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2. Effect of 2020-21 and 2021-22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands

Author

Caliendo, Valentina, Kleyheeg, Erik, Beerens, Nancy, Camphuysen, Kees C.J., Cazemier, Rommert, Elbers, Armin R.W., Fouchier, Ron A.M., Kelder, Leon, Kuiken, Thijs, Leopold, Mardik, Slaterus, Roy, Spierenburg, Marcel A.H., van der Jeugd, Henk, Verdaat, Hans, and Rijks, Jolianne M.

Subjects
Avian influenza -- Analysis, Epidemics -- Netherlands, Geese -- Analysis, Health
Abstract

The dynamics of highly pathogenic avian influenza (HPAI) virus infection of the H5 GS/GD lineage (clade 2.3.4.4b) have dramatically changed for wild birds. For 2 recent epidemic seasons (2020-21 and [...]

Published
2024
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3. Defining the risk of SARS-CoV-2 variants on immune protection

Author

DeGrace, Marciela M, Ghedin, Elodie, Frieman, Matthew B, Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R, Baric, Ralph S, Barouch, Dan H, Bloom, Jesse D, Bloyet, Louis-Marie, Bonenfant, Gaston, Boon, Adrianus CM, Boritz, Eli A, Bratt, Debbie L, Bricker, Traci L, Brown, Liliana, Buchser, William J, Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L, Davis-Gardner, Meredith E, Dearlove, Bethany L, Di, Han, Dittmann, Meike, Doria-Rose, Nicole A, Douek, Daniel C, Drosten, Christian, Edara, Venkata-Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P, Ferrari, Guido, Fischer, Will M, Florence, William C, Fouchier, Ron AM, Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L, Halfmann, Peter J, Ho, David D, Holbrook, Michael R, Huang, Yaoxing, James, Sarah L, Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M, Jones, Terry C, Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion PG, Korber, Bette, Koren, Eilay, Koup, Richard A, LeGresley, Eric B, Lemieux, Jacob E, Liebeskind, Mariel J, Liu, Zhuoming, Livingston, Brandi, Logue, James P, Luo, Yang, McDermott, Adrian B, McElrath, Margaret J, Meliopoulos, Victoria A, Menachery, Vineet D, Montefiori, David C, Mühlemann, Barbara, Munster, Vincent J, Munt, Jenny E, Nair, Manoj S, Netzl, Antonia, Niewiadomska, Anna M, O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C, Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W, Sacharen, Sinai, Scheuermann, Richard H, Schmidt, Stephen D, Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A, Sedova, Mayya, Sette, Alessandro, Shabman, Reed S, Shen, Xiaoying, Shi, Pei-Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J, Thackray, Larissa B, and Theiler, James

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Emerging Infectious Diseases, Pneumonia, Vaccine Related, Pneumonia & Influenza, Infectious Diseases, Biodefense, Immunization, Biotechnology, Prevention, Lung, Prevention of disease and conditions, and promotion of well-being, 2.1 Biological and endogenous factors, 3.4 Vaccines, Aetiology, Infection, Good Health and Well Being, Animals, Biological Evolution, COVID-19, COVID-19 Vaccines, Humans, National Institute of Allergy and Infectious Diseases (U.S.), Pandemics, Pharmacogenomic Variants, SARS-CoV-2, United States, Virulence, General Science & Technology
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.

Published
2022

4. US National Institutes of Health Prioritization of SARS-CoV-2 Variants

Author

Turner, Sam, Alisoltani, Arghavan, Bratt, Debbie, Cohen-Lavi, Liel, Dearlove, Bethany L., Drosten, Christian, Fischer, Will M., Fouchier, Ron A.M., Gonzalez-Reiche, Ana Silvia, Jaroszewski, Lukasz, Khalil, Zain, LeGresley, Eric, Johnson, Marc, Jones, Terry C., Muhlemann, Barbara, O'Connor, David, Sedova, Mayya, Shukla, Maulik, Theiler, James, Wallace, Zachary S., Yoon, Hyejin, Zhang, Yun, van Bakel, Harm, Degrace, Marciela M., Ghedin, Elodie, Godzik, Adam, Hertz, Tomer, Korber, Bette, Lemieux, Jacob, Niewiadomska, Anna M., Post, Diane J., Rolland, Morgane, Scheuermann, Richard, and Smith, Derek J.

Subjects
Values -- Analysis, Microbial mutation -- Health aspects, Epidemiology -- Methods, Health
Abstract

As part of the US National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) SARS-CoV-2 Assessment of Viral Evolution (SAVE) effort to combat the SARS-CoV-2 pandemic, [...]

Published
2023
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5. Mass Mortality Caused by Highly Pathogenic Influenza A(H5N1) Virus in Sandwich Terns, the Netherlands, 2022

Author

Rijks, Jolianne M., Leopold, Mardik F., Kuhn, Susanne, In't Veld, Ronald, Schenk, Fred, Brenninkmeijer, Allix, Lilipaly, Sander J., Ballmann, Monika Z., Kelder, Leon, de Jong, Job W., Courtens, Wouter, Slaterus, Roy, Kleyheeg, Erik, Vreman, Sandra, Kik, Marja J.L., Grone, Andrea, Fouchier, Ron A.M., Engelsma, Marc, de Jong, Mart C.M., Kuiken, Thijs, and Beerens, Nancy

Subjects
Avian influenza -- Patient outcomes -- Statistics -- Causes of, Epidemics -- Statistics -- Causes of -- Netherlands, Avian influenza viruses -- Identification and classification -- Genetic aspects -- Distribution, Terns -- Statistics -- Health aspects -- Death of, Company distribution practices, Health
Abstract

The 2021-2022 epidemic of highly pathogenic avian influenza (HPAI) A(H5Nl) virus clade 2.3.4.4b has been unprecedented in terms of numbers of dead wild birds, species affected, spatial extent, and incidence [...]

Published
2022
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7. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H, Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V, Amarasinghe, Gaya K, Anthony, Simon J, Avšič-Županc, Tatjana, Ayllón, María A, Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J, Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A, Bergeron, Éric, Bird, Brian H, Blair, Carol, Blasdell, Kim R, Bradfute, Steven B, Breyta, Rachel, Briese, Thomas, Brown, Paul A, Buchholz, Ursula J, Buchmeier, Michael J, Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H, Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N, Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, Clegg, J Christopher S, Crozier, Ian, da Graça, John V, Dal Bó, Elena, Dávila, Alberto MR, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L, Di Bello, Patrick L, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G, Digiaro, Michele, Dolja, Valerian V, Dolnik, Olga, Drebot, Michael A, Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G, Duprex, W Paul, Dye, John M, Easton, Andrew J, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R, Formenty, Pierre BH, Forth, Leonie F, Fouchier, Ron AM, Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R, Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean-Paul J, Griffiths, Anthony, Groschup, Martin H, Günther, Stephan, Guterres, Alexandro, Hall, Roy A, Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R, Hyndman, Timothy H, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, and Jonson, Gilda B

Subjects
Biotechnology, Mononegavirales, Terminology as Topic, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
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

10. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays

Author

Mühlemann, Barbara, primary, Wilks, Samuel H., additional, Baracco, Lauren, additional, Bekliz, Meriem, additional, Carreño, Juan Manuel, additional, Corman, Victor M., additional, Davis-Gardner, Meredith E., additional, Dejnirattisai, Wanwisa, additional, Diamond, Michael S., additional, Douek, Daniel C., additional, Drosten, Christian, additional, Eckerle, Isabella, additional, Edara, Venkata-Viswanadh, additional, Ellis, Madison, additional, Fouchier, Ron A. M., additional, Frieman, Matthew, additional, Godbole, Sucheta, additional, Haagmans, Bart, additional, Halfmann, Peter J., additional, Henry, Amy R., additional, Jones, Terry C., additional, Katzelnick, Leah C., additional, Kawaoka, Yoshihiro, additional, Kimpel, Janine, additional, Krammer, Florian, additional, Lai, Lilin, additional, Liu, Chang, additional, Lusvarghi, Sabrina, additional, Meyer, Benjamin, additional, Mongkolsapaya, Juthathip, additional, Montefiori, David C., additional, Mykytyn, Anna, additional, Netzl, Antonia, additional, Pollett, Simon, additional, Rössler, Annika, additional, Screaton, Gavin R., additional, Shen, Xiaoying, additional, Sigal, Alex, additional, Simon, Viviana, additional, Subramanian, Rahul, additional, Supasa, Piyada, additional, Suthar, Mehul S., additional, Türeli, Sina, additional, Wang, Wei, additional, Weiss, Carol D., additional, and Smith, Derek J., additional

Published
2024
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12. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Author

Oude Munnink, Bas B., Worp, Nathalie, Nieuwenhuijse, David F., Sikkema, Reina S., Haagmans, Bart, Fouchier, Ron A. M., and Koopmans, Marion

Subjects
Molecular diagnostic techniques -- Usage, Epidemiology -- Methods -- Forecasts and trends, Market trend/market analysis, Biological sciences, Health
Abstract

The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of pandemic surveillance with a focus on genotype-to-phenotype characterization., Author(s): Bas B. Oude Munnink [sup.1] , Nathalie Worp [sup.1] , David F. Nieuwenhuijse [sup.1] , Reina S. Sikkema [sup.1] , Bart Haagmans [sup.1] , Ron A. M. Fouchier [sup.1] [...]

Published
2021
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13. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Author

Postler, Thomas S, Clawson, Anna N, Amarasinghe, Gaya K, Basler, Christopher F, Bavari, Sbina, Benko, Mária, Blasdell, Kim R, Briese, Thomas, Buchmeier, Michael J, Bukreyev, Alexander, Calisher, Charles H, Chandran, Kartik, Charrel, Rémi, Clegg, Christopher S, Collins, Peter L, Juan Carlos, De La Torre, Derisi, Joseph L, Dietzgen, Ralf G, Dolnik, Olga, Dürrwald, Ralf, Dye, John M, Easton, Andrew J, Emonet, Sébastian, Formenty, Pierre, Fouchier, Ron AM, Ghedin, Elodie, Gonzalez, Jean-Paul, Harrach, Balázs, Hewson, Roger, Horie, Masayuki, Jiang, Dàohóng, Kobinger, Gary, Kondo, Hideki, Kropinski, Andrew M, Krupovic, Mart, Kurath, Gael, Lamb, Robert A, Leroy, Eric M, Lukashevich, Igor S, Maisner, Andrea, Mushegian, Arcady R, Netesov, Sergey V, Nowotny, Norbert, Patterson, Jean L, Payne, Susan L, PaWeska, Janusz T, Peters, Clarence J, Radoshitzky, Sheli R, Rima, Bertus K, Romanowski, Victor, Rubbenstroth, Dennis, Sabanadzovic, Sead, Sanfaçon, Hélène, Salvato, Maria S, Schwemmle, Martin, Smither, Sophie J, Stenglein, Mark D, Stone, David M, Takada, Ayato, Tesh, Robert B, Tomonaga, Keizo, Tordo, Noël, Towner, Jonathan S, Vasilakis, Nikos, Volchkov, Viktor E, Wahl-Jensen, Victoria, Walker, Peter J, Wang, Lin-Fa, Varsani, Arvind, Whitfield, Anna E, Zerbini, F Murilo, and Kuhn, Jens H

Subjects
Classification, Terminology as Topic, Viruses, Arenaviridae, binomials, ICTV, International Committee on Taxonomy of Viruses, Mononegavirales, virus nomenclature, virus taxonomy, Evolutionary Biology, Genetics
Abstract

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].

Published
2017

14. Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity

Author

Vigeveno, René M, Han, Alvin X, de Vries, Robert P, Parker, Edyth, de Haan, Karen, van Leeuwen, Sarah, Hulme, Katina D, Lauring, Adam S, Te Velthuis, Aartjan J W, Boons, Geert-Jan, Fouchier, Ron A M, Russell, Colin A, de Jong, Menno D, Eggink, Dirk, Vigeveno, René M, Han, Alvin X, de Vries, Robert P, Parker, Edyth, de Haan, Karen, van Leeuwen, Sarah, Hulme, Katina D, Lauring, Adam S, Te Velthuis, Aartjan J W, Boons, Geert-Jan, Fouchier, Ron A M, Russell, Colin A, de Jong, Menno D, and Eggink, Dirk

Abstract

Since the influenza pandemic in 1968, influenza A(H3N2) viruses have become endemic. In this state, H3N2 viruses continuously evolve to overcome immune pressure as a result of prior infection or vaccination, as is evident from the accumulation of mutations in the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). However, phylogenetic studies have also demonstrated ongoing evolution in the influenza A(H3N2) virus RNA polymerase complex genes. The RNA polymerase complex of seasonal influenza A(H3N2) viruses produces mRNA for viral protein synthesis and replicates the negative sense viral RNA genome (vRNA) through a positive sense complementary RNA intermediate (cRNA). Presently, the consequences and selection pressures driving the evolution of the polymerase complex remain largely unknown. Here, we characterize the RNA polymerase complex of seasonal influenza A(H3N2) viruses representative of nearly 50 years of influenza A(H3N2) virus evolution. The H3N2 polymerase complex is a reassortment of human and avian influenza virus genes. We show that since 1968, influenza A(H3N2) viruses have increased the transcriptional activity of the polymerase complex while retaining a close balance between mRNA, vRNA, and cRNA levels. Interestingly, the increased polymerase complex activity did not result in increased replicative ability on differentiated human airway epithelial (HAE) cells. We hypothesize that the evolutionary increase in polymerase complex activity of influenza A(H3N2) viruses may compensate for the reduced HA receptor binding and avidity that is the result of the antigenic evolution of influenza A(H3N2) viruses.

Published
2024

15. Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity

Author

Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Vigeveno, René M, Han, Alvin X, de Vries, Robert P, Parker, Edyth, de Haan, Karen, van Leeuwen, Sarah, Hulme, Katina D, Lauring, Adam S, Te Velthuis, Aartjan J W, Boons, Geert-Jan, Fouchier, Ron A M, Russell, Colin A, de Jong, Menno D, Eggink, Dirk, Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Vigeveno, René M, Han, Alvin X, de Vries, Robert P, Parker, Edyth, de Haan, Karen, van Leeuwen, Sarah, Hulme, Katina D, Lauring, Adam S, Te Velthuis, Aartjan J W, Boons, Geert-Jan, Fouchier, Ron A M, Russell, Colin A, de Jong, Menno D, and Eggink, Dirk

Published
2024

16. Seasonal influenza vaccine performance and the potential benefits of mRNA vaccines

Author

Russell, Colin A., Fouchier, Ron A. M., Ghaswalla, Parinaz, Park, Yoonyoung, Vicic, Nevena, Ananworanich, Jintanat, Nachbagauer, Raffael, Rudin, Deborah, Russell, Colin A., Fouchier, Ron A. M., Ghaswalla, Parinaz, Park, Yoonyoung, Vicic, Nevena, Ananworanich, Jintanat, Nachbagauer, Raffael, and Rudin, Deborah

Abstract

Influenza remains a public health threat, partly due to suboptimal effectiveness of vaccines. One factor impacting vaccine effectiveness is strain mismatch, occurring when vaccines no longer match circulating strains due to antigenic drift or the incorporation of inadvertent (eg, egg-adaptive) mutations during vaccine manufacturing. In this review, we summarize the evidence for antigenic drift of circulating viruses and/or egg-adaptive mutations occurring in vaccine strains during the 2011-2020 influenza seasons. Evidence suggests that antigenic drift led to vaccine mismatch during four seasons and that egg-adaptive mutations caused vaccine mismatch during six seasons. These findings highlight the need for alternative vaccine development platforms. Recently, vaccines based on mRNA technology have demonstrated efficacy against SARS-CoV-2 and respiratory syncytial virus and are under clinical evaluation for seasonal influenza. We discuss the potential for mRNA vaccines to address strain mismatch, as well as new multi-component strategies using the mRNA platform to improve vaccine effectiveness.

Published
2024

17. High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe—Why trends of virus evolution are more difficult to predict

Author

Fusaro, Alice, Zecchin, Bianca, Giussani, Edoardo, Palumbo, Elisa, Agüero-García, Montserrat, Bachofen, Claudia, Bálint, Ádám, Banihashem, Fereshteh, Banyard, Ashley, Beerens, Nancy, Bourg, Manon, Briand, Francois-Xavier, Bröjer, Caroline, Brown, Ian, Brugger, Brigitte, Byrne, Alexander, Cana, Armend, Christodoulou, Vasiliki, Dirbakova, Zuzana, Fagulha, Teresa, Fouchier, Ron, Garza-Cuartero, Laura, Georgiades, George, Gjerset, Britt, Grasland, Beatrice, Groza, Oxana, Harder, Timm, Henriques, Ana M., Hjulsager, Charlotte K., Ivanova, Emiliya, Janeliunas, Zygimantas, Krivko, Laura, Lemon, Ken, Liang, Yuan, Lika, Aldin, Malik, Péter, Mcmenamy, Michael, Nagy, Alexander, Nurmoja, Imbi, Onita, Iuliana, Pohlmann, Anne, Revilla-Fernández, Sandra, Sánchez-Sánchez, Azucena, Savic, Vladimir, Slavec, Brigita, Smietanka, Krzysztof, Snoeck, Chantal, Steensels, Mieke, Svansson, Vilhjálmur, Swieton, Edyta, Tammiranta, Niina, Tinak, Martin, van Borm, Steven, Zohari, Siamak, Adlhoch, Cornelia, Baldinelli, Francesca, Terregino, Calogero, Monne, Isabella, Fusaro, Alice, Zecchin, Bianca, Giussani, Edoardo, Palumbo, Elisa, Agüero-García, Montserrat, Bachofen, Claudia, Bálint, Ádám, Banihashem, Fereshteh, Banyard, Ashley, Beerens, Nancy, Bourg, Manon, Briand, Francois-Xavier, Bröjer, Caroline, Brown, Ian, Brugger, Brigitte, Byrne, Alexander, Cana, Armend, Christodoulou, Vasiliki, Dirbakova, Zuzana, Fagulha, Teresa, Fouchier, Ron, Garza-Cuartero, Laura, Georgiades, George, Gjerset, Britt, Grasland, Beatrice, Groza, Oxana, Harder, Timm, Henriques, Ana M., Hjulsager, Charlotte K., Ivanova, Emiliya, Janeliunas, Zygimantas, Krivko, Laura, Lemon, Ken, Liang, Yuan, Lika, Aldin, Malik, Péter, Mcmenamy, Michael, Nagy, Alexander, Nurmoja, Imbi, Onita, Iuliana, Pohlmann, Anne, Revilla-Fernández, Sandra, Sánchez-Sánchez, Azucena, Savic, Vladimir, Slavec, Brigita, Smietanka, Krzysztof, Snoeck, Chantal, Steensels, Mieke, Svansson, Vilhjálmur, Swieton, Edyta, Tammiranta, Niina, Tinak, Martin, van Borm, Steven, Zohari, Siamak, Adlhoch, Cornelia, Baldinelli, Francesca, Terregino, Calogero, and Monne, Isabella

Abstract

Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020–2021 and 2021–2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020–2021 and 2021–2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020–2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.

Published
2024

18. Asymmetrical Biantennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses

Author

Chemical Biology and Drug Discovery, Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Ma, Shengzhou, Liu, Lin, Eggink, Dirk, Herfst, Sander, Fouchier, Ron A. M., Vries, Robert P. de, Boons, Geert-Jan, Chemical Biology and Drug Discovery, Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Ma, Shengzhou, Liu, Lin, Eggink, Dirk, Herfst, Sander, Fouchier, Ron A. M., Vries, Robert P. de, and Boons, Geert-Jan

Published
2024

19. Effect of 2020-21 and 2021-22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands

Author

VPDC pathologie, Pathology, Caliendo, Valentina, Kleyheeg, Erik, Beerens, Nancy, Camphuysen, Kees C J, Cazemier, Rommert, Elbers, Armin R W, Fouchier, Ron A M, Kelder, Leon, Kuiken, Thijs, Leopold, Mardik, Slaterus, Roy, Spierenburg, Marcel A H, van der Jeugd, Henk, Verdaat, Hans, Rijks, Jolianne M, VPDC pathologie, Pathology, Caliendo, Valentina, Kleyheeg, Erik, Beerens, Nancy, Camphuysen, Kees C J, Cazemier, Rommert, Elbers, Armin R W, Fouchier, Ron A M, Kelder, Leon, Kuiken, Thijs, Leopold, Mardik, Slaterus, Roy, Spierenburg, Marcel A H, van der Jeugd, Henk, Verdaat, Hans, and Rijks, Jolianne M

Published
2024

20. Human metapneumovirus infection of organoid-derived human bronchial epithelium represents cell tropism and cytopathology as observed in in vivo models

Author

Ribo-Molina, Pau, van Nieuwkoop, Stefan, Mykytyn, Anna Z., van Run, Peter, Lamers, Mart M., Haagmans, Bart L., Fouchier, Ron A. M., van den Hoogen, Bernadette G., Ribo-Molina, Pau, van Nieuwkoop, Stefan, Mykytyn, Anna Z., van Run, Peter, Lamers, Mart M., Haagmans, Bart L., Fouchier, Ron A. M., and van den Hoogen, Bernadette G.

Abstract

Human metapneumovirus (HMPV), a member of the Pneumoviridae family, causes upper and lower respiratory tract infections in humans. In vitro studies with HMPV have mostly been performed in monolayers of undifferentiated epithelial cells. In vivo studies in cynomolgus macaques and cotton rats have shown that ciliated epithelial cells are the main target of HMPV infection, but these observations cannot be studied in monolayer systems. Here, we established an organoid-derived bronchial culture model that allows physiologically relevant studies on HMPV. Inoculation with multiple prototype HMPV viruses and recent clinical virus isolates led to differences in replication among HMPV isolates. Prolific HMPV replication in this model caused damage to the ciliary layer, including cilia loss at advanced stages post-infection. These cytopathic effects correlated with those observed in previous in vivo studies with cynomolgus macaques. The assessment of the innate immune responses in three donors upon HMPV and RSV inoculation highlighted the importance of incorporating multiple donors to account for donor-dependent variation. In conclusion, these data indicate that the organoid-derived bronchial cell culture model resembles in vivo findings and is therefore a suitable and robust model for future HMPV studies.

Published
2024

21. Species-specific emergence of H7 highly pathogenic avian influenza virus is driven by intrahost selection differences between chickens and ducks

Author

de Bruin, Anja C M, Spronken, Monique I, Kok, Adinda, Rosu, Miruna E, de Meulder, Dennis, van Nieuwkoop, Stefan, Lexmond, Pascal, Funk, Mathis, Leijten, Lonneke M, Bestebroer, Theo M, Herfst, Sander, van Riel, Debby, Fouchier, Ron A M, Richard, Mathilde, de Bruin, Anja C M, Spronken, Monique I, Kok, Adinda, Rosu, Miruna E, de Meulder, Dennis, van Nieuwkoop, Stefan, Lexmond, Pascal, Funk, Mathis, Leijten, Lonneke M, Bestebroer, Theo M, Herfst, Sander, van Riel, Debby, Fouchier, Ron A M, and Richard, Mathilde

Abstract

Highly pathogenic avian influenza viruses (HPAIVs) cause severe hemorrhagic disease in terrestrial poultry and are a threat to the poultry industry, wild life, and human health. HPAIVs arise from low pathogenic avian influenza viruses (LPAIVs), which circulate in wild aquatic birds. HPAIV emergence is thought to occur in poultry and not wild aquatic birds, but the reason for this species-restriction is not known. We hypothesized that, due to species-specific tropism and replication, intrahost HPAIV selection is favored in poultry and disfavored in wild aquatic birds. We tested this hypothesis by co-inoculating chickens, representative of poultry, and ducks, representative of wild aquatic birds, with a mixture of H7N7 HPAIV and LPAIV, mimicking HPAIV emergence in an experimental setting. Virus selection was monitored in swabs and tissues by RT-qPCR and immunostaining of differential N-terminal epitope tags that were added to the hemagglutinin protein. HPAIV was selected in four of six co-inoculated chickens, whereas LPAIV remained the major population in co-inoculated ducks on the long-term, despite detection of infectious HPAIV in tissues at early time points. Collectively, our data support the hypothesis that HPAIVs are more likely to be selected at the intrahost level in poultry than in wild aquatic birds and point towards species-specific differences in HPAIV and LPAIV tropism and replication levels as possible explanations.

Published
2024

22. Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity

Author

Aguilar-Bretones, Muriel, Fouchier, Ron A.M., Koopmans, Marion P.G., and van Nierop, Gijsbert P.

Subjects
Immunologic memory -- Research, Antigenic determinants -- Health aspects -- Physiological aspects, Immune response -- Research, Health care industry
Abstract

Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against coronavirus disease 2019 (COVID-19). This immunity may further be shaped by cross-reactivity with common cold coronaviruses. Mutations arising in S that are associated with altered intrinsic virus properties and immune escape result in the continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will be required to protect against future variants of concern, as for influenza. To offer potent protection against future variants, these second-generation vaccines may need to redirect immunity to epitopes associated with immune escape and not merely boost immunity toward conserved domains in preimmune individuals. For influenza, efficacy of repeated vaccination is hampered by original antigenic sin, an attribute of immune memory that leads to greater induction of antibodies specific to the first-encountered variant of an immunogen compared with subsequent variants. In this Review, recent findings on original antigenic sin are discussed in the context of SARS-CoV-2 evolution. Unanswered questions and future directions are highlighted, with an emphasis on the impact on disease outcome and vaccine design., SARS-CoV-2 immunity and memory recall upon exposure to variant viruses The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in the pandemic of coronavirus disease 2019 (COVID-19) (1). [...]

Published
2023
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30. High number of HPAI H5 Virus Infections and Antibodies in Wild Carnivores in the Netherlands, 2020-2022

Author

Chestakova, Irina V., primary, van der Linden, Anne, additional, Martin, Beatriz Bellido, additional, Caliendo, Valentina, additional, Vuong, Oanh, additional, Thewessen, Sanne, additional, Hartung, Tijmen, additional, Bestebroer, Theo, additional, Dekker, Jasja, additional, Poerink, Bob Jonge, additional, Gröne, Andrea, additional, Koopmans, Marion, additional, Fouchier, Ron, additional, van den Brand, Judith M. A., additional, and Sikkema, Reina S., additional

Published
2023
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31. 4-Octyl itaconate reduces influenza A replication by targeting the nuclear export protein CRM1

Author

Ribó-Molina, Pau, primary, Weiss, Hauke J., additional, Susma, Balasubramanian, additional, van Nieuwkoop, Stefan, additional, Persoons, Leentje, additional, Zheng, Yunan, additional, Ruzek, Melanie, additional, Daelemans, Dirk, additional, Fouchier, Ron A. M., additional, O'Neill, Luke A. J., additional, and van den Hoogen, Bernadette G., additional

Published
2023
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32. Mapping SARS-CoV-2 antigenic relationships and serological responses

Author

Wilks, Samuel H., primary, Mühlemann, Barbara, additional, Shen, Xiaoying, additional, Türeli, Sina, additional, LeGresley, Eric B., additional, Netzl, Antonia, additional, Caniza, Miguela A., additional, Chacaltana-Huarcaya, Jesus N., additional, Corman, Victor M., additional, Daniell, Xiaoju, additional, Datto, Michael B., additional, Dawood, Fatimah S., additional, Denny, Thomas N., additional, Drosten, Christian, additional, Fouchier, Ron A. M., additional, Garcia, Patricia J., additional, Halfmann, Peter J., additional, Jassem, Agatha, additional, Jeworowski, Lara M., additional, Jones, Terry C., additional, Kawaoka, Yoshihiro, additional, Krammer, Florian, additional, McDanal, Charlene, additional, Pajon, Rolando, additional, Simon, Viviana, additional, Stockwell, Melissa S., additional, Tang, Haili, additional, van Bakel, Harm, additional, Veguilla, Vic, additional, Webby, Richard, additional, Montefiori, David C., additional, and Smith, Derek J., additional

Published
2023
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33. Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera

Author

Mühlemann, Barbara, primary, Wilks, Samuel Hedley, additional, Baracco, Lauren, additional, Bekliz, Meriem, additional, Carreno, Juan Manuel, additional, Corman, Victor M, additional, Davis-Gardner, Meredith E, additional, Dejnirattisai, Wanwisa, additional, Diamond, Michael, additional, Doueck, Danny, additional, Drosten, Christian, additional, Eckerle, Isabella, additional, Edara, Venkata Vishwanadh, additional, Ellis, Madison, additional, Fouchier, Ron AM, additional, Frieman, Matthew, additional, Godbole, Sucheta, additional, Haagmans, Bart, additional, Halfmann, Peter, additional, Henry, Amy R, additional, Jones, Terry C, additional, Katzelnick, Leah, additional, Kawaoka, Yoshihiro, additional, Kimpel, Janine, additional, Krammer, Florian, additional, Lai, Lilin, additional, Liu, Chang, additional, Lusvarghi, Sabrina, additional, Meyer, Benjamin, additional, Mongkolsapaya, Juthathip, additional, Montefiori, David, additional, Mykytyn, Anna Z, additional, Netzl, Antonia, additional, Pollett, Simon, additional, Rössler, Annika, additional, Screaton, Gavin, additional, Shen, Xiaoying, additional, Sigal, Alex, additional, Simon, Viviana, additional, Subramanian, Rahul, additional, Supasa, Piyada, additional, Suthar, Mehul, additional, Tureli, Sina, additional, Wang, Wei, additional, Weiss, Carol D., additional, and Smith, Derek J, additional

Published
2023
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35. Induction of Cross-Clade Antibody and T-Cell Responses by a Modified Vaccinia Virus Ankara–Based Influenza A(H5N1) Vaccine in a Randomized Phase 1/2a Clinical Trial

Author

de Vries, Rory D., Altenburg, Arwen F., Nieuwkoop, Nella J., de Bruin, Erwin, van Trierum, Stella E., Pronk, Mark R., Lamers, Mart M., Richard, Mathilde, Nieuwenhuijse, David F., Koopmans, Marion P. G., Kreijtz, Joost H. C. M., Fouchier, Ron A. M., Osterhaus, Albert D. M. E., Sutter, Gerd, and Rimmelzwaan, Guus F.

Published
2018

37. Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Author

Mühlemann, Barbara, Margaryan, Ashot, de Barros Damgaard, Peter, Allentoft, Morten E., Vinner, Lasse, Hansen, Anders J., Weber, Andrzej, Bazaliiskii, Vladimir I., Molak, Martyna, Arneborg, Jette, Bogdanowicz, Wieslaw, Falys, Ceri, Sablin, Mikhail, Smrčka, Václav, Sten, Sabine, Tashbaeva, Kadicha, Lynnerup, Niels, Sikora, Martin, Smith, Derek J., Fouchier, Ron A. M., Drosten, Christian, Sjögren, Karl-Göran, Kristiansen, Kristian, Willerslev, Eske, and Jones, Terry C.

Published
2018

38. Taxonomy of the order Mononegavirales: update 2019

Author

Amarasinghe, Gaya K., Ayllón, María A., Bào, Yīmíng, Basler, Christopher F., Bavari, Sina, Blasdell, Kim R., Briese, Thomas, Brown, Paul A., Bukreyev, Alexander, Balkema-Buschmann, Anne, Buchholz, Ursula J., Chabi-Jesus, Camila, Chandran, Kartik, Chiapponi, Chiara, Crozier, Ian, de Swart, Rik L., Dietzgen, Ralf G., Dolnik, Olga, Drexler, Jan F., Dürrwald, Ralf, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Fooks, Anthony R., Formenty, Pierre B. H., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Griffiths, Anthony, Hewson, Roger, Horie, Masayuki, Hyndman, Timothy H., Jiāng, Dàohóng, Kitajima, Elliott W., Kobinger, Gary P., Kondō, Hideki, Kurath, Gael, Kuzmin, Ivan V., Lamb, Robert A., Lavazza, Antonio, Lee, Benhur, Lelli, Davide, Leroy, Eric M., Lǐ, Jiànróng, Maes, Piet, Marzano, Shin-Yi L., Moreno, Ana, Mühlberger, Elke, Netesov, Sergey V., Nowotny, Norbert, Nylund, Are, Økland, Arnfinn L., Palacios, Gustavo, Pályi, Bernadett, Pawęska, Janusz T., Payne, Susan L., Prosperi, Alice, Ramos-González, Pedro Luis, Rima, Bertus K., Rota, Paul, Rubbenstroth, Dennis, Shī, Mǎng, Simmonds, Peter, Smither, Sophie J., Sozzi, Enrica, Spann, Kirsten, Stenglein, Mark D., Stone, David M., Takada, Ayato, Tesh, Robert B., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., van den Hoogen, Bernadette, Vasilakis, Nikos, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Whitfield, Anna E., Williams, John V., Zerbini, F. Murilo, Zhāng, Tāo, Zhang, Yong-Zhen, and Kuhn, Jens H.

Published
2019
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39. Taxonomy of the order Mononegavirales: second update 2018

Author

Maes, Piet, Amarasinghe, Gaya K., Ayllón, María A., Basler, Christopher F., Bavari, Sina, Blasdell, Kim R., Briese, Thomas, Brown, Paul A., Bukreyev, Alexander, Balkema-Buschmann, Anne, Buchholz, Ursula J., Chandran, Kartik, Crozier, Ian, de Swart, Rik L., Dietzgen, Ralf G., Dolnik, Olga, Domier, Leslie L., Drexler, Jan F., Dürrwald, Ralf, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Fooks, Anthony R., Formenty, Pierre B. H., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Ghedin, Elodie, Griffiths, Anthony, Hewson, Roger, Horie, Masayuki, Hurwitz, Julia L., Hyndman, Timothy H., Jiāng, Dàohóng, Kobinger, Gary P., Kondō, Hideki, Kurath, Gael, Kuzmin, Ivan V., Lamb, Robert A., Lee, Benhur, Leroy, Eric M., Lǐ, Jiànróng, Marzano, Shin-Yi L., Mühlberger, Elke, Netesov, Sergey V., Nowotny, Norbert, Palacios, Gustavo, Pályi, Bernadett, Pawęska, Janusz T., Payne, Susan L., Rima, Bertus K., Rota, Paul, Rubbenstroth, Dennis, Simmonds, Peter, Smither, Sophie J., Song, Qisheng, Song, Timothy, Spann, Kirsten, Stenglein, Mark D., Stone, David M., Takada, Ayato, Tesh, Robert B., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., van den Hoogen, Bernadette, Vasilakis, Nikos, Wahl, Victoria, Walker, Peter J., Wang, David, Wang, Lin-Fa, Whitfield, Anna E., Williams, John V., Yè, Gōngyín, Zerbini, F. Murilo, Zhang, Yong-Zhen, and Kuhn, Jens H.

Published
2019
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41. A Dutch highly pathogenic H5N6 avian influenza virus showed remarkable tropism for extra-respiratory organs and caused severe disease but was not transmissible via air in the ferret model

Author

Herfst, Sander, primary, Begeman, Lineke, additional, Spronken, Monique I., additional, Poen, Marjolein J., additional, Eggink, Dirk, additional, de Meulder, Dennis, additional, Lexmond, Pascal, additional, Bestebroer, Theo M., additional, Koopmans, Marion P. G., additional, Kuiken, Thijs, additional, Richard, Mathilde, additional, and Fouchier, Ron A. M., additional

Published
2023
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42. Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution

Author

Kok, Adinda, primary, Scheuer, Rachel, additional, Bestebroer, Theo M., additional, Burke, David F., additional, Wilks, Samuel H., additional, Spronken, Monique I., additional, de Meulder, Dennis, additional, Lexmond, Pascal, additional, Pronk, Mark, additional, Smith, Derek J., additional, Herfst, Sander, additional, Fouchier, Ron A. M., additional, and Richard, Mathilde, additional

Published
2023
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43. Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection

Author

Spruit, Cindy M, primary, Sweet, Igor R, additional, Maliepaard, Joshua C L, additional, Bestebroer, Theo, additional, Lexmond, Pascal, additional, Qiu, Boning, additional, Damen, Mirjam J A, additional, Fouchier, Ron A M, additional, Reiding, Karli R, additional, Snijder, Joost, additional, Herfst, Sander, additional, Boons, Geert-Jan, additional, and de Vries, Robert P, additional

Published
2023
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44. Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome

Author

Rota, Paul A., Oberste, M. Steven, Monroe, Stephan S., Nix, W. Allan, Campagnoli, Ray, Icenogle, Joseph P., Peñaranda, Silvia, Bankamp, Bettina, Maher, Kaija, Chen, Min-hsin, Tong, Suxiong, Tamin, Azaibi, Lowe, Luis, Frace, Michael, DeRisi, Joseph L., Chen, Qi, Wang, David, Erdman, Dean D., Burns, Cara, Ksiazek, Thomas G., Rollin, Pierre E., Sanchez, Anthony, Liffick, Stephanie, Holloway, Brian, Limor, Josef, McCaustland, Karen, Olsen-Rasmussen, Melissa, Fouchier, Ron, Günther, Stephan, Drosten, Christian, Pallansch, Mark A., Anderson, Larry J., and Bellini, William J.

Published
2003

45. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance

Author

Abraham, Ashta Mary, Baraket, Amal, Bialasiewicz, Seweryn, Caniza, Miguela A, Chan, Paul KS, Cohen, Cheryl, Corriveau, André, Cowling, Benjamin J, Drews, Steven J, Echavarria, Marcela, Fouchier, Ron, Fraaij, Pieter LA, Hachette, Todd F, Heraud, Jean-Michel, Jalal, Hamid, Jennings, Lance, Kabanda, Alice, Kadjo, Herve A, Khanani, Mohammed Rafiq, Koay, Evelyn SC, Koopmans, Marion P, Krajden, Mel, Lam, Tommy T, Lee, Hong Kai, Lipkin, W. Ian, Lutwama, Julius, Marchant, David, Nishimura, Hidekazu, Nymadawa, Pagbajabyn, Pinsky, Benjamin A, Rughooputh, Sanjiv, Rukelibuga, Joseph, Saiyed, Taslimarif, Shet, Anita, Sloots, Theo, Tamfum, JJ Muyembe, Tang, Julian W, Tempia, Stefano, Tozer, Sarah, Treurnicht, Florette, Waris, Matti, Watanabe, Aripuana, Wemakoy, Emile Okitolonda, Zaraket, Hassan, Lipkin, W Ian, and Hatchette, Todd F

Published
2017
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49. Seasonal coronavirus-specific B cells with limited SARS-CoV-2 cross-reactivity dominate the IgG response in severe COVID-19

Author

Aguilar-Bretones, Muriel, Westerhuis, Brenda M., Raadsen, Matthijs P., de Bruin, Erwin, Chandler, Felicity D., Okba, Nisreen M.A., Haagmans, Bart L., Langerak, Thomas, Endeman, Henrik, van den Akker, Johannes P.C., Gommers, Diederik A.M.P.J., van Gorp, Eric C.M., GeurtsvanKessel, Corine H., de Vries, Rory D., Fouchier, Ron A.M., Rockx, Barry H.G., Koopmans, Marion P.G., and van Nierop, Gijsbert P.

Subjects
Immune response -- Health aspects, Immunoglobulin G -- Physiological aspects -- Health aspects, Health care industry
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19). Little is known about the interplay between preexisting immunity to endemic seasonal coronaviruses and the development of a SARS-CoV-2-specific IgG response. We investigated the kinetics, breadth, magnitude, and level of cross-reactivity of IgG antibodies against SARS-CoV-2 and heterologous seasonal and epidemic coronaviruses at the clonal level in patients with mild or severe COVID-19 as well as in disease control patients. We assessed antibody reactivity to nucleocapsid and spike antigens and correlated this IgG response to SARS-CoV-2 neutralization. Patients with COVID-19 mounted a mostly typespecific SARS-CoV-2 response. Additionally, IgG clones directed against a seasonal coronavirus were boosted in patients with severe COVID-19. These boosted clones showed limited cross-reactivity and did not neutralize SARS-CoV-2. These findings indicate a boost of poorly protective CoV-specific antibodies in patients with COVID-19 that correlated with disease severity, revealing 'original antigenic sin.', Introduction The introduction of the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a pandemic of coronavirus disease 2019 (COVID-19) (1). The majority of patients with COVID-19 [...]

Published
2021
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50. Species-specific emergence of H7 highly pathogenic avian influenza virus is driven by intrahost selection differences between chickens and ducks.

Author

de Bruin, Anja C. M., Spronken, Monique I., Kok, Adinda, Rosu, Miruna E., de Meulder, Dennis, van Nieuwkoop, Stefan, Lexmond, Pascal, Funk, Mathis, Leijten, Lonneke M., Bestebroer, Theo M., Herfst, Sander, van Riel, Debby, Fouchier, Ron A. M., and Richard, Mathilde

Subjects
AVIAN influenza, AVIAN influenza A virus, WATER birds, CHICKENS, DUCKS, BIRD populations, POULTRY breeding, POULTRY farms
Abstract

Highly pathogenic avian influenza viruses (HPAIVs) cause severe hemorrhagic disease in terrestrial poultry and are a threat to the poultry industry, wild life, and human health. HPAIVs arise from low pathogenic avian influenza viruses (LPAIVs), which circulate in wild aquatic birds. HPAIV emergence is thought to occur in poultry and not wild aquatic birds, but the reason for this species-restriction is not known. We hypothesized that, due to species-specific tropism and replication, intrahost HPAIV selection is favored in poultry and disfavored in wild aquatic birds. We tested this hypothesis by co-inoculating chickens, representative of poultry, and ducks, representative of wild aquatic birds, with a mixture of H7N7 HPAIV and LPAIV, mimicking HPAIV emergence in an experimental setting. Virus selection was monitored in swabs and tissues by RT-qPCR and immunostaining of differential N-terminal epitope tags that were added to the hemagglutinin protein. HPAIV was selected in four of six co-inoculated chickens, whereas LPAIV remained the major population in co-inoculated ducks on the long-term, despite detection of infectious HPAIV in tissues at early time points. Collectively, our data support the hypothesis that HPAIVs are more likely to be selected at the intrahost level in poultry than in wild aquatic birds and point towards species-specific differences in HPAIV and LPAIV tropism and replication levels as possible explanations. Author summary: Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease in poultry with mortality rates reaching 100% and, therefore, pose a large burden on the poultry industry. Additionally, some HPAIVs have spilled back from poultry into wild bird populations, increasing their geographic spread. HPAIVs arise from low pathogenic avian influenza viruses (LPAIVs), which circulate in wild aquatic birds and occasionally spillover into poultry. LPAIV to HPAIV conversion is associated with terrestrial poultry species, but the reasons underlying this species-restriction are unknown. The second step of HPAIV emergence, following HPAIV genesis, constitutes of the intrahost selection of the HPAIV from the large pool of replicating LPAIVs. Here, we investigated whether the intrahost selection efficiency differs between chickens and ducks, models for poultry and wild aquatic birds respectively, by co-inoculating them with HPAIV and LPAIV. Tagged viruses were utilized to monitor LPAIV and HPAIV frequencies at both the RNA and protein level. The HPAIV was selected in a majority of the chickens, demonstrated by the development of canonical HPAI disease and infectious HPAIV shedding, whereas all ducks solely shed infectious LPAIV. These results confirm that intrahost selection of HPAIVs is species-specific, which likely contributes to the restriction of HPAIV-emergence to poultry populations. [ABSTRACT FROM AUTHOR]

Published
2024
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