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1. 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

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, Rijks, Jolianne M, 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
Abstract: The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020-September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020-21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021-22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
Published: 2024

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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, Rijks, Jolianne, 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
Abstract: The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020–September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020–21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021–22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
Published: 2024

10. 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

11. 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, Rijks, Jolianne M., 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.
Abstract: The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020–September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020–21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021–22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
Published: 2024

12. High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020-2022

Author: Chestakova, Irina V, van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M A, Sikkema, Reina S, Chestakova, Irina V, van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M A, and Sikkema, Reina S
Abstract: In October 2020, a new lineage of a clade 2.3.4.4b HPAI virus of the H5 subtype emerged in Europe, resulting in the largest global outbreak of HPAI to date, with unprecedented mortality in wild birds and poultry. The virus appears to have become enzootic in birds, continuously yielding novel HPAI virus variants. The recently increased abundance of infected birds worldwide increases the probability of bird-mammal contact, particularly in wild carnivores. Here, we performed molecular and serological screening of over 500 dead wild carnivores and sequencing of RNA positive materials. We show virological evidence for HPAI H5 virus infection in 0.8%, 1.4%, and 9.9% of animals tested in 2020, 2021, and 2022 respectively, with the highest proportion of positives in foxes, polecats and stone martens. We obtained near full genomes of 7 viruses and detected PB2 amino acid substitutions known to play a role in mammalian adaptation in three sequences. Infections were also found in without neurological signs or mortality. Serological evidence for infection was detected in 20% of the study population. These findings suggests that a high proportion of wild carnivores is infected but undetected in current surveillance programmes. We recommend increased surveillance in susceptible mammals, irrespective of neurological signs or encephalitis.
Published: 2023

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

Author: Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Ma, Shengzhou, Liu, Lin, Eggink, Dirk, Herfst, Sander, Fouchier, Ron A M, de Vries, Robert P, Boons, Geert-Jan, Afd Chemical Biology and Drug Discovery, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Ma, Shengzhou, Liu, Lin, Eggink, Dirk, Herfst, Sander, Fouchier, Ron A M, de Vries, Robert P, and Boons, Geert-Jan
Published: 2023

14. Continued adaptation of A/H2N2 viruses during pandemic circulation in humans

Author: Afd Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Kutter, Jasmin S., Linster, Martin, de Meulder, Dennis, Bestebroer, Theo M., Lexmond, Pascal, Rosu, Miruna E., Richard, Mathilde, de Vries, Robert P., Fouchier, Ron A.M., Herfst, Sander, Afd Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Kutter, Jasmin S., Linster, Martin, de Meulder, Dennis, Bestebroer, Theo M., Lexmond, Pascal, Rosu, Miruna E., Richard, Mathilde, de Vries, Robert P., Fouchier, Ron A.M., and Herfst, Sander
Published: 2023

15. High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020–2022

Author: Chestakova, Irina V., van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M.A., Sikkema, Reina S., Chestakova, Irina V., van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M.A., and Sikkema, Reina S.
Abstract: In October 2020, a new lineage of a clade 2.3.4.4b HPAI virus of the H5 subtype emerged in Europe, resulting in the largest global outbreak of HPAI to date, with unprecedented mortality in wild birds and poultry. The virus appears to have become enzootic in birds, continuously yielding novel HPAI virus variants. The recently increased abundance of infected birds worldwide increases the probability of bird–mammal contact, particularly in wild carnivores. Here, we performed molecular and serological screening of over 500 dead wild carnivores and sequencing of RNA positive materials. We show virological evidence for HPAI H5 virus infection in 0.8%, 1.4%, and 9.9% of animals tested in 2020, 2021, and 2022 respectively, with the highest proportion of positives in foxes, polecats and stone martens. We obtained near full genomes of 7 viruses and detected PB2 amino acid substitutions known to play a role in mammalian adaptation in three sequences. Infections were also found in without neurological signs or mortality. Serological evidence for infection was detected in 20% of the study population. These findings suggests that a high proportion of wild carnivores is infected but undetected in current surveillance programmes. We recommend increased surveillance in susceptible mammals, irrespective of neurological signs or encephalitis.
Published: 2023

16. Contemporary human H3N2 influenza a viruses require a low threshold of suitable glycan receptors for efficient infection

Author: Afd Chemical Biology and Drug Discovery, Afd Biomol.Mass Spect. and Proteomics, Afd Pharmaceutics, Sub Biomol.Mass Spectrometry & Proteom., Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Pharmaceutics, Spruit, Cindy M, Sweet, Igor R, Maliepaard, Joshua C L, Bestebroer, Theo, Lexmond, Pascal, Qiu, Boning, Damen, Mirjam J A, Fouchier, Ron A M, Reiding, Karli R, Snijder, Joost, Herfst, Sander, Boons, Geert-Jan, de Vries, Robert P, Afd Chemical Biology and Drug Discovery, Afd Biomol.Mass Spect. and Proteomics, Afd Pharmaceutics, Sub Biomol.Mass Spectrometry & Proteom., Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Pharmaceutics, Spruit, Cindy M, Sweet, Igor R, Maliepaard, Joshua C L, Bestebroer, Theo, Lexmond, Pascal, Qiu, Boning, Damen, Mirjam J A, Fouchier, Ron A M, Reiding, Karli R, Snijder, Joost, Herfst, Sander, Boons, Geert-Jan, and de Vries, Robert P
Published: 2023

17. High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020-2022

Author: VPDC pathologie, Dutch Wildlife Health Centre (DWHC), Pathology, Chestakova, Irina V, van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M A, Sikkema, Reina S, VPDC pathologie, Dutch Wildlife Health Centre (DWHC), Pathology, Chestakova, Irina V, van der Linden, Anne, Bellido Martin, Beatriz, Caliendo, Valentina, Vuong, Oanh, Thewessen, Sanne, Hartung, Tijmen, Bestebroer, Theo, Dekker, Jasja, Jonge Poerink, Bob, Gröne, Andrea, Koopmans, Marion, Fouchier, Ron, van den Brand, Judith M A, and Sikkema, Reina S
Published: 2023

18. Antigenic evolution of SARS coronavirus 2

Author: Mykytyn, Anna Z., Fouchier, Ron AM, Haagmans, Bart L., Mykytyn, Anna Z., Fouchier, Ron AM, and Haagmans, Bart L.
Abstract: SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
Published: 2023

19. Field Research Is Essential to Counter Virological Threats

Author: Runstadler, Jonathan A., Lowen, Anice C., Kayali, Ghazi, Tompkins, S. Mark, Albrecht, Randy A., Fouchier, Ron A.M., Stallknecht, David E., Lakdawala, Seema S., Goodrum, Felicia D., Casadevall, Arturo, Enquist, Lynn W., Alwine, James C., Imperiale, Michael J., Schultz-Cherry, Stacey, Webby, Richard J., Runstadler, Jonathan A., Lowen, Anice C., Kayali, Ghazi, Tompkins, S. Mark, Albrecht, Randy A., Fouchier, Ron A.M., Stallknecht, David E., Lakdawala, Seema S., Goodrum, Felicia D., Casadevall, Arturo, Enquist, Lynn W., Alwine, James C., Imperiale, Michael J., Schultz-Cherry, Stacey, and Webby, Richard J.
Abstract: The interface between humans and wildlife is changing and, with it, the potential for pathogen introduction into humans has increased. Avian influenza is a prominent example, with an ongoing outbreak showing the unprecedented expansion of both geographic and host ranges. Research in the field is essential to understand this and other zoonotic threats. Only by monitoring dynamic viral populations and defining their biology in situ can we gather the information needed to ensure effective pandemic preparation.
Published: 2023

20. Conserved Expression and Functionality of Furin between Chickens and Ducks as an Activating Protease of Highly Pathogenic Avian Influenza Virus Hemagglutinins

Author: de Bruin, Anja C M, Spronken, Monique I, Bestebroer, Theo M, Fouchier, Ron A M, Richard, Mathilde, de Bruin, Anja C M, Spronken, Monique I, Bestebroer, Theo M, Fouchier, Ron A M, and Richard, Mathilde
Abstract: Highly pathogenic avian influenza viruses (HPAIVs) typically emerge from low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes upon spillover from wild aquatic birds into poultry. The conversion from LPAIV to HPAIV is characterized by the acquisition of a multibasic cleavage site (MBCS) at the proteolytic cleavage site in the viral binding and fusion protein, hemagglutinin (HA), resulting in cleavage and activation of HA by ubiquitously expressed furin-like proteases. The ensuing HPAIVs disseminate systemically in gallinaceous poultry, are endotheliotropic, and cause hemorrhagic disease with high mortality. HPAIV infections in wild aquatic birds are generally milder, often asymptomatic, and generally not associated with systemic dissemination nor endotheliotropic. As MBCS cleavage by host proteases is the main virulence determinant of HPAIVs in poultry, we set out to determine whether cleavage of HPAIV HA by host proteases might influence the observed species-specific pathogenesis and tropism. Here, we sequenced, cloned, and characterized the expression and functionality of duck furin. The furin sequence was strongly conserved between chickens and ducks, and duck furin cleaved HPAIV and tetrabasic HA in an overexpression system, confirming its functionality. Furin was expressed ubiquitously and to similar extents in duck and chicken tissues, including in primary duck endothelial cells, which sustained multicycle replication of H5N1 HPAIV but not LPAIVs. In conclusion, differences in furin-like protease biology between wild aquatic birds and gallinaceous poultry are unlikely to largely determine the stark differences observed in species-specific pathogenesis of HPAIVs. IMPORTANCE HPAIV outbreaks are a global concern due to the health risks for poultry, wildlife, and humans and their major economic impact. The number of LPAIV-to-HPAIV conversions, which is associated with spillover from wild birds to poultry, has been increasing over recent deca
Published: 2023

21. 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, Begeman, Lineke, Spronken, Monique I, Poen, Marjolein J, Eggink, Dirk, de Meulder, Dennis, Lexmond, Pascal, Bestebroer, Theo M, Koopmans, Marion P G, Kuiken, Thijs, Richard, Mathilde, Fouchier, Ron A M, Herfst, Sander, Begeman, Lineke, Spronken, Monique I, Poen, Marjolein J, Eggink, Dirk, de Meulder, Dennis, Lexmond, Pascal, Bestebroer, Theo M, Koopmans, Marion P G, Kuiken, Thijs, Richard, Mathilde, and Fouchier, Ron A M
Abstract: Continued circulation of A/H5N1 influenzaviruses of the A/goose/Guangdong/1/96 lineage in poultry has resulted in the diversificationin multiple genetic and antigenic clades. Since 2009, clade 2.3.4.4 hemagglutinin (HA) containing viruses harboring the internal and neuraminidase (NA) genes of other avian influenzaA viruses have been detected. As a result, various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8 have been identified.As of January 2023, 83 humans have been infected with A/H5N6 viruses, thereby posing an apparent risk for public health. Here, as part of a risk assessment, the in vitro and in vivo characterization of A/H5N6 A/black-headed gull/Netherlands/29/2017 is described. This A/H5N6 virus was not transmitted between ferrets via the air but was of unexpectedly high pathogenicity compared to other described A/H5N6 viruses. The virus replicated and caused severe lesions not only in respiratory tissues but also in multiple extra-respiratory tissues, including brain, liver, pancreas, spleen, lymph nodes, and adrenal gland. Sequence analyses demonstrated that the well-known mammalian adaptation substitution D701N was positively selected in almost all ferrets. In the in vitro experiments, no other known viral phenotypic properties associated with mammalian adaptation or increased pathogenicity were identified.The lack of transmission via the air and the absence of mammalian adaptation markers suggest that the public health risk of this virus is low. The high pathogenicity of this virus in ferrets could not be explained by the known mammalian pathogenicity factors and should be further studied.
Published: 2023

22. 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., Mühlemann, 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, Smith, Derek J., 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., Mühlemann, 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.
Abstract: Since late 2020, SARS-CoV-2 variants have regularly emerged with competitive and phenotypic differences from previously circulating strains, sometimes with the potential to escape from immunity produced by prior exposure and infection. The Early Detection group is one of the constituent groups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution program. The group uses bioinformatic methods to monitor the emergence, spread, and potential phenotypic properties of emerging and circulating strains to identify the most relevant variants for experimental groups within the program to phenotypically characterize. Since April 2021, the group has prioritized variants monthly. Prioritization successes include rapidly identifying most major variants of SARS-CoV-2 and providing experimental groups within the National Institutes of Health program easy access to regularly updated information on the recent evolution and epidemiology of SARS-CoV-2 that can be used to guide phenotypic investigations.
Published: 2023

23. Emergence and Potential Extinction of Genetic Lineages of Human Metapneumovirus between 2005 and 2021

Author: Groen, Kevin, Van Nieuwkoop, Stefan, Meijer, Adam, Van Der Veer, Bas, van Kampen, Jeroen J.A., Fraaij, Pieter L., Fouchier, Ron A.M., Van Den Hoogen, Bernadette G., Groen, Kevin, Van Nieuwkoop, Stefan, Meijer, Adam, Van Der Veer, Bas, van Kampen, Jeroen J.A., Fraaij, Pieter L., Fouchier, Ron A.M., and Van Den Hoogen, Bernadette G.
Abstract: Human metapneumovirus (HMPV) is one of the leading causes of respiratory illness (RI), primarily in infants. Worldwide, two genetic lineages (A and B) of HMPV are circulating that are antigenically distinct and can each be further divided into genetic sublineages. Surveillance combined with large-scale whole-genome sequencing studies of HMPV are scarce but would help to identify viral evolutionary dynamics. Here, we analyzed 130 whole HMPV genome sequences obtained from samples collected from individuals hospitalized with RI and partial fusion (n = 144) and attachment (n = 123) protein gene sequences obtained from samples collected from patients with RI visiting general practitioners between 2005 and 2021 in the Netherlands. Phylogenetic analyses demonstrated that HMPV continued to group in the four sublineages described in 2004 (A1, A2, B1, and B2). However, one sublineage (A1) was no longer detected in the Netherlands after 2006, while the others continued to evolve. No differences were observed in dominant (sub)lineages between samples obtained from patients with RI being hospitalized and those consulting general practitioners. In both populations, viruses of lineage A2 carrying a 180-nucleotide or 111-nucleotide duplication in the attachment protein gene became the most frequently detected genotypes. In the past, different names for the newly energing lineages have been proposed, demonstrating the need for a consistent naming convention. Here, criteria are proposed for the designation of new genetic lineages to aid in moving toward a systematic HMPV classification.
Published: 2023

24. Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1

Author: Mykytyn, Anna Z., Rosu, Miruna E., Kok, Adinda, Rissmann, Melanie, van Amerongen, Geert, Geurtsvankessel, Corine, de Vries, Rory D., Munnink, Bas B.Oude, Smith, Derek J., Koopmans, Marion P.G., Lamers, Mart M., Fouchier, Ron A.M., Haagmans, Bart L., Mykytyn, Anna Z., Rosu, Miruna E., Kok, Adinda, Rissmann, Melanie, van Amerongen, Geert, Geurtsvankessel, Corine, de Vries, Rory D., Munnink, Bas B.Oude, Smith, Derek J., Koopmans, Marion P.G., Lamers, Mart M., Fouchier, Ron A.M., and Haagmans, Bart L.
Published: 2023

25. Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds

Author: Wille, Michelle, Lisovski, Simeon, Roshier, David, Ferenczi, Marta, Hoye, Bethany J., Leen, Trent, Warner, Simone, Fouchier, Ron A.M., Hurt, Aeron C., Holmes, Edward C., Klaassen, Marcel, Wille, Michelle, Lisovski, Simeon, Roshier, David, Ferenczi, Marta, Hoye, Bethany J., Leen, Trent, Warner, Simone, Fouchier, Ron A.M., Hurt, Aeron C., Holmes, Edward C., and Klaassen, Marcel
Abstract: Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum samples collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño-Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.
Published: 2023

26. 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., van Nierop, Gijsbert P., Aguilar-Bretones, Muriel, Fouchier, Ron A.M., Koopmans, Marion P.G., and van Nierop, Gijsbert P.
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.
Published: 2023

27. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: National Institute of Allergy and Infectious Diseases (US), National Cancer Institute (US), National Institutes of Health (US), Frederick National Laboratory for Cancer Research (US), US Department of Homeland Security, National Institute of Food and Agriculture (US), Kuhn, Jens H. [0000-0002-7800-6045], Adkins, Scott [0000-0003-0095-8414], Alioto, Daniela [0000-0002-4954-8363], Alkhovsky, Sergey V. [0000-0001-6913-5841], Amarasinghe, Gaya K. [0000-0002-0418-9707], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bartonička, Tomáš [0000-0001-7335-2435], Basler, Christopher F. [0000-0003-4195-425X], Bavari, Sina [0000-0001-8424-5635], Beer, Martin [0000-0002-0598-5254], Bente, Dennis A. [0000-0002-5150-7368], Bergeron, Éric [0000-0003-3398-8628], Bird, Brian H. [0000-0001-8170-8710], Blair, Carol D. [0000-0002-2803-0354], Blasdell, Kim R. [0000-0003-2121-0376], Bradfute, Steven B. [0000-0002-1985-751X], Breyta, Rachel [0000-0002-9106-1014], Briese, Thomas [0000-0002-4819-8963], Brown, Paul A. [0000-0002-6697-7688], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J. [0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Buzkan, Nihal [0000-0002-0428-0447], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chamberlain, John [0000-0002-7387-6420], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N. [0000-0002-7675-8251], Chen, Biao [0000-0002-2450-9296], Chiumenti, Michela [0000-0002-8412-3037], Choi, Il-Ryong [0000-0002-8035-7573], Clegg, J Christopher S. [0000-0003-3765-1862], Crozier, Ian [0000-0003-2485-4011], da Graça, John V. [0000-0003-0743-1519], Dávila, Alberto M.R. [0000-0002-6918-7673], de la Torre, J. C. [0000-0002-8171-8115], de Lamballerie, Xavier [0000-0001-7895-2720], De Swart, Rik L. [0000-0003-3599-8969], Di Bello, Patrick L. [0000-0002-4773-8040], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G. [0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Dolja, Valerian V. [0000-0002-8148-4670], Dolnik, Olga [0000-0001-7739-4798], Drexler, J. Felix [0000-0002-3509-0232], Dürrwald, Ralf [0000-0002-3432-0438], Dufkova, Lucie [0000-0001-7302-2057], Dundon, William G. [0000-0002-2776-169X], Duprex, W. Paul [0000-0003-1716-6376], Dye, John M. [0000-0002-0883-5016], Easton, Andrew J. [0000-0002-2288-3882], Ebihara, Hideki [0000-0002-2576-9735], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Fernandes, Jorlan [0000-0002-5039-0604], Fooks, Anthony R. [0000-0002-3243-6154], Formenty, Pierre B.H. [0000-0002-9482-5411], Forth, Leonie F [0000-0002-2708-2515], Fouchier, Ron A.M. [0000-0001-8095-2869], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], Gāo, George Fú [0000-0002-3869-615X], García, María Laura [0000-0001-6468-6943], García-Sastre, Adolfo [0000-0002-6551-1827], Garrison, Aura R. [0000-0003-3034-6400], Gbakima, Aiah [0000-0002-7642-0752], Goldstein, Tracey [0000-0002-1672-7410], Gonzalez, Jean-Paul J. [0000-0003-3063-1770], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H. [0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Guterres, Alexandro [0000-0001-8323-1477], Hall, Roy A. [0000-0001-5778-1387], Hammond, John [0000-0001-7593-747X], Hassan, Mohamed [0000-0002-1289-0878], Hepojoki, Jussi [0000-0001-5699-214X], Hepojoki, Satu [0000-0002-0696-1879], Hetzel, Udo [0000-0001-9142-560X], Hewson, Roger [0000-0003-2273-3152], Höper, Dirk [0000-0001-8408-2274], Horie, Masayuki [0000-0003-4682-7698], Hyndman, Timothy [0000-0002-7047-5023], Hughes, Holly R. [0000-0003-1380-8263], Hyndman, Timothy [0000-0003-4083-562X], Jambai, Amara [0000-0003-3754-2500], Jardim, Rodrigo [0000-0002-0943-5356], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B. [0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B. [0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kobinger, Gary [0000-0003-0612-2298], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Langevin, Stanley L. [0000-0002-6833-271X], Lee, Benhur [0000-0003-0760-1709], Lemos, Elba R.S. [0000-0003-3761-0200], Lukashevich, Igor S. [0000-0001-6523-5116], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mielke-Ehret, Nicole [0000-0003-0096-0696], Minafra, Angelantonio [0000-0002-0547-7129], Minutolo, Maria [0000-0001-7816-2657], Mühlberger, Elke [0000-0003-3547-9376], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Nunes, Márcio R.T. [0000-0003-0529-0230], Nylund, Are [0000-0002-1932-6604], Okland, Arnfinn Lodden [0000-0003-3062-4386], Oliveira, Renata C. [0000-0002-1904-7533], Pallás, Vicente [0000-0003-4954-989X], Pályi, Bernadett [0000-0003-1975-4198], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Radoshitzky, Sheli R. [0000-0001-8976-8056], Rahman, Aziz-Ul [0000-0002-3342-4462], Ramos-González, Pedro L. [0000-0002-9640-6587], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Robles Luna, Gabriel [0000-0003-3409-5557], Rota, Paul [0000-0002-8595-4094], Rubbenstroth, Dennis [0000-0002-8209-6274], Runstadler, Jonathan A. [0000-0002-6747-7765], Ruzek, Daniel [0000-0003-4655-2380], Sabanadzovic, Sead [0000-0002-2995-2633], Salát, Jiří [0000-0002-9915-8953], Sarpkaya, Kamil [0000-0001-5794-668X], Sasaya, Takahide [0000-0002-5020-9377], Shabbir, Muhammad Z. [0000-0003-4908-3313], Shí, Zhènglì [0000-0002-7309-6838], Sironi, Manuela [0000-0002-2267-5266], Smither, Sophie [0000-0002-7835-3581], Smura, Teemu [0000-0002-9187-3151], Spann, Kirsten [0000-0003-0567-8382], Spengler, Jessica R. [0000-0002-5383-0513], Stenglein, Mark D. [0000-0002-0993-813X], Takada, Ayato [0000-0003-2464-6642], Tesh, Robert B. [0000-0002-9226-397X], Thornburg, Natalie J. [0000-0003-3523-3616], Tomonaga, Keizō [0000-0003-0405-7103], Tordo, Noël [0000-0001-5873-059X], Towner, Jonathan S. [0000-0002-6473-3049], Turina, Massimo [0000-0002-9659-9470], Tzanetakis, Ioannis E. [0000-0002-5970-1763], Ulrich, R. G. [0000-0002-5620-1528], Vaira, Anna Maria [0000-0003-2526-4419], Van den Hoogen, Bernadette [0000-0003-1996-8559], Varsani, Arvind [0000-0003-4111-2415], Verbeek, Martin [0000-0002-8973-3803], Wahl, Victoria [0000-0002-6588-4308], Whitfield, Anna E. [0000-0002-3538-015X], Wolf, Yuri I. [0000-0002-0247-8708], Yutin, Natalya [0000-0002-3633-5123], Zerbini, F. Murilo [0000-0001-8617-0200], Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher F., Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., 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 M.R., de la Torre, J. C., 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, J. 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 B.H., Forth, Leonie F., Fouchier, Ron A.M., 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, M. 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, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, B., Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R.S., Leroy, Eric M., Li, Dexin, Li, Jianrong, Liang, Mifang, Liú, Wénwén, Liu, Yang, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P, Martin, Robert R., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Nylund, Are, Okland, Arnfinn Lodden, Oliveira, Renata C., Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz-Ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis E., Ulrich, R. G., Vaira, Anna Maria, Van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, Zhou, Xueping, National Institute of Allergy and Infectious Diseases (US), National Cancer Institute (US), National Institutes of Health (US), Frederick National Laboratory for Cancer Research (US), US Department of Homeland Security, National Institute of Food and Agriculture (US), Kuhn, Jens H. [0000-0002-7800-6045], Adkins, Scott [0000-0003-0095-8414], Alioto, Daniela [0000-0002-4954-8363], Alkhovsky, Sergey V. [0000-0001-6913-5841], Amarasinghe, Gaya K. [0000-0002-0418-9707], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bartonička, Tomáš [0000-0001-7335-2435], Basler, Christopher F. [0000-0003-4195-425X], Bavari, Sina [0000-0001-8424-5635], Beer, Martin [0000-0002-0598-5254], Bente, Dennis A. [0000-0002-5150-7368], Bergeron, Éric [0000-0003-3398-8628], Bird, Brian H. [0000-0001-8170-8710], Blair, Carol D. [0000-0002-2803-0354], Blasdell, Kim R. [0000-0003-2121-0376], Bradfute, Steven B. [0000-0002-1985-751X], Breyta, Rachel [0000-0002-9106-1014], Briese, Thomas [0000-0002-4819-8963], Brown, Paul A. [0000-0002-6697-7688], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J. [0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Buzkan, Nihal [0000-0002-0428-0447], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chamberlain, John [0000-0002-7387-6420], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N. [0000-0002-7675-8251], Chen, Biao [0000-0002-2450-9296], Chiumenti, Michela [0000-0002-8412-3037], Choi, Il-Ryong [0000-0002-8035-7573], Clegg, J Christopher S. [0000-0003-3765-1862], Crozier, Ian [0000-0003-2485-4011], da Graça, John V. [0000-0003-0743-1519], Dávila, Alberto M.R. [0000-0002-6918-7673], de la Torre, J. C. [0000-0002-8171-8115], de Lamballerie, Xavier [0000-0001-7895-2720], De Swart, Rik L. [0000-0003-3599-8969], Di Bello, Patrick L. [0000-0002-4773-8040], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G. [0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Dolja, Valerian V. [0000-0002-8148-4670], Dolnik, Olga [0000-0001-7739-4798], Drexler, J. Felix [0000-0002-3509-0232], Dürrwald, Ralf [0000-0002-3432-0438], Dufkova, Lucie [0000-0001-7302-2057], Dundon, William G. [0000-0002-2776-169X], Duprex, W. Paul [0000-0003-1716-6376], Dye, John M. [0000-0002-0883-5016], Easton, Andrew J. [0000-0002-2288-3882], Ebihara, Hideki [0000-0002-2576-9735], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Fernandes, Jorlan [0000-0002-5039-0604], Fooks, Anthony R. [0000-0002-3243-6154], Formenty, Pierre B.H. [0000-0002-9482-5411], Forth, Leonie F [0000-0002-2708-2515], Fouchier, Ron A.M. [0000-0001-8095-2869], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], Gāo, George Fú [0000-0002-3869-615X], García, María Laura [0000-0001-6468-6943], García-Sastre, Adolfo [0000-0002-6551-1827], Garrison, Aura R. [0000-0003-3034-6400], Gbakima, Aiah [0000-0002-7642-0752], Goldstein, Tracey [0000-0002-1672-7410], Gonzalez, Jean-Paul J. [0000-0003-3063-1770], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H. [0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Guterres, Alexandro [0000-0001-8323-1477], Hall, Roy A. [0000-0001-5778-1387], Hammond, John [0000-0001-7593-747X], Hassan, Mohamed [0000-0002-1289-0878], Hepojoki, Jussi [0000-0001-5699-214X], Hepojoki, Satu [0000-0002-0696-1879], Hetzel, Udo [0000-0001-9142-560X], Hewson, Roger [0000-0003-2273-3152], Höper, Dirk [0000-0001-8408-2274], Horie, Masayuki [0000-0003-4682-7698], Hyndman, Timothy [0000-0002-7047-5023], Hughes, Holly R. [0000-0003-1380-8263], Hyndman, Timothy [0000-0003-4083-562X], Jambai, Amara [0000-0003-3754-2500], Jardim, Rodrigo [0000-0002-0943-5356], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B. [0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B. [0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kobinger, Gary [0000-0003-0612-2298], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Langevin, Stanley L. [0000-0002-6833-271X], Lee, Benhur [0000-0003-0760-1709], Lemos, Elba R.S. [0000-0003-3761-0200], Lukashevich, Igor S. [0000-0001-6523-5116], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mielke-Ehret, Nicole [0000-0003-0096-0696], Minafra, Angelantonio [0000-0002-0547-7129], Minutolo, Maria [0000-0001-7816-2657], Mühlberger, Elke [0000-0003-3547-9376], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Nunes, Márcio R.T. [0000-0003-0529-0230], Nylund, Are [0000-0002-1932-6604], Okland, Arnfinn Lodden [0000-0003-3062-4386], Oliveira, Renata C. [0000-0002-1904-7533], Pallás, Vicente [0000-0003-4954-989X], Pályi, Bernadett [0000-0003-1975-4198], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Radoshitzky, Sheli R. [0000-0001-8976-8056], Rahman, Aziz-Ul [0000-0002-3342-4462], Ramos-González, Pedro L. [0000-0002-9640-6587], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Robles Luna, Gabriel [0000-0003-3409-5557], Rota, Paul [0000-0002-8595-4094], Rubbenstroth, Dennis [0000-0002-8209-6274], Runstadler, Jonathan A. [0000-0002-6747-7765], Ruzek, Daniel [0000-0003-4655-2380], Sabanadzovic, Sead [0000-0002-2995-2633], Salát, Jiří [0000-0002-9915-8953], Sarpkaya, Kamil [0000-0001-5794-668X], Sasaya, Takahide [0000-0002-5020-9377], Shabbir, Muhammad Z. [0000-0003-4908-3313], Shí, Zhènglì [0000-0002-7309-6838], Sironi, Manuela [0000-0002-2267-5266], Smither, Sophie [0000-0002-7835-3581], Smura, Teemu [0000-0002-9187-3151], Spann, Kirsten [0000-0003-0567-8382], Spengler, Jessica R. [0000-0002-5383-0513], Stenglein, Mark D. [0000-0002-0993-813X], Takada, Ayato [0000-0003-2464-6642], Tesh, Robert B. [0000-0002-9226-397X], Thornburg, Natalie J. [0000-0003-3523-3616], Tomonaga, Keizō [0000-0003-0405-7103], Tordo, Noël [0000-0001-5873-059X], Towner, Jonathan S. [0000-0002-6473-3049], Turina, Massimo [0000-0002-9659-9470], Tzanetakis, Ioannis E. [0000-0002-5970-1763], Ulrich, R. G. [0000-0002-5620-1528], Vaira, Anna Maria [0000-0003-2526-4419], Van den Hoogen, Bernadette [0000-0003-1996-8559], Varsani, Arvind [0000-0003-4111-2415], Verbeek, Martin [0000-0002-8973-3803], Wahl, Victoria [0000-0002-6588-4308], Whitfield, Anna E. [0000-0002-3538-015X], Wolf, Yuri I. [0000-0002-0247-8708], Yutin, Natalya [0000-0002-3633-5123], Zerbini, F. Murilo [0000-0001-8617-0200], Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher F., Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., 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 M.R., de la Torre, J. C., 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, J. 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 B.H., Forth, Leonie F., Fouchier, Ron A.M., 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, M. 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, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, B., Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R.S., Leroy, Eric M., Li, Dexin, Li, Jianrong, Liang, Mifang, Liú, Wénwén, Liu, Yang, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P, Martin, Robert R., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Nylund, Are, Okland, Arnfinn Lodden, Oliveira, Renata C., Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz-Ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis E., Ulrich, R. G., Vaira, Anna Maria, Van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou, Xueping
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

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

Author: Rijks, Jolianne M, Leopold, Mardik F, Kühn, Susanne, In 't Veld, Ronald, Schenk, Fred, Brenninkmeijer, Allix, Lilipaly, Sander J, Ballmann, Mónika Z, Kelder, Leon, de Jong, Job W, Courtens, Wouter, Slaterus, Roy, Kleyheeg, Erik, Vreman, Sandra, Kik, Marja J L, Gröne, Andrea, Fouchier, Ron A M, Engelsma, Marc, de Jong, Mart C M, Kuiken, Thijs, Beerens, Nancy, Rijks, Jolianne M, Leopold, Mardik F, Kühn, Susanne, In 't Veld, Ronald, Schenk, Fred, Brenninkmeijer, Allix, Lilipaly, Sander J, Ballmann, Mónika Z, Kelder, Leon, de Jong, Job W, Courtens, Wouter, Slaterus, Roy, Kleyheeg, Erik, Vreman, Sandra, Kik, Marja J L, Gröne, Andrea, Fouchier, Ron A M, Engelsma, Marc, de Jong, Mart C M, Kuiken, Thijs, and Beerens, Nancy
Abstract: We collected data on mass mortality in Sandwich terns (Thalasseus sandvicensis) during the 2022 breeding season in the Netherlands. Mortality was associated with at least 2 variants of highly pathogenic avian influenza A(H5N1) virus clade 2.3.4.4b. We report on carcass removal efforts relative to survival in colonies. Mitigation strategies urgently require structured research.
Published: 2022

29. Contribution of neuraminidase to the efficacy of seasonal split influenza vaccines in the ferret model

Author: Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, Herfst, Sander, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, and Herfst, Sander
Abstract: Seasonal influenza vaccination takes into account primarily hemagglutinin (HA)-specific neutralizing antibody responses. However, the accumulation of substitutions in the antigenic regions of HA (i.e., antigenic drift) occasionally results in a mismatch between the vaccine and circulating strains. To prevent poor vaccine performance, we investigated whether an antigenically matched neuraminidase (NA) may compensate for reduced vaccine efficacy due to a mismatched HA. Ferrets were vaccinated twice with adjuvanted split inactivated influenza vaccines containing homologous HA and NA (vacH3N2), only homologous HA (vacH3N1), only homologous NA (vacH1N2), heterologous HA and NA (vacH1N1), or phosphate-buffered saline (vacPBS), followed by challenge with H3N2 virus (A/Netherlands/16190/1968). Ferrets vaccinated with homologous HA (vacH3N2 and vacH3N1) displayed minimum fever and weight loss compared to vacH1N1 and vacPBS ferrets, while ferrets vaccinated with NA-matched vacH1N2 displayed intermediate fever and weight loss. Vaccination with vacH1N2 further led to a reduction in virus shedding from the nose and undetectable virus titers in the lower respiratory tract, similarly to when the homologous vacH3N2 was used. Some protection was observed upon vacH1N1 vaccination, but this was not comparable to that observed for vacH1N2, again highlighting the important role of NA in vaccine-induced protection. These results illustrate that NA antibodies can prevent severe disease caused by influenza virus infection and that an antigenically matched NA in seasonal vaccines might prevent lower respiratory tract complications. This underlines the importance of considering NA during the yearly vaccine strain selection process, which may be particularly beneficial in seasons when the HA component of the vaccine is mismatched. IMPORTANCE Despite the availability of vaccines, influenza virus infections continue to cause substantial morbidity and mortality in humans. Currently available
Published: 2022

30. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Abstract: Highly pathogenic avian influenza (HPAI) in wild birds is a major emerging disease, and a cause of increased mortality during outbreaks. The Common buzzard (Buteo buteo) has a considerable chance of acquiring the infection and therefore may function as bio-sentinel for the presence of virus in wildlife. This study aimed to determine the virus distribution and associated pathological changes in the tissues of Common buzzards that died with HPAI H5 virus infection during the 2020-2021 epizootic. Eleven freshly dead, HPAI H5 virus-positive Common buzzards were necropsied. Based on RT-PCR, all birds were systemically infected with HPAI H5N8 virus, as viral RNA was detected in cloacal and pharyngeal swabs and in all 10 selected tissues of the birds, with mean Ct values per tissue ranging from 22 for heart to 32 for jejunum. Based on histology and immunohistochemistry, the most common virus-associated pathological changes were necrotizing encephalitis (9/11 birds) and necrotizing myocarditis (7/11 birds). The proventriculus of two birds showed virus-associated necrosis, indicating tropism of this virus for the digestive tract. Our advice is to collect at least a miniset of samples including brain, heart, liver, and spleen, as these tissues were positive both by RT-PCR and for virus-antigen-associated lesions.
Published: 2022

31. Contribution of neuraminidase to the efficacy of seasonal split influenza vaccines in the ferret model

Author: VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, Herfst, Sander, VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, and Herfst, Sander
Published: 2022

32. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Published: 2022

33. Contribution of neuraminidase to the efficacy of seasonal split influenza vaccines in the ferret model

Author: VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, Herfst, Sander, VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, and Herfst, Sander
Published: 2022

34. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Published: 2022

35. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

36. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

37. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

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

Author: Afd Chemical Biology and Drug Discovery, Afd Pharmaceutics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Pharmaceutics, Biomolecular Mass Spectrometry and Proteomics, Spruit, Cindy M., Sweet, Igor R., Bestebroer, Theo, Lexmond, Pascal, Qiu, Boning, Damen, Mirjam J.A., Fouchier, Ron A. M., Snijder, Joost, Herfst, Sander, Boons, Geert-Jan, Vries, Robert P. de, Afd Chemical Biology and Drug Discovery, Afd Pharmaceutics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Pharmaceutics, Biomolecular Mass Spectrometry and Proteomics, Spruit, Cindy M., Sweet, Igor R., Bestebroer, Theo, Lexmond, Pascal, Qiu, Boning, Damen, Mirjam J.A., Fouchier, Ron A. M., Snijder, Joost, Herfst, Sander, Boons, Geert-Jan, and Vries, Robert P. de
Published: 2022

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

Author: VPDC pathologie, Rijks, Jolianne M, Leopold, Mardik F, Kühn, Susanne, In 't Veld, Ronald, Schenk, Fred, Brenninkmeijer, Allix, Lilipaly, Sander J, Ballmann, Mónika Z, Kelder, Leon, de Jong, Job W, Courtens, Wouter, Slaterus, Roy, Kleyheeg, Erik, Vreman, Sandra, Kik, Marja J L, Gröne, Andrea, Fouchier, Ron A M, Engelsma, Marc, de Jong, Mart C M, Kuiken, Thijs, Beerens, Nancy, VPDC pathologie, Rijks, Jolianne M, Leopold, Mardik F, Kühn, Susanne, In 't Veld, Ronald, Schenk, Fred, Brenninkmeijer, Allix, Lilipaly, Sander J, Ballmann, Mónika Z, Kelder, Leon, de Jong, Job W, Courtens, Wouter, Slaterus, Roy, Kleyheeg, Erik, Vreman, Sandra, Kik, Marja J L, Gröne, Andrea, Fouchier, Ron A M, Engelsma, Marc, de Jong, Mart C M, Kuiken, Thijs, and Beerens, Nancy
Published: 2022

40. Contribution of neuraminidase to the efficacy of seasonal split influenza vaccines in the ferret model

Author: VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, Herfst, Sander, VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, and Herfst, Sander
Published: 2022

41. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Published: 2022

42. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Published: 2022

43. Contribution of neuraminidase to the efficacy of seasonal split influenza vaccines in the ferret model

Author: VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, Herfst, Sander, VPDC pathologie, dPB CR, dPB I&I, Rosu, Miruna E, Kok, Adinda, Bestebroer, Theo M, de Meulder, Dennis, Verveer, Elwin P, Pronk, Mark R, Dekker, Lennard J M, Luider, Theo M, Richard, Mathilde, van den Brand, Judith M A, Fouchier, Ron A M, and Herfst, Sander
Published: 2022

44. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Björn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

45. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

46. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

47. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

Author: Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, Waldenström, Jonas, Wille, Michelle, Tolf, Conny, Latorre-Margalef, Neus, Fouchier, Ron A. M., Halpin, Rebecca A., Wentworth, David E., Ragwani, Jayna, Pybus, Oliver G., Olsen, Bjorn, and Waldenström, Jonas
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Published: 2022
Full Text: View/download PDF

48. Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Author: VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, Kuiken, Thijs, VPDC pathologie, dPB I&I, Caliendo, Valentina, Leijten, Lonneke, van de Bildt, Marco W G, Fouchier, Ron A M, Rijks, Jolianne M, and Kuiken, Thijs
Published: 2022

49. Defining the risk of SARS-CoV-2 variants on immune protection.

Author: DeGrace, Marciela M, 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, Theiler, James, DeGrace, Marciela M, 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
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

50. Active wild bird surveillance of avian influenza viruses, a report

Author: Waldenström, Jonas, van Toor, Mariëlle L., Lewis, Nicola, Lopes, Sara, Javakhishvili, Zura, Muzika, Denys, Fouchier, Ron A. M., Brouwer, Adam, Waldenström, Jonas, van Toor, Mariëlle L., Lewis, Nicola, Lopes, Sara, Javakhishvili, Zura, Muzika, Denys, Fouchier, Ron A. M., and Brouwer, Adam
Abstract: This report summarises the potential for an EU-wide active surveillance of highly pathogenic avian influenza (HPAI) virus in wild birds. As basis for the analyses, we collected and analysed virological and ornithological data and carried out fieldwork in two countries outside the EU: Ukraine and Georgia. We show that it is possible to build capacity and logistics for sampling nodes that can provide rapid detection and identification of HPAI, that are key features for an early warning system. Based on the data presented here, it is suggested that an EU-level surveillance network in wild birds is constructed, where surveillance nodes are chosen to reflect the epidemiological benefit of the whole EU. Selection of sampling nodes in the surveillance network should incorporate ornithological and virological background data, and that on-site development should include combined local ornithology and virology expertise and a minimised analytic time frame from sample to result. Ideally, surveillance nodes should be constructed with operational flexibility in what type of material that can be collected, such as active surveillance of wild birds (cloacal, oropharyngeal, blood samples), sampling of hunting bags, and the possibility to take environmental samples or to sample carcasses. This way a surveillance node could be adapted to changes in virus epidemiology, such as shifts in what hosts need to be sampled and at what times of the year sampling should occur. In times of enzootic virus circulation, the network should be tuned to monitor waves of infections and provide warning signals when increased activity is anticipated based on migratory bird movements. Based on the above assumptions, we provide a set of suitable regions, both within and outside the EU, that should be considered.
Published: 2022
Full Text: View/download PDF

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