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1. A systematic review of interventions in the early course of bipolar disorder I or II: a report of the International Society for Bipolar Disorders Taskforce on early intervention.

Author: Ratheesh, A, Ratheesh, A, Hett, D, Ramain, J, Wong, E, Berk, L, Conus, P, Fristad, MA, Goldstein, T, Hillegers, M, Jauhar, S, Kessing, LV, Miklowitz, DJ, Murray, G, Scott, J, Tohen, M, Yatham, LN, Young, AH, Berk, M, Marwaha, S, Ratheesh, A, Ratheesh, A, Hett, D, Ramain, J, Wong, E, Berk, L, Conus, P, Fristad, MA, Goldstein, T, Hillegers, M, Jauhar, S, Kessing, LV, Miklowitz, DJ, Murray, G, Scott, J, Tohen, M, Yatham, LN, Young, AH, Berk, M, and Marwaha, S
Abstract: BackgroundGiven the likelihood of progressive illness in bipolar disorder (BD), it is important to understand the benefits and risks of interventions administered early in illness course. We conducted a systematic review of the effectiveness of interventions in the early course of BD I or II.MethodsWe completed a systematic search on MEDLINE, PsycINFO, EMBASE, the Cochrane Central Register of Controlled Trials, CINAHL and Google Scholar from 1/1/1979 till 14/9/2022. We included controlled trials examining intervention effects on symptomatic, course, functional and tolerability outcomes of patients in the 'early course' of BD I or II. We classified patients to be in early course if they (a) were seeking help for the first time for a manic episode, (b) had a lifetime history of up to 3 manic episodes, or (c) had up to 6 lifetime mood episodes. Evidence quality was assessed using the GRADE approach.ResultsFrom 4135 unique publications we included 25 reports representing 2212 participants in 16 randomized studies, and 17,714 participants from nine non-randomized studies. Available evidence suggested that in early illness course, lithium use was associated with lower recurrence risk compared with other mood stabilizers. Mood stabilizers were also associated with better global functioning, compared with the use of antipsychotics in the medium term. While summative findings regarding psychological therapies were limited by heterogeneity, family-focused and cognitive-behavioral interventions were associated with reduced recurrence risk or improved symptomatic outcomes. There was some evidence that the same pharmacological interventions were more efficacious in preventing recurrences when utilized in earlier rather than later illness course.Conclusions and recommendationsWhile there are promising initial findings, there is a need for more adequately powered trials to examine the efficacy and tolerability of interventions in youth and adults in early illness course. Specifica
Published: 2023

2. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

Author: Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., Marwaha, S., Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., and Marwaha, S.
Abstract: Background: Given the likelihood of progressive illness in bipolar disorder (BD), it is important to understand the benefits and risks of interventions administered early in illness course. We conducted a systematic review of the effectiveness of interventions in the early course of BD I or II. Methods: We completed a systematic search on MEDLINE, PsycINFO, EMBASE, the Cochrane Central Register of Controlled Trials, CINAHL and Google Scholar from 1/1/1979 till 14/9/2022. We included controlled trials examining intervention effects on symptomatic, course, functional and tolerability outcomes of patients in the ‘early course’ of BD I or II. We classified patients to be in early course if they (a) were seeking help for the first time for a manic episode, (b) had a lifetime history of up to 3 manic episodes, or (c) had up to 6 lifetime mood episodes. Evidence quality was assessed using the GRADE approach. Results: From 4135 unique publications we included 25 reports representing 2212 participants in 16 randomized studies, and 17,714 participants from nine non-randomized studies. Available evidence suggested that in early illness course, lithium use was associated with lower recurrence risk compared with other mood stabilizers. Mood stabilizers were also associated with better global functioning, compared with the use of antipsychotics in the medium term. While summative findings regarding psychological therapies were limited by heterogeneity, family-focused and cognitive-behavioral interventions were associated with reduced recurrence risk or improved symptomatic outcomes. There was some evidence that the same pharmacological interventions were more efficacious in preventing recurrences when utilized in earlier rather than later illness course. Conclusions and recommendations: While there are promising initial findings, there is a need for more adequately powered trials to examine the efficacy and tolerability of interventions in youth and adults in early illness cou
Published: 2023

3. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

Author: Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., Marwaha, S., Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., and Marwaha, S.
Abstract: Background: Given the likelihood of progressive illness in bipolar disorder (BD), it is important to understand the benefits and risks of interventions administered early in illness course. We conducted a systematic review of the effectiveness of interventions in the early course of BD I or II. Methods: We completed a systematic search on MEDLINE, PsycINFO, EMBASE, the Cochrane Central Register of Controlled Trials, CINAHL and Google Scholar from 1/1/1979 till 14/9/2022. We included controlled trials examining intervention effects on symptomatic, course, functional and tolerability outcomes of patients in the ‘early course’ of BD I or II. We classified patients to be in early course if they (a) were seeking help for the first time for a manic episode, (b) had a lifetime history of up to 3 manic episodes, or (c) had up to 6 lifetime mood episodes. Evidence quality was assessed using the GRADE approach. Results: From 4135 unique publications we included 25 reports representing 2212 participants in 16 randomized studies, and 17,714 participants from nine non-randomized studies. Available evidence suggested that in early illness course, lithium use was associated with lower recurrence risk compared with other mood stabilizers. Mood stabilizers were also associated with better global functioning, compared with the use of antipsychotics in the medium term. While summative findings regarding psychological therapies were limited by heterogeneity, family-focused and cognitive-behavioral interventions were associated with reduced recurrence risk or improved symptomatic outcomes. There was some evidence that the same pharmacological interventions were more efficacious in preventing recurrences when utilized in earlier rather than later illness course. Conclusions and recommendations: While there are promising initial findings, there is a need for more adequately powered trials to examine the efficacy and tolerability of interventions in youth and adults in early illness cou
Published: 2023

4. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

Author: Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., Marwaha, S., Ratheesh, A., Hett, D., Ramain, J., Wong, E., Berk, L., Conus, P., Fristad, M. A., Goldstein, T., Hillegers, M., Jauhar, S., Kessing, L. V., Miklowitz, D. J., Murray, G., Scott, J., Tohen, M., Yatham, L. N., Young, A. H., Berk, M., and Marwaha, S.
Abstract: Background: Given the likelihood of progressive illness in bipolar disorder (BD), it is important to understand the benefits and risks of interventions administered early in illness course. We conducted a systematic review of the effectiveness of interventions in the early course of BD I or II. Methods: We completed a systematic search on MEDLINE, PsycINFO, EMBASE, the Cochrane Central Register of Controlled Trials, CINAHL and Google Scholar from 1/1/1979 till 14/9/2022. We included controlled trials examining intervention effects on symptomatic, course, functional and tolerability outcomes of patients in the ‘early course’ of BD I or II. We classified patients to be in early course if they (a) were seeking help for the first time for a manic episode, (b) had a lifetime history of up to 3 manic episodes, or (c) had up to 6 lifetime mood episodes. Evidence quality was assessed using the GRADE approach. Results: From 4135 unique publications we included 25 reports representing 2212 participants in 16 randomized studies, and 17,714 participants from nine non-randomized studies. Available evidence suggested that in early illness course, lithium use was associated with lower recurrence risk compared with other mood stabilizers. Mood stabilizers were also associated with better global functioning, compared with the use of antipsychotics in the medium term. While summative findings regarding psychological therapies were limited by heterogeneity, family-focused and cognitive-behavioral interventions were associated with reduced recurrence risk or improved symptomatic outcomes. There was some evidence that the same pharmacological interventions were more efficacious in preventing recurrences when utilized in earlier rather than later illness course. Conclusions and recommendations: While there are promising initial findings, there is a need for more adequately powered trials to examine the efficacy and tolerability of interventions in youth and adults in early illness cou
Published: 2023

5. 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

6. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats

Author: Zhu, F, Duong, V, Lim, XF, Hul, V, Chawla, T, Keatts, L, Goldstein, T, Hassanin, A, Tu, VT, Buchy, P, Sessions, OM, Wang, L-F, Dussart, P, Anderson, DE, Zhu, F, Duong, V, Lim, XF, Hul, V, Chawla, T, Keatts, L, Goldstein, T, Hassanin, A, Tu, VT, Buchy, P, Sessions, OM, Wang, L-F, Dussart, P, and Anderson, DE
Abstract: Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
Published: 2022

7. Predicting the potential for zoonotic transmission and host associations for novel viruses

Author: Pandit, PS, Anthony, SJ, Goldstein, T, Olival, KJ, Doyle, MM, Gardner, NR, Bird, B, Smith, WA, Wolking, D, Gilardi, K, Monagin, C, Kelly, T, Uhart, M, Epstein, JH, Machalaba, C, Rostal, MK, Dawson, P, Hagan, E, Sullivan, A, Li, H, Chmura, AA, Latinne, A, Lange, C, O'Rourke, T, Olson, SH, Keatts, L, Mendoza, AP, Perez, A, de Paula, CD, Zimmerman, D, Valitutto, M, LeBreton, M, McIver, D, Islam, A, Duong, V, Mouiche, M, Shi, Z, Mulembakani, P, Kumakamba, C, Ali, M, Kebede, N, Tamoufe, U, Bel-Nono, S, Camara, A, Pamungkas, J, Coulibaly, K, Abu-Basha, E, Kamau, J, Silithammavong, S, Desmond, J, Hughes, T, Shiilegdamba, E, Aung, O, Karmacharya, D, Nziza, J, Ndiaye, D, Gbakima, A, Sijali, Z, Wacharapluesadee, S, Robles, EA, Ssebide, B, Suzan, G, Aguirre, LF, Solorio, MR, Dhole, TN, Nga, NTT, Hitchens, PL, Joly, DO, Saylors, K, Fine, A, Murray, S, Karesh, W, Daszak, P, Mazet, JAK, Johnson, CK, Pandit, PS, Anthony, SJ, Goldstein, T, Olival, KJ, Doyle, MM, Gardner, NR, Bird, B, Smith, WA, Wolking, D, Gilardi, K, Monagin, C, Kelly, T, Uhart, M, Epstein, JH, Machalaba, C, Rostal, MK, Dawson, P, Hagan, E, Sullivan, A, Li, H, Chmura, AA, Latinne, A, Lange, C, O'Rourke, T, Olson, SH, Keatts, L, Mendoza, AP, Perez, A, de Paula, CD, Zimmerman, D, Valitutto, M, LeBreton, M, McIver, D, Islam, A, Duong, V, Mouiche, M, Shi, Z, Mulembakani, P, Kumakamba, C, Ali, M, Kebede, N, Tamoufe, U, Bel-Nono, S, Camara, A, Pamungkas, J, Coulibaly, K, Abu-Basha, E, Kamau, J, Silithammavong, S, Desmond, J, Hughes, T, Shiilegdamba, E, Aung, O, Karmacharya, D, Nziza, J, Ndiaye, D, Gbakima, A, Sijali, Z, Wacharapluesadee, S, Robles, EA, Ssebide, B, Suzan, G, Aguirre, LF, Solorio, MR, Dhole, TN, Nga, NTT, Hitchens, PL, Joly, DO, Saylors, K, Fine, A, Murray, S, Karesh, W, Daszak, P, Mazet, JAK, and Johnson, CK
Abstract: Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.
Published: 2022

8. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

Author: Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, Anthony, SJ, Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, and Anthony, SJ
Abstract: Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
Published: 2021

9. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

Author: Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, Anthony, SJ, Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, and Anthony, SJ
Abstract: Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
Published: 2021

10. 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

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. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.

Author: Yu, K, Yu, K, Chen, B, Aran, D, Charalel, J, Yau, C, Wolf, DM, van 't Veer, LJ, Butte, AJ, Goldstein, T, Sirota, M, Yu, K, Yu, K, Chen, B, Aran, D, Charalel, J, Yau, C, Wolf, DM, van 't Veer, LJ, Butte, AJ, Goldstein, T, and Sirota, M
Abstract: Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models.
Published: 2019

13. Viral emergence in marine mammals in the North Pacific may be linked to Arctic sea ice reduction.

Author: VanWormer, E, VanWormer, E, Mazet, JAK, Hall, A, Gill, VA, Boveng, PL, London, JM, Gelatt, T, Fadely, BS, Lander, ME, Sterling, J, Burkanov, VN, Ream, RR, Brock, PM, Rea, LD, Smith, BR, Jeffers, A, Henstock, M, Rehberg, MJ, Burek-Huntington, KA, Cosby, SL, Hammond, JA, Goldstein, T, VanWormer, E, VanWormer, E, Mazet, JAK, Hall, A, Gill, VA, Boveng, PL, London, JM, Gelatt, T, Fadely, BS, Lander, ME, Sterling, J, Burkanov, VN, Ream, RR, Brock, PM, Rea, LD, Smith, BR, Jeffers, A, Henstock, M, Rehberg, MJ, Burek-Huntington, KA, Cosby, SL, Hammond, JA, and Goldstein, T
Abstract: Climate change-driven alterations in Arctic environments can influence habitat availability, species distributions and interactions, and the breeding, foraging, and health of marine mammals. Phocine distemper virus (PDV), which has caused extensive mortality in Atlantic seals, was confirmed in sea otters in the North Pacific Ocean in 2004, raising the question of whether reductions in sea ice could increase contact between Arctic and sub-Arctic marine mammals and lead to viral transmission across the Arctic Ocean. Using data on PDV exposure and infection and animal movement in sympatric seal, sea lion, and sea otter species sampled in the North Pacific Ocean from 2001-2016, we investigated the timing of PDV introduction, risk factors associated with PDV emergence, and patterns of transmission following introduction. We identified widespread exposure to and infection with PDV across the North Pacific Ocean beginning in 2003 with a second peak of PDV exposure and infection in 2009; viral transmission across sympatric marine mammal species; and association of PDV exposure and infection with reductions in Arctic sea ice extent. Peaks of PDV exposure and infection following 2003 may reflect additional viral introductions among the diverse marine mammals in the North Pacific Ocean linked to change in Arctic sea ice extent.
Published: 2019

14. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.

Author: Yu, K, Yu, K, Chen, B, Aran, D, Charalel, J, Yau, C, Wolf, DM, van 't Veer, LJ, Butte, AJ, Goldstein, T, Sirota, M, Yu, K, Yu, K, Chen, B, Aran, D, Charalel, J, Yau, C, Wolf, DM, van 't Veer, LJ, Butte, AJ, Goldstein, T, and Sirota, M
Abstract: Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models.
Published: 2019

15. Viral emergence in marine mammals in the North Pacific may be linked to Arctic sea ice reduction.

Author: VanWormer, E, VanWormer, E, Mazet, JAK, Hall, A, Gill, VA, Boveng, PL, London, JM, Gelatt, T, Fadely, BS, Lander, ME, Sterling, J, Burkanov, VN, Ream, RR, Brock, PM, Rea, LD, Smith, BR, Jeffers, A, Henstock, M, Rehberg, MJ, Burek-Huntington, KA, Cosby, SL, Hammond, JA, Goldstein, T, VanWormer, E, VanWormer, E, Mazet, JAK, Hall, A, Gill, VA, Boveng, PL, London, JM, Gelatt, T, Fadely, BS, Lander, ME, Sterling, J, Burkanov, VN, Ream, RR, Brock, PM, Rea, LD, Smith, BR, Jeffers, A, Henstock, M, Rehberg, MJ, Burek-Huntington, KA, Cosby, SL, Hammond, JA, and Goldstein, T
Abstract: Climate change-driven alterations in Arctic environments can influence habitat availability, species distributions and interactions, and the breeding, foraging, and health of marine mammals. Phocine distemper virus (PDV), which has caused extensive mortality in Atlantic seals, was confirmed in sea otters in the North Pacific Ocean in 2004, raising the question of whether reductions in sea ice could increase contact between Arctic and sub-Arctic marine mammals and lead to viral transmission across the Arctic Ocean. Using data on PDV exposure and infection and animal movement in sympatric seal, sea lion, and sea otter species sampled in the North Pacific Ocean from 2001-2016, we investigated the timing of PDV introduction, risk factors associated with PDV emergence, and patterns of transmission following introduction. We identified widespread exposure to and infection with PDV across the North Pacific Ocean beginning in 2003 with a second peak of PDV exposure and infection in 2009; viral transmission across sympatric marine mammal species; and association of PDV exposure and infection with reductions in Arctic sea ice extent. Peaks of PDV exposure and infection following 2003 may reflect additional viral introductions among the diverse marine mammals in the North Pacific Ocean linked to change in Arctic sea ice extent.
Published: 2019

16. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

Author: Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., Phillips, M. L., Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., and Phillips, M. L.
Published: 2018

17. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

Author: Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., Phillips, M. L., Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., and Phillips, M. L.
Published: 2018

18. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

Author: Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., Phillips, M. L., Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., and Phillips, M. L.
Published: 2018

19. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

Author: Imago ISI, Brain, Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., Phillips, M. L., Imago ISI, Brain, Versace, A., Ladouceur, C. D., Graur, S., Acuff, H. E., Bonar, L. K., Monk, K., McCaffrey, A., Yendiki, A., Leemans, A., Travis, M. J., Diwadkar, V. A., Holland, S. K., Sunshine, J. L., Kowatch, R. A., Horwitz, S. M., Frazier, T. W., Arnold, L. E., Fristad, M. A., Youngstrom, E. A., Findling, R. L., Goldstein, B. I., Goldstein, T., Axelson, D., Birmaher, B., and Phillips, M. L.
Published: 2018

20. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

Author: Anthony, SJ, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, Mazet, JAK, Anthony, SJ, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, and Mazet, JAK
Abstract: The evolutionary origins of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) are unknown. Current evidence suggests that insectivorous bats are likely to be the original source, as several 2c CoVs have been described from various species in the family Vespertilionidae Here, we describe a MERS-like CoV identified from a Pipistrellus cf. hesperidus bat sampled in Uganda (strain PREDICT/PDF-2180), further supporting the hypothesis that bats are the evolutionary source of MERS-CoV. Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Indeed, several amino acid substitutions were identified in key binding residues that were predicted to block PREDICT/PDF-2180 from attaching to the MERS-CoV DPP4 receptor. To experimentally test this hypothesis, an infectious MERS-CoV clone expressing the PREDICT/PDF-2180 spike protein was generated. Recombinant viruses derived from the clone were replication competent but unable to spread and establish new infections in Vero cells or primary human airway epithelial cells. Our findings suggest that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans.IMPORTANCE Global surveillance efforts for undiscovered viruses are an important component of pandemic prevention initiatives. These surveys can be useful for finding novel viruses and for gaining insights into the ecological and evolutionary factors driving viral diversity; however, finding a viral sequence is not sufficient to determine whether it can infect people (i.e., poses a zoonotic threat). Here, we invest
Published: 2017

21. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

Author: Anthony, SJ, Schultz-Cherry, Stacey1, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, Mazet, JAK, Anthony, SJ, Schultz-Cherry, Stacey1, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, and Mazet, JAK
Abstract: The evolutionary origins of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) are unknown. Current evidence suggests that insectivorous bats are likely to be the original source, as several 2c CoVs have been described from various species in the family Vespertilionidae Here, we describe a MERS-like CoV identified from a Pipistrellus cf. hesperidus bat sampled in Uganda (strain PREDICT/PDF-2180), further supporting the hypothesis that bats are the evolutionary source of MERS-CoV. Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Indeed, several amino acid substitutions were identified in key binding residues that were predicted to block PREDICT/PDF-2180 from attaching to the MERS-CoV DPP4 receptor. To experimentally test this hypothesis, an infectious MERS-CoV clone expressing the PREDICT/PDF-2180 spike protein was generated. Recombinant viruses derived from the clone were replication competent but unable to spread and establish new infections in Vero cells or primary human airway epithelial cells. Our findings suggest that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans.IMPORTANCE Global surveillance efforts for undiscovered viruses are an important component of pandemic prevention initiatives. These surveys can be useful for finding novel viruses and for gaining insights into the ecological and evolutionary factors driving viral diversity; however, finding a viral sequence is not sufficient to determine whether it can infect people (i.e., poses a zoonotic threat). Here, we invest
Published: 2017

22. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

Author: Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., Hillegers, M. H. J., Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., and Hillegers, M. H. J.
Published: 2016

23. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

Author: Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., Hillegers, M. H. J., Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., and Hillegers, M. H. J.
Published: 2016

24. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

Author: Diagnostiek & Vroege Psychose Medisch, Onderzoeksgroep 3, Brain, Onderzoek, Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., Hillegers, M. H. J., Diagnostiek & Vroege Psychose Medisch, Onderzoeksgroep 3, Brain, Onderzoek, Mesman, E., Birmaher, B. B., Derks, E. M., Vleeschouwer, M., Hickey, M. B., Goldstein, B. I., Goldstein, T., Axelson, D., Monk, K., Diller, R., Hafeman, D., Sakolsky, D. J., Vink, M., Reichart, C. G., Wals, M., Verhulst, F. C., Nolen, W. A., and Hillegers, M. H. J.
Published: 2016

25. Non-random patterns in viral diversity

Author: Anthony, SJ, Islam, A, Johnson, C, Navarrete-Macias, I, Liang, E, Jain, K, Hitchens, PL, Che, X, Soloyvov, A, Hicks, AL, Ojeda-Flores, R, Zambrana-Torrelio, C, Ulrich, W, Rostal, MK, Petrosov, A, Garcia, J, Haider, N, Wolfe, N, Goldstein, T, Morse, SS, Rahman, M, Epstein, JH, Mazet, JK, Daszak, P, Lipkin, WI, Anthony, SJ, Islam, A, Johnson, C, Navarrete-Macias, I, Liang, E, Jain, K, Hitchens, PL, Che, X, Soloyvov, A, Hicks, AL, Ojeda-Flores, R, Zambrana-Torrelio, C, Ulrich, W, Rostal, MK, Petrosov, A, Garcia, J, Haider, N, Wolfe, N, Goldstein, T, Morse, SS, Rahman, M, Epstein, JH, Mazet, JK, Daszak, P, and Lipkin, WI
Abstract: It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.
Published: 2015

26. Spillover and pandemic properties of zoonotic viruses with high host plasticity

Author: Johnson, CK, Hitchens, PL, Evans, TS, Goldstein, T, Thomas, K, Clements, A, Joly, DO, Wolfe, ND, Daszak, P, Karesh, WB, Mazet, JK, Johnson, CK, Hitchens, PL, Evans, TS, Goldstein, T, Thomas, K, Clements, A, Joly, DO, Wolfe, ND, Daszak, P, Karesh, WB, and Mazet, JK
Abstract: Most human infectious diseases, especially recently emerging pathogens, originate from animals, and ongoing disease transmission from animals to people presents a significant global health burden. Recognition of the epidemiologic circumstances involved in zoonotic spillover, amplification, and spread of diseases is essential for prioritizing surveillance and predicting future disease emergence risk. We examine the animal hosts and transmission mechanisms involved in spillover of zoonotic viruses to date, and discover that viruses with high host plasticity (i.e. taxonomically and ecologically diverse host range) were more likely to amplify viral spillover by secondary human-to-human transmission and have broader geographic spread. Viruses transmitted to humans during practices that facilitate mixing of diverse animal species had significantly higher host plasticity. Our findings suggest that animal-to-human spillover of new viruses that are capable of infecting diverse host species signal emerging disease events with higher pandemic potential in that these viruses are more likely to amplify by human-to-human transmission with spread on a global scale.
Published: 2015

27. Phocine distemper Virus: Current knowledge and future directions

Author: Duignan, P., Van Bressem, M.-F. (Marie-Françoise), Baker, J.D. (Jason), Barbieri, M. (Michelle), Colegrove, K.M. (Kathleen M), De Guise, S. (Sylvain), Swart, R.L. (Rik) de, di Guardo, G. (Giovanni), Dobson, A.P. (Andrew), Duprex, W.P. (Paul), Early, G. (Greg), Fauquier, D. (Deborah), Goldstein, T. (Tracey), Goodman, S.J. (Simon J.), Grenfell, B.T. (Bryan), Groch, K.R. (Kátia R.), Gulland, F. (Frances), Hall, A. (Ailsa), Jensen, B.A. (Brenda A.), Lamy, K. (Karina), Matassa, K. (Keith), Mazzariol, S. (Sandro), Morris, S.E. (Sinead E.), Nielsen, O. (Ole), Rotstein, D. (David), Rowles, T.K. (Teresa K), Saliki, J. (Jeremy), Siebert, U. (Ursula), Waltzek, T. (Thomas), Wellehan, J.F.X. (James F. X.), Duignan, P., Van Bressem, M.-F. (Marie-Françoise), Baker, J.D. (Jason), Barbieri, M. (Michelle), Colegrove, K.M. (Kathleen M), De Guise, S. (Sylvain), Swart, R.L. (Rik) de, di Guardo, G. (Giovanni), Dobson, A.P. (Andrew), Duprex, W.P. (Paul), Early, G. (Greg), Fauquier, D. (Deborah), Goldstein, T. (Tracey), Goodman, S.J. (Simon J.), Grenfell, B.T. (Bryan), Groch, K.R. (Kátia R.), Gulland, F. (Frances), Hall, A. (Ailsa), Jensen, B.A. (Brenda A.), Lamy, K. (Karina), Matassa, K. (Keith), Mazzariol, S. (Sandro), Morris, S.E. (Sinead E.), Nielsen, O. (Ole), Rotstein, D. (David), Rowles, T.K. (Teresa K), Saliki, J. (Jeremy), Siebert, U. (Ursula), Waltzek, T. (Thomas), and Wellehan, J.F.X. (James F. X.)
Abstract: Phocine distemper virus (PDV) was first recognized in 1988 following a massive epidemic in harbor and grey seals in north-western Europe. Since then, the epidemiology of infection in North Atlantic and Arctic pinnipeds has been investigated. In the western North Atlantic endemic infection in harp and grey seals predates the European epidemic, with relatively small, localized mortality events occurring primarily in harbor seals. By contrast, PDV seems not to have become established in European harbor seals following the 1988 epidemic and a second event of similar magnitude and extent occurred in 2002. PDV is a distinct species within the Morbillivirus genus with minor sequence variation between outbreaks over time. There is now mounting evidence of PDV-like viruses in the North Pacific/Western Arctic with serological and molecular evidence of infection in pinnipeds and sea otters. However, despite the absence of associated mortality in the region, there is concern that the virus may infect the large Pacific harbor seal and northern elephant seal populations or the endangered Hawaiian monk seals. Here, we review the current state of knowledge on PDV with particular focus on developments in diagnostics, pathogenesis, immune response, vaccine development, phylogenetics and modeling over the past 20 years.
Published: 2014
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28. Cetacean morbillivirus: Current knowledge and future directions

Author: Van Bressem, M-F, Duignan, P., Banyard, A., Barbieri, M., Colegrove, K., De Guise, S., Di Guardo, G., Dobson, A., Domingo, M., Fauquier, D., Fernandez, A., Goldstein, T., Grenfell, B., Groch, K., Gulland, F., Jensen, B., Jepson, P., Hall, A., Kuiken, T., Mazzariol, S., Morris, S., Nielsen, O., Raga, J., Rowles, T., Saliki, J., Sierra, E., Stephens, N., Stone, B., Tomo, I., Wang, J., Waltzek, T., Wellehan, J., Van Bressem, M-F, Duignan, P., Banyard, A., Barbieri, M., Colegrove, K., De Guise, S., Di Guardo, G., Dobson, A., Domingo, M., Fauquier, D., Fernandez, A., Goldstein, T., Grenfell, B., Groch, K., Gulland, F., Jensen, B., Jepson, P., Hall, A., Kuiken, T., Mazzariol, S., Morris, S., Nielsen, O., Raga, J., Rowles, T., Saliki, J., Sierra, E., Stephens, N., Stone, B., Tomo, I., Wang, J., Waltzek, T., and Wellehan, J.
Abstract: We review the molecular and epidemiological characteristics of cetacean morbillivirus (CeMV) and the diagnosis and pathogenesis of associated disease, with six different strains detected in cetaceans worldwide. CeMV has caused epidemics with high mortality in odontocetes in Europe, the USAand Australia. It represents a distinct species within the Morbillivirusgenus. Although most CeMV strains are phylogenetically closely related, recent data indicate that morbilliviruses recovered from Indo-Pacific bottlenose dolphins (Tursiops aduncus), from Western Australia, and a Guiana dolphin (Sotalia guianensis), from Brazil, are divergent. The signaling lymphocyte activation molecule (SLAM) cell receptor for CeMV has been characterized in cetaceans. It shares higher amino acid identity with the ruminant SLAM than with the receptors of carnivores or humans, reflecting the evolutionary history of these mammalian taxa. In Delphinidae, three amino acid substitutions may result in a higher affinity for the virus. Infection is diagnosed by histology, immunohistochemistry, virus isolation, RT-PCR, and serology. Classical CeMV-associated lesions include bronchointerstitial pneumonia, encephalitis, syncytia, and lymphoid depletion associated with immunosuppression. Cetaceans that survive the acute disease may develop fatal secondary infections and chronic encephalitis. Endemicallyinfected, gregarious odontocetes probably serve as reservoirs and vectors. Transmission likely occurs through the inhalation of aerosolized virus but mother to fetus transmission was also reported.
Published: 2014

29. Evaluation of local media surveillance for improved disease recognition and monitoring in global hotspot regions

Author: Schwind, JS, Wolking, DJ, Brownstein, JS, Predict, C, Mazet, JAK, Smith, WA, Aguirre, A, Aguirre, L, Akongo, MJ, Robles, EA, Ambu, L, Anthony, S, Antonjaya, U, Aguilar, GA, Barcena, L, Barradas, R, Bogich, T, Bounga, G, Buchy, P, Bunn, D, Byaruba, D, Cameron, K, Carroll, D, Cavero, N, Cespedes, M, Che, X, Chea, S, Chiu, C, Chmura, A, Chor, K, Clements, A, Cranfield, M, Acevedo, LD, Daszak, P, Campos, ACA, De La Puente, M, de Lamballerie, X, de Paula, C, Delwart, E, Le Doux, JD, Doyle-Capitman, C, Duengkae, P, Durigon, E, Epstein, JH, Fair, J, Ferrer-Paris, JR, Fine, A, Formenty, P, Galarza, I, Garcia, J, Gilardi, K, Gilbert, M, Gillis, A, Goldstein, T, Goossens, B, Grard, G, Greatorex, Z, Greig, D, Hagan, E, Harris, L, He, Q, Hemachudha, T, Hitchens, P, Ho, M, Hosseini, P, Hughes, T, In, S, Iñíguez, V, Iskandriati, D, Islam, Ariful, Iyanya, J, Jain, K, Johnson, C, Joly, D, Jones, K, Joyner, P, Kaba, S, Kambale, E, Karesh, W, Karmacharya, D, Kataregga, A, Kazwala, R, Ke, C, Kelly, T, Khammavong, K, Kilpatrick, AM, LeBreton, M, Lee, H, Lee, MH, Lee, J, LeRoy, E, Levinson, J, Levy, M, Liang, E, Liang, N, Limachi, R, Lipkin, WI, Loh, E, Lowenstine, LJ, Mollericona, JL, Schwind, JS, Wolking, DJ, Brownstein, JS, Predict, C, Mazet, JAK, Smith, WA, Aguirre, A, Aguirre, L, Akongo, MJ, Robles, EA, Ambu, L, Anthony, S, Antonjaya, U, Aguilar, GA, Barcena, L, Barradas, R, Bogich, T, Bounga, G, Buchy, P, Bunn, D, Byaruba, D, Cameron, K, Carroll, D, Cavero, N, Cespedes, M, Che, X, Chea, S, Chiu, C, Chmura, A, Chor, K, Clements, A, Cranfield, M, Acevedo, LD, Daszak, P, Campos, ACA, De La Puente, M, de Lamballerie, X, de Paula, C, Delwart, E, Le Doux, JD, Doyle-Capitman, C, Duengkae, P, Durigon, E, Epstein, JH, Fair, J, Ferrer-Paris, JR, Fine, A, Formenty, P, Galarza, I, Garcia, J, Gilardi, K, Gilbert, M, Gillis, A, Goldstein, T, Goossens, B, Grard, G, Greatorex, Z, Greig, D, Hagan, E, Harris, L, He, Q, Hemachudha, T, Hitchens, P, Ho, M, Hosseini, P, Hughes, T, In, S, Iñíguez, V, Iskandriati, D, Islam, Ariful, Iyanya, J, Jain, K, Johnson, C, Joly, D, Jones, K, Joyner, P, Kaba, S, Kambale, E, Karesh, W, Karmacharya, D, Kataregga, A, Kazwala, R, Ke, C, Kelly, T, Khammavong, K, Kilpatrick, AM, LeBreton, M, Lee, H, Lee, MH, Lee, J, LeRoy, E, Levinson, J, Levy, M, Liang, E, Liang, N, Limachi, R, Lipkin, WI, Loh, E, Lowenstine, LJ, and Mollericona, JL
Published: 2014

30. Capacity building efforts and perceptions for wildlife surveillance to detect zoonotic pathogens: comparing stakeholder perspectives

Author: Schwind, JS, Goldstein, T, Thomas, K, Mazet, JAK, Smith, WA, Schwind, JS, Goldstein, T, Thomas, K, Mazet, JAK, and Smith, WA
Abstract: BACKGROUND: The capacity to conduct zoonotic pathogen surveillance in wildlife is critical for the recognition and identification of emerging health threats. The PREDICT project, a component of United States Agency for International Development's Emerging Pandemic Threats program, has introduced capacity building efforts to increase zoonotic pathogen surveillance in wildlife in global 'hot spot' regions where zoonotic disease emergence is likely to occur. Understanding priorities, challenges, and opportunities from the perspectives of the stakeholders is a key component of any successful capacity building program. METHODS: A survey was administered to wildlife officials and to PREDICT-implementing in-country project scientists in 16 participating countries in order to identify similarities and differences in perspectives between the groups regarding capacity needs for zoonotic pathogen surveillance in wildlife. RESULTS: Both stakeholder groups identified some human-animal interfaces (i.e. areas of high contact between wildlife and humans with the potential risk for disease transmission), such as hunting and markets, as important for ongoing targeting of wildlife surveillance. Similarly, findings regarding challenges across stakeholder groups showed some agreement in that a lack of sustainable funding across regions was the greatest challenge for conducting wildlife surveillance for zoonotic pathogens (wildlife officials: 96% and project scientists: 81%). However, the opportunity for improving zoonotic pathogen surveillance capacity identified most frequently by wildlife officials as important was increasing communication or coordination among agencies, sectors, or regions (100% of wildlife officials), whereas the most frequent opportunities identified as important by project scientists were increasing human capacity, increasing laboratory capacity, and the growing interest or awareness regarding wildlife disease or surveillance programs (all identified by 69% of pro
Published: 2014

31. Cetacean morbillivirus: Current knowledge and future directions

Author: Van Bressem, M-F, Duignan, P., Banyard, A., Barbieri, M., Colegrove, K., De Guise, S., Di Guardo, G., Dobson, A., Domingo, M., Fauquier, D., Fernandez, A., Goldstein, T., Grenfell, B., Groch, K., Gulland, F., Jensen, B., Jepson, P., Hall, A., Kuiken, T., Mazzariol, S., Morris, S., Nielsen, O., Raga, J., Rowles, T., Saliki, J., Sierra, E., Stephens, N., Stone, B., Tomo, I., Wang, J., Waltzek, T., Wellehan, J., Van Bressem, M-F, Duignan, P., Banyard, A., Barbieri, M., Colegrove, K., De Guise, S., Di Guardo, G., Dobson, A., Domingo, M., Fauquier, D., Fernandez, A., Goldstein, T., Grenfell, B., Groch, K., Gulland, F., Jensen, B., Jepson, P., Hall, A., Kuiken, T., Mazzariol, S., Morris, S., Nielsen, O., Raga, J., Rowles, T., Saliki, J., Sierra, E., Stephens, N., Stone, B., Tomo, I., Wang, J., Waltzek, T., and Wellehan, J.
Abstract: We review the molecular and epidemiological characteristics of cetacean morbillivirus (CeMV) and the diagnosis and pathogenesis of associated disease, with six different strains detected in cetaceans worldwide. CeMV has caused epidemics with high mortality in odontocetes in Europe, the USAand Australia. It represents a distinct species within the Morbillivirusgenus. Although most CeMV strains are phylogenetically closely related, recent data indicate that morbilliviruses recovered from Indo-Pacific bottlenose dolphins (Tursiops aduncus), from Western Australia, and a Guiana dolphin (Sotalia guianensis), from Brazil, are divergent. The signaling lymphocyte activation molecule (SLAM) cell receptor for CeMV has been characterized in cetaceans. It shares higher amino acid identity with the ruminant SLAM than with the receptors of carnivores or humans, reflecting the evolutionary history of these mammalian taxa. In Delphinidae, three amino acid substitutions may result in a higher affinity for the virus. Infection is diagnosed by histology, immunohistochemistry, virus isolation, RT-PCR, and serology. Classical CeMV-associated lesions include bronchointerstitial pneumonia, encephalitis, syncytia, and lymphoid depletion associated with immunosuppression. Cetaceans that survive the acute disease may develop fatal secondary infections and chronic encephalitis. Endemicallyinfected, gregarious odontocetes probably serve as reservoirs and vectors. Transmission likely occurs through the inhalation of aerosolized virus but mother to fetus transmission was also reported.
Published: 2014

32. A strategy to estimate unknown viral diversity in mammals

Author: Anthony, SJ, Epstein, JH, Murray, KA, Navarrete-Macias, I, Zambrana-Torrelio, CM, Solovyov, A, Ojeda-Flores, R, Arrigo, NC, Islam, Ariful, Khan, SA, Hosseini, P, Bogich, TL, Olival, KJ, Sanchez-Leon, MD, Karesh, WB, Goldstein, T, Luby, SP, Morse, SS, Mazet, JAK, Daszak, P, Lipkin, WI, Anthony, SJ, Epstein, JH, Murray, KA, Navarrete-Macias, I, Zambrana-Torrelio, CM, Solovyov, A, Ojeda-Flores, R, Arrigo, NC, Islam, Ariful, Khan, SA, Hosseini, P, Bogich, TL, Olival, KJ, Sanchez-Leon, MD, Karesh, WB, Goldstein, T, Luby, SP, Morse, SS, Mazet, JAK, Daszak, P, and Lipkin, WI
Abstract: ABSTRACT The majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed “virodiversity”) for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox, Pteropus giganteus ) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families in P. giganteus to be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses. IMPORTANCE Recent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever est
Published: 2013

33. Comprehensivemolecular characterization of clear cell renal cell carcinoma

Author: Creighton, C., Morgan, M., Gunaratne, P., Wheeler, D., Gibbs, R., Robertson, A., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H., Raphael, B., Verhaak, R., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J., Reuter, V., Hsieh, J., Brannon, A., Hakimi, A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C., Linehan, W., Stuart, J., Rathmell, W., Shen, H., Laird, P., Muzny, D., Davis, C., Xi, L., Chang, K., Kakkar, N., Trevino, L., Benton, S., Reid, J., Morton, D., Doddapaneni, H., Han, Y., Lewis, L., Dinh, H., Kovar, C., Zhu, Y., Santibanez, J., Wang, M., Hale, W., Kalra, D., Getz, G., Lawrence, M., Sougnez, C., Carter, S., Sivachenko, A., Lichtenstein, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S., Lander, E., Schumacher, S., Tabak, B., Saksena, G., Onofrio, R., Cherniack, A., Gentry, J., Ardlie, K., Meyerson, M., Chun, H., Mungall, A., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chuah, E., Coope, R., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R., Lebovitz, C., Lee, D., Li, H., Mayo, M., Moore, R., Pleasance, E., Plettner, P., Schein, J., Shafiei, A., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zhao, Y., Birol, I., Jones, S., Marra, M., Auman, J., Tan, D., Jones, C., Hoadley, K., Mieczkowski, P., Mose, L., Jefferys, S., Topal, M., Liquori, C., Turman, Y., Shi, Y., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A., Simons, J., Soloway, M., Balu, S., Parker, J., Hayes, D., Perou, C., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D., Lai, P., Bootwalla, M., Maglinte, D., Mahurkar, S., Berman, B., Van den Berg, D., Cope, L., Baylin, S., Noble, M., DiCara, D., Zhang, H., Cho, J., Heiman, D., Gehlenborg, N., Mallard, W., Lin, P., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S., Shmulevich, I., Vegesna, R., Kim, H., Zhang, W., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A., Casasent, T., Wakefield, C., Tsavachidou, D., Mills, G., Schultz, N., Antipin, Y., Gao, J., Cerami, E., Gross, B., Aksoy, B., Sinha, R., Weinhold, N., Sumer, S., Taylor, B., Shen, R., Ostrovnaya, I., Berger, M., Ladanyi, M., Sander, C., Fei, S., Stout, A., Spellman, P., Rubin, D., Liu, T., Sam, N., Paull, E., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Zhu, J., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W., Choueiri, T., Atkins, M., Curley, E., Tickoo, S., Thorne, L., Boice, L., Huang, M., Fisher, J., Vocke, C., Peterson, J., Worrell, R., Merino, M., Schmidt, L., Czerniak, B., Aldape, K., Wood, C., Boyd, J., Weaver, J., Iacocca, M., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, O., Fedosenko, K., Cheville, J., Thompson, R., Mosquera, J., Rubin, M., Blute, M., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R., Zhang, J., Eley, G., Ferguson, M., Shaw, K., Guyer, M., Ozenberger, B., Sofia, H., Creighton, C., Morgan, M., Gunaratne, P., Wheeler, D., Gibbs, R., Robertson, A., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H., Raphael, B., Verhaak, R., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J., Reuter, V., Hsieh, J., Brannon, A., Hakimi, A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C., Linehan, W., Stuart, J., Rathmell, W., Shen, H., Laird, P., Muzny, D., Davis, C., Xi, L., Chang, K., Kakkar, N., Trevino, L., Benton, S., Reid, J., Morton, D., Doddapaneni, H., Han, Y., Lewis, L., Dinh, H., Kovar, C., Zhu, Y., Santibanez, J., Wang, M., Hale, W., Kalra, D., Getz, G., Lawrence, M., Sougnez, C., Carter, S., Sivachenko, A., Lichtenstein, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S., Lander, E., Schumacher, S., Tabak, B., Saksena, G., Onofrio, R., Cherniack, A., Gentry, J., Ardlie, K., Meyerson, M., Chun, H., Mungall, A., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chuah, E., Coope, R., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R., Lebovitz, C., Lee, D., Li, H., Mayo, M., Moore, R., Pleasance, E., Plettner, P., Schein, J., Shafiei, A., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zhao, Y., Birol, I., Jones, S., Marra, M., Auman, J., Tan, D., Jones, C., Hoadley, K., Mieczkowski, P., Mose, L., Jefferys, S., Topal, M., Liquori, C., Turman, Y., Shi, Y., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A., Simons, J., Soloway, M., Balu, S., Parker, J., Hayes, D., Perou, C., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D., Lai, P., Bootwalla, M., Maglinte, D., Mahurkar, S., Berman, B., Van den Berg, D., Cope, L., Baylin, S., Noble, M., DiCara, D., Zhang, H., Cho, J., Heiman, D., Gehlenborg, N., Mallard, W., Lin, P., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S., Shmulevich, I., Vegesna, R., Kim, H., Zhang, W., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A., Casasent, T., Wakefield, C., Tsavachidou, D., Mills, G., Schultz, N., Antipin, Y., Gao, J., Cerami, E., Gross, B., Aksoy, B., Sinha, R., Weinhold, N., Sumer, S., Taylor, B., Shen, R., Ostrovnaya, I., Berger, M., Ladanyi, M., Sander, C., Fei, S., Stout, A., Spellman, P., Rubin, D., Liu, T., Sam, N., Paull, E., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Zhu, J., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W., Choueiri, T., Atkins, M., Curley, E., Tickoo, S., Thorne, L., Boice, L., Huang, M., Fisher, J., Vocke, C., Peterson, J., Worrell, R., Merino, M., Schmidt, L., Czerniak, B., Aldape, K., Wood, C., Boyd, J., Weaver, J., Iacocca, M., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, O., Fedosenko, K., Cheville, J., Thompson, R., Mosquera, J., Rubin, M., Blute, M., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R., Zhang, J., Eley, G., Ferguson, M., Shaw, K., Guyer, M., Ozenberger, B., and Sofia, H.
Abstract: Genetic changes underlying clear cell renal cell carcinoma(ccRCC) include alterations in genes controlling cellularoxygen sensing (for example, VHL) and the maintenance of chromatin states (for example, PBRM1). We surveyed more than 400 tumours using different genomic platforms and identified 19 significantly mutated genes. The PI(3)K/AKT pathway was recurrently mutated, suggesting this pathway as a potential therapeutic target. Widespread DNA hypomethylation was associated with mutation of the H3K36 methyltransferase SETD2, and integrative analysis suggested that mutations involving the SWI/SNF chromatin remodelling complex (PBRM1, ARID1A, SMARCA4) could have far-reaching effects on other pathways. Aggressive cancers demonstrated evidence of a metabolic shift, involving downregulation of genes involved in the TCA cycle, decreasedAMPK and PTEN protein levels, upregulation of the pentose phosphate pathway and the glutamine transporter genes, increased acetyl-CoA carboxylase protein, and altered promoter methylation of miR-21 (also known as MIR21) and GRB10. Remodelling cellular metabolism thus constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment. Â© 2013 Macmillan Publishers Limited. All rights reserved.
Published: 2013

34. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

Author: Collisson, Eric, Collisson, Eric, Ng, S, Collisson, EA, Sokolov, A, Goldstein, T, onzalez-Perez, A, Lopez-Bigas, N, Benz, C, Haussler, D, Stuart, JM, Collisson, Eric, Collisson, Eric, Ng, S, Collisson, EA, Sokolov, A, Goldstein, T, onzalez-Perez, A, Lopez-Bigas, N, Benz, C, Haussler, D, and Stuart, JM
Abstract: Motivation: A current challenge in understanding cancer processes is to pinpoint which mutations influence the onset and progression of disease. Toward this goal, we describe a method called PARADIGMSHIFT that can predict whether a mutational event is neut
Published: 2012

35. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

Author: Collisson, Eric, Collisson, Eric, Ng, S, Collisson, EA, Sokolov, A, Goldstein, T, onzalez-Perez, A, Lopez-Bigas, N, Benz, C, Haussler, D, Stuart, JM, Collisson, Eric, Collisson, Eric, Ng, S, Collisson, EA, Sokolov, A, Goldstein, T, onzalez-Perez, A, Lopez-Bigas, N, Benz, C, Haussler, D, and Stuart, JM
Abstract: Motivation: A current challenge in understanding cancer processes is to pinpoint which mutations influence the onset and progression of disease. Toward this goal, we describe a method called PARADIGMSHIFT that can predict whether a mutational event is neut
Published: 2012

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35 results on '"Goldstein T"'

1. A systematic review of interventions in the early course of bipolar disorder I or II: a report of the International Society for Bipolar Disorders Taskforce on early intervention.

2. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

3. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

4. A systematic review of interventions in the early course of bipolar disorder I or II:a report of the International Society for Bipolar Disorders Taskforce on early intervention

5. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

6. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats

7. Predicting the potential for zoonotic transmission and host associations for novel viruses

8. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

9. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

10. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

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

12. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.

13. Viral emergence in marine mammals in the North Pacific may be linked to Arctic sea ice reduction.

14. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.

15. Viral emergence in marine mammals in the North Pacific may be linked to Arctic sea ice reduction.

16. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

17. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

18. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

19. Diffusion imaging markers of bipolar versus general psychopathology risk in youth at-risk

20. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

21. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

22. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

23. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

24. Psychopathology in the Dutch bipolar offspring study and the Pittsburgh bipolar offspring study (BIOS): similarities and differences

25. Non-random patterns in viral diversity

26. Spillover and pandemic properties of zoonotic viruses with high host plasticity

27. Phocine distemper Virus: Current knowledge and future directions

28. Cetacean morbillivirus: Current knowledge and future directions

29. Evaluation of local media surveillance for improved disease recognition and monitoring in global hotspot regions

30. Capacity building efforts and perceptions for wildlife surveillance to detect zoonotic pathogens: comparing stakeholder perspectives

31. Cetacean morbillivirus: Current knowledge and future directions

32. A strategy to estimate unknown viral diversity in mammals

33. Comprehensivemolecular characterization of clear cell renal cell carcinoma

34. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

35. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

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