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1. Double-blinded, randomised, placebo-controlled trial of convalescent plasma for COVID-19: analyses by neutralising antibodies homologous to recipients’ variants.

Author: Khawaja, T., Kajova, M., Levonen, I., Pietilä, J. P., Välimaa, H., Paajanen, J., Pakkanen, S. H., Patjas, A., Montonen, R., Miettinen, S., Virtanen, J., Smura, T., Sironen, T., Fagerlund, R., Ugurlu, H., Iheozor-Ejiofor, R., Saksela, K., Vahlberg, T., Ranki, A., and Vierikko, A.
Subjects: CONVALESCENT plasma, COVID-19, COVID-19 treatment, ANTIBODY titer, IMMUNOGLOBULINS
Abstract: Introduction: Convalescent plasma (CP) emerged as potential treatment for COVID-19 early in the pandemic. While efficacy in hospitalised patients has been lacklustre, CP may be beneficial at the first stages of disease. Despite multiple new variants emerging, no trials have involved analyses on variant-specific antibody titres of CP. Methods: We recruited hospitalised COVID-19 patients within 10 days of symptom onset and, employing a double-blinded approach, randomised them to receive 200 ml convalescent plasma with high (HCP) or low (LCP) neutralising antibody (NAb) titre against the ancestral strain (Wuhan-like variant) or placebo in 1:1:1 ratio. Primary endpoints comprised intubation, corticosteroids for symptom aggravation, and safety assessed as serious adverse events. For a pre-planned ad hoc analysis, the patients were regrouped by infused CP’s NAb titers to variants infecting the recipients i.e. by titres of homologous HCP (hHCP) or LCP (hLCP). Results: Of the 57 patients, 18 received HCP, 19 LCP and 20 placebo, all groups smaller than planned. No significant differences were found for primary endpoints. In ad hoc analysis, hHCPrecipients needed significantly less respiratory support, and appeared to be given corticosteroids less frequently (1/14; 7.1%) than those receiving hLCP (9/23; 39.1%) or placebo (8/20; 40%), (p = 0.077). Discussion: Our double-blinded, placebo-controlled CP therapy trial remained underpowered and does not allow any firm conclusions for early-stage hospitalised COVID-19 patients. Interestingly, however, regrouping by homologous – recipients’ variant-specific – CP titres suggested benefits for hHCP. We encourage similar re-analysis of ongoing/previous larger CP studies. [ABSTRACT FROM AUTHOR]
Published: 2024
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2. Visual pigments of Arctic charr (Salvelinus alpinus (L.)) and whitefish (Coregonus lavaretus (L.)) morphs in subarctic lakes

Author: Kahilainen, K. K., Smura, T., Knudsen, R., Amundsen, P.-A., Jokela-Määttä, M., and Donner, K.
Published: 2016
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3. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: Kuhn, J, Adkins, S, Alioto, D, Alkhovsky, S, Amarasinghe, G, Anthony, S, Avsic-Aupanc, T, Ayllon, M, Bahl, J, Balkema-Buschmann, A, Ballinger, M, Bartonicka, T, Basler, C, Bavari, S, Beer, M, Bente, D, Bergeron, E, Bird, B, Blair, C, Blasdell, K, Bradfute, S, Breyta, R, Briese, T, Brown, P, Buchholz, U, Buchmeier, M, Bukreyev, A, Burt, F, Buzkan, N, Calisher, C, Cao, M, Casas, I, Chamberlain, J, Chandran, K, Charrel, R, Chen, B, Chiumenti, M, Choi, I, Clegg, J, Crozier, I, da Graca, J, Dal Bo, E, Davila, A, de la Torre, J, de Lamballerie, X, de Swart, R, Di Bello, P, Di Paola, N, Di Serio, F, Dietzgen, R, Digiaro, M, Dolja, V, Dolnik, O, Drebot, M, Drexler, J, Durrwald, R, Dufkova, L, Dundon, W, Duprex, W, Dye, J, Easton, A, Ebihara, H, Elbeaino, T, Ergunay, K, Fernandes, J, Fooks, A, Formenty, P, Forth, L, Fouchier, R, Freitas-Astua, J, Gago-Zachert, S, Gao, G, Garcia, M, Garcia-Sastre, A, Garrison, A, Gbakima, A, Goldstein, T, Gonzalez, J, Griffiths, A, Groschup, M, Gunther, S, Guterres, A, Hall, R, Hammond, J, Hassan, M, Hepojoki, J, Hepojoki, S, Hetzel, U, Hewson, R, Hoffmann, B, Hongo, S, Hoper, D, Horie, M, Hughes, H, Hyndman, T, Jambai, A, Jardim, R, Jiang, D, Jin, Q, Jonson, G, Junglen, S, Karadag, S, Keller, K, Klempa, B, Klingstrom, J, Kobinger, G, Kondo, H, Koonin, E, Krupovic, M, Kurath, G, Kuzmin, I, Laenen, L, Lamb, R, Lambert, A, Langevin, S, Lee, B, Lemos, E, Leroy, E, Li, D, Li, J, Liang, M, Liu, W, Liu, Y, Lukashevich, I, Maes, P, de Souza, W, Marklewitz, M, Marshall, S, Martelli, G, Martin, R, Marzano, S, Massart, S, Mccauley, J, Mielke-Ehret, N, Minafra, A, Minutolo, M, Mirazimi, A, Muhlbach, H, Muhlberger, E, Naidu, R, Natsuaki, T, Navarro, B, Navarro, J, Netesov, S, Neumann, G, Nowotny, N, Nunes, M, Nylund, A, Okland, A, Oliveira, R, Palacios, G, Pallas, V, Palyi, B, Papa, A, Parrish, C, Pauvolid-Correa, A, Paweska, J, Payne, S, Perez, D, Pfaff, F, Radoshitzky, S, Aziz-ul, R, Ramos-Gonzalez, P, Resende, R, Reyes, C, Rima, B, Romanowski, V, Luna, G, Rota, P, Rubbenstroth, D, Runstadler, J, Ruzek, D, Sabanadzovic, S, Salat, J, Sall, A, Salvato, M, Sarpkaya, K, Sasaya, T, Schwemmle, M, Shabbir, M, Shi, X, Shi, Z, Shirako, Y, Simmonds, P, Sirmarovaa, J, Sironi, M, Smither, S, Smura, T, Song, J, Spann, K, Spengler, J, Stenglein, M, Stone, D, Strakova, P, Takada, A, Tesh, R, Thornburg, N, Tomonaga, K, Tordo, N, Towner, J, Turina, M, Tzanetakis, I, Ulrich, R, Vaira, A, van den Hoogen, B, Varsani, A, Vasilakis, N, Verbeek, M, Wahl, V, Walker, P, Wang, H, Wang, J, Wang, X, Wang, L, Wei, T, Wells, H, Whitfield, A, Williams, J, Wolf, Y, Wu, Z, Yang, X, Yu, X, Yutin, N, Zerbini, F, Zhang, T, Zhang, Y, Zhou, G, Zhou, X, Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avsic-Aupanc T, Ayllon MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonicka T, Basler C, Bavari S, Beer M, Bente DA, Bergeron E, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao MJ, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi I, Clegg JCS, Crozier I, da Graca JV, Dal Bo E, Davila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Durrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergunay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astua J, Gago-Zachert S, Gao GF, Garcia ML, Garcia-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Gunther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Hoper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiang DH, Jin Q, Jonson GB, Junglen S, Karadag S, Keller KE, Klempa B, Klingstrom J, Kobinger G, Kondo H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee BH, Lemos ERS, Leroy EM, Li DX, Li JR, Liang MF, Liu WW, Liu Y, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Muhlbach HP, Muhlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Okland AL, Oliveira RC, Palacios G, Pallas V, Palyi B, Papa A, Parrish CR, Pauvolid-Correa A, Paweska JT, Payne S, Perez DR, Pfaff F, Radoshitzky SR, Aziz-ul Rahman, Ramos-Gonzalez PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Luna GR, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salat J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shi XH, Shi ZL, Shirako Y, Simmonds P, Sirmarovaa J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Strakova P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang JW, Wang XF, Wang LF, Wei TY, Wells H, Whitfield AE, Williams JV, Wolf YI, Wu ZQ, Yang X, Yu XJ, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou GH, Zhou XP, Kuhn, J, Adkins, S, Alioto, D, Alkhovsky, S, Amarasinghe, G, Anthony, S, Avsic-Aupanc, T, Ayllon, M, Bahl, J, Balkema-Buschmann, A, Ballinger, M, Bartonicka, T, Basler, C, Bavari, S, Beer, M, Bente, D, Bergeron, E, Bird, B, Blair, C, Blasdell, K, Bradfute, S, Breyta, R, Briese, T, Brown, P, Buchholz, U, Buchmeier, M, Bukreyev, A, Burt, F, Buzkan, N, Calisher, C, Cao, M, Casas, I, Chamberlain, J, Chandran, K, Charrel, R, Chen, B, Chiumenti, M, Choi, I, Clegg, J, Crozier, I, da Graca, J, Dal Bo, E, Davila, A, de la Torre, J, de Lamballerie, X, de Swart, R, Di Bello, P, Di Paola, N, Di Serio, F, Dietzgen, R, Digiaro, M, Dolja, V, Dolnik, O, Drebot, M, Drexler, J, Durrwald, R, Dufkova, L, Dundon, W, Duprex, W, Dye, J, Easton, A, Ebihara, H, Elbeaino, T, Ergunay, K, Fernandes, J, Fooks, A, Formenty, P, Forth, L, Fouchier, R, Freitas-Astua, J, Gago-Zachert, S, Gao, G, Garcia, M, Garcia-Sastre, A, Garrison, A, Gbakima, A, Goldstein, T, Gonzalez, J, Griffiths, A, Groschup, M, Gunther, S, Guterres, A, Hall, R, Hammond, J, Hassan, M, Hepojoki, J, Hepojoki, S, Hetzel, U, Hewson, R, Hoffmann, B, Hongo, S, Hoper, D, Horie, M, Hughes, H, Hyndman, T, Jambai, A, Jardim, R, Jiang, D, Jin, Q, Jonson, G, Junglen, S, Karadag, S, Keller, K, Klempa, B, Klingstrom, J, Kobinger, G, Kondo, H, Koonin, E, Krupovic, M, Kurath, G, Kuzmin, I, Laenen, L, Lamb, R, Lambert, A, Langevin, S, Lee, B, Lemos, E, Leroy, E, Li, D, Li, J, Liang, M, Liu, W, Liu, Y, Lukashevich, I, Maes, P, de Souza, W, Marklewitz, M, Marshall, S, Martelli, G, Martin, R, Marzano, S, Massart, S, Mccauley, J, Mielke-Ehret, N, Minafra, A, Minutolo, M, Mirazimi, A, Muhlbach, H, Muhlberger, E, Naidu, R, Natsuaki, T, Navarro, B, Navarro, J, Netesov, S, Neumann, G, Nowotny, N, Nunes, M, Nylund, A, Okland, A, Oliveira, R, Palacios, G, Pallas, V, Palyi, B, Papa, A, Parrish, C, Pauvolid-Correa, A, Paweska, J, Payne, S, Perez, D, Pfaff, F, Radoshitzky, S, Aziz-ul, R, Ramos-Gonzalez, P, Resende, R, Reyes, C, Rima, B, Romanowski, V, Luna, G, Rota, P, Rubbenstroth, D, Runstadler, J, Ruzek, D, Sabanadzovic, S, Salat, J, Sall, A, Salvato, M, Sarpkaya, K, Sasaya, T, Schwemmle, M, Shabbir, M, Shi, X, Shi, Z, Shirako, Y, Simmonds, P, Sirmarovaa, J, Sironi, M, Smither, S, Smura, T, Song, J, Spann, K, Spengler, J, Stenglein, M, Stone, D, Strakova, P, Takada, A, Tesh, R, Thornburg, N, Tomonaga, K, Tordo, N, Towner, J, Turina, M, Tzanetakis, I, Ulrich, R, Vaira, A, van den Hoogen, B, Varsani, A, Vasilakis, N, Verbeek, M, Wahl, V, Walker, P, Wang, H, Wang, J, Wang, X, Wang, L, Wei, T, Wells, H, Whitfield, A, Williams, J, Wolf, Y, Wu, Z, Yang, X, Yu, X, Yutin, N, Zerbini, F, Zhang, T, Zhang, Y, Zhou, G, Zhou, X, Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avsic-Aupanc T, Ayllon MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonicka T, Basler C, Bavari S, Beer M, Bente DA, Bergeron E, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao MJ, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi I, Clegg JCS, Crozier I, da Graca JV, Dal Bo E, Davila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Durrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergunay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astua J, Gago-Zachert S, Gao GF, Garcia ML, Garcia-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Gunther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Hoper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiang DH, Jin Q, Jonson GB, Junglen S, Karadag S, Keller KE, Klempa B, Klingstrom J, Kobinger G, Kondo H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee BH, Lemos ERS, Leroy EM, Li DX, Li JR, Liang MF, Liu WW, Liu Y, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Muhlbach HP, Muhlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Okland AL, Oliveira RC, Palacios G, Pallas V, Palyi B, Papa A, Parrish CR, Pauvolid-Correa A, Paweska JT, Payne S, Perez DR, Pfaff F, Radoshitzky SR, Aziz-ul Rahman, Ramos-Gonzalez PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Luna GR, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salat J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shi XH, Shi ZL, Shirako Y, Simmonds P, Sirmarovaa J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Strakova P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang JW, Wang XF, Wang LF, Wei TY, Wells H, Whitfield AE, Williams JV, Wolf YI, Wu ZQ, Yang X, Yu XJ, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou GH, and Zhou XP
Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Published: 2020

4. Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022

Author: Lindh, E. (Erika), Smura, T. (Teemu), Blomqvist, S. (Soile), Liitsola, K. (Kirsi), Vauhkonen, H. (Hanna), Savolainen, L. (Laura), Ikonen, J. (Jaana), Ronkainen, J. (Jukka), Taskila, J. (Jyri), Sakaranaho, P. (Pertti), Savolainen-Kopra, C. (Carita), Vapalahti, O. (Olli), Ikonen, N. (Niina), Lindh, E. (Erika), Smura, T. (Teemu), Blomqvist, S. (Soile), Liitsola, K. (Kirsi), Vauhkonen, H. (Hanna), Savolainen, L. (Laura), Ikonen, J. (Jaana), Ronkainen, J. (Jukka), Taskila, J. (Jyri), Sakaranaho, P. (Pertti), Savolainen-Kopra, C. (Carita), Vapalahti, O. (Olli), and Ikonen, N. (Niina)
Abstract: Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.
Published: 2022

5. Zika Virus Infection With Prolonged Maternal Viremia and Fetal Brain Abnormalities

Author: Driggers, R.W., Ho, C.-Y., Korhonen, E.M., Kuivanen, S., Jääskeläinen, A.J., Smura, T., Rosenberg, A., Hill, D.A., DeBiasi, R.L., Vezina, G., Timofeev, J., Rodriguez, F.J., Levanov, L., Razak, J., Iyengar, P., Hennenfent, A., Kennedy, R., Lanciotti, R., du Plessis, A., and Vapalahti, O.
Published: 2017
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6. COVID-19 cases in spectators returning to Finland from UEFA Euro 2020 matches in Saint Petersburg

Author: Sarvikivi, E., primary, Salminen, M., additional, Savolainen-Kopra, C., additional, Ikonen, N., additional, Kontio, M., additional, Isosomppi, S., additional, Jamanca, S., additional, Hannila-Handelberg, T., additional, Vapalahti, O., additional, Smura, T., additional, Lappalainen, M., additional, and Helve, O., additional
Published: 2022
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7. Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction

Author: Ylipaasto, P., Smura, T., Gopalacharyulu, P., Paananen, A., Seppänen-Laakso, T., Kaijalainen, S., Ahlfors, H., Korsgren, O., Lakey, J. R. T., Lahesmaa, R., Piemonti, L., Oresic, M., Galama, J., and Roivainen, M.
Published: 2012
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8. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

Author: O'Toole, Á, Hill, V, Pybus, OG, Watts, A, Bogoch, II, Khan, K, Messina, JP, COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally, H, Lessells, RR, Giandhari, J, Pillay, S, Tumedi, KA, Nyepetsi, G, Kebabonye, M, Matsheka, M, Mine, M, Tokajian, S, Hassan, H, Salloum, T, Merhi, G, Koweyes, J, Geoghegan, JL, de Ligt, J, Ren, X, Storey, M, Freed, NE, Pattabiraman, C, Prasad, P, Desai, AS, Vasanthapuram, R, Schulz, TF, Steinbrück, L, Stadler, T, Swiss Viollier Sequencing Consortium, Parisi, A, Bianco, A, García de Viedma, D, Buenestado-Serrano, S, Borges, V, Isidro, J, Duarte, S, Gomes, JP, Zuckerman, NS, Mandelboim, M, Mor, O, Seemann, T, Arnott, A, Draper, J, Gall, M, Rawlinson, W, Deveson, I, Schlebusch, S, McMahon, J, Leong, L, Lim, CK, Chironna, M, Loconsole, D, Bal, A, Josset, L, Holmes, E, St George, K, Lasek-Nesselquist, E, Sikkema, RS, Oude Munnink, B, Koopmans, M, Brytting, M, Sudha Rani, V, Pavani, S, Smura, T, Heim, A, Kurkela, S, Umair, M, Salman, M, Bartolini, B, Rueca, M, Drosten, C, Wolff, T, Silander, O, Eggink, D, Reusken, C, Vennema, H, Park, A, Carrington, C, Sahadeo, N, Carr, M, Gonzalez, G, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), de Oliveira, T, Faria, N, Rambaut, A, Kraemer, MUG, O'Toole, Á, Hill, V, Pybus, OG, Watts, A, Bogoch, II, Khan, K, Messina, JP, COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally, H, Lessells, RR, Giandhari, J, Pillay, S, Tumedi, KA, Nyepetsi, G, Kebabonye, M, Matsheka, M, Mine, M, Tokajian, S, Hassan, H, Salloum, T, Merhi, G, Koweyes, J, Geoghegan, JL, de Ligt, J, Ren, X, Storey, M, Freed, NE, Pattabiraman, C, Prasad, P, Desai, AS, Vasanthapuram, R, Schulz, TF, Steinbrück, L, Stadler, T, Swiss Viollier Sequencing Consortium, Parisi, A, Bianco, A, García de Viedma, D, Buenestado-Serrano, S, Borges, V, Isidro, J, Duarte, S, Gomes, JP, Zuckerman, NS, Mandelboim, M, Mor, O, Seemann, T, Arnott, A, Draper, J, Gall, M, Rawlinson, W, Deveson, I, Schlebusch, S, McMahon, J, Leong, L, Lim, CK, Chironna, M, Loconsole, D, Bal, A, Josset, L, Holmes, E, St George, K, Lasek-Nesselquist, E, Sikkema, RS, Oude Munnink, B, Koopmans, M, Brytting, M, Sudha Rani, V, Pavani, S, Smura, T, Heim, A, Kurkela, S, Umair, M, Salman, M, Bartolini, B, Rueca, M, Drosten, C, Wolff, T, Silander, O, Eggink, D, Reusken, C, Vennema, H, Park, A, Carrington, C, Sahadeo, N, Carr, M, Gonzalez, G, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), de Oliveira, T, Faria, N, Rambaut, A, and Kraemer, MUG
Abstract: Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Published: 2021

9. Human enterovirus infections in children at increased risk for type 1 diabetes: the Babydiet study

Author: Simonen-Tikka, M.-L., Pflueger, M., Klemola, P., Savolainen-Kopra, C., Smura, T., Hummel, S., Kaijalainen, S., Nuutila, K., Natri, O., Roivainen, M., and Ziegler, A.-G.
Published: 2011
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10. Chikungunya virus infections in Finnish travellers 2009-2019 : Infection Ecology & Epidemiology

Author: Jääskeläinen, A. J., Kareinen, L., Smura, T., Kallio-Kokko, H., Vapalahti, O., Medicum, HUSLAB, Viral Zoonosis Research Unit, Department of Virology, University of Helsinki, Helsinki University Hospital Area, Faculty of Medicine, Doctoral Programme in Microbiology and Biotechnology, Helsinki One Health (HOH), Veterinary Microbiology and Epidemiology, and Veterinary Biosciences
Subjects: 11832 Microbiology and virology, virus diseases, 3111 Biomedicine
Abstract: The mosquito-borne chikungunya virus (CHIKV) causes an acute febrile illness with rash, joint and muscle pain.A realtime RT-PCR assay for CHIKV detecting non-structural protein (nsP2; CHIKV nsP2-RT-qPCR) was set up. All the serodiagnosed CHIKV cases detected during 2009-2019 in Finland were screened with the assay, followed by isolations attempts and sequencing using Sanger and next generation sequencing (NGS). To validate the assay external and in-house quality control samples were used and all were correctly identified. Specificity of the assay was 100%. Assay was sensitive to detect CHIKV RNA in dilution of 10-8.During years 2009-2019 34 patients were diagnosed for acute CHIKV infection. Twelve out of 34 cases were positive by CHIKV nsP2-RT-qPCR.Two CHIKV isolations succeeded from two individuals infected originally in Thailand, 2019. From 12 CHIKV nsP2-RT-qPCR positive samples, five (42%) CHIKVs were successfully sequenced. In this study, CHIKVs from year 2019 clustered with CHIKV ECSA-lineage forming sub-cluster with strains from ones detected in Bangladesh 2017, and the ones from Jamaica (2014) within Asian lineage showing highest similarity to strains detected in Caribbean outbreak 2013-15. Majority of the CHIKV infections detected in Finland originates from Asia and virus lineages reflect the global circulation of the pathogen.
Published: 2020

11. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: Kuhn, J.H., Adkins, S., Alioto, D., Alkhovsky, S.V., Amarasinghe, G.K., Anthony, S.J., Avšič-Županc, T., Ayllón, M.A., Bahl, J., Balkema-Buschmann, A., Ballinger, M.J., Bartonička, T., Basler, C., Bavari, S., Beer, M., Bente, D.A., Bergeron, É., Bird, B.H., Blair, C., Blasdell, K.R., Bradfute, S.B., Breyta, R., Briese, T., Brown, P.A., Buchholz, U.J., Buchmeier, M.J., Bukreyev, A., Burt, F., Buzkan, N., Calisher, C.H., Cao, M., Casas, I., Chamberlain, J., Chandran, K., Charrel, R.N., Chen, B., Chiumenti, M., Choi, I-R, Clegg, J.C.S., Crozier, I., da Graça, J.V., Dal Bó, E., Dávila, A.M.R., de la Torre, J.C., de Lamballerie, X., de Swart, R.L., Di Bello, P.L., Di Paola, N., Di Serio, F., Dietzgen, R.G., Digiaro, M., Dolja, V.V., Dolnik, O., Drebot, M.A., Drexler, J.F., Dürrwald, R., Dufkova, L., Dundon, W.G., Duprex, W.P., Dye, J.M., Easton, A.J., Ebihara, H., Elbeaino, T., Ergünay, K., Fernandes, J., Fooks, A.R., Formenty, P.B.H., Forth, L.F., Fouchier, R.A.M., Freitas-Astúa, J., Gago-Zachert, S., Gāo, G.F., García, M.L., García-Sastre, A., Garrison, A.R., Gbakima, A., Goldstein, T., Gonzalez, J-P.J., Griffiths, A., Groschup, M.H., Günther, S., Guterres, A., Hall, R.A., Hammond, J., Hassan, M., Hepojoki, J., Hepojoki, S., Hetzel, U., Hewson, R., Hoffmann, B., Hongo, S., Höper, D., Horie, M., Hughes, H.R., Hyndman, T.H., Jambai, A., Jardim, R., Jiāng, D., Jin, Q., Jonson, G.B., Junglen, S., Karadağ, S., Keller, K.E., Klempa, B., Klingström, J., Kobinger, G., Kondō, H., Koonin, E.V., Krupovic, M., Kurath, G., Kuzmin, I.V., Laenen, L., Lamb, R.A., Lambert, A.J., Langevin, S.L., Lee, B., Lemos, E.R.S., Leroy, E.M., Li, D., Lǐ, J., Liang, M., Liú, W., Liú, Y., Lukashevich, I.S., Maes, P., Marciel de Souza, W., Marklewitz, M., Marshall, S.H., Martelli, G.P., Martin, R.R., Marzano, S-Y.L., Massart, S., McCauley, J.W., Mielke-Ehret, N., Minafra, A., Minutolo, M., Mirazimi, A., Mühlbach, H-P, Mühlberger, E., Naidu, R., Natsuaki, T., Navarro, B., Navarro, J.A., Netesov, S.V., Neumann, G., Nowotny, N., Nunes, M.R.T., Nylund, A., Økland, A.L., Oliveira, R.C., Palacios, G., Pallas, V., Pályi, B., Papa, A., Parrish, C.R., Pauvolid-Corrêa, A., Pawęska, J.T., Payne, S., Perez, D.R., Pfaff, F., Radoshitzky, S.R., Rahman, A-U, Ramos-González, P.L., Resende, R.O., Reyes, C.A., Rima, B.K., Romanowski, V., Robles Luna, G., Rota, P., Rubbenstroth, D., Runstadler, J.A., Ruzek, D., Sabanadzovic, S., Salat, J., Sall, A.A., Salvato, M.S., Sarpkaya, K., Sasaya, T., Schwemmle, M., Shabbir, M.Z., Shí, X., Shí, Z., Shirako, Y., Simmonds, P., Širmarová, J., Sironi, M., Smither, S., Smura, T., Song, J-W, Spann, K.M., Spengler, J.R., Stenglein, M.D., Stone, D.M., Straková, P., Takada, A., Tesh, R.B., Thornburg, N.J., Tomonaga, K., Tordo, N., Towner, J.S., Turina, M., Tzanetakis, I., Ulrich, R.G., Vaira, A.M., van den Hoogen, B., Varsani, A., Vasilakis, N., Verbeek, M., Wahl, V., Walker, P.J., Wang, H., Wang, J., Wang, X., Wang, L-F, Wèi, T., Wells, H., Whitfield, A.E., Williams, J.V., Wolf, Y.I., Wú, Z., Yang, X., Yáng, X., Yu, X., Yutin, N., Zerbini, F.M., Zhang, T., Zhang, Y-Z, Zhou, G., Zhou, X., Kuhn, J.H., Adkins, S., Alioto, D., Alkhovsky, S.V., Amarasinghe, G.K., Anthony, S.J., Avšič-Županc, T., Ayllón, M.A., Bahl, J., Balkema-Buschmann, A., Ballinger, M.J., Bartonička, T., Basler, C., Bavari, S., Beer, M., Bente, D.A., Bergeron, É., Bird, B.H., Blair, C., Blasdell, K.R., Bradfute, S.B., Breyta, R., Briese, T., Brown, P.A., Buchholz, U.J., Buchmeier, M.J., Bukreyev, A., Burt, F., Buzkan, N., Calisher, C.H., Cao, M., Casas, I., Chamberlain, J., Chandran, K., Charrel, R.N., Chen, B., Chiumenti, M., Choi, I-R, Clegg, J.C.S., Crozier, I., da Graça, J.V., Dal Bó, E., Dávila, A.M.R., de la Torre, J.C., de Lamballerie, X., de Swart, R.L., Di Bello, P.L., Di Paola, N., Di Serio, F., Dietzgen, R.G., Digiaro, M., Dolja, V.V., Dolnik, O., Drebot, M.A., Drexler, J.F., Dürrwald, R., Dufkova, L., Dundon, W.G., Duprex, W.P., Dye, J.M., Easton, A.J., Ebihara, H., Elbeaino, T., Ergünay, K., Fernandes, J., Fooks, A.R., Formenty, P.B.H., Forth, L.F., Fouchier, R.A.M., Freitas-Astúa, J., Gago-Zachert, S., Gāo, G.F., García, M.L., García-Sastre, A., Garrison, A.R., Gbakima, A., Goldstein, T., Gonzalez, J-P.J., Griffiths, A., Groschup, M.H., Günther, S., Guterres, A., Hall, R.A., Hammond, J., Hassan, M., Hepojoki, J., Hepojoki, S., Hetzel, U., Hewson, R., Hoffmann, B., Hongo, S., Höper, D., Horie, M., Hughes, H.R., Hyndman, T.H., Jambai, A., Jardim, R., Jiāng, D., Jin, Q., Jonson, G.B., Junglen, S., Karadağ, S., Keller, K.E., Klempa, B., Klingström, J., Kobinger, G., Kondō, H., Koonin, E.V., Krupovic, M., Kurath, G., Kuzmin, I.V., Laenen, L., Lamb, R.A., Lambert, A.J., Langevin, S.L., Lee, B., Lemos, E.R.S., Leroy, E.M., Li, D., Lǐ, J., Liang, M., Liú, W., Liú, Y., Lukashevich, I.S., Maes, P., Marciel de Souza, W., Marklewitz, M., Marshall, S.H., Martelli, G.P., Martin, R.R., Marzano, S-Y.L., Massart, S., McCauley, J.W., Mielke-Ehret, N., Minafra, A., Minutolo, M., Mirazimi, A., Mühlbach, H-P, Mühlberger, E., Naidu, R., Natsuaki, T., Navarro, B., Navarro, J.A., Netesov, S.V., Neumann, G., Nowotny, N., Nunes, M.R.T., Nylund, A., Økland, A.L., Oliveira, R.C., Palacios, G., Pallas, V., Pályi, B., Papa, A., Parrish, C.R., Pauvolid-Corrêa, A., Pawęska, J.T., Payne, S., Perez, D.R., Pfaff, F., Radoshitzky, S.R., Rahman, A-U, Ramos-González, P.L., Resende, R.O., Reyes, C.A., Rima, B.K., Romanowski, V., Robles Luna, G., Rota, P., Rubbenstroth, D., Runstadler, J.A., Ruzek, D., Sabanadzovic, S., Salat, J., Sall, A.A., Salvato, M.S., Sarpkaya, K., Sasaya, T., Schwemmle, M., Shabbir, M.Z., Shí, X., Shí, Z., Shirako, Y., Simmonds, P., Širmarová, J., Sironi, M., Smither, S., Smura, T., Song, J-W, Spann, K.M., Spengler, J.R., Stenglein, M.D., Stone, D.M., Straková, P., Takada, A., Tesh, R.B., Thornburg, N.J., Tomonaga, K., Tordo, N., Towner, J.S., Turina, M., Tzanetakis, I., Ulrich, R.G., Vaira, A.M., van den Hoogen, B., Varsani, A., Vasilakis, N., Verbeek, M., Wahl, V., Walker, P.J., Wang, H., Wang, J., Wang, X., Wang, L-F, Wèi, T., Wells, H., Whitfield, A.E., Williams, J.V., Wolf, Y.I., Wú, Z., Yang, X., Yáng, X., Yu, X., Yutin, N., Zerbini, F.M., Zhang, T., Zhang, Y-Z, Zhou, G., and Zhou, X.
Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Published: 2020

12. A single amino acid substitution in viral VP1 protein alters the lytic potential of clone-derived variants of echovirus 9 DM strain in human pancreatic islets

Author: Paananen, A., Ylipaasto, P., Smura, T., Lempinen, M., Galama, J., and Roivainen, M.
Published: 2013
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13. Chikungunya virus infections in Finnish travellers 2009-2019

Author: Jääskeläinen, A. J., primary, Kareinen, L., additional, Smura, T., additional, Kallio-Kokko, H., additional, and Vapalahti, O., additional
Published: 2020
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14. Techno-Economic Analysis of Fixed WiMAX Networks

Author: Katsianis, D, primary, Rokkas, T, additional, H√§mm√§inen, H, additional, and Smura, T, additional
Published: 2007
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15. Techno-Economic Analysis of Fixed WiMAX Networks

Author: Smura, T., primary, Hämmäinen, Heikki, additional, Rokkas, T., additional, and Katsianis, D., additional
Published: 2007
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16. No association between Ljungan virus seropositivity and the beta-cell damaging process in the Finnish Type 1 Diabetes Prediction and Prevention Study cohort

Author: Jääskeläinen, A. J. (Anne J.), Nurminen, N. (Noora), Kolehmainen, P. (Pekka), Smura, T. (Teemu), Tauriainen, S. (Sisko), Toppari, J. (Jorma), Ilonen, J. (Jorma), Veijola, R. (Riitta), Knip, M. (Mikael), Hyöty, H. (Heikki), Vapalahti, O. (Olli), Kallio-Kokko, H. (Hannimari), Jääskeläinen, A. J. (Anne J.), Nurminen, N. (Noora), Kolehmainen, P. (Pekka), Smura, T. (Teemu), Tauriainen, S. (Sisko), Toppari, J. (Jorma), Ilonen, J. (Jorma), Veijola, R. (Riitta), Knip, M. (Mikael), Hyöty, H. (Heikki), Vapalahti, O. (Olli), and Kallio-Kokko, H. (Hannimari)
Abstract: Background: Ljungan virus (LV) has not confirmed to associate with any human disease, but a possible connection with type 1 diabetes has been suggested. LV is a rodent-borne picornavirus that induces a diabetes-like condition in rodents. Approximately 30% of adults and 60% of children are seropositive in Finland. The Finnish Type 1 Diabetes Prediction and Prevention study enabled the use of very well characterized sample panels from children seroconverted to positivity for multiple islet autoantibodies during their prospective observation from birth; in addition, samples from age, sex, human leukocyte antigen (HLA), and residence area matched control children. Methods: We analyzed LV IgG seroprevalence in 102 case children (65 had also developed type 1 diabetes), in addition to nondiabetic control children. LV and human parechovirus (HPeV) immunofluorescence assays were used to analyze LV and HPeV-specific IgG from 102 plasma samples taken at the time of islet autoantibody appearance and from 204 samples from the matched control children. Results: Altogether 46.1% of the case and 50.7% of the control children were positive for LV IgG (odds ratio 0.8; 95% confidence interval, 0.47–1.36; P = 0.416) and 67.6% versus 79.8% were positive for HPeV IgG, respectively (odds ratio 0.49, 0.27–0.9, P = 0.023). Conclusions: Thus, no risk associations between LV or HPeV-specific IgG and islet autoimmunity were observed. However, a trend for significantly higher prevalence of HPeV antibodies in control children (P = 0.023) suggests a possible protective association of this virus with islet autoimmunity.
Published: 2019

17. Visual pigments of Arctic charr (Salvelinus alpinus (L.)) and whitefish (Coregonus lavaretus (L.)) morphs in subarctic lakes

Author: Kahilainen, K. K., primary, Smura, T., additional, Knudsen, R., additional, Amundsen, P.-A., additional, Jokela-Määttä, M., additional, and Donner, K., additional
Published: 2015
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18. Human islet metabolic profiles in progression to type 1 diabetes

Author: Lindfors, Erno, Mattila, Ismo, Castillo, Sandra, Smura, T., Ylipaasto, T., Seppänen-Laakso, Tuulikki, Hyötyläinen, Tuulia, Oresic, Matej, and Roivainen, M.
Subjects: SDG 3 - Good Health and Well-being
Published: 2011

19. Arbovirus seroprevalence in Nasiriyah Iraq

Author: Barakat, A.M., primary, Smura, T., additional, Kuivanen, S., additional, Huhtamo, E., additional, Kurkela, S., additional, and Putkuri, N., additional
Published: 2015
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20. Human parechovirus type 4 sequences from infants with sepsis-like disease indicates intertypic recombination

Author: Kolehmainen, P., primary, Siponen, A., additional, Smura, T., additional, Kallio-Kokko, H., additional, Vapalahti, O., additional, Jääskeläinen, A., additional, and Tauriainen, Sisko, additional
Published: 2015
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21. Alternatives for mobile operators in the competitive 3G and beyond business

Author: Harno, J. Katsianis, D. Smura, T. Eskedal, T.G. Venturin, R. Pohjola, O.P. Kumar, K.R.R. Varoutas, D.
Abstract: The importance of analyzing different business models and technologies in the mobile industry has become more crucial for the investment policy of the telecom operators. This paper aims to cover some of the most interesting business alternatives in providing the new 3G and beyond services including cases where the operator already has an existing second-generation cellular network and perhaps even a license for the 3G UMTS network, and cases where the operator does not have any existing network. Three cases for incumbents and new entrants are foreseen, leaving alternatives for new competing 3G technology deployment or acting as a mobile virtual network operator (MVNO) without owning any radio infrastructure. A techno-economic approach has been used to identify business opportunities and quantify the potential profitability of different kind of business players. The scenarios have been analyzed in the Western European context by different country groups that are not exactly representative of any defined country, but rather share typical demographic characteristics. © 2009 Springer Science+Business Media, LLC.
Published: 2009

22. On the economics of fixed-mobile convergence

Author: Rokkas, T. Varoutas, D. Katsianis, D. Smura, T. Renjish, K. Heikkinen, M. Harno, J. Kind, M. von Hugo, D. Monath, T.
Abstract: Purpose: The purpose of this paper is to show that fixed-mobile convergence (FMC) has gathered much interest in the telecommunications industry lately. Integrated operators (who own both fixed and mobile networks), are keen to exploit FMC benefits in order to save costs and generate new revenues. This paper aims to analyze the effects of converged network and service environment on the business of existing telecommunication operators. Design/methodology/approach: After an introduction to the regulatory, market, and technology related issues of convergence, the authors focus on analyzing the role of FMC technologies and services in their businesses of an integrated operator with existing fixed and mobile operations in a large Western European country. Findings: Results reveal that an integrated operator can benefit from cost savings, customer retention and prevent revenue erosion by migrating to FMC. Originality/value: This paper examines the effects of fixed-mobile convergence to an integrated operator. © Emerald Group Publishing Limited.
Published: 2009

23. Zika virus infection in a traveller returning from the Maldives, June 2015.

Author: Korhonen, E. M., Huhtamo, E., Smura, T., Kallio-Kokko, H., Raassina, M., and Vapalahti, O.
Published: 2016
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24. Mobile handset features as service enablers - Conceptual model of feature diffusion.

Author: Riikonen, A., Smura, T., and Juntunen, A.
Published: 2011
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25. Value Network Configurations in wireless local area access.

Author: Casey, T., Smura, T., and Sorri, A.
Published: 2010
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26. Diffusion of Mobile Handset Features in Finland.

Author: Kivi, A., Smura, T., and Toyli, J.
Published: 2009
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27. Future Scenarios for Local Area Access: Industry Structure and Access Fragmentation.

Author: Smura, T. and Sorri, A.
Published: 2009
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28. Fixed-Mobile Convergence: An Integrated Operator Case Study.

Author: Renjish Kumar, K.R., Rokkas, T., Varoutas, D., Kind, M., Von Hugo, D., Harno, J., Smura, T., and Heikkinen, M.
Published: 2007
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29. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Author: Alm E., Broberg E.K., Connor T., Hodcroft E.B., Komissarov A.B., Maurer-Stroh S., Melidou A., Neher R.A., O'Toole A., Pereyaslov D., Beerenwinkel N., Posada-Cespedes S., Jablonski K.P., Ferreira P.F., Topolsky I., Avsic-Zupanc T., Korva M., Poljak M., Zakotnik S., Zorec T.M., Bragstad K., Hungnes O., Stene-Johansen K., Reusken C., Meijer A., Vennema H., Ruiz-Roldan L., Bracho M.A., Garcia-Gonzalez N., Chiner-Oms A., Cancino-Munoz I., Comas I., Goig G.A., Torres-Puente M., Lopez M.G., Martinez-Priego L., D'Auria G., Ruiz-Hueso P., Ferrus-Abad L., de Marco G., Galan-Vendrell I., Carbo-Ramirez S., Ruiz-Rodriguez P., Coscolla M., Polackova K., Kramna L., Cinek O., Richter J., Krashias G., Tryfonos C., Bashiardes S., Koptides D., Christodoulou C., Bartolini B., Gruber C.E., Di Caro A., Castilletti C., Stefani F., Rimoldi S.G., Romeri F., Salerno F., Polesello S., Nagy A., Jirincova H., Vecerova J., Novakova L., Cordey S., Murtskhvaladze M., Kotaria N., Schar T., Beisel C., Vugrek O., Rokic F., Trgovec-Greif L., Jurak I., Rukavina T., Sucic N., Schonning K., Karst S.M., Kirkegaard R.H., Michaelsen T.Y., Sorensen E.A., Knutson S., Brandt J., Le-Quy V., Sorensen T., Petersen C., Pedersen M.S., Larsen S.L., Skov M.N., Rasmussen M., Fonager J., Fomsgaard A., Maksyutov R.A., Gavrilova E.V., Pyankov O.V., Bodnev S.A., Tregubchak T.V., Shvalov A.N., Antonets D.V., Resende P.C., Goya S., Perrin A., Lee R.T., Yadahalli S., Han A.X., Russell C.A., Schmutz S., Zaheri M., Kufner V., Huber M., Trkola A., Antwerpen M., Walter M.C., van der Werf S., Gambaro F., Behillil S., Enouf V., Donati F., Ustinova M., Rovite V., Klovins J., Savicka O., Wienecke-Baldacchino A.K., Ragimbeau C., Fournier G., Mossong J., Aberle S.W., Haukland M., Enkirch T., Advani A., Karlberg M.L., Lindsjo O.K., Broddesson S., Slavikova M., Lickova M., Klempa B., Staronova E., Ticha E., Szemes T., Rusnakova D., Stadler T., Quer J., Anton A., Andres C., Pinana M., Garcia-Cehic D., Pumarola T., Izopet J., Gioula G., Exindari M., Papa A., Chatzidimitriou D., Metallidis S., Pappa S., Macek M., Geryk J., Broz P., Briksi A., Hubacek P., Drevinek P., Zajac M., Kvapil P., Holub M., Kvapilova K., Novotny A., Kasny M., Klempt P., Vapalahti O., Smura T., Sironen T., Selhorst P., Anthony C., Arien K., Simon-Loriere E., Rabalski L., Bienkowska-Szewczyk K., Borges V., Isidro J., Gomes J.P., Guiomar R., Pechirra P., Costa I., Duarte S., Vieira L., Pyrc K., Zuckerman N.S., Turdikulova S., Abdullaev A., Dalimova D., Abdurakhimov A., Tagliabracci A., Alessandrini F., Melchionda F., Onofri V., Turchi C., Bagnarelli P., Menzo S., Caucci S., Di Sante L., Popa A., Genger J.-W., Agerer B., Lercher A., Endler L., Smyth M., Penz T., Schuster M., Senekowitsch M., Laine J., Bock C., Bergthaler A., Shevtsov A., Kalendar R., Ramanculov Y., Graf A., Muenchhoff M., Keppler O.T., Krebs S., Blum H., Marcello A., Licastro D., D'Agaro P., Laubscher F., Vidanovic D., Tesovic B., Volkening J., Clementi N., Mancini N., Rupnik M., Mahnic A., Walker A., Houwaart T., Wienemann T., Vasconcelos M.K., Strelow D., Jensen B.-E.O., Senff T., Hulse L., Adams O., Andree M., Hauka S., Feldt T., Keitel V., Kindgen-Milles D., Timm J., Pfeffer K., Dilthey A.T., Moore C., Ozdarendeli A., Pavel S.T.I., Yetiskin H., Aydin G., Holyavkin C., Uygut M.A., Cevik C., Shchetinin A., Gushchin V., Dinler-Doganay G., Doganay L., Kizilboga-Akgun T., Karacan I., Pancer K., Maes P., Marti-Carreras J., Wawina-Bokalanga T., Vanmechelen B., Thurmer A., Wedde M., Durrwald R., von Kleist M., Drechsel O., Wolff T., Fuchs S., Kmiecinski R., Michel J., Nitsche A., Casas I., Caballero M.I., Zaballos A., Jimenez P., Jimenez M., Fernandez S.M., Fernandez S.V., de la Plaza I.C., Fadeev A., Ivanova A., Sergeeva M., Stefanelli P., Estee Torok M., Hall G., da Silva Filipe A., Turtle L., Afifi S., McCluggage K., Beer R., Ledesma J., Maksimovic J., Spellman K., Hamilton W.L., Marchbank A., Southgate J.A., Underwood A., Taylor B., Yeats C., Abudahab K., Gemmell M.R., Eccles R., Lucaci A., Nelson C.A., Rainbow L., Whitehead M., Gregory R., Haldenby S., Paterson S., Hughes M.A., Curran M.D., Baker D., Tucker R., Green L.R., Feltwell T., Halstead F.D., Wyles M., Jahun A.S., Ahmad S.S.Y., Georgana I., Goodfellow I., Yakovleva A., Meredith L.W., Gavriil A., Awan A.R., Fisher C., Edgeworth J., Lynch J., Moore N., Williams R., Kidd S.P., Cortes N., Brunker K., McCrone J.T., Quick J., Duckworth N., Walsh S., Sloan T., Ludden C., George R.P., Eltringham G., Brown J.R., Aranday-Cortes E., Shepherd J.G., Hughes J., Li K.K., Williams T.C., Johnson N., Jesudason N., Mair D., Thomson E., Shah R., Parr Y.A., Carmichael S., Robertson D.L., Nomikou K., Broos A., Niebel M., Smollett K., Tong L., Miah S., Wittner A., Phillips N., Payne B., Dewar R., Holmes A., Bolt F., Price J.R., Mookerjee S., Sethi D.K., Potter W., Stanley R., Prakash R., Dervisevic S., Graham J.C., Nelson A., Smith D., Young G.R., Yew W.C., Todd J.A., Trebes A., Andersson M., Bull M., Watkins J., Birchley A., Gatica-Wilcox B., Gilbert L., Kumziene-Summerhayes S., Rey S., Chauhan A., Butcher E., Bicknell K., Elliott S., Glaysher S., Lackenby A., Bibby D., Platt S., Mohamed H., Machin N.W., Mbisa J.L., Evans J., Perry M., Pacchiarini N., Corden S., Adams A.G., Gaskin A., Coombs J., Graham L.J., Cottrell S., Morgan M., Gifford L., Kolyva A., Rudder S.J., Trotter A.J., Mather A.E., Aydin A., Page A.J., Kay G.L., de Oliveira Martins L., Yasir M., Alikhan N.-F., Thomson N.M., Gilroy R., Kingsley R.A., O'Grady J., Gutierrez A.V., Diaz M., Viet T.L., Tedim A.P., Adriaenssens E.M., Patrick Mcclure C., Sang F., Clark G., Howson-Wells H.C., Debebe J., Ball J., Chappell J., Khakh M., Carlile M., Loose M., Lister M.M., Holmes N., Tsoleridis T., Fleming V.M., Wright V., Smith W., Gallagher M.D., Parker M., Partridge D.G., Evans C., Baker P., Essex S., Liggett S., Keeley A.J., Bashton M., Rooke S., Dervisavic S., Meader E.J., Lopez C.E.B., Angyal A., Kristiansen M., Tutill H.J., Findlay J., Mestek-Boukhibar L., Forrest L., Dyal P., Williams R.J., Panchbhaya Y., Williams C.A., Roy S., Pandey S., Stockton J., Loman N.J., Poplawski R., Nicholls S., Rowe W.P.M., Khokhar F., Pinckert M.L., Hosmillo M., Chaudhry Y., Caller L.G., Davidson R.K., Griffith L., Rambaut A., Jackson B., Colquhoun R., Hill V., Nichols J., Asamaphan P., Darby A., Jackson K.A., Iturriza-Gomara M., Vamos E.E., Green A., Aanensen D., Bonsall D., Buck D., Macintyre-Cockett G., de Cesare M., Pybus O., Golubchik T., Scarlett G., Loveson K.F., Robson S.C., Beckett A., Lindsey B., Groves D.C., Parsons P.J., McHugh M.P., Barnes J.D., Manso C.F., Grammatopoulos D., Menger K.E., Harrison E., Gunson R., Peacock S.J., Gonzalez G., Carr M., Mihaela L., Popovici O., Brytting M., Bresner C., Fuller W., Workman T., Mentis A.F., Kossyvakis A., Karamitros T., Pogka V., Kalliaropoulos A., Horefti E., Kontou A., Martinez-Gonzalez B., Labropoulou V., Voulgari-Kokota A., Evangelidou M., Bizta P., Belimezi M., Lambrechts L., Doymaz M.Z., Yazici M.K., Cetin N.S., Karaaslan E., Kallio-Kokko H., Virtanen J., Suvanto M., Nguyen P.T., Ellonen P., Hannula S., Kangas H., Sreenu V.B., Burian K., Terhes G., Gombos K., Gyenesei A., Urban P., Herczeg R., Jakab F., Kemenesi G., Toth G.E., Somogyi B., Zana B., Zeghbib S., Kuczmog A., Foldes F., Lanszki Z., Madai M., Papp H., Pereszlenyi C.I., Babinszky G.C., Dudas G., Csoma E., Abou Tayoun A.N., Alsheikh-Ali A.A., Loney T., Nowotny N., Abdul-Wahab O., Gonzalez-Candelas F., Andersen M.H., Taylor S., MARTI CARRERAS, Joan, Vanmechelen, Bert, Wawina, Tony, Medical Microbiology and Infection Prevention, AII - Infectious diseases, WHO European Region Sequencing Lab, GISAID EpiCoV Grp, Erik, Alm, Eeva K, Broberg, Thomas, Connor, Emma B, Hodcroft, Andrey B, Komissarov, Sebastian, Maurer-Stroh, Angeliki, Melidou, Richard A, Neher, Áine, O’Toole, Dmitriy, Pereyaslov, WHO European Region sequencing laboratories and GISAID EpiCoV group (Niko Beerenwinkel, The, Posada-Céspedes, Susana, Philipp, Kim, Jablonski, Falé Ferreira, Pedro, Topolsky, Ivan, Avšičžupanc, Tatjana, Korva, Miša, Poljak, Mario, Zakotnik, Samo, Tomaž, Zorec, Mark, Bragstad, Karoline, Hungnes, Olav, Stene-Johansen, Kathrine, Reusken, Chantal, Meijer, Adam, Vennema, Harry, Ruiz-Roldán, Lidia, Alma Bracho, María, García-González, Neri, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, A Goig, Galo, Torres-Puente, Manuela, G López, Mariana, Martínez-Priego, Llúcia, D’Auria, Giuseppe, LoretoFerrús-Abad, de Marco, Griselda, Galan-Vendrell, Inmaculada, Carbó-Ramirez, Sandra, Ruíz-Hueso, Paula, Coscollá, Mireia, Polackova, Katerina, Kramna, Lenka, Cinek, Ondrej, Richter, Jan, Krashias, George, Tryfonos, Christina, Bashiardes, Stavro, Koptides, Dana, Christodoulou, Christina, Bartolini, Barbara, Em Gruber, Cesare, Di Caro, Antonino, Castilletti, Concetta, Stefani, Fabrizio, Giordana Rimoldi, Sara, Romeri, Francesca, Salerno, Franco, Polesello, Stefano, Nagy, Alexander, Jirincova, Helena, Vecerova, Jaromira, Novakova, Ludmila, Cordey, Samuel, Murtskhvaladze, Marine, Kotaria, Nato, Schär, Tobia, Beisel, Christian, Vugrek, Oliver, Rokić, Filip, Trgovecgreif, Lovro, Jurak, Igor, Rukavina, Tomislav, Sučić, Neven, Schønning, Kristian, M Karst, Søren, H Kirkegaard, Rasmu, Y Michaelsen, Thoma, Aa Sørensen, Emil, Knutson, Simon, Brandt, Jakob, Le-Quy, Vang, Sørensen, Trine, Petersen, Celine, Schou Pedersen, Martin, Løkkegaard Larsen, Sanne, Nielsine Skov, Marianne, Rasmussen, Morten, Fonager, Jannik, Fomsgaard, Ander, Amirovich Maksyutov, Rinat, Vasil’Evna Gavrilova, Elena, Victorovich Pyankov, Oleg, Alexandrovich Bodnev, Sergey, Vladimirovna Tregubchak, Tatyana, Nikolayevich Shvalov, Alexander, Victorovich Antonets, Deni, Cristina Resende, Paola, Goya, Stephanie, Perrin, Amandine, Tc Lee, Raphael, Yadahalli, Shilpa, X Han, Alvin, A Russell, Colin, Schmutz, Stefan, Zaheri, Maryam, Kufner, Verena, Huber, Michael, Trkola, Alexandra, Antwerpen, Marku, C Walter, Mathia, van der Werf, Sylvie, Gambaro, Fabiana, Behillil, Sylvie, Enouf, Vincent, Donati, Flora, Ustinova, Monta, Rovite, Vita, Klovins, Jani, Savicka, Oksana, K Wienecke-Baldacchino, Anke, Ragimbeau, Catherine, Fournier, Guillaume, Mossong, Joël, W Aberle, Stephan, Haukland, Mattia, Enkirch, Theresa, Advani, Abdolreza, Lind Karlberg, Maria, Karlsson Lindsjö, Oskar, Broddesson, Sandra, Sláviková, Monika, Ličková, Martina, Klempa, Bori, Staroňová, Edita, Tichá, Elena, Szemes, Tomáš, Rusňáková, Diana, Stadler, Tanja, Quer, Josep, Anton, Andre, Andres, Cristina, Piñana, Maria, Garcia-Cehic, Damir, Pumarola, Toma, Izopet, Jacque, Gioula, Georgia, Exindari, Maria, Papa, Anna, Chatzidimitriou, Dimitrio, Metallidis, Symeon, Pappa, Stella, Macek Jr, Milan, Geryk, Jan, Brož, Petr, Briksí, Aleš, Hubáček, Petr, Dřevínek, Pavel, Zajac, Miroslav, Kvapil, Petr, Holub, Michal, Kvapilová, Kateřina, Novotný, Adam, Kašný, Martin, Klempt, Petr, Vapalahti, Olli, Smura, Teemu, Sironen, Tarja, Selhorst, Philippe, Anthony, Colin, Ariën, Kevin, Simon-Loriere, Etienne, Rabalski, Lukasz, Bienkowska-Szewczyk, Krystyna, Borges, Vítor, Isidro, Joana, Paulo Gomes, João, Guiomar, Raquel, Pechirra, Pedro, Costa, Inê, Duarte, Sílvia, Vieira, Luí, Pyrc, Krzysztof, S Zuckerman, Neta, Turdikulova, Shahlo, Abdullaev, Alisher, Dalimova, Dilbar, Abdurakhimov, Abror, Tagliabracci, Adriano, Alessandrini, Federica, Melchionda, Filomena, Onofri, Valerio, Turchi, Chiara, Bagnarelli, Patrizia, Menzo, Stefano, Caucci, Sara, Di Sante, Laura, Popa, Alexandra, Genger, Jakob-Wendelin, Agerer, Benedikt, Lercher, Alexander, Endler, Luka, Smyth, Mark, Penz, Thoma, Schuster, Michael, Senekowitsch, Martin, Laine, Jan, Bock, Christoph, Bergthaler, Andrea, Shevtsov, Alexandr, Kalendar, Ruslan, Ramanculov, Yerlan, Graf, Alexander, Muenchhoff, Maximilian, T Keppler, Oliver, Krebs, Stefan, Blum, Helmut, Marcello, Alessandro, Licastro, Danilo, D’Agaro, Pierlanfranco, Laubscher, Florian, Vidanovic, Dejan, Tesovic, Bojana, Volkening, Jeremy, Clementi, Nicola, Mancini, Nicasio, Rupnik, Maja, Mahnic, Aleksander, Walker, Andrea, Houwaart, Torsten, Wienemann, Tobia, Kohns Vasconcelos, Malte, Strelow, Daniel, Ole Jensen, Björn-Erik, Senff, Tina, Hülse, Lisanna, Adams, Ortwin, Andree, Marcel, Hauka, Sandra, Feldt, Torsten, Keitel, Verena, Kindgen-Milles, Detlef, Timm, Jörg, Pfeffer, Klau, T Dilthey, Alexander, Moore, Catherine, Ozdarendeli, Aykut, Terkis Islam Pavel, Shaikh, Yetiskin, Hazel, Aydin, Gunsu, Holyavkin, Can, Ali Uygut, Muhammet, Cevik, Ceren, Shchetinin, Alexey, Gushchin, Vladimir, Dinler-Doganay, Gizem, Doganay, Levent, Kizilboga-Akgun, Tugba, Karacan, Ilker, Pancer, Katarzyna, Maes, Piet, Martí-Carreras, Joan, Wawina-Bokalanga, Tony, Thürmer, Andrea, Wedde, Marianne, Dürrwald, Ralf, Von Kleist, Max, Drechsel, Oliver, Wolff, Thorsten, Fuchs, Stephan, Kmiecinski, Rene, Michel, Janine, Nitsche, Andrea, Casas, Inmaculada, Iglesias Caballero, María, Zaballos, Ángel, Jiménez, Pilar, Jiménez, Mercede, Monzón Fernández, Sara, Varona Fernández, Sarai, Cuesta De La Plaza, Isabel, Fadeev, Artem, Ivanova, Anna, Sergeeva, Mariia, Stefanelli, Paola, Estee Torok, M, Hall, Grant, da Silva Filipe, Ana, Turtle, Lance, Afifi, Safiah, Mccluggage, Kathryn, Beer, Robert, Ledesma, Juan, Maksimovic, Joshua, Spellman, Karla, L Hamilton, William, Marchbank, Angela, Alexander Southgate, Joel, Underwood, Anthony, Taylor, Ben, Yeats, Corin, Abudahab, Khalil, R Gemmell, Matthew, Eccles, Richard, Lucaci, Anita, Abigail Nelson, Charlotte, Rainbow, Lucille, Whitehead, Mark, Gregory, Richard, Haldenby, Sam, Paterson, Steve, A Hughes, Margaret, D Curran, Martin, Baker, David, Tucker, Rachel, R Green, Luke, Feltwell, Theresa, D Halstead, Fenella, Wyles, Matthew, S Jahun, Aminu, Y Ahmad, Shazaad S, Georgana, Iliana, Goodfellow, Ian, Yakovleva, Anna, W Meredith, Luke, Gavriil, Artemi, Raza Awan, Ali, Fisher, Chloe, Jonathan, European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Cardiff University, Public Health Wales [Cardiff, Royaume uni], University of Basel (Unibas), Research Institute of Influenza, St. Petersburg, Russia, Agency for science, technology and research [Singapore] (A*STAR), National University of Singapore (NUS), University of Edinburgh, WHO Regional Office for Europe [Copenhagen], We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible, The WHO European Region sequencing laboratories and GISAID EpiCoV group*: Niko Beerenwinkel, Susana Posada-Céspedes, Kim Philipp Jablonski, Pedro Falé Ferreira, Ivan Topolsky, Tatjana Avšič-Županc, Miša Korva, Mario Poljak, Samo Zakotnik, Tomaž Mark Zorec, Karoline Bragstad, Olav Hungnes, Kathrine Stene-Johansen, Chantal Reusken, Adam Meijer, Harry Vennema, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Álvaro Chiner-Oms, Irving Cancino-Muñoz, Iñaki Comas, Galo A Goig, Manuela Torres-Puente, Mariana G López, Llúcia Martínez-Priego, Giuseppe D'Auria, Paula Ruíz-Hueso, Loreto Ferrús-Abad, Griselda de Marco, Inmaculada Galan-Vendrell, Sandra Carbó-Ramirez, Paula Ruiz-Rodriguez, Mireia Coscollá, Katerina Polackova, Lenka Kramna, Ondrej Cinek, Jan Richter, George Krashias, Christina Tryfonos, Stavros Bashiardes, Dana Koptides, Christina Christodoulou, Barbara Bartolini, Cesare Em Gruber, Antonino Di Caro, Concetta Castilletti, Fabrizio Stefani, Sara Giordana Rimoldi, Francesca Romeri, Franco Salerno, Stefano Polesello, Alexander Nagy, Helena Jirincova, Jaromira Vecerova, Ludmila Novakova, Samuel Cordey, Marine Murtskhvaladze, Nato Kotaria, Tobias Schär, Christian Beisel, Oliver Vugrek, Filip Rokić, Lovro Trgovec-Greif, Igor Jurak, Tomislav Rukavina, Neven Sučić, Kristian Schønning, Søren M Karst, Rasmus H Kirkegaard, Thomas Y Michaelsen, Emil Aa Sørensen, Simon Knutson, Jakob Brandt, Vang Le-Quy, Trine Sørensen, Celine Petersen, Martin Schou Pedersen, Sanne Løkkegaard Larsen, Marianne Nielsine Skov, Morten Rasmussen, Jannik Fonager, Anders Fomsgaard, Rinat Amirovich Maksyutov, Elena Vasil'Evna Gavrilova, Oleg Victorovich Pyankov, Sergey Alexandrovich Bodnev, Tatyana Vladimirovna Tregubchak, Alexander Nikolayevich Shvalov, Denis Victorovich Antonets, Paola Cristina Resende, Stephanie Goya, Amandine Perrin, Raphael Tc Lee, Shilpa Yadahalli, Alvin X Han, Colin A Russell, Stefan Schmutz, Maryam Zaheri, Verena Kufner, Michael Huber, Alexandra Trkola, Markus Antwerpen, Mathias C Walter, Sylvie van der Werf, Fabiana Gambaro, Sylvie Behillil, Vincent Enouf, Flora Donati, Monta Ustinova, Vita Rovite, Janis Klovins, Oksana Savicka, Anke K Wienecke-Baldacchino, Catherine Ragimbeau, Guillaume Fournier, Joël Mossong, Stephan W Aberle, Mattias Haukland, Theresa Enkirch, Abdolreza Advani, Maria Lind Karlberg, Oskar Karlsson Lindsjö, Sandra Broddesson, Monika Sláviková, Martina Ličková, Boris Klempa, Edita Staroňová, Elena Tichá, Tomáš Szemes, Diana Rusňáková, Tanja Stadler, Josep Quer, Andres Anton, Cristina Andres, Maria Piñana, Damir Garcia-Cehic, Tomas Pumarola, Jacques Izopet, Georgia Gioula, Maria Exindari, Anna Papa, Dimitrios Chatzidimitriou, Symeon Metallidis, Stella Pappa, Milan Macek Jr, Jan Geryk, Petr Brož, Aleš Briksí, Petr Hubáček, Pavel Dřevínek, Miroslav Zajac, Petr Kvapil, Michal Holub, Kateřina Kvapilová, Adam Novotný, Martin Kašný, Petr Klempt, Olli Vapalahti, Teemu Smura, Tarja Sironen, Philippe Selhorst, Colin Anthony, Kevin Ariën, Etienne Simon-Loriere, Lukasz Rabalski, Krystyna Bienkowska-Szewczyk, Vítor Borges, Joana Isidro, João Paulo Gomes, Raquel Guiomar, Pedro Pechirra, Inês Costa, Sílvia Duarte, Luís Vieira, Krzysztof Pyrc, Neta S Zuckerman, Shahlo Turdikulova, Alisher Abdullaev, Dilbar Dalimova, Abror Abdurakhimov, Adriano Tagliabracci, Federica Alessandrini, Filomena Melchionda, Valerio Onofri, Chiara Turchi, Patrizia Bagnarelli, Stefano Menzo, Sara Caucci, Laura Di Sante, Alexandra Popa, Jakob-Wendelin Genger, Benedikt Agerer, Alexander Lercher, Lukas Endler, Mark Smyth, Thomas Penz, Michael Schuster, Martin Senekowitsch, Jan Laine, Christoph Bock, Andreas Bergthaler, Alexandr Shevtsov, Ruslan Kalendar, Yerlan Ramanculov, Alexander Graf, Maximilian Muenchhoff, Oliver T Keppler, Stefan Krebs, Helmut Blum, Alessandro Marcello, Danilo Licastro, Pierlanfranco D'Agaro, Florian Laubscher, Dejan Vidanovic, Bojana Tesovic, Jeremy Volkening, Nicola Clementi, Nicasio Mancini, Maja Rupnik, Aleksander Mahnic, Andreas Walker, Torsten Houwaart, Tobias Wienemann, Malte Kohns Vasconcelos, Daniel Strelow, Björn-Erik Ole Jensen, Tina Senff, Lisanna Hülse, Ortwin Adams, Marcel Andree, Sandra Hauka, Torsten Feldt, Verena Keitel, Detlef Kindgen-Milles, Jörg Timm, Klaus Pfeffer, Alexander T Dilthey, Catherine Moore, Aykut Ozdarendeli, Shaikh Terkis Islam Pavel, Hazel Yetiskin, Gunsu Aydin, Can Holyavkin, Muhammet Ali Uygut, Ceren Cevik, Alexey Shchetinin, Vladimir Gushchin, Gizem Dinler-Doganay, Levent Doganay, Tugba Kizilboga-Akgun, Ilker Karacan, Katarzyna Pancer, Piet Maes, Joan Martí-Carreras, Tony Wawina-Bokalanga, Bert Vanmechelen, Andrea Thürmer, Marianne Wedde, Ralf Dürrwald, Max Von Kleist, Oliver Drechsel, Thorsten Wolff, Stephan Fuchs, Rene Kmiecinski, Janine Michel, Andreas Nitsche, Inmaculada Casas, María Iglesias Caballero, Ángel Zaballos, Pilar Jiménez, Mercedes Jiménez, Sara Monzón Fernández, Sarai Varona Fernández, Isabel Cuesta De La Plaza, Artem Fadeev, Anna Ivanova, Mariia Sergeeva, Paola Stefanelli, M Estee Torok, Grant Hall, Ana da Silva Filipe, Lance Turtle, Safiah Afifi, Kathryn Mccluggage, Robert Beer, Juan Ledesma, Joshua Maksimovic, Karla Spellman, William L Hamilton, Angela Marchbank, Joel Alexander Southgate, Anthony Underwood, Ben Taylor, Corin Yeats, Khalil Abudahab, Matthew R Gemmell, Richard Eccles, Anita Lucaci, Charlotte Abigail Nelson, Lucille Rainbow, Mark Whitehead, Richard Gregory, Sam Haldenby, Steve Paterson, Margaret A Hughes, Martin D Curran, David Baker, Rachel Tucker, Luke R Green, Theresa Feltwell, Fenella D Halstead, Matthew Wyles, Aminu S Jahun, Shazaad S Y Ahmad, Iliana Georgana, Ian Goodfellow, Anna Yakovleva, Luke W Meredith, Artemis Gavriil, Ali Raza Awan, Chloe Fisher, Jonathan Edgeworth, Jessica Lynch, Nathan Moore, Rebecca Williams, Stephen P Kidd, Nicholas Cortes, Kirstyn Brunker, John T Mccrone, Joshua Quick, Nichola Duckworth, Sarah Walsh, Tim Sloan, Catherine Ludden, Ryan P George, Gary Eltringham, Julianne R Brown, Elihu Aranday-Cortes, James G Shepherd, Joseph Hughes, Kathy K Li, Thomas C Williams, Natasha Johnson, Natasha Jesudason, Daniel Mair, Emma Thomson, Rajiv Shah, Yasmin A Parr, Stephen Carmichael, David L Robertson, Kyriaki Nomikou, Alice Broos, Marc Niebel, Katherine Smollett, Lily Tong, Shahjahan Miah, Anita Wittner, Nicole Phillips, Brendan Payne, Rebecca Dewar, Alison Holmes, Frances Bolt, James R Price, Siddharth Mookerjee, Dheeraj K Sethi, Will Potter, Rachael Stanley, Reenesh Prakash, Samir Dervisevic, Jonathan Clive Graham, Andrew Nelson, Darren Smith, Gregory R Young, Wen Chyin Yew, John A Todd, Amy Trebes, Monique Andersson, Matthew Bull, Joanne Watkins, Alec Birchley, Bree Gatica-Wilcox, Lauren Gilbert, Sara Kumžiene-Summerhayes, Sara Rey, Anoop Chauhan, Ethan Butcher, Kelly Bicknell, Scott Elliott, Sharon Glaysher, Angie Lackenby, David Bibby, Steven Platt, Hodan Mohamed, Nicholas William Machin, Jean Lutamyo Mbisa, Jonathan Evans, Malorie Perry, Nicole Pacchiarini, Sally Corden, Alexander Geraint Adams, Amy Gaskin, Jason Coombs, Lee John Graham, Simon Cottrell, Mari Morgan, Laura Gifford, Anastasia Kolyva, Steven John Rudder, Alexander J Trotter, Alison E Mather, Alp Aydin, Andrew J Page, Gemma L Kay, Leonardo de Oliveira Martins, Muhammad Yasir, Nabil-Fareed Alikhan, Nicholas M Thomson, Rachel Gilroy, Robert A Kingsley, Justin O'Grady, Ana Victoria Gutierrez, Maria Diaz, Thanh Le Viet, Ana P Tedim, Evelien M Adriaenssens, C Patrick Mcclure, Christopher Moore, Fei Sang, Gemma Clark, Hannah C Howson-Wells, Johnny Debebe, Jonathan Ball, Joseph Chappell, Manjinder Khakh, Matthew Carlile, Matthew Loose, Michelle M Lister, Nadine Holmes, Theocharis Tsoleridis, Vicki M Fleming, Victoria Wright, Wendy Smith, Michael D Gallagher, Matthew Parker, David G Partridge, Cariad Evans, Paul Baker, Sarah Essex, Steven Liggett, Alexander J Keeley, Matthew Bashton, Stefan Rooke, Samir Dervisevic, Emma Jane Meader, Carlos Enrique Balcazar Lopez, Adrienn Angyal, Mark Kristiansen, Helena J Tutill, Jacqueline Findlay, Lamia Mestek-Boukhibar, Leysa Forrest, Patricia Dyal, Rachel J Williams, Yasmin Panchbhaya, Charlotte A Williams, Sunando Roy, Sarojini Pandey, Jo Stockton, Nicholas J Loman, Radoslaw Poplawski, Samuel Nicholls, W P M Rowe, Fahad Khokhar, Malte Lars Pinckert, Myra Hosmillo, Yasmin Chaudhry, Laura G Caller, Rose K Davidson, Luke Griffith, Andrew Rambaut, Ben Jackson, Rachel Colquhoun, Verity Hill, Jenna Nichols, Patawee Asamaphan, Alistair Darby, Kathryn A Jackson, Miren Iturriza-Gomara, Ecaterina Edith Vamos, Angie Green, David Aanensen, David Bonsall, David Buck, George Macintyre-Cockett, Mariateresa de Cesare, Oliver Pybus, Tanya Golubchik, Garry Scarlett, Katie F Loveson, Samuel C Robson, Angela Beckett, Benjamin Lindsey, Danielle C Groves, Paul J Parsons, Martin P Mchugh, James Daniel Barnes, Carmen F Manso, Dimitris Grammatopoulos, Katja Elisabeth Menger, Ewan Harrison, Rory Gunson, Sharon J Peacock, Gabriel Gonzalez, Michael Carr, Lazar Mihaela, Odette Popovici, Mia Brytting, Catherine Bresner, William Fuller, Trudy Workman, Andreas F Mentis, Athanasios Kossyvakis, Timokratis Karamitros, Vasiliki Pogka, Antonios Kalliaropoulos, Elina Horefti, Aspasia Kontou, Beatriz Martinez-Gonzalez, Voula Labropoulou, Androniki Voulgari-Kokota, Maria Evangelidou, Panagiota Bizta, Maria Belimezi, Laurens Lambrechts, Mehmet Z Doymaz, Merve Kalkan Yazici, Nesibe S Cetin, Elif Karaaslan, Hannimari Kallio-Kokko, Jenni Virtanen, Maija Suvanto, Phuoc Truong Nguyen, Pekka Ellonen, Sari Hannula, Harri Kangas, Vattipally B Sreenu, Katalin Burián, Gabriella Terhes, Katalin Gombos, Attila Gyenesei, Péter Urbán, Róbert Herczeg, Ferenc Jakab, Gábor Kemenesi, Gábor Endre Tóth, Balázs Somogyi, Brigitta Zana, Safia Zeghbib, Anett Kuczmog, Fanni Földes, Zsófia Lanszki, Mónika Madai, Henrietta Papp, Ágnes Nagy, Csaba István Pereszlényi, Gergely Csaba Babinszky, Gábor Dudás, Eszter Csoma, Ahmad N Abou Tayoun, Alawi A Alsheikh-Ali, Tom Loney, Norbert Nowotny, Osama Abdul-Wahab, Fernando Gonzalez-Candelas, Martin H Andersen, Sarah Taylor, Comas, Iñaki [0000-0001-5504-9408], Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., Melidou, A., Neher, R. A., O'Toole, A., Pereyaslov, D., Beerenwinkel, N., Posada-Cespedes, S., Jablonski, K. P., Ferreira, P. F., Topolsky, I., Avsic-Zupanc, T., Korva, M., Poljak, M., Zakotnik, S., Zorec, T. M., Bragstad, K., Hungnes, O., Stene-Johansen, K., Reusken, C., Meijer, A., Vennema, H., Ruiz-Roldan, L., Bracho, M. A., Garcia-Gonzalez, N., Chiner-Oms, A., Cancino-Munoz, I., Comas, I., Goig, G. A., Torres-Puente, M., Lopez, M. G., Martinez-Priego, L., D'Auria, G., Ruiz-Hueso, P., Ferrus-Abad, L., de Marco, G., Galan-Vendrell, I., Carbo-Ramirez, S., Ruiz-Rodriguez, P., Coscolla, M., Polackova, K., Kramna, L., Cinek, O., Richter, J., Krashias, G., Tryfonos, C., Bashiardes, S., Koptides, D., Christodoulou, C., Bartolini, B., Gruber, C. E., Di Caro, A., Castilletti, C., Stefani, F., Rimoldi, S. G., Romeri, F., Salerno, F., Polesello, S., Nagy, A., Jirincova, H., Vecerova, J., Novakova, L., Cordey, S., Murtskhvaladze, M., Kotaria, N., Schar, T., Beisel, C., Vugrek, O., Rokic, F., Trgovec-Greif, L., Jurak, I., Rukavina, T., Sucic, N., Schonning, K., Karst, S. M., Kirkegaard, R. H., Michaelsen, T. Y., Sorensen, E. A., Knutson, S., Brandt, J., Le-Quy, V., Sorensen, T., Petersen, C., Pedersen, M. S., Larsen, S. L., Skov, M. N., Rasmussen, M., Fonager, J., Fomsgaard, A., Maksyutov, R. A., Gavrilova, E. V., Pyankov, O. V., Bodnev, S. A., Tregubchak, T. V., Shvalov, A. N., Antonets, D. V., Resende, P. C., Goya, S., Perrin, A., Lee, R. T., Yadahalli, S., Han, A. X., Russell, C. A., Schmutz, S., Zaheri, M., Kufner, V., Huber, M., Trkola, A., Antwerpen, M., Walter, M. C., van der Werf, S., Gambaro, F., Behillil, S., Enouf, V., Donati, F., Ustinova, M., Rovite, V., Klovins, J., Savicka, O., Wienecke-Baldacchino, A. K., Ragimbeau, C., Fournier, G., Mossong, J., Aberle, S. W., Haukland, M., Enkirch, T., Advani, A., Karlberg, M. L., Lindsjo, O. K., Broddesson, S., Slavikova, M., Lickova, M., Klempa, B., Staronova, E., Ticha, E., Szemes, T., Rusnakova, D., Stadler, T., Quer, J., Anton, A., Andres, C., Pinana, M., Garcia-Cehic, D., Pumarola, T., Izopet, J., Gioula, G., Exindari, M., Papa, A., Chatzidimitriou, D., Metallidis, S., Pappa, S., Macek, M., Geryk, J., Broz, P., Briksi, A., Hubacek, P., Drevinek, P., Zajac, M., Kvapil, P., Holub, M., Kvapilova, K., Novotny, A., Kasny, M., Klempt, P., Vapalahti, O., Smura, T., Sironen, T., Selhorst, P., Anthony, C., Arien, K., Simon-Loriere, E., Rabalski, L., Bienkowska-Szewczyk, K., Borges, V., Isidro, J., Gomes, J. P., Guiomar, R., Pechirra, P., Costa, I., Duarte, S., Vieira, L., Pyrc, K., Zuckerman, N. S., Turdikulova, S., Abdullaev, A., Dalimova, D., Abdurakhimov, A., Tagliabracci, A., Alessandrini, F., Melchionda, F., Onofri, V., Turchi, C., Bagnarelli, P., Menzo, S., Caucci, S., Di Sante, L., Popa, A., Genger, J. -W., Agerer, B., Lercher, A., Endler, L., Smyth, M., Penz, T., Schuster, M., Senekowitsch, M., Laine, J., Bock, C., Bergthaler, A., Shevtsov, A., Kalendar, R., Ramanculov, Y., Graf, A., Muenchhoff, M., Keppler, O. T., Krebs, S., Blum, H., Marcello, A., Licastro, D., D'Agaro, P., Laubscher, F., Vidanovic, D., Tesovic, B., Volkening, J., Clementi, N., Mancini, N., Rupnik, M., Mahnic, A., Walker, A., Houwaart, T., Wienemann, T., Vasconcelos, M. K., Strelow, D., Jensen, B. -E. O., Senff, T., Hulse, L., Adams, O., Andree, M., Hauka, S., Feldt, T., Keitel, V., Kindgen-Milles, D., Timm, J., Pfeffer, K., Dilthey, A. T., Moore, C., Ozdarendeli, A., Pavel, S. T. I., Yetiskin, H., Aydin, G., Holyavkin, C., Uygut, M. A., Cevik, C., Shchetinin, A., Gushchin, V., Dinler-Doganay, G., Doganay, L., Kizilboga-Akgun, T., Karacan, I., Pancer, K., Maes, P., Marti-Carreras, J., Wawina-Bokalanga, T., Vanmechelen, B., Thurmer, A., Wedde, M., Durrwald, R., von Kleist, M., Drechsel, O., Wolff, T., Fuchs, S., Kmiecinski, R., Michel, J., Nitsche, A., Casas, I., Caballero, M. I., Zaballos, A., Jimenez, P., Jimenez, M., Fernandez, S. M., Fernandez, S. V., de la Plaza, I. C., Fadeev, A., Ivanova, A., Sergeeva, M., Stefanelli, P., Estee Torok, M., Hall, G., da Silva Filipe, A., Turtle, L., Afifi, S., Mccluggage, K., Beer, R., Ledesma, J., Maksimovic, J., Spellman, K., Hamilton, W. L., Marchbank, A., Southgate, J. A., Underwood, A., Taylor, B., Yeats, C., Abudahab, K., Gemmell, M. R., Eccles, R., Lucaci, A., Nelson, C. A., Rainbow, L., Whitehead, M., Gregory, R., Haldenby, S., Paterson, S., Hughes, M. A., Curran, M. D., Baker, D., Tucker, R., Green, L. R., Feltwell, T., Halstead, F. D., Wyles, M., Jahun, A. S., Ahmad, S. S. Y., Georgana, I., Goodfellow, I., Yakovleva, A., Meredith, L. W., Gavriil, A., Awan, A. R., Fisher, C., Edgeworth, J., Lynch, J., Moore, N., Williams, R., Kidd, S. P., Cortes, N., Brunker, K., Mccrone, J. T., Quick, J., Duckworth, N., Walsh, S., Sloan, T., Ludden, C., George, R. P., Eltringham, G., Brown, J. R., Aranday-Cortes, E., Shepherd, J. G., Hughes, J., Li, K. K., Williams, T. C., Johnson, N., Jesudason, N., Mair, D., Thomson, E., Shah, R., Parr, Y. A., Carmichael, S., Robertson, D. L., Nomikou, K., Broos, A., Niebel, M., Smollett, K., Tong, L., Miah, S., Wittner, A., Phillips, N., Payne, B., Dewar, R., Holmes, A., Bolt, F., Price, J. R., Mookerjee, S., Sethi, D. K., Potter, W., Stanley, R., Prakash, R., Dervisevic, S., Graham, J. C., Nelson, A., Smith, D., Young, G. R., Yew, W. C., Todd, J. A., Trebes, A., Andersson, M., Bull, M., Watkins, J., Birchley, A., Gatica-Wilcox, B., Gilbert, L., Kumziene-Summerhayes, S., Rey, S., Chauhan, A., Butcher, E., Bicknell, K., Elliott, S., Glaysher, S., Lackenby, A., Bibby, D., Platt, S., Mohamed, H., Machin, N. W., Mbisa, J. L., Evans, J., Perry, M., Pacchiarini, N., Corden, S., Adams, A. G., Gaskin, A., Coombs, J., Graham, L. J., Cottrell, S., Morgan, M., Gifford, L., Kolyva, A., Rudder, S. J., Trotter, A. J., Mather, A. E., Aydin, A., Page, A. J., Kay, G. L., de Oliveira Martins, L., Yasir, M., Alikhan, N. -F., Thomson, N. M., Gilroy, R., Kingsley, R. A., O'Grady, J., Gutierrez, A. V., Diaz, M., Viet, T. L., Tedim, A. P., Adriaenssens, E. M., Patrick Mcclure, C., Sang, F., Clark, G., Howson-Wells, H. C., Debebe, J., Ball, J., Chappell, J., Khakh, M., Carlile, M., Loose, M., Lister, M. M., Holmes, N., Tsoleridis, T., Fleming, V. M., Wright, V., Smith, W., Gallagher, M. D., Parker, M., Partridge, D. G., Evans, C., Baker, P., Essex, S., Liggett, S., Keeley, A. J., Bashton, M., Rooke, S., Dervisavic, S., Meader, E. J., Lopez, C. E. B., Angyal, A., Kristiansen, M., Tutill, H. J., Findlay, J., Mestek-Boukhibar, L., Forrest, L., Dyal, P., Williams, R. J., Panchbhaya, Y., Williams, C. A., Roy, S., Pandey, S., Stockton, J., Loman, N. J., Poplawski, R., Nicholls, S., Rowe, W. P. M., Khokhar, F., Pinckert, M. L., Hosmillo, M., Chaudhry, Y., Caller, L. G., Davidson, R. K., Griffith, L., Rambaut, A., Jackson, B., Colquhoun, R., Hill, V., Nichols, J., Asamaphan, P., Darby, A., Jackson, K. A., Iturriza-Gomara, M., Vamos, E. E., Green, A., Aanensen, D., Bonsall, D., Buck, D., Macintyre-Cockett, G., de Cesare, M., Pybus, O., Golubchik, T., Scarlett, G., Loveson, K. F., Robson, S. C., Beckett, A., Lindsey, B., Groves, D. C., Parsons, P. J., Mchugh, M. P., Barnes, J. D., Manso, C. F., Grammatopoulos, D., Menger, K. E., Harrison, E., Gunson, R., Peacock, S. J., Gonzalez, G., Carr, M., Mihaela, L., Popovici, O., Brytting, M., Bresner, C., Fuller, W., Workman, T., Mentis, A. F., Kossyvakis, A., Karamitros, T., Pogka, V., Kalliaropoulos, A., Horefti, E., Kontou, A., Martinez-Gonzalez, B., Labropoulou, V., Voulgari-Kokota, A., Evangelidou, M., Bizta, P., Belimezi, M., Lambrechts, L., Doymaz, M. Z., Yazici, M. K., Cetin, N. S., Karaaslan, E., Kallio-Kokko, H., Virtanen, J., Suvanto, M., Nguyen, P. T., Ellonen, P., Hannula, S., Kangas, H., Sreenu, V. B., Burian, K., Terhes, G., Gombos, K., Gyenesei, A., Urban, P., Herczeg, R., Jakab, F., Kemenesi, G., Toth, G. E., Somogyi, B., Zana, B., Zeghbib, S., Kuczmog, A., Foldes, F., Lanszki, Z., Madai, M., Papp, H., Pereszlenyi, C. I., Babinszky, G. C., Dudas, G., Csoma, E., Abou Tayoun, A. N., Alsheikh-Ali, A. A., Loney, T., Nowotny, N., Abdul-Wahab, O., Gonzalez-Candelas, F., Andersen, M. H., Taylor, S., European Centre for Disease Prevention and Control (ECDC), Public Health Wales Microbiology Cardiff, Faculty of Agriculture and Forestry, Department of Agricultural Sciences, and Institute of Biotechnology
Subjects: Infecções Respiratórias, 0301 basic medicine, MESH: Coronavirus Infections, Epidemiology, [SDV]Life Sciences [q-bio], Distribution (economics), Wastewater, MESH: Base Sequence, Severe Acute Respiratory Syndrome, MESH: World Health Organization, Pandemic, MESH: Coronavirus, MESH: COVID-19, Sequencing, Viral, Clade, Nomenclature, Genome, biology, COVID-19, Europe, NGS, SARS-CoV-2, WGS, nomenclature, sequencing, Base Sequence, Betacoronavirus, Coronavirus, Coronavirus Infections, Genome, Viral, Humans, Phylogeography, Pneumonia, Viral, RNA, Viral, RNA-Dependent RNA Polymerase, Spatio-Temporal Analysis, World Health Organization, Pandemics, C500, European region, 3. Good health, Geography, MESH: Phylogeography, MESH: RNA-Dependent RNA Polymerase, MESH: RNA, Viral, MESH: Betacoronavirus, Spatio-Temporal Analysi, MESH: Genome, Viral, Cartography, Human, Bioquímica, MESH: Pandemics, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronaviru, 030106 microbiology, 03 medical and health sciences, MESH: Spatio-Temporal Analysis, MESH: Severe Acute Respiratory Syndrome, Virology, MESH: SARS-CoV-2, Whole genome sequencing, MESH: Humans, Whole Genome Sequencing, Betacoronaviru, Coronavirus Infection, business.industry, Public Health, Environmental and Occupational Health, Pneumonia, biology.organism_classification, B900, 030104 developmental biology, MESH: Pneumonia, Viral, RNA, SARS_CoV-2, 3111 Biomedicine, MESH: Europe, Human medicine, business
Abstract: 8 páginas, 3 figuras, We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2., We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible.
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30. Kırklareli Bölgesindeki Hyalomma Scupense ve Rhipicephalus Bursa Kenelerinin RNAVirom Analizi

Author: AKYILDIZ, GÜRKAN and Özdemir A., Erdin M., POLAT C., AKYILDIZ G., Smura T., KAR S., PINAR A., Sironen T., ERGÜNAY K.
Published: 2022

31. Zika Virus Infection with Prolonged Maternal Viremia and Fetal Brain Abnormalities.

Author: Driggers, R. W., Ho, C.-Y., Korhonen, E. M., Kuivanen, S., Jääskeläinen, A. J., Smura, T., Rosenberg, A., Hill, D. A., DeBiasi, R. L., Vezina, G., Timofeev, J., Rodriguez, F. J., Levanov, L., Razak, J., Iyengar, P., Hennenfent, A., Kennedy, R., Lanciotti, R., du Plessis, A., and Vapalahti, O.
Subjects: *BRAIN abnormalities, *BRAIN, *COMMUNICABLE diseases, *EPIDEMICS, *FETAL ultrasonic imaging, *MAGNETIC resonance imaging, *PREGNANCY complications, *QUESTIONNAIRES, *VIREMIA, *CRANIOFACIAL abnormalities
Abstract: The current outbreak of Zika virus (ZIKV) infection has been associated with an apparent increased risk of congenital microcephaly. We describe a case of a pregnant woman and her fetus infected with ZIKV during the 11th gestational week. The fetal head circumference decreased from the 47th percentile to the 24th percentile between 16 and 20 weeks of gestation. ZIKV RNA was identified in maternal serum at 16 and 21 weeks of gestation. At 19 and 20 weeks of gestation, substantial brain abnormalities were detected on ultrasonography and magnetic resonance imaging (MRI) without the presence of microcephaly or intracranial calcifications. On postmortem analysis of the fetal brain, diffuse cerebral cortical thinning, high ZIKV RNA loads, and viral particles were detected, and ZIKV was subsequently isolated. [ABSTRACT FROM AUTHOR]
Published: 2016
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32. Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction

Author: Riitta Lahesmaa, Teemu Smura, Jonathan R. T. Lakey, Svetlana Kaijalainen, Helena Ahlfors, Olle Korsgren, Lorenzo Piemonti, Petri Ylipaasto, Peddinti Gopalacharyulu, Anja Paananen, Matej Orešič, Tuulikki Seppänen-Laakso, Merja Roivainen, Jochem M. D. Galama, Ylipaasto, P, Smura, T, Gopalacharyulu, P, Paananen, A, Seppanen Laakso, T, Kaijalainen, S, Ahlfors, H, Korsgren, O, Lakey, Jrt, Lahesmaa, R, Piemonti, Lorenzo, Oresic, M, Galama, J, and Roivainen, M.
Subjects: Male, Echovirus, type 1 diabetes, viruses, Endocrinology, Diabetes and Metabolism, Interleukin-1beta, medicine.disease_cause, Mice, tumour necrosis factor, Cytopathogenic Effect, Viral, Interleukin-1alpha, Coxsackievirus, Cells, Cultured, geography.geographical_feature_category, biology, enterovirus, echovirus, Middle Aged, Islet, Immunohistochemistry, Enterovirus B, Human, medicine.anatomical_structure, Female, Beta cell, pancreatic beta cells, interleukin 1, Virus, Necrosis, Immune system, SDG 3 - Good Health and Well-being, Enterovirus Infections, Internal Medicine, medicine, Animals, Humans, Inflammation, geography, pancreatic islets, Tumor Necrosis Factor-alpha, Pancreatic islets, biology.organism_classification, Virology, Immunity, Innate, Diabetes Mellitus, Type 1, Gene Expression Regulation, Immunology, Enterovirus, microarray analysis
Abstract: Aims/hypothesisVirally induced inflammatory responses, beta cell destruction and release of beta cell autoantigens may lead to autoimmune reactions culminating in type 1 diabetes. Therefore, viral capability to induce beta cell death and the nature of virus-induced immune responses are among key determinants of diabetogenic viruses. We hypothesised that enterovirus infection induces a specific gene expression pattern that results in islet destruction and that such a host response pattern is not shared among all enterovirus infections but varies between virus strains.MethodsThe changes in global gene expression and secreted cytokine profiles induced by lytic or benign enterovirus infections were studied in primary human pancreatic islet using DNA microarrays and viral strains either isolated at the clinical onset of type 1 diabetes or capable of causing a diabetes-like condition in mice.ResultsThe expression of pro-inflammatory cytokine genes (IL-1-α, IL-1-β and TNF-α) that also mediate cytokine-induced beta cell dysfunction correlated with the lytic potential of a virus. Temporally increasing gene expression levels of double-stranded RNA recognition receptors, antiviral molecules, cytokines and chemokines were detected for all studied virus strains. Lytic coxsackievirus B5 (CBV-5)-DS infection also downregulated genes involved in glycolysis and insulin secretion.Conclusions/interpretationThe results suggest a distinct, virus-strain-specific, gene expression pattern leading to pancreatic islet destruction and pro-inflammatory effects after enterovirus infection. However, neither viral replication nor cytotoxic cytokine production alone are sufficient to induce necrotic cell death. More likely the combined effect of these and possibly cellular energy depletion lie behind the enterovirus-induced necrosis of islets.
Published: 2012

33. CELLULAR TROPISM OF HUMAN ENTEROVIRUS D SPECIES SEROTYPES EV-94, EV-70 AND EV-68 IN VITRO – IMPLICATIONS FOR PATHOGENESIS

Author: Lorenzo Piemonti, Päivi Klemola, Valeria Sordi, Lauri Kyllönen, Petri Ylipaasto, Svetlana Kaijalainen, Merja Roivainen, Teemu Smura, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare [Helsinki], Surgical Hospital, Division of Transplantation, University of Helsinki, San Raffaele Scientific Institute, Diabetes Research Institute (HSR-DRI), Smura, T, Ylipaasto, P, Klemola, P, Kaijalainen, S, Kyllonen, L, Sordi, V, Piemonti, Lorenzo, and Roivainen, M.
Subjects: Cell type, Umbilical Veins, Enterovirus D, Biology, medicine.disease_cause, Virus Replication, Virus, Cell Line, 03 medical and health sciences, Islets of Langerhans, Species Specificity, Seroepidemiologic Studies, Virology, medicine, Enterovirus Infections, Leukocytes, Animals, Humans, Serotyping, Tropism, Cells, Cultured, 030304 developmental biology, Enterovirus D, Human, 0303 health sciences, 030306 microbiology, Pancreatic islets, Endothelial Cells, 3. Good health, Endothelial stem cell, Infectious Diseases, medicine.anatomical_structure, Diabetes Mellitus, Type 1, Tissue tropism, Enterovirus, Medicine
Abstract: Enterovirus 94 (EV-94) is an enterovirus serotype described recently which, together with EV-68 and EV-70, forms human enterovirus D species. This study investigates the seroprevalences of these three serotypes and their abilities to infect, replicate, and damage cell types considered to be essential for enterovirus-induced diseases. The cell types studied included human leukocyte cell lines, primary endothelial cells, and pancreatic islets. High prevalence of neutralizing antibodies against EV-68 and EV-94 was found in the Finnish population. The virus strains studied had wide leukocyte tropism. EV-94 and EV-68 were able to produce infectious progeny in leukocyte cell lines with monocytic, granulocytic, T-cell, or B-cell characteristics. EV-94 and EV-70 were capable of infecting primary human umbilical vein endothelial cells, whereas EV-68 had only marginal progeny production and did not induce cytopathic effects in these cells. Intriguingly, EV-94 was able to damage pancreatic islet beta-cells, to infect, replicate, and cause necrosis in human pancreatic islets, and to induce proinflammatory and chemoattractive cytokine expression in endothelial cells. These results suggest that HEV-D viruses may be more prevalent than has been thought previously, and they provide in vitro evidence that EV-94 may be a potent pathogen and should be considered a potentially diabetogenic enterovirus type. J. Med. Virol. 82: 1940-1949, 2010. (C) 2010 Wiley-Liss, Inc.
Published: 2010

34. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Author: Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, and Iqbal Z
Abstract: The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org . Each genome was constructed using a novel assembly tool called Viridian ( https://github.com/iqbal-lab-org/viridian ), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.
Published: 2024
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35. No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota.

Author: Parry RH, Lytras S, Petrone ME, Wille M, Crits-Christoph A, Gifford RJ, Saito A, Smura T, and Peacock TP
Abstract: Understanding the origin and evolution of mutations in SARS-CoV-2 variants of concern (VOCs) is a critical area of research. B. Cao, X. Wang, W. Yin, Z. Gao, and B. Xia (mBio 15:e03187-23, 2024, https://doi.org/10.1128/mbio.03187-23) proposed that these mutations originated from bacterial sequences incorporated into the viral genome through stochastic template-switching by the viral RNA-dependent RNA polymerase (RdRp). Their analysis suggested that 62% of the viral mutation fragments (VMFs) in key SARS-CoV-2 proteins were identical to bacterial protein sequences. Given the implications of this finding, we re-examined the methods employed and argue that they resulted in false-positive findings. Specifically, the short query length of VMFs, seven amino acids, leads to spurious matches in large protein databases, as indicated by high BLAST Expect values. Furthermore, we analyzed the nucleotide sequence of VMFs, revealing no unique homology between SARS-CoV-2 and bacterial sequences. Consequently, the evidence does not support the hypothesis that bacterial sequences contribute to the evolution of SARS-CoV-2 VOCs. Instead, the emergence of these variants is more plausibly attributed to factors intrinsic to viral replication and evolution, such as the error-prone nature of RdRp, intrahost diversity, and recombination of related viral sublineages.
Published: 2024
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36. Infective SARS-CoV-2 in Skull Sawdust at Autopsy, Finland.

Author: Kantonen JN, Kuivanen S, Smura T, Puttonen H, Kekäläinen E, Sajantila A, Myllykangas L, Kantele A, Vapalahti O, Mäyränpää MI, and Carpén O
Subjects: Humans, Finland epidemiology, Male, Female, Occupational Exposure, Middle Aged, Aged, Adult, Personal Protective Equipment, Aged, 80 and over, COVID-19 epidemiology, COVID-19 virology, COVID-19 pathology, SARS-CoV-2 genetics, SARS-CoV-2 isolation & purification, Autopsy, Skull pathology, Skull virology
Abstract: We assessed the distribution of SARS-CoV-2 at autopsy in 22 deceased persons with confirmed COVID-19. SARS-CoV-2 was found by PCR (2/22, 9.1%) and by culture (1/22, 4.5%) in skull sawdust, suggesting that live virus is present in tissues postmortem, including bone. Occupational exposure risk is low with appropriate personal protective equipment.
Published: 2024
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37. Complete coding sequence of an Aedes flavivirus strain isolated from Aedes albopictus collected in Northern Italy.

Author: Korhonen EM, Truong Nguyen PT, Faolotto G, Suvanto MT, Nicosia AM, Crobu MG, Grasso I, Vapalahti O, Smura T, Ravanini P, and Huhtamo E
Abstract: Complete genome data for the globally distributed Aedes flavivirus (AEFV) is scarce. We analyzed a new Italian AEFV strain isolated from Aedes albopictus . The results demonstrated genetic diversity among Italian AEFVs. The high similarity between AEFV genomes across geographically distant regions suggests long distance spreading via invasive host mosquito species., Competing Interests: The authors declare no conflict of interest.
Published: 2024
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38. Evolution and genetic characterization of Seoul virus in wild rats Rattus norvegicus from an urban park in Lyon, France 2020-2022.

Author: Alburkat H, Smura T, Bouilloud M, Pradel J, Anfray G, Berthier K, Dutra L, Loiseau A, Niamsap T, Olander V, Sepulveda D, Venkat V, Charbonnel N, Castel G, and Sironen T
Subjects: Animals, Rats virology, France epidemiology, Animals, Wild virology, Humans, Cities epidemiology, Rodent Diseases virology, Rodent Diseases epidemiology, Seoul virus genetics, Seoul virus isolation & purification, Seoul virus classification, Phylogeny, Hemorrhagic Fever with Renal Syndrome epidemiology, Hemorrhagic Fever with Renal Syndrome virology, Hemorrhagic Fever with Renal Syndrome veterinary, Hemorrhagic Fever with Renal Syndrome transmission, Parks, Recreational
Abstract: Background: Seoul virus (SEOV) is an orthohantavirus primarily carried by rats. In humans, it may cause hemorrhagic fever with renal syndrome (HFRS). Its incidence is likely underestimated and given the expansion of urban areas, a better knowledge of SEOV circulation in rat populations is called for. Beyond the need to improve human case detection, we need to deepen our comprehension of the ecological, epidemiological, and evolutionary processes involved in the transmission of SEOV., Methodology / Principal Findings: We performed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus in a popular urban park within a large city (Lyon, France) to provide essential information to design surveillance strategies regarding SEOV. We sampled rats within the urban park of 'La Tête d'Or' in Lyon city from 2020 to 2022. We combined rat population genetics, immunofluorescence assays, SEOV high-throughput sequencing (S, M, and L segments), and phylogenetic analyses. We found low structuring of wild rat populations within Lyon city. Only one sampling site within the park (building created in 2021) showed high genetic differentiation and deserves further attention. We confirmed the circulation of SEOV in rats from the park with high seroprevalence (17.2%) and high genetic similarity with the strain previously described in 2011 in Lyon city., Conclusion/significance: This study confirms the continuous circulation of SEOV in a popular urban park where the risk for SEOV transmission to humans is present. Implementing a surveillance of this virus could provide an efficient early warning system and help prepare risk-based interventions. As we reveal high gene flow between rat populations from the park and the rest of the city, we advocate for SEOV surveillance to be conducted at the scale of the entire city., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Alburkat et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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39. Increasing Restorative Sleep Among Adults With Depressive Symptoms: A Quality Improvement Project.

Author: Smura T, Hammonds LS, and Griffin CM
Abstract: The Centers for Disease Control and Prevention estimates that 34.8% of adults in the United States experience non-restorative sleep. The restorative theory of sleep is based on sleep as a means for the restoration of cellular function that is needed for activities when awake. Non-restorative sleep leads to awakening feeling unrefreshed and not ready for the activities of the day three or more times weekly. Aims: The aim of this quality improvement project was to increase restorative sleep by increasing the average amount of sleep over units of 24 h, decreasing perceived insufficient sleep, and decreasing episodes of unintended daytime sleep among patients with depressive symptoms ages 18 to 80 years in an outpatient mental health clinic. Methods: Ten patients with depressive symptoms and reporting non-restorative sleep volunteered to participate in the project. Participants kept a sleep diary and followed principles of healthy sleep such as limiting time in bed and going to bed at the same time nightly. The change in and the average amount of sleep over 24 h and daytime sleepiness were evaluated using the Behavioral Risk Factor Surveillance System. Results: All participants achieved at least one more day of restorative sleep, with nine increasing restorative sleep by at least 30 min per day, and nine having no episodes of unintentionally falling asleep.
Published: 2024
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40. Epstein-Barr Virus in the Cerebrospinal Fluid and Blood Compartments of Patients With Multiple Sclerosis and Controls.

Author: Lehikoinen J, Nurmi K, Ainola M, Clancy J, Nieminen JK, Jansson L, Vauhkonen H, Vaheri A, Smura T, Laakso SM, Eklund KK, and Tienari PJ
Subjects: Humans, Herpesvirus 4, Human, DNA, Viral, RNA, Viral, Epstein-Barr Virus Infections complications, Multiple Sclerosis
Abstract: Background and Objectives: Epstein-Barr virus (EBV) infection is a major risk factor of multiple sclerosis (MS). We examined the presence of EBV DNA in the CSF and blood of patients with MS and controls. We analyzed whether EBV DNA is more common in the CSF of patients with MS than in controls and estimated the proportions of EBV-positive B cells in the CSF and blood., Methods: CSF supernatants and cells were collected at diagnostic lumbar punctures from 45 patients with MS and 45 HLA-DR15 matched controls with other conditions, all participants were EBV seropositive. Cellular DNA was amplified by Phi polymerase targeting both host and viral DNA, and representative samples were obtained in 28 cases and 28 controls. Nonamplified DNA from CSF cells (14 cases, 14 controls) and blood B cells (10 cases, 10 controls) were analyzed in a subset of participants. Multiple droplet digital PCR (ddPCR) runs were performed per sample to assess the cumulative EBV positivity rate. To detect viral RNA as a sign of activation, RNA sequencing was performed in blood CD4-positive, CD8-positive, and CD19-positive cells from 21 patients with MS and 3 controls., Results: One of the 45 patients with MS and none of the 45 controls were positive for EBV DNA in CSF supernatants (1 mL). CSF cellular DNA was analyzed in 8 independent ddPCRs: EBV DNA was detected at least once in 18 (64%) of the 28 patients with MS and in 15 (54%) of the 28 controls ( p = 0.59, Fisher test). The cumulative EBV positivity increased steadily up to 59% in the successive ddPCRs, suggesting that all individuals would have reached EBV positivity in the CSF cells, if more DNA would have been analyzed. The estimated proportion of EBV-positive B cells was >1/10,000 in both the CSF and blood. We did not detect viral RNA, except from endogenous retroviruses, in the blood lymphocyte subpopulations., Discussion: EBV-DNA is equally detectable in the CSF cells of both patients with MS and controls with ddPCR, and the probabilistic approach indicates that the true positivity rate approaches 100% in EBV-positive individuals. The proportion of EBV-positive B cells seems higher than previously estimated.
Published: 2024
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41. Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland.

Author: Lipponen A, Kolehmainen A, Oikarinen S, Hokajärvi AM, Lehto KM, Heikinheimo A, Halkilahti J, Juutinen A, Luomala O, Smura T, Liitsola K, Blomqvist S, Savolainen-Kopra C, and Pitkänen T
Subjects: Humans, Wastewater, Finland epidemiology, Pandemics, RNA, Viral genetics, High-Throughput Nucleotide Sequencing, SARS-CoV-2 genetics, COVID-19 epidemiology
Abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating the importance of variant detection at the population level. Wastewater-based surveillance of SARS-CoV-2 RNA fragments has been shown to be an effective way to monitor the COVID-19 pandemic at the population level. Wastewater is a complex sample matrix affected by environmental factors and PCR inhibitors, causing insufficient coverage in sequencing, for example. Subsequently, results where part of the genome does not have sufficient coverage are not uncommon. To identify variants and their proportions in wastewater over time, we utilized next-generation sequencing with the ARTIC Network's primer set and bioinformatics pipeline to evaluate the presence of variants in partial genome data. Based on the wastewater data from November 2021 to February 2022, the Delta variant was dominant until mid-December in Helsinki, Finland's capital, and thereafter in late December 2022 Omicron became the most common variant. At the same time, the Omicron variant of SARS-CoV-2 outcompeted the previous Delta variant in Finland in new COVID-19 cases. The SARS-CoV-2 variant findings from wastewater are in agreement with the variant information obtained from the patient samples when visually comparing trends in the sewerage network area. This indicates that the sequencing of wastewater is an effective way to monitor temporal and spatial trends of SARS-CoV-2 variants at the population level., (© 2024. The Author(s).)
Published: 2024
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42. Phylogenetic Characterization of Orthohantavirus dobravaense (Dobrava Virus).

Author: Erdin M, Polat C, Smura T, Irmak S, Cetintas O, Cogal M, Colak F, Karatas A, Sozen M, Matur F, Vapalahti O, Sironen T, and Oktem IMA
Subjects: Phylogeny, Cluster Analysis, Public Health, Orthohantavirus, RNA Viruses
Abstract: We report complete coding sequences of Orthohantavirus dobravaense (Dobrava virus) Igneada strains and phylogenetic characterization of all available complete coding sequences. Our analyses suggested separation of host-dependent lineages, followed by geographic clustering. Surveillance of orthohantaviruses using complete genomes would be useful for assessing public health threats from Dobrava virus.
Published: 2024
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43. The combination of pleconaril, rupintrivir, and remdesivir efficiently inhibits enterovirus infections in vitro, delaying the development of drug-resistant virus variants.

Author: Ianevski A, Frøysa IT, Lysvand H, Calitz C, Smura T, Schjelderup Nilsen HJ, Høyer E, Afset JE, Sridhar A, Wolthers KC, Zusinaite E, Tenson T, Kurg R, Oksenych V, Galabov AS, Stoyanova A, Bjørås M, and Kainov DE
Subjects: Animals, Humans, Enterovirus B, Human, Antiviral Agents pharmacology, Antiviral Agents therapeutic use, Drug Combinations, Enterovirus A, Human, Enterovirus, Enterovirus Infections drug therapy, Adenosine Monophosphate analogs & derivatives, Oxadiazoles, Pyrrolidinones, Oxazoles, Valine analogs & derivatives, Isoxazoles, Phenylalanine analogs & derivatives, Alanine analogs & derivatives
Abstract: Enteroviruses are a significant global health concern, causing a spectrum of diseases from the common cold to more severe conditions like hand-foot-and-mouth disease, meningitis, myocarditis, pancreatitis, and poliomyelitis. Current treatment options for these infections are limited, underscoring the urgent need for effective therapeutic strategies. To find better treatment option we analyzed toxicity and efficacy of 12 known broad-spectrum anti-enterovirals both individually and in combinations against different enteroviruses in vitro. We identified several novel, synergistic two-drug and three-drug combinations that demonstrated significant inhibition of enterovirus infections in vitro. Specifically, the triple-drug combination of pleconaril, rupintrivir, and remdesivir exhibited remarkable efficacy against echovirus (EV) 1, EV6, EV11, and coxsackievirus (CV) B5, in human lung epithelial A549 cells. This combination surpassed the effectiveness of single-agent or dual-drug treatments, as evidenced by its ability to protect A549 cells from EV1-induced cytotoxicity across seven passages. Additionally, this triple-drug cocktail showed potent antiviral activity against EV-A71 in human intestinal organoids. Thus, our findings highlight the therapeutic potential of the pleconaril-rupintrivir-remdesivir combination as a broad-spectrum treatment option against a range of enterovirus infections. The study also paves the way towards development of strategic antiviral drug combinations with virus family coverage and high-resistance barriers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
Published: 2024
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44. ICTV Virus Taxonomy Profile: Kolmioviridae 2024.

Author: Kuhn JH, Babaian A, Bergner LM, Dény P, Glebe D, Horie M, Koonin EV, Krupovic M, Paraskevopoulou S, de la Peña M, Smura T, and Hepojoki J
Subjects: Animals, Humans, Biological Evolution, Negative-Sense RNA Viruses, RNA Polymerase II, Mammals, Helper Viruses, Viroids
Abstract: Kolmioviridae is a family for negative-sense RNA viruses with circular, viroid-like genomes of about 1.5-1.7 kb that are maintained in mammals, amphibians, birds, fish, insects and reptiles. Deltaviruses, for instance, can cause severe hepatitis in humans. Kolmiovirids encode delta antigen (DAg) and replicate using host-cell DNA-directed RNA polymerase II and ribozymes encoded in their genome and antigenome. They require evolutionary unrelated helper viruses to provide envelopes and incorporate helper virus proteins for infectious particle formation. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Kolmioviridae , which is available at ictv.global/report/kolmioviridae.
Published: 2024
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45. Novel Ozark Orthohantavirus in Hispid Cotton Rats (Sigmodon hispidus), Arkansas, USA.

Author: Mull N, Erdin M, Smura T, Sironen T, and Forbes KM
Subjects: Animals, Humans, Arkansas epidemiology, Antibodies, Viral, Sigmodontinae, RNA Viruses, Orthohantavirus, Hantavirus Infections
Abstract: We report a novel orthohantavirus, putatively named Ozark orthohantavirus, in hispid cotton rats captured within the Ozark Plateau in Arkansas, USA. This virus phylogenetically clusters with other orthohantaviruses that cause severe human disease. Continued orthohantavirus surveillance and virus sequencing are needed to address the potential public health threat of this virus.
Published: 2023
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46. Equine dermatitis outbreak associated with parapoxvirus.

Author: Virtanen J, Hautala K, Utriainen M, Dutra L, Eskola K, Airas N, Uusitalo R, Ahvenainen E, Smura T, Sironen T, Vapalahti O, Kant R, Virtala AK, and Kinnunen PM
Subjects: Humans, Animals, Horses, Disease Outbreaks, Skin, Coinfection epidemiology, Coinfection veterinary, Dermatitis epidemiology, Dermatitis veterinary, Parapoxvirus genetics
Abstract: Parapoxviruses (PPV) cause skin and mucous membrane lesions in several animal species, and of the five recognized PPVs, at least three are zoonotic. Equine PPV (EqPPV) is the sixth one initially described in humans in the United States and later in a severely sick horse in Finland in 2013-2015. In 2021-2022, a large-scale pustulo-vesicular pastern dermatitis outbreak occurred in horses all over Finland. This study aimed at analysing the outbreak, identifying and describing the causative agent, describing clinical signs, and searching for risk factors. EqPPV was identified as a probable causative agent and co-infections with several potentially pathogenic and zoonotic bacteria were observed. Histopathologically, suppurative and ulcerative dermatitis was diagnosed. Due to the lack of specific tests for this virus, we developed a novel diagnostic EqPPV-PCR with sensitivity of 10 copies/reaction. Based on a large proportion of the genome sequenced directly from clinical samples, very little variation was detected between the sequences of the case from 2013 and the cases from 2021 to 2022. Based on an epidemiological survey, the main risk factor for pastern dermatitis was having racehorses. Approximately one third of the horses at each affected stable got clinical dermatitis, manifesting as severe skin lesions. Skin lesions were also occasionally reported in humans, indicating potential zoonotic transmission. Case stables commonly reported attendance at race events before acquiring the disease. Survey also identified differences in practises between case and control stables. Taken together, these results enable a better preparedness, diagnostics, and guidelines for future outbreaks.
Published: 2023
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47. Boosted production of antibodies that neutralized different SARS-CoV-2 variants in a COVID-19 convalescent following messenger RNA vaccination - a case study.

Author: Ravlo E, Ianevski A, Starheim E, Wang W, Ji P, Lysvand H, Smura T, Kivi G, Voolaid ML, Plaan K, Ustav M, Ustav M Jr, Zusinaite E, Tenson T, Kurg R, Oksenych V, Walstad K, Nordbø SA, Kaarbø M, Ernits K, Bjørås M, Kainov DE, and Fenstad MH
Subjects: Humans, COVID-19 Serotherapy, Antibodies, Neutralizing, Vaccination, Epitopes, RNA, Messenger genetics, Antibodies, Viral, SARS-CoV-2 genetics, COVID-19 prevention & control
Abstract: Vaccinated convalescents do not develop severe COVID-19 after infection with new SARS-CoV-2 variants. We questioned how messenger RNA (mRNA) vaccination of convalescents provides protection from emerging virus variants. From the cohort of 71 convalescent plasma donors, we identified a patient who developed immune response to infection with SARS-CoV-2 variant of 20A clade and who subsequently received mRNA vaccine encoding spike (S) protein of strain of 19A clade. We showed that vaccination increased the production of immune cells and anti-S antibodies in the serum. Serum antibodies neutralized not only 19A and 20A, but also 20B, 20H, 21J, and 21K virus variants. One of the serum antibodies (100F8) completely neutralized 20A, 21J, and partially 21K strains. 100F8 was structurally similar to published Ab188 antibody, which recognized non-conserved epitope on the S protein. We proposed that 100F8 and other serum antibodies of the patient which recognized non- and conserved epitopes of the S protein, could have additive or synergistic effects to neutralize various virus variants. Thus, mRNA vaccination could be beneficial for convalescents because it boosts production of neutralizing antibodies with broad-spectrum activity., Competing Interests: Declarations of Competing Interest The authors have no competing interests to declare., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
Published: 2023
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48. Molecular detection of pathogens from ticks collected from dogs and cats at veterinary clinics in Finland.

Author: Zakham F, Korhonen EM, Puonti PT, Castrén RS, Uusitalo R, Smura T, Kant R, Vapalahti O, Sironen T, and Kinnunen PM
Subjects: Humans, Cats, Dogs, Animals, Finland epidemiology, Hospitals, Animal, Ehrlichia canis, Cat Diseases epidemiology, Dog Diseases epidemiology, Ixodes, Anaplasmataceae, Babesia genetics, Encephalitis Viruses, Tick-Borne
Abstract: Background: Ticks carry microbes, some of which are pathogenic for humans and animals. To assess this One Health challenge, 342 ticks were collected from pet dogs and cats at 10 veterinary clinics in Finland as part of the European project "Protect Our Future Too"., Methods: The tick species were identified, and ticks were screened with quantitative PCR (qPCR) for tick-borne pathogens, including Borrelia burgdorferi sensu lato, Borrelia miyamotoi, Ehrlichia canis, Anaplasma spp., Candidatus Neoehrlichia mikurensis, tick-borne encephalitis virus (TBEV), and Babesia spp. For comparison, a subset of tick DNA (20 qPCR-positive samples) was analysed with 16S next-generation sequencing (NGS)., Results: Most ticks were Ixodes ricinus (289, 84.5%), followed by Ixodes persulcatus (51, 14.9%). One hybrid tick (I. ricinus/I. persulcatus, 0.3%) and one Rhipicephalus sanguineus tick (0.3%) were identified. We found one or more of the analysed pathogens in 17% (59/342) of the ticks. The most prevalent pathogen was B. burgdorferi s.l. (36, 10.5%), followed by Anaplasma phagocytophilum (12, 3.5%), B. miyamotoi (5, 1.5%), Babesia venatorum (4, 1.2%), and TBEV (1, 0.3%). Candidatus Neoehrlichia mikurensis DNA was amplified from three (0.9%) ticks. Ehrlichia canis was not detected. In the 16S NGS, six samples produced enough reads for the analysis. In these six samples, we confirmed all the positive qPCR findings of Borrelia spp. and Ca. N. mikurensis., Conclusions: The high prevalence of pathogenic microorganisms in the ticks of this study emphasizes the importance of awareness of ticks and tick-borne diseases and prevention. Furthermore, the results show that veterinary surveillance can facilitate early detection of tick-borne pathogens and new tick species and draw attention to possible co-infections that should be considered both in symptomatic humans and animals after tick bites., (© 2023. BioMed Central Ltd., part of Springer Nature.)
Published: 2023
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49. Partial Genome Characterization of Novel Parapoxvirus in Horse, Finland.

Author: Virtanen J, Hautaniemi M, Dutra L, Plyusnin I, Hautala K, Smura T, Vapalahti O, Sironen T, Kant R, and Kinnunen PM
Subjects: Horses, Animals, Finland epidemiology, Phylogeny, Parapoxvirus genetics, Poxviridae, Communicable Diseases
Abstract: We report a sequencing protocol and 121-kb poxvirus sequence from a clinical sample from a horse in Finland with dermatitis. Based on phylogenetic analyses, the virus is a novel parapoxvirus associated with a recent epidemic; previous data suggest zoonotic potential. Increased awareness of this virus and specific diagnostic protocols are needed.
Published: 2023
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50. Superspreading of SARS-CoV-2 Omicron BA.2.23 among vaccinated Finnish adults: symptomatic COVID-19 only contracted by those without recent infection.

Author: Riekkinen M, Kajova M, Eriksson M, Luukkainen A, Holmberg V, Aro T, Pakkanen SH, Miettinen S, Montonen R, Smura T, Lääveri T, and Kantele A
Subjects: Humans, SARS-CoV-2 genetics, Finland epidemiology, Disease Outbreaks, Fever, COVID-19 prevention & control
Abstract: An outbreak of SARS-CoV-2 was confirmed after an academic party in Helsinki, Finland, in 2022. All 70 guests were requested to fill in follow-up questionnaires; serologic analyses and whole-genome sequencing (WGS) were conducted when possible.Of those participating - all but one with ≥3 vaccine doses - 21/53 (40%) had test-confirmed symptomatic COVID-19: 7% of those with earlier episodes and 76% of those without. Half (11/21) were febrile, but none needed hospitalisation. WGS revealed subvariant BA.2.23.Compared to vaccination alone, our data suggest remarkable protection by hybrid immunity against symptomatic infection, particularly in instances of recent infections with homologous variants.
Published: 2023
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