H5N1 and highly pathogenic avian influenza
H5N1 has moved from a poultry problem to a panzootic affecting wild birds, marine mammals and now dairy cattle across the United States. We use genomic surveillance and phylodynamic inference to ask which reassortant genotypes carry pandemic potential, how the virus is moving between herds and what adaptations accompany each jump into a new mammalian host.
Featured publications
Featured publication
Can H5N1 avian influenza in dairy cattle be contained in the US?
Pekar JE, Crespo-Bellido A, Lemey P, Bowman AS, Peacock TP, Ochoa JN, Rambaut A, Pybus OG, Worobey M, Nelson MI
Cell 2026 189(3):699-705
Featured publication
Cross-species and mammal-to-mammal transmission of clade 2.3.4.4b highly pathogenic avian influenza A/H5N1 with PB2 adaptations
Pardo-Roa C, Nelson MI, Ariyama N, Aguayo C, Almonacid LI, Gonzalez-Reiche AS, Muñoz G, Ulloa M, Ávila C, Navarro C, Reyes R, Castillo-Torres PN, Mathieu C, Vergara R, González Á, González CG, Araya H, Castillo A, Torres JC, Covarrubias P, Bustos P, van Bakel H, Fernández J, Fasce RA, Johow M, Neira V, Medina RA
Nat Commun 2025 16(1):2232
Featured publication
The global H5N1 influenza panzootic in mammals
Peacock TP, Moncla L, Dudas G, VanInsberghe D, Sukhova K, Lloyd-Smith JO, Worobey M, Lowen AC, Nelson MI
Nature 2025 637(8045):304-313
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2026
Featured publication
Can H5N1 avian influenza in dairy cattle be contained in the US?
Pekar JE, Crespo-Bellido A, Lemey P, Bowman AS, Peacock TP, Ochoa JN, Rambaut A, Pybus OG, Worobey M, Nelson MI
Cell 2026 189(3):699-705
CEIRR Risk Assessment Pipeline executive reports on H5N1 highly pathogenic avian influenza 2.3.4.4b, swine H1 1B.2, and H9N2 low pathogenicity avian influenza B4.7.2
Centers of Excellence for Influenza Research and Response Risk Assessment Pipeline
J Virol 2026 100(6):e0054526
Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica
Clessin A, Brusselmans M, Hong SL, Tornos J, Lejeune M, Shao Y, Briand FX, Abolnik C, Kaza B, Suchard MA, Aguado B, Alcamí A, Barbraud C, Beer M, Bennison A, Bonadonna F, Bonnet T, Bost CA, Boucheron S, Bralet T, Catry P, Cleeland J, Connan M, Coombes HA, Delord K, de Pasquale C, Dewar ML, Dong X, Emerit J, Fischer R, Fountain-Jones N, Galimberti F, González-Solís J, Guinet C, Gunn C, Günther A, Iervolino M, James J, Ji X, Jonsen I, Jones CW, Kuepfer A, Kuiken T, Lebohec C, Lisovski S, Llorente Zubiri L, Lynton-Jenkins JG, Martinez-García P, McCulley M, McMahon CR, Mollett BC, Moraga-Quintanilla AI, Nichol R, Noiret A, Ogrzewalska M, Owen K, Pardo-Roa C, Peroteau S, Phillips RA, Poulin E, Rambaut A, Reid SM, Riehle E, Risi M, Rumianowski O, Ryan PG, Sanvito S, Stanworth A, Steinfurth A, Stevenson J, Stier A, Uhart MM, Vanstreels RET, Vázquez-Calvo A, Vianna JA, Wells K, White J, Whitelaw P, Wille M, Younger J, Roberts LC, Grasland B, Banyard AC, Nelson MI, Gamble A, Boulinier T, Baele G
bioRxiv 2026
Emergence of D1.1 reassortant H5N1 avian influenza viruses in North America
Crespo-Bellido A, Trovão NS, Puryear W, Maksiaev A, Pekar JE, Baele G, Dellicour S, Nelson MI
bioRxiv 2026
Highly pathogenic avian influenza (HPAI H5N1, clade 2.3.4.4b, genotype C2.1) in commercial ring-necked pheasants during the 2022 outbreak in the United States
Niel K, St Charles K, Elissa J, Lighty M, Ssematimba A, Culhane M, Crespo-Bellido A, Trovão N, Nelson M, Cardona C
Can J Microbiol 2026 72:1-17
The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle
Pekar JE, Gangavarapu K, Crespo-Bellido A, Peacock TP, Wertheim JO, Dudas G, Joy JB, Chand M, Débarre F, Gangavarapu P, Goldhill DH, Groves N, Ji X, Serrano LM, Moncla L, Rasmussen AL, Ruis C, Venkatesh D, Kraemer MUG, Pybus OG, Andersen KG, Suchard MA, Nelson MI, Lemey P, Worobey M, Rambaut A
bioRxiv 2026
2025
Controlling bird flu is urgent-for dairy, wildlife, poultry, pets, and people
Lowen AC, Bowman AS, Runstadler JA, Baker AL, García-Sastre A, Hensley SE, Lakdawala SS, Moncla LH, Nelson M, Pekosz A, Poulson RL, Puryear WB, Sutton TC, Tompkins SM, Webby RJ
J Am Vet Med Assoc 2025 263(9):1192-1195
Featured publication
Cross-species and mammal-to-mammal transmission of clade 2.3.4.4b highly pathogenic avian influenza A/H5N1 with PB2 adaptations
Pardo-Roa C, Nelson MI, Ariyama N, Aguayo C, Almonacid LI, Gonzalez-Reiche AS, Muñoz G, Ulloa M, Ávila C, Navarro C, Reyes R, Castillo-Torres PN, Mathieu C, Vergara R, González Á, González CG, Araya H, Castillo A, Torres JC, Covarrubias P, Bustos P, van Bakel H, Fernández J, Fasce RA, Johow M, Neira V, Medina RA
Nat Commun 2025 16(1):2232
Enhancing the response to avian influenza in the US and globally
Bartlett ML, Palese P, Davis MF, Vermund SH, Bréchot C, Evans JD, Sauer LM, Osterhaus A, Pekosz A, Nelson M, Stachler E, Krammer F, Moreno G, Olinger G, Koopmans M
Lancet Reg Health Am 2025 46:101100
Novel Highly Pathogenic Avian Influenza A(H5N1) Virus, Argentina, 2025
Vanstreels RET, Nelson MI, Artuso MC, Marchione VD, Piccini LE, Benedetti E, Crespo-Bellido A, Pierdomenico A, Wolff T, Uhart MM, Rimondi A
Emerg Infect Dis 2025 31(12):2279-2283
Pandemic risk stemming from the bovine H5N1 outbreak: an account of the knowns and unknowns
Lowen AC, Baker AL, Bowman AS, García-Sastre A, Hensley SE, Lakdawala SS, Moncla LH, Nelson MI, Pekosz A, Poulson RL, Puryear WB, Runstadler JA, Sutton TC, Tompkins SM, Webby RJ, Risk Assessment Pipeline working group of the NIAID Centers of Excellence for Influenza Research and Response (CEIRR) Network
J Virol 2025 99(4):e0005225
Persistence and spillback of mammal-adapted H5N1 genotype B3.2 viruses among South American seabirds and marine mammals
Rimondi A, Vanstreets R, Nelson M, Olivera V, Gallo L, Durant A, Quintana F, Brogger M, Campana J, Dellicour S, Wolff T, Uhart MM
Res Sq 2025
Featured publication
The global H5N1 influenza panzootic in mammals
Peacock TP, Moncla L, Dudas G, VanInsberghe D, Sukhova K, Lloyd-Smith JO, Worobey M, Lowen AC, Nelson MI
Nature 2025 637(8045):304-313
2024
Avian Influenza A(H5N1) Virus among Dairy Cattle, Texas, USA
Oguzie JU, Marushchak LV, Shittu I, Lednicky JA, Miller AL, Hao H, Nelson MI, Gray GC
Emerg Infect Dis 2024 30(7):1425-1429
Epidemiological data of an influenza A/H5N1 outbreak in elephant seals in Argentina indicates mammal-to-mammal transmission
Uhart MM, Vanstreels RET, Nelson MI, Olivera V, Campagna J, Zavattieri V, Lemey P, Campagna C, Falabella V, Rimondi A
Nat Commun 2024 15(1):9516
2023
Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru
Leguia M, Garcia-Glaessner A, Muñoz-Saavedra B, Juarez D, Barrera P, Calvo-Mac C, Jara J, Silva W, Ploog K, Amaro L, Colchao-Claux P, Johnson CK, Uhart MM, Nelson MI, Lescano J
Nat Commun 2023 14(1):5489
2020
Evolution of highly pathogenic H7N3 avian influenza viruses in Mexico
Trovão NS, Talavera GA, Nelson MI, Perez de la Rosa JD
Zoonoses Public Health 2020 67(3):318-323
2014
Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor
Monne I, Fusaro A, Nelson MI, Bonfanti L, Mulatti P, Hughes J, Murcia PR, Schivo A, Valastro V, Moreno A, Holmes EC, Cattoli G
J Virol 2014 88(8):4375-88
2010
Evolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria from 2006 to 2008
Fusaro A, Nelson MI, Joannis T, Bertolotti L, Monne I, Salviato A, Olaleye O, Shittu I, Sulaiman L, Lombin LH, Capua I, Holmes EC, Cattoli G
J Virol 2010 84(7):3239-47
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