Genomics of Influenza A and Influenza B Viruses

Influenza viruses are members of the Orthomyxoviridae family whose genomes consist of 8 segments of single-stranded negative-sense RNA. Influenza A virus (IAV) and influenza B virus (IBV) are responsible for seasonal epidemics of respiratory illness among humans. While IBV circulates only among humans, IAV circulates among many mammalian and avian hosts. Global surveillance of these viruses is necessary for maintaining a well-matched annual influenza vaccine, as well as for detecting the emergence of new influenza strains that may cause a human pandemic. Hemagglutinin (HA) and neuraminidase (NA) are the two predominant viral glycoproteins found in the viral envelope, and are the primary targets of the host immune system and are key factors in the entry and exit of influenza particles from host cells. HA and NA are also used to classify influenza A viruses into subtypes (e.g., H3N2, H5N1).

Our collaborative influenza projects: 1) characterizing the temporal and spatial evolutionary dynamics of the IAV and IBV circulating globally in humans and wild birds, 2) identifying the IAV genotypes circulating in pigs at county fairs (swine-human interface) to determine if fairs produce novel reassortants or enable zoonosis/reverse zoonosis, 3) determining if specific internal gene segment constellations enhance viral fitness, 4) detecting epistatic interactions between gene segments, and 5) assessing the impact of inter-hemispheric migration of viruses/gene segments.

The accumulation of mutations at antigenic sites (antigenic drift) and the reassortment of segments with differing evolutionary histories (antigenic shift) allow influenza viruses to continually evade the host immune response. Annual human epidemics are currently caused by two IAV subtypes (A/H3N2, A/H1N1) and by two diverging IBV lineages (B/Yamagata, B/Victoria). IAVs circulating in avian and swine hosts are also important because of frequent interspecies transmission, which periodically causes human pandemics (e.g., pandemics of 1957, 1968, and 2009). Complete genome sequencing is required to identify fitness advantages conferred by genes and how antigenic drift in HA/NA drive mutations throughout the genome. Genomic sequence data will be generated from the diverse subtypes/strains (H1-H16, N1-N9) in avian reservoirs, which are a source of viruses with pandemic potential (e.g., H5N1). Swine are 'mixing vessels' for reassortment between avian and human viruses because they express sialic acid molecules that act as receptors for both avian and human viruses. Human, avian, and classical swine lineage viruses are co-circulating in North American swine populations, generating novel reassortants and leading to hundreds of zoonotic infections (e.g., H3N2v). The large number of co-circulating viruses in swine is the most genetically dynamic situation observed in North America over the last 90 years.

Publications

The Journal of general virology. 2017-04-01; 98.4: 577-584.
Pathogenicity of modified bat influenza virus with different M genes and its reassortment potential with swine influenza A virus
Yang J, Lee J, Ma J, Lang Y, Nietfeld J, Li Y, Duff M, Li Y, Yang Y, Liu H, Zhou B, Wentworth DE, Richt JA, Li Z, Ma W
PMID: 28100299
PLoS pathogens. 2017-03-22; 13.3: e1006292.
The blood DNA virome in 8,000 humans
Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A
PMID: 28328962
Journal of virology. 2017-02-01; 91.3:
Potential for Low-Pathogenic Avian H7 Influenza A Viruses To Replicate and Cause Disease in a Mammalian Model
Zanin M, Koçer ZA, Poulson RL, Gabbard JD, Howerth EW, Jones CA, Friedman K, Seiler J, Danner A, Kercher L, McBride R, Paulson JC, Wentworth DE, Krauss S, Tompkins SM, Stallknecht DE, Webster RG
PMID: 27852855
PLoS pathogens. 2017-02-01; 13.2: e1006203.
The effective rate of influenza reassortment is limited during human infection
Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K, Illingworth CJ
PMID: 28170438
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH
PMID: 27679478
Journal of virology. 2016-12-15; 90.24: 11247-11258.
Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification
Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K
PMID: 27707932
mSphere. 2016-12-14; 1.6:
A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL
PMID: 27981236
Journal of virology. 2016-12-01; 90.23: 10963-10971.
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
PMID: 27681134
Journal of virology. 2016-10-01; 90.19: 8454-63.
Reversion of Cold-Adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus
Zhou B, Meliopoulos VA, Wang W, Lin X, Stucker KM, Halpin RA, Stockwell TB, Schultz-Cherry S, Wentworth DE
PMID: 27440882
PLoS pathogens. 2016-05-01; 12.5: e1005620.
Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential
Bahl J, Pham TT, Hill NJ, Hussein IT, Ma EJ, Easterday BC, Halpin RA, Stockwell TB, Wentworth DE, Kayali G, Krauss S, Schultz-Cherry S, Webster RG, Webby RJ, Swartz MD, Smith GJ, Runstadler JA
PMID: 27166585
Journal of virology. 2016-02-15; 90.4: 1997-2007.
Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States
Tan Y, Hassan F, Schuster JE, Simenauer A, Selvarangan R, Halpin RA, Lin X, Fedorova N, Stockwell TB, Lam TT, Chappell JD, Hartert TV, Holmes EC, Das SR
PMID: 26656685
Nature genetics. 2016-02-01; 48.2: 195-200.
Quantifying influenza virus diversity and transmission in humans
Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E
PMID: 26727660
The Journal of infectious diseases. 2016-01-15; 213.2: 173-82.
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
PMID: 26243317
Microbiome. 2015-12-15; 3.74.
The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles
Tarabichi Y, Li K, Hu S, Nguyen C, Wang X, Elashoff D, Saira K, Frank B, Bihan M, Ghedin E, Methé BA, Deng JC
PMID: 26667497
Journal of virology. 2015-12-01; 89.23: 11935-44.
Differential Susceptibilities of Human Lung Primary Cells to H1N1 Influenza Viruses
Travanty E, Zhou B, Zhang H, Di YP, Alcorn JF, Wentworth DE, Mason R, Wang J
PMID: 26378172
Nature. 2015-10-01; 526.7571: 122-5.
The soft palate is an important site of adaptation for transmissible influenza viruses
Lakdawala SS, Jayaraman A, Halpin RA, Lamirande EW, Shih AR, Stockwell TB, Lin X, Simenauer A, Hanson CT, Vogel L, Paskel M, Minai M, Moore I, Orandle M, Das SR, Wentworth DE, Sasisekharan R, Subbarao K
PMID: 26416728
Journal of virology. 2015-09-01; 89.18: 9689-92.
Evolution of Influenza B Virus in Kuala Lumpur, Malaysia, between 1995 and 2008
Sam IC, Su YC, Chan YF, Nor'E SS, Hassan A, Jafar FL, Joseph U, Halpin RA, Ghedin E, Hooi PS, Fourment M, Hassan H, AbuBakar S, Wentworth DE, Smith GJ
PMID: 26136576
The Journal of general virology. 2015-08-01; 96.8: 2050-60.
Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data
Lewis NS, Verhagen JH, Javakhishvili Z, Russell CA, Lexmond P, Westgeest KB, Bestebroer TM, Halpin RA, Lin X, Ransier A, Fedorova NB, Stockwell TB, Latorre-Margalef N, Olsen B, Smith G, Bahl J, Wentworth DE, Waldenström J, Fouchier RA, de Graaf M
PMID: 25904147
Journal of virology. 2015-07-01; 89.13: 6860-73.
Equine and Canine Influenza H3N8 Viruses Show Minimal Biological Differences Despite Phylogenetic Divergence
Feng KH, Gonzalez G, Deng L, Yu H, Tse VL, Huang L, Huang K, Wasik BR, Zhou B, Wentworth DE, Holmes EC, Chen X, Varki A, Murcia PR, Parrish CR
PMID: 25903329
Emerging microbes & infections. 2015-06-17; 4.e35.
Long-term surveillance of H7 influenza viruses in American wild aquatic birds: are the H7N3 influenza viruses in wild birds the precursors of highly pathogenic strains in domestic poultry?
Krauss S, Stucker KM, Schobel SA, Danner A, Friedman K, Knowles JP, Kayali G, Niles LJ, Dey AD, Raven G, Pryor P, Lin X, Das SR, Stockwell TB, Wentworth DE, Webster RG
PMID: 26954883
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin. 2015-05-07; 20.18:
Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas
Stucker KM, Schobel SA, Olsen RJ, Hodges HL, Lin X, Halpin RA, Fedorova N, Stockwell TB, Tovchigrechko A, Das SR, Wentworth DE, Musser JM
PMID: 25990233
Journal of virology. 2015-05-01; 89.10: 5651-67.
Swine Influenza Virus PA and Neuraminidase Gene Reassortment into Human H1N1 Influenza Virus Is Associated with an Altered Pathogenic Phenotype Linked to Increased MIP-2 Expression
Dlugolenski D, Jones L, Howerth E, Wentworth D, Tompkins SM, Tripp RA
PMID: 25762737
Journal of virology. 2015-05-01; 89.10: 5427-40.
Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans
Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH
PMID: 25741011
Journal of virology. 2015-05-01; 89.10: 5371-81.
Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway
Fries AC, Nolting JM, Bowman AS, Lin X, Halpin RA, Wester E, Fedorova N, Stockwell TB, Das SR, Dugan VG, Wentworth DE, Gibbs HL, Slemons RD
PMID: 25741003
Journal of virology. 2015-04-01; 89.8: 4706.
Correction for Joseph et al., Adaptation of pandemic H2N2 influenza A viruses in humans
Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ
PMID: 25792756
Nature communications. 2015-03-27; 6.6696.
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
PMID: 25813399
Evolutionary bioinformatics online. 2015-03-16; 11.43-8.
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA
PMID: 25861210
Journal of virology. 2015-02-01; 89.4: 2442-7.
Adaptation of pandemic H2N2 influenza A viruses in humans
Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ, CEIRS H2N2 Working Group
PMID: 25505070
The Journal of general virology. 2015-02-01; 96.Pt 2: 269-76.
H7N9 influenza A virus in turkeys in Minnesota
Lebarbenchon C, Pedersen JC, Sreevatsan S, Ramey AM, Dugan VG, Halpin RA, Ferro PJ, Lupiani B, Enomoto S, Poulson RL, Smeltzer M, Cardona CJ, Tompkins SM, Wentworth DE, Stallknecht DE, Brown JD
PMID: 25351723
eLife. 2015-01-16; 4.e05055.
The contrasting phylodynamics of human influenza B viruses
Vijaykrishna D, Holmes EC, Joseph U, Fourment M, Su YC, Halpin R, Lee RT, Deng YM, Gunalan V, Lin X, Stockwell TB, Fedorova NB, Zhou B, Spirason N, Kühnert D, Bošková V, Stadler T, Costa AM, Dwyer DE, Huang QS, Jennings LC, Rawlinson W, Sullivan SG, Hurt AC, Maurer-Stroh S, Wentworth DE, Smith GJ, Barr IG
PMID: 25594904
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2014-12-01; 28.351-7.
Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus
Squires RB, Pickett BE, Das S, Scheuermann RH
PMID: 25064525
Scientific data. 2014-10-14; 1.140033.
A comprehensive collection of systems biology data characterizing the host response to viral infection
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH
PMID: 25977790
PLoS pathogens. 2014-10-01; 10.10: e1004420.
Characterization of uncultivable bat influenza virus using a replicative synthetic virus
Zhou B, Ma J, Liu Q, Bawa B, Wang W, Shabman RS, Duff M, Lee J, Lang Y, Cao N, Nagy A, Lin X, Stockwell TB, Richt JA, Wentworth DE, Ma W
PMID: 25275541
Journal of virology. 2014-09-01; 88.17: 10110-9.
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
PMID: 24965467
Virology. 2014-08-01; 462-463.81-90.
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
PMID: 24959982
Journal of virology. 2014-07-01; 88.14: 8153-65.
Analysis of recombinant H7N9 wild-type and mutant viruses in pigs shows that the Q226L mutation in HA is important for transmission
Liu Q, Zhou B, Ma W, Bawa B, Ma J, Wang W, Lang Y, Lyoo Y, Halpin RA, Lin X, Stockwell TB, Webby R, Wentworth DE, Richt JA
PMID: 24807722
Journal of clinical microbiology. 2014-05-01; 52.5: 1330-7.
Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics
Zhou B, Lin X, Wang W, Halpin RA, Bera J, Stockwell TB, Barr IG, Wentworth DE
PMID: 24501036
PloS one. 2014-01-01; 9.3: e92075.
North Atlantic migratory bird flyways provide routes for intercontinental movement of avian influenza viruses
Dusek RJ, Hallgrimsson GT, Ip HS, Jónsson JE, Sreevatsan S, Nashold SW, Teslaa JL, Enomoto S, Halpin RA, Lin X, Fedorova N, Stockwell TB, Dugan VG, Wentworth DE, Hall JS
PMID: 24647410
Virology. 2013-12-01; 447.1-2: 45-51.
Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes
Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH
PMID: 24210098
Virology journal. 2013-06-06; 10.181.
Sequencing viral genomes from a single isolated plaque
Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE
PMID: 23742765
PloS one. 2013-01-01; 8.5: e67616.
Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus
Zhou B, Pearce MB, Li Y, Wang J, Mason RJ, Tumpey TM, Wentworth DE
PMID: 23799150
Molecular ecology. 2012-12-01; 21.24: 5905-7.
A robust tool highlights the influence of bird migration on influenza A virus evolution
Dugan VG
PMID: 23355978
Nucleic acids research. 2012-07-01; 40.Web Server issue: W186-92.
VIGOR extended to annotate genomes for additional 12 different viruses
Wang S, Sundaram JP, Stockwell TB
PMID: 22669909
Future virology. 2012-06-01; 7.6: 563-573.
Large-scale sequencing and the natural history of model human RNA viruses
Dugan VG, Saira K, Ghedin E
PMID: 23682295
Methods in molecular biology (Clifton, N.J.). 2012-01-01; 944.175-92.
Influenza A virus molecular virology techniques
Zhou B, Wentworth DE
PMID: 22528160
PloS one. 2009-09-29; 4.9: e7264.
Metagenomic analysis of RNA viruses in a fresh water lake
Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ
PMID: 19787045

Funding

This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Award Numbers N01-AI30071 and U19AI110819.

Principal Investigator

Key Staff

  • Torrey Williams

Collaborators

Ian Barr, PhD

Aubree Gordon, PhD

Jonathan Runstadler, PhD

Richard Slemons, PhD

David Stallknecht, PhD

Andrew Bowman, PhD

Susan Detmer, PhD

Stacey Schultz-Cherry, PhD

Kirsten St. George, PhD

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