Genomic-based #biosurveillance for avian #influenza: whole genome sequencing from wild #mallards sampled during autumn migration in 2022–23 reveals a high co-infection rate on migration stopover site in #Georgia
Abstract 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 comb...