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

H5N1 and highly pathogenic avian influenza Review

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

H5N1 and highly pathogenic avian influenza

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

H5N1 and highly pathogenic avian influenza Preprint

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

H5N1 and highly pathogenic avian influenza Preprint

Genomic analysis reveals dynamics of SARS-CoV-2 during the initial phases of the COVID-19 outbreak in the Dominican Republic

Kreitman A, Mushegian A, Nelson MI, Banakis S, Mederos C, Chung M, Roder A, Peguero A, Mueses S, Cuevas P, Paulino-Ramírez R, Ghedin E

Microbiol Spectr · 2026 · 14(3):e0110525

SARS-CoV-2 in humans

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

H5N1 and highly pathogenic avian influenza

Outbreak of H9N2 avian influenza viruses in lesser rhea in Peru, June-July 2025

Garcia-Glaessner A, Crespo-Bellido A, Muñoz-Saavedra B, Juarez D, Barrera P, Salmon-Mulanovich G, Checahuari-Jaratai SE, Cruz D, Huisa D, Idme G, Nelson MI, Lescano J, Leguia M

bioRxiv · 2026

Other influenza Preprint

★ Featured publication

SARS-CoV-2 Delta variant re-emerges in US farmed mink and free-ranging white-tailed deer in 2022-2023

Crespo-Bellido A, Owsiany MC, Chillson NN, Huey D, McBride DS, Lemey P, Rekant SI, Korslund J, Neafsey M, Killian ML, Chandler JC, Hobbs C, Hildebrandt HH, Easley J, Yount JS, Nelson MI, Bowman AS

Nat Commun · 2026 · 17(1)

SARS-CoV-2 in non-human reservoirs

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

H5N1 and highly pathogenic avian influenza Preprint

Zoonotic infections and genomic evolution of novel reassortant swine influenza A viruses in Spain

Encinas PA, O'Boyle B, Maksaiev A, Nelson MI, García-Sastre A, Del Real G

bioRxiv · 2026

Swine influenza Preprint

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

H5N1 and highly pathogenic avian influenza

Cross-reactivity between antibodies induced by European swine influenza vaccines and Spanish swine influenza strains

Encinas P, Nogales A, Nelson MI, García-Sastre A, Del Real G

Front Vet Sci · 2025 · 12:1725563

Swine influenza

★ 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

H5N1 and highly pathogenic avian influenza

Ecology and evolution of influenza A viruses in wild waterfowl in Argentina reveals novel viral genotypes

Kreps L, Batsche LO, Olivera VS, Crespo-Bellido A, Nelson MI, Perez DR, Rimondi A

Virus Evol · 2025 · 11(1):veaf088

Other influenza

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

H5N1 and highly pathogenic avian influenza Review

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

H5N1 and highly pathogenic avian influenza

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

H5N1 and highly pathogenic avian influenza Review

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

H5N1 and highly pathogenic avian influenza Preprint

Persistence of SARS-CoV-2 Alpha Variant in White-Tailed Deer, Ohio, USA

Tarbuck NN, Garushyants SK, McBride DS, Dennis PM, Franks J, Woodard K, Shamblin A, Sovic MG, Collins DT, Van Why K, Webby RJ, Nelson MI, Bowman AS

Emerg Infect Dis · 2025 · 31(7):1319-1329

SARS-CoV-2 in non-human reservoirs

Repeated introductions and widespread transmission of human metapneumovirus in Côte d'Ivoire

Kadjo HA, Khan SM, Tamim S, Ar Gouilh M, Adagba M, Adjogoua E, Coulibaly D, Vabret A, Cherry JL, Nelson MI, Trovão NS

BMC Infect Dis · 2025 · 25(1):1092

Other disease systems

Seasonal Influenza Vaccine 2021/2022 Provides Limited Cross Reactivity Against Contemporary Swine Influenza A Virus Strains in Spain

Encinas P, Lalueza-Blanco A, García-Vaquero AI, Nelson MI, García-Sastre A, Del Real G

Influenza Other Respir Viruses · 2025 · 19(12):e70158

Swine influenza

★ 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

H5N1 and highly pathogenic avian influenza Review

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

H5N1 and highly pathogenic avian influenza

Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species

Trovão NS, Khan SM, Lemey P, Nelson MI, Cherry JL

mBio · 2024 · 15(1):e0264923

Other influenza

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

H5N1 and highly pathogenic avian influenza

Genomic analysis of the early COVID-19 pandemic in Haiti reveals Caribbean-specific variant dynamics

Mushegian A, Kreitman A, Nelson MI, Chung M, Mederos C, Roder A, Banakis S, Desormeaux AM, Jean Charles NL, Grant-Greene Y, Marseille S, Pierre K, Lafontant D, Boncy J, Journel I, Buteau J, Juin S, Ghedin E

PLOS Glob Public Health · 2024 · 4(11):e0003536

SARS-CoV-2 in humans

The Evolution of SARS-CoV-2 and Influenza A Virus at the Human–Animal Interface

Anderson TK, Medina RA, Nelson MI

In: Genetics and Evolution of Infectious Diseases (Third Edition) · Tibayrenc M, ed. · Elsevier · 2024 · ch. 22 · pp. 549–572

SARS-CoV-2 in non-human reservoirs Swine influenza Book chapter

Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

McBride DS, Garushyants SK, Franks J, Magee AF, Overend SH, Huey D, Williams AM, Faith SA, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting JM, Tonkovich MJ, Genders JT, Montoney AJ, Kasnyik K, Linder TJ, Bevins SN, Lenoch JB, Chandler JC, DeLiberto TJ, Koonin EV, Suchard MA, Lemey P, Webby RJ, Nelson MI, Bowman AS

Nat Commun · 2023 · 14(1):5105

SARS-CoV-2 in non-human reservoirs

Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses

Ortiz L, Geiger G, Ferreri L, Moran D, Mendez D, Gonzalez-Reiche AS, Alvarez D, Motta M, Escobar F, Rajao D, Cordon-Rosales C, Nelson MI, Perez DR

Viruses · 2023 · 15(2)

Other influenza

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

H5N1 and highly pathogenic avian influenza

Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States

Rasmussen EA, Czaja A, Cuthbert FJ, Tan GS, Lemey P, Nelson MI, Culhane MR

Front Genet · 2023 · 14:1172048

Other influenza

SARS-CoV-2 Neutralizing Antibodies in Free-Ranging Fallow Deer (Dama dama) and Red Deer (Cervus elaphus) in Suburban and Rural Areas in Spain

Encinas P, Escalera A, Aydillo T, Iglesias I, Nelson MI, García-Sastre A, Del Real G

Transbound Emerg Dis · 2023 · 2023:3324790

SARS-CoV-2 in non-human reservoirs

Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil

Pillai TK, Johnson KE, Song T, Gregianini TS, Tatiana G B, Wang G, Medina RA, Van Bakel H, García-Sastre A, Nelson MI, Ghedin E, Veiga ABG

Virus Evol · 2023 · 9(1):vead027

Human influenza

Birth cohort relative to an influenza A virus's antigenic cluster introduction drives patterns of children's antibody titers

Brouwer AF, Balmaseda A, Gresh L, Patel M, Ojeda S, Schiller AJ, Lopez R, Webby RJ, Nelson MI, Kuan G, Gordon A

PLoS Pathog · 2022 · 18(2):e1010317

Human influenza

Evolution of influenza A virus in intensive and free-range swine farms in Spain

Encinas P, Del Real G, Dutta J, Khan Z, van Bakel H, Del Burgo MÁM, García-Sastre A, Nelson MI

Virus Evol · 2022 · 7(2):veab099

Swine influenza

Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua

Wraith S, Balmaseda A, Carrillo FAB, Kuan G, Huddleston J, Kubale J, Lopez R, Ojeda S, Schiller A, Lopez B, Sanchez N, Webby R, Nelson MI, Harris E, Gordon A

Nat Commun · 2022 · 13(1):1190

Human influenza

Origins and Evolution of Seasonal Human Coronaviruses

Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS

Viruses · 2022 · 14(7)

SARS-CoV-2 in humans

★ Featured publication

SARS-CoV-2 infection in free-ranging white-tailed deer

Hale VL, Dennis PM, McBride DS, Nolting JM, Madden C, Huey D, Ehrlich M, Grieser J, Winston J, Lombardi D, Gibson S, Saif L, Killian ML, Lantz K, Tell RM, Torchetti M, Robbe-Austerman S, Nelson MI, Faith SA, Bowman AS

Nature · 2022 · 602(7897):481-486

SARS-CoV-2 in non-human reservoirs

Coordinating SARS-CoV-2 genomic surveillance in the United States

Nelson MI, Thielen P

Virus Evol · 2021 · 7(2):veab053

SARS-CoV-2 in humans

Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan

Trovão NS, Khuri-Bulos N, Tan Y, Puri V, Shilts MH, Halpin RA, Fedorova NB, Nelson MI, Halasa N, Das SR

Microb Genom · 2021 · 7(6)

Other disease systems

★ Featured publication

Tracing the Source of Influenza A Virus Zoonoses in Interconnected Circuits of Swine Exhibitions

McBride DS, Perofsky AC, Nolting JM, Nelson MI, Bowman AS

J Infect Dis · 2021 · 224(3):458-468

Swine influenza

A Heterogeneous Swine Show Circuit Drives Zoonotic Transmission of Influenza A Viruses in the United States

Nelson MI, Perofsky A, McBride DS, Rambo-Martin BL, Wilson MM, Barnes JR, van Bakel H, Khan Z, Dutta J, Nolting JM, Bowman AS

J Virol · 2020 · 94(24)

Swine influenza

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA

Nat Commun · 2020 · 11(1):5110

SARS-CoV-2 in humans

Beyond clinical trials: Evolutionary and epidemiological considerations for development of a universal influenza vaccine

Viboud C, Gostic K, Nelson MI, Price GE, Perofsky A, Sun K, Sequeira Trovão N, Cowling BJ, Epstein SL, Spiro DJ

PLoS Pathog · 2020 · 16(9):e1008583

Human influenza Review

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P

Nat Commun · 2020 · 11(1):5620

Other disease systems

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

H5N1 and highly pathogenic avian influenza

Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market

Nirmala J, Bender JB, Lynfield R, Yang M, Rene Culhane M, Nelson MI, Sreevatsan S, Torremorell M

Zoonoses Public Health · 2020 · 67(3):243-250

Swine influenza

The emergence of SARS-CoV-2 in Europe and North America

Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P

Science · 2020 · 370(6516):564-570

SARS-CoV-2 in humans

The Evolutionary Dynamics of Influenza A Viruses Circulating in Mallards in Duck Hunting Preserves in Maryland, USA

Trovão NS, Nolting JM, Slemons RD, Nelson MI, Bowman AS

Microorganisms · 2020 · 9(1)

Other influenza

When Pigs Fly: Pandemic influenza enters the 21st century

Trovão NS, Nelson MI

PLoS Pathog · 2020 · 16(3):e1008259

Swine influenza Review

Characterization of swine-origin H1N1 canine influenza viruses

Wang G, Dos Anjos Borges LG, Stadlbauer D, Ramos I, Bermúdez González MC, He J, Ding Y, Wei Z, Ouyang K, Huang W, Simon V, Fernandez-Sesma A, Krammer F, Nelson MI, Chen Y, García-Sastre A

Emerg Microbes Infect · 2019 · 8(1):1017-1026

Other influenza

Evolution of rotavirus C in humans and several domestic animal species

Trovão NS, Shepherd FK, Herzberg K, Jarvis MC, Lam HC, Rovira A, Culhane MR, Nelson MI, Marthaler DG

Zoonoses Public Health · 2019 · 66(5):546-557

Other disease systems

Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building

Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B, Viboud C

Epidemics · 2019 · 26:116-127

Other disease systems Review

Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit

Altman MO, Angel M, Košík I, Trovão NS, Zost SJ, Gibbs JS, Casalino L, Amaro RE, Hensley SE, Nelson MI, Yewdell JW

mBio · 2019 · 10(2)

Human influenza

Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico

Nelson MI, Souza CK, Trovão NS, Diaz A, Mena I, Rovira A, Vincent AL, Torremorell M, Marthaler D, Culhane MR

Emerg Infect Dis · 2019 · 25(4):691-700

Swine influenza

Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes

Bose ME, Shrivastava S, He J, Nelson MI, Bera J, Fedorova N, Halpin R, Town CD, Lorenzi HA, Amedeo P, Gupta N, Noyola DE, Videla C, Kok T, Buys A, Venter M, Vabret A, Cordey S, Henrickson KJ

PLoS One · 2019 · 14(7):e0220057

Other disease systems

Emergence and Evolution of Novel Reassortant Influenza A Viruses in Canines in Southern China

Chen Y, Trovão NS, Wang G, Zhao W, He P, Zhou H, Mo Y, Wei Z, Ouyang K, Huang W, García-Sastre A, Nelson MI

mBio · 2018 · 9(3)

Other influenza

Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006-2016)

Rimondi A, Gonzalez-Reiche AS, Olivera VS, Decarre J, Castresana GJ, Romano M, Nelson MI, van Bakel H, Pereda AJ, Ferreri L, Geiger G, Perez DR

Emerg Microbes Infect · 2018 · 7(1):194

Other influenza

Genetic Diversity of Noroviruses Circulating in a Pediatric Cohort in Bangladesh

Nelson MI, Mahfuz M, Chhabra P, Haque R, Seidman JC, Hossain I, McGrath M, Ahmed AMS, Knobler S, Vinjé J, Ahmed T

J Infect Dis · 2018 · 218(12):1937-1942

Other disease systems

Origins of the 1918 Pandemic: Revisiting the Swine "Mixing Vessel" Hypothesis

Nelson MI, Worobey M

Am J Epidemiol · 2018 · 187(12):2498-2502

Human influenza Review

The transmission dynamics and diversity of human metapneumovirus in Peru

Pollett S, Trovão NS, Tan Y, Eden JS, Halpin RA, Bera J, Das SR, Wentworth D, Ocaña V, Mendocilla SM, Álvarez C, Calisto ME, Garcia J, Halsey E, Ampuero JS, Nelson MI, Leguia M

Influenza Other Respir Viruses · 2018 · 12(4):508-513

Other disease systems

Evidence of Intercontinental Spread and Uncommon Variants of Low-Pathogenicity Avian Influenza Viruses in Ducks Overwintering in Guatemala

Gonzalez-Reiche AS, Nelson MI, Angel M, Müller ML, Ortiz L, Dutta J, van Bakel H, Cordon-Rosales C, Perez DR

mSphere · 2017 · 2(2)

Other influenza

Pandemic (H1N1) 2009 influenza A virus infection associated with respiratory signs in sloth bears (Melursus ursinus)

Boedeker NC, Nelson MI, Killian ML, Torchetti MK, Barthel T, Murray S

Zoonoses Public Health · 2017 · 64(7):566-571

Other influenza

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

Nelson MI, Culhane MR, Trovão NS, Patnayak DP, Halpin RA, Lin X, Shilts MH, Das SR, Detmer SE

J Gen Virol · 2017 · 98(11):2663-2675

Swine influenza

Characterization and evolution of porcine deltacoronavirus in the United States

Homwong N, Jarvis MC, Lam HC, Diaz A, Rovira A, Nelson M, Marthaler D

Prev Vet Med · 2016 · 123:168-174

Other disease systems

Evolutionary Dynamics of Influenza A Viruses in US Exhibition Swine

Nelson MI, Wentworth DE, Das SR, Sreevatsan S, Killian ML, Nolting JM, Slemons RD, Bowman AS

J Infect Dis · 2016 · 213(2):173-82

Swine influenza

Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country

Pollett S, Leguia M, Nelson MI, Maljkovic Berry I, Rutherford G, Bausch DG, Kasper M, Jarman R, Melendrez M

Int J Infect Dis · 2016 · 42:24-27

Other disease systems

Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

Jarvis MC, Lam HC, Zhang Y, Wang L, Hesse RA, Hause BM, Vlasova A, Wang Q, Zhang J, Nelson MI, Murtaugh MP, Marthaler D

Prev Vet Med · 2016 · 123:175-184

Other disease systems

Introduction, Evolution, and Dissemination of Influenza A Viruses in Exhibition Swine in the United States during 2009 to 2013

Nelson MI, Stucker KM, Schobel SA, Trovão NS, Das SR, Dugan VG, Nelson SW, Sreevatsan S, Killian ML, Nolting JM, Wentworth DE, Bowman AS

J Virol · 2016 · 90(23):10963-10971

Swine influenza

★ Featured publication

Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H, García-Sastre A

Elife · 2016 · 5

Swine influenza

★ Featured publication

Reassortment in segmented RNA viruses: mechanisms and outcomes

McDonald SM, Nelson MI, Turner PE, Patton JT

Nat Rev Microbiol · 2016 · 14(7):448-60

Other disease systems Review

The Genetic Diversity of Influenza A Viruses in Wild Birds in Peru

Nelson MI, Pollett S, Ghersi B, Silva M, Simons MP, Icochea E, Gonzalez AE, Segovia K, Kasper MR, Montgomery JM, Bausch DG

PLoS One · 2016 · 11(1):e0146059

Other influenza

Transmission dynamics of pandemic influenza A(H1N1)pdm09 virus in humans and swine in backyard farms in Tumbes, Peru

Tinoco YO, Montgomery JM, Kasper MR, Nelson MI, Razuri H, Guezala MC, Azziz-Baumgartner E, Widdowson MA, Barnes J, Gilman RH, Bausch DG, Gonzalez AE

Influenza Other Respir Viruses · 2016 · 10(1):47-56

Swine influenza

Characterization of co-circulating swine influenza A viruses in North America and the identification of a novel H1 genetic clade with antigenic significance

Anderson TK, Campbell BA, Nelson MI, Lewis NS, Janas-Martindale A, Killian ML, Vincent AL

Virus Res · 2015 · 201:24-31

Swine influenza

Continual Reintroduction of Human Pandemic H1N1 Influenza A Viruses into Swine in the United States, 2009 to 2014

Nelson MI, Stratton J, Killian ML, Janas-Martindale A, Vincent AL

J Virol · 2015 · 89(12):6218-26

Swine influenza

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

Diaz A, Enomoto S, Romagosa A, Sreevatsan S, Nelson M, Culhane M, Torremorell M

J Gen Virol · 2015 · 96(10):2982-2993

Swine influenza

★ Featured publication

Global migration of influenza A viruses in swine

Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P

Nat Commun · 2015 · 6:6696

Swine influenza

Influenza A Viruses of Human Origin in Swine, Brazil

Nelson MI, Schaefer R, Gava D, Cantão ME, Ciacci-Zanella JR

Emerg Infect Dis · 2015 · 21(8):1339-47

Swine influenza

Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile

Nelson M, Culhane MR, Rovira A, Torremorell M, Guerrero P, Norambuena J

PLoS Curr · 2015 · 7

Swine influenza

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012

Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG

Emerg Infect Dis · 2015 · 21(8):1330-8

Human influenza

★ Featured publication

Reverse zoonosis of influenza to swine: new perspectives on the human-animal interface

Nelson MI, Vincent AL

Trends Microbiol · 2015 · 23(3):142-53

Swine influenza Review

Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes

Bose ME, He J, Shrivastava S, Nelson MI, Bera J, Halpin RA, Town CD, Lorenzi HA, Noyola DE, Falcone V, Gerna G, De Beenhouwer H, Videla C, Kok T, Venter M, Williams JV, Henrickson KJ

PLoS One · 2015 · 10(3):e0120098

Other disease systems

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

H5N1 and highly pathogenic avian influenza

Equine influenza A(H3N8) virus isolated from Bactrian camel, Mongolia

Yondon M, Zayat B, Nelson MI, Heil GL, Anderson BD, Lin X, Halpin RA, McKenzie PP, White SK, Wentworth DE, Gray GC

Emerg Infect Dis · 2014 · 20(12):2144-7

Other influenza

Introductions and evolution of human-origin seasonal influenza a viruses in multinational swine populations

Nelson MI, Wentworth DE, Culhane MR, Vincent AL, Viboud C, LaPointe MP, Lin X, Holmes EC, Detmer SE

J Virol · 2014 · 88(17):10110-9

Swine influenza

Molecular epidemiology of influenza A/H3N2 viruses circulating in Mexico from 2003 to 2012

Escalera-Zamudio M, Nelson MI, Cobián Güemes AG, López-Martínez I, Cruz-Ortiz N, Iguala-Vidales M, García ER, Barrera-Badillo G, Díaz-Quiñonez JA, López S, Arias CF, Isa P, Members of Colegio de Pediatría del Estado de Veracruz

PLoS One · 2014 · 9(7):e102453

Human influenza

★ Featured publication

Multiyear persistence of 2 pandemic A/H1N1 influenza virus lineages in West Africa

Nelson MI, Njouom R, Viboud C, Niang MN, Kadjo H, Ampofo W, Adebayo A, Tarnagda Z, Miller MA, Holmes EC, Diop OM

J Infect Dis · 2014 · 210(1):121-5

Human influenza

Risks of avian influenza transmission in areas of intensive free-ranging duck production with wild waterfowl

Cappelle J, Zhao D, Gilbert M, Nelson MI, Newman SH, Takekawa JY, Gaidet N, Prosser DJ, Liu Y, Li P, Shu Y, Xiao X

Ecohealth · 2014 · 11(1):109-19

Other influenza

The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua

Nelson MI, Balmaseda A, Kuan G, Saborio S, Lin X, Halpin RA, Stockwell TB, Wentworth DE, Harris E, Gordon A

Virology · 2014 · 462-463:81-90

Human influenza

The role of viral introductions in sustaining community-based HIV epidemics in rural Uganda: evidence from spatial clustering, phylogenetics, and egocentric transmission models

Grabowski MK, Lessler J, Redd AD, Kagaayi J, Laeyendecker O, Ndyanabo A, Nelson MI, Cummings DA, Bwanika JB, Mueller AC, Reynolds SJ, Munshaw S, Ray SC, Lutalo T, Manucci J, Tobian AA, Chang LW, Beyrer C, Jennings JM, Nalugoda F, Serwadda D, Wawer MJ, Quinn TC, Gray RH, Rakai Health Sciences Program

PLoS Med · 2014 · 11(3):e1001610

Other disease systems

Widespread rotavirus H in commercially raised pigs, United States

Marthaler D, Rossow K, Culhane M, Goyal S, Collins J, Matthijnssens J, Nelson M, Ciarlet M

Emerg Infect Dis · 2014 · 20(7):1195-8

Other disease systems

Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission

Viboud C, Nelson MI, Tan Y, Holmes EC

Philos Trans R Soc Lond B Biol Sci · 2013 · 368(1614):20120199

Human influenza Review

Epidemiological dynamics and phylogeography of influenza virus in southern China

Cheng X, Tan Y, He M, Lam TT, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, Kung HF, Holmes EC, Cheng J

J Infect Dis · 2013 · 207(1):106-14

Human influenza

Genotype patterns of contemporary reassorted H3N2 virus in US swine

Kitikoon P, Nelson MI, Killian ML, Anderson TK, Koster L, Culhane MR, Vincent AL

J Gen Virol · 2013 · 94(Pt 6):1236-41

Swine influenza

Human rhinoviruses and enteroviruses in influenza-like illness in Latin America

Garcia J, Espejo V, Nelson M, Sovero M, Villaran MV, Gomez J, Barrantes M, Sanchez F, Comach G, Arango AE, Aguayo N, de Rivera IL, Chicaiza W, Jimenez M, Aleman W, Rodriguez F, Gonzales MS, Kochel TJ, Halsey ES

Virol J · 2013 · 10:305

Other disease systems

Population dynamics of cocirculating swine influenza A viruses in the United States from 2009 to 2012

Anderson TK, Nelson MI, Kitikoon P, Swenson SL, Korslund JA, Vincent AL

Influenza Other Respir Viruses · 2013 · 7 Suppl 4(Suppl 4):42-51

Swine influenza

Characterization of an influenza A virus in Mexican swine that is related to the A/H1N1/2009 pandemic clade

Escalera-Zamudio M, Cobián-Güemes G, de los Dolores Soto-del Río M, Isa P, Sánchez-Betancourt I, Parissi-Crivelli A, Martínez-Cázares MT, Romero P, Velázquez-Salinas L, Huerta-Lozano B, Nelson M, Montero H, Vinuesa P, López S, Arias CF

Virology · 2012 · 433(1):176-82

Swine influenza

Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011

Nelson MI, Vincent AL, Kitikoon P, Holmes EC, Gramer MR

J Virol · 2012 · 86(16):8872-8

Swine influenza

Genome sequencing and phylogenetic analysis of 39 human parainfluenza virus type 1 strains isolated from 1997-2010

Beck ET, He J, Nelson MI, Bose ME, Fan J, Kumar S, Henrickson KJ

PLoS One · 2012 · 7(9):e46048

Other disease systems

Genomic reassortment of influenza A virus in North American swine, 1998-2011

Nelson MI, Detmer SE, Wentworth DE, Tan Y, Schwartzbard A, Halpin RA, Stockwell TB, Lin X, Vincent AL, Gramer MR, Holmes EC

J Gen Virol · 2012 · 93(Pt 12):2584-2589

Swine influenza

Global transmission of influenza viruses from humans to swine

Nelson MI, Gramer MR, Vincent AL, Holmes EC

J Gen Virol · 2012 · 93(Pt 10):2195-2203

Swine influenza

Global influenza seasonality: reconciling patterns across temperate and tropical regions

Tamerius J, Nelson MI, Zhou SZ, Viboud C, Miller MA, Alonso WJ

Environ Health Perspect · 2011 · 119(4):439-45

Human influenza Review

Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States

Nelson MI, Tan Y, Ghedin E, Wentworth DE, St George K, Edelman L, Beck ET, Fan J, Lam TT, Kumar S, Spiro DJ, Simonsen L, Viboud C, Holmes EC, Henrickson KJ, Musser JM

J Virol · 2011 · 85(2):828-34

Human influenza

Spatial dynamics of human-origin H1 influenza A virus in North American swine

Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC, Gramer M

PLoS Pathog · 2011 · 7(6):e1002077

Swine influenza

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JS, Riley S, Rambaut A, Holmes EC, Smith GJ

Proc Natl Acad Sci U S A · 2011 · 108(48):19359-64

Human influenza

Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010

Rebuffo-Scheer C, Bose M, He J, Khaja S, Ulatowski M, Beck ET, Fan J, Kumar S, Nelson MI, Henrickson KJ

PLoS One · 2011 · 6(10):e25468

Other disease systems

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

H5N1 and highly pathogenic avian influenza

The early diversification of influenza A/H1N1pdm

Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, Viboud C, Holmes E, Henrickson K

PLoS Curr · 2009 · 1:RRN1126

Human influenza

The origin and global emergence of adamantane resistant A/H3N2 influenza viruses

Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC

Virology · 2009 · 388(2):270-8

Human influenza

Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States

Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Sengamalay N, Ghedin E, Miller MA, Simonsen L, Viboud C, Holmes EC

PLoS Pathog · 2008 · 4(8):e1000133

Human influenza

★ Featured publication

Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918

Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, St George K, Taylor J, Spiro DJ, Sengamalay NA, Ghedin E, Taubenberger JK, Holmes EC

PLoS Pathog · 2008 · 4(2):e1000012

Human influenza

The genomic and epidemiological dynamics of human influenza A virus

Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC

Nature · 2008 · 453(7195):615-9

Human influenza

Phylogenetic analysis reveals the global migration of seasonal influenza A viruses

Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC

PLoS Pathog · 2007 · 3(9):1220-8

Human influenza

★ Featured publication

The evolution of epidemic influenza

Nelson MI, Holmes EC

Nat Rev Genet · 2007 · 8(3):196-205

Human influenza Review

Stochastic processes are key determinants of short-term evolution in influenza a virus

Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC

PLoS Pathog · 2006 · 2(12):e125

Human influenza