{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T09:21:54Z","timestamp":1771924914535,"version":"3.50.1"},"reference-count":29,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:00:00Z","timestamp":1769558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The Caucasus region, including Georgia, is an important intersection for migratory waterbirds, offering potential for avian influenza virus (AIV) transmission between populations from different geographic areas. In 2022 and 2023, wild ducks were sampled during autumn migration events in Georgia to study the genetic relationships and molecular characteristics of influenza strains. Sequencing and phylogenetic analysis were used to compare the sampled strains to reference sequences from Africa, Asia, and Europe, allowing assessment of genetic relationships and virus transmission between migratory birds. Protein language modeling identified potential co-infections. Of 225 duck samples, 128 tested positive for the influenza M gene. 55 influenza-positive samples underwent whole-genome sequencing, revealing significant diversity. Analysis of the hemagglutinin (HA) segment showed notable differences among subtypes. Most samples were H6N1 and H6N6, but co-infections with combinations like H6H3, N8N1, N6H9, N2N6, and H9H6\/N1N2 were also identified. These findings demonstrate the high variability of influenza viruses in migratory waterbirds in Georgia, including a notable rate of co-infections. Some samples exhibited uncommon genetic characteristics compared to other strains from the same year, suggesting Georgia\u2019s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1735728","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T06:43:19Z","timestamp":1769582599000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic-based biosurveillance for avian influenza: whole genome sequencing from wild mallards sampled during autumn migration in 2022\u20132023 reveals a high co-infection rate on migration stopover site in Georgia"],"prefix":"10.3389","volume":"17","author":[{"given":"Ana","family":"Papkiauri","sequence":"first","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lela","family":"Urushadze","sequence":"additional","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tea","family":"Tevdoradze","sequence":"additional","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ketevan","family":"Sidamonidze","sequence":"additional","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgi","family":"Tomashvili","sequence":"additional","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mari","family":"Gavashelidze","sequence":"additional","affiliation":[{"name":"National Center for Disease Control and Public Health","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Levan","family":"Ninua","sequence":"additional","affiliation":[{"name":"Center for Wildlife Disease Ecology, Ilia State University","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivane","family":"Daraselia","sequence":"additional","affiliation":[{"name":"Center for Wildlife Disease Ecology, Ilia State University","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sopio","family":"Kiknavelidze","sequence":"additional","affiliation":[{"name":"Center for Wildlife Disease Ecology, Ilia State University","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nika","family":"Melikishvili","sequence":"additional","affiliation":[{"name":"Center for Wildlife Disease Ecology, Ilia State University","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Hu","sequence":"additional","affiliation":[{"name":"Genomics and Bioanalytics, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Chain","sequence":"additional","affiliation":[{"name":"Genomics and Bioanalytics, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaetlyn","family":"Gibson","sequence":"additional","affiliation":[{"name":"Genomics and Bioanalytics, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martha","family":"Dix","sequence":"additional","affiliation":[{"name":"Genomics and Bioanalytics, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valerie","family":"Li","sequence":"additional","affiliation":[{"name":"Genomics and Bioanalytics, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeanne","family":"Fair","sequence":"additional","affiliation":[{"name":"Modeling and Observation of Earth Systems, Los Alamos National Laboratory","place":["Los Alamos, NM, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer","family":"Owen","sequence":"additional","affiliation":[{"name":"Department of Fisheries and Wildlife, Michigan State University","place":["East Lansing, MI, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zurab","family":"Javakhishvili","sequence":"additional","affiliation":[{"name":"Center for Wildlife Disease Ecology, Ilia State University","place":["Tbilisi, Georgia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,28]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"833","DOI":"10.3390\/v15040833","article-title":"Avian influenza virus tropism in humans","volume":"15","author":"AbuBakar","year":"2023","journal-title":"Viruses"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-3-642-74542-3_22","article-title":"Optimal bird migration: the relative importance of time","volume-title":"Energy, and safety, in bird migration","author":"Alerstam","year":"1990"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1016\/j.cels.2021.05.017","article-title":"Learning the protein language: evolution, structure, and function","volume":"12","author":"Bepler","year":"2021","journal-title":"Cell Syst"},{"key":"ref4","author":"Bub","year":"1995"},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.1128\/AEM.01929-09","article-title":"Detection and Quantification of Infectious Avian Influenza A (H5N1) Virus in Environmental Water by Using Real-Time Reverse Transcription-PCR","volume":"76","author":"Dovas","year":"2010","journal-title":"Applied and Environmental Microbiology"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"100043","DOI":"10.1016\/j.soh.2023.100043","article-title":"An overview of avian influenza surveillance strategies and modes","volume":"2","author":"Duan","year":"2023","journal-title":"Sci. One Health"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1002\/gch2.1018","article-title":"Data, disease and diplomacy: GISAID\u2019S innovative contribution to global health","volume":"1","author":"Elbe","year":"2017","journal-title":"Global Chall."},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3390\/v16010009","article-title":"Viral Zoonoses: Interactions and Factors Driving Virus Transmission","volume":"16","author":"Ermonval","year":"2023","journal-title":"Viruses"},{"key":"ref8","year":"2025"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"196","DOI":"10.3389\/fviro.2021.751196","article-title":"A non-phylogeny-dependent reassortment detection method for influenza a viruses","volume":"1","author":"Gong","year":"2021","journal-title":"Front. Virol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1006\/jtbi.1997.0505","article-title":"Optimum fuel loads in migratory birds: distinguishing between time and energy minimization","volume":"189","author":"Hedenstr\u00f6m","year":"1997","journal-title":"J. Theor. Biol."},{"key":"ref9004","doi-asserted-by":"publisher","first-page":"104505","DOI":"10.1016\/j.meegid.2020.104505","article-title":"Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs","volume":"90","author":"Hopken","year":"2021","journal-title":"Infect Genet Evol"},{"key":"ref9005","doi-asserted-by":"publisher","first-page":"1827","DOI":"10.3201\/eid1612.100589","article-title":"Surveillance of wild birds for avian influenza virus","volume":"16","author":"Hoye","year":"2010","journal-title":"Emerg Infect Dis"},{"key":"ref9006","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s13073-018-0560-3","article-title":"Genomic surveillance of avian-origin influenza A viruses causing human disease","volume":"10","author":"Lam","year":"2018","journal-title":"Genome Medicine"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e58534","DOI":"10.1371\/journal.pone.0058534","article-title":"Avian influenza virus surveillance in wild birds in Georgia: 2009\u20132011","volume":"8","author":"Lewis","year":"2013","journal-title":"PLoS One"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"ref9007","doi-asserted-by":"publisher","first-page":"e141415","DOI":"10.3201\/eid2104.141415","article-title":"Global Avian Influenza Surveillance in Wild Birds: A Strategy to Capture Viral Diversity","volume":"21","author":"Machalaba","year":"2015","journal-title":"Emerg Infect Dis"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"205","DOI":"10.21105\/joss.00205","article-title":"Hdbscan: hierarchical density based clustering","volume":"2","author":"McInnes","year":"2017","journal-title":"J. Open Source Softw."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e0244669","DOI":"10.1371\/journal.pone.0244669","article-title":"A universal RT-qPCR assay for \u201cone health\u201d detection of influenza a viruses","volume":"16","author":"Nagy","year":"2021","journal-title":"PLoS One"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"D134","DOI":"10.1093\/nar\/gkad903","article-title":"GenBank 2024 Update","volume":"52","author":"Sayers","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data \u2013 from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Eurosurveillance"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"3256","DOI":"10.1128\/JCM.40.9.3256-3260.2002","article-title":"Development of a real-time reverse transcriptase PCR assay for type a influenza virus and the avian H5 and H7 hemagglutinin subtypes","volume":"40","author":"Spackman","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref19","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"Van der Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"ref9008","doi-asserted-by":"publisher","first-page":"212","DOI":"10.3390\/v13020212","article-title":"Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance","volume":"13","author":"Verhagen","year":"2021","journal-title":"Viruses"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/82_2014_396","article-title":"Evolution and ecology of influenza a viruses","volume-title":"Influenza pathogenesis and control","author":"Yoon","year":"2014"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1007\/s42770-020-00338-6","article-title":"Serological evidence of the infection of H7 virus and the co-infection of H7 and H9 viruses in farmed fur\u2013bearing animals in eastern China","volume":"51","author":"Yu","year":"2020","journal-title":"Braz. J. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"10309","DOI":"10.1128\/jvi.01109-09","article-title":"Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza a viruses","volume":"83","author":"Zhou","year":"2009","journal-title":"J. Virol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1735728\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T08:32:07Z","timestamp":1771921927000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1735728\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,28]]},"references-count":29,"alternative-id":["10.3389\/fmicb.2026.1735728"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1735728","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,28]]},"article-number":"1735728"}}