{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T09:40:15Z","timestamp":1790070015967,"version":"4.0.1"},"reference-count":44,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,3,19]],"date-time":"2021-03-19T00:00:00Z","timestamp":1616112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI127799"],"award-info":[{"award-number":["R01 AI127799"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centers of Excellence for Influenza Research and Surveillance","award":["HHSN272201400004C"],"award-info":[{"award-number":["HHSN272201400004C"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian IAVs within their natural host (mallards) and a mammalian model system (guinea pigs). Animals were co-inoculated with A\/wildbird\/California\/187718-36\/2008 (H3N8) and A\/mallard\/Colorado\/P66F1-5\/2008 (H4N6) viruses. Longitudinal samples were collected from the cloaca of mallards or the nasal tract of guinea pigs and viral genetic exchange was monitored by genotyping clonal isolates from these samples. Relative to those in guinea pigs, viral populations in mallards showed higher frequencies of reassortant genotypes and were characterized by higher genotype richness and diversity. In line with these observations, analysis of pairwise segment combinations revealed lower linkage disequilibrium in mallards as compared to guinea pigs. No clear longitudinal patterns in richness, diversity or linkage disequilibrium were present in either host. Our results reveal mallards to be a highly permissive host for IAV reassortment and suggest that reduced viral mixing limits avian IAV reassortment in a mammalian host.<\/jats:p>","DOI":"10.3390\/v13030509","type":"journal-article","created":{"date-parts":[[2021,3,21]],"date-time":"2021-03-21T23:47:41Z","timestamp":1616370461000},"page":"509","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9687-3505","authenticated-orcid":false,"given":"Ketaki","family":"Ganti","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1355-7452","authenticated-orcid":false,"given":"Anish","family":"Bagga","sequence":"additional","affiliation":[{"name":"Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana","family":"DaSilva","sequence":"additional","affiliation":[{"name":"Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel S.","family":"Shepard","sequence":"additional","affiliation":[{"name":"Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R.","family":"Barnes","sequence":"additional","affiliation":[{"name":"Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0349-7182","authenticated-orcid":false,"given":"Susan","family":"Shriner","sequence":"additional","affiliation":[{"name":"National Wildlife Research Center, US Department of Agriculture-Animal and Plant Health Inspection Service, Fort Collins, CO 80521, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0254-6141","authenticated-orcid":false,"given":"Katia","family":"Koelle","sequence":"additional","affiliation":[{"name":"Department of Biology, Emory University, Atlanta, GA 30322, USA"},{"name":"Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anice C.","family":"Lowen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA"},{"name":"Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,19]]},"reference":[{"key":"ref_1","first-page":"461","article-title":"Influenza viruses from avian and porcine sources and their possible role in the origin of human pandemic strains","volume":"39","author":"Webster","year":"1977","journal-title":"Dev. 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