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 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’s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.

Source: 

Link: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1735728/full

____

#Replication and #Transmission of #Influenza A Virus in Farmed #Mink

 

Abstract

Farmed mink are frequently exposed to circulating influenza A viruses (IAVs), as confirmed by viral isolation and serological evidence. Previous work reveals that naïve mink serve as susceptible hosts for both avian and human influenza strains, highlighting their potential role in influenza ecology. In this study, we investigated whether farmed mink naturally pre-exposed to H9 retain the capacity to serve as “mixing vessels” for reassorting human and avian IAVs. Our results demonstrate that they remain fully susceptible and permissive to infection by both avian H6N6 and human H1N1 influenza strains. Notably, efficient transmission of these viruses occurred among farmed mink, confirming their potential to sustain viral exchange. These findings indicate that farmed mink represent highly permissive hosts capable of facilitating reassortment between circulating human and avian IAVs. Given this risk, current mink farming practices may substantially increase the likelihood of a pandemic emergence. We therefore urge immediate revision, stringent enhancement, and rigorous enforcement of biosecurity protocols and active surveillance systems in fur farming operations.

Source: 

Link: https://www.mdpi.com/1999-4915/18/1/9

____

Active #Surveillance for Emerging #Influenza A Viruses – Findings from a #OneHealth Study in #Vietnam’s Live Bird #Markets

 

Highlights

-- We conducted surveillance for influenza A viruses at live bird markets in northern Vietnam.

-- Six different subtypes of influenza A virus were found co-circulating in the markets.

-- Notable genetic mutations were found across many genes.

-- These markets have great potential to generate new pandemic influenza A virus strains.

Abstract

Objectives

Live bird markets (LBMs) in Asia have often been the source of human infections with avian influenza virus (AIV).

Methods

From July 2021 to August 2023, we employed a One Health approach in conducting periodic surveillance for novel influenza A viruses in five LBMs in northern Vietnam. Specimens were studied with egg culture, molecular assays, Sanger sequencing, and next-generation sequencing.

Results

We studied a total of 688 human, avian, and bioaerosol specimens. Among these, 118 (17.2%) were found to have molecular evidence of AIVs. Next-generation sequencing of 92 isolates revealed multiple AIV subtypes, including H4N6 (n=1), H5N1 (n=3), H5N8 (n=6), H6N2 (n=3), H6N6 (n=18), and H9N2 (n=61) and mix infections (n=7). Our H5Nx sequences belonged to the Eurasian lineage clade 2.3.4.4b, while our H6N2 sequences were of group III, H6N6 of group II, and H9N2 of the BJ94-lineage clade 4.6.14.

Conclusions

The relatively high prevalence of AIV, particularly highly pathogenic H5N1 and H5N8 viruses, along with the subtype diversity, frequent co-infections and notable mutations, highlights the urgent need for continued monitoring and control of AIV in Vietnam’s poultry farms and LBMs.

Source: International Journal of Infectious Diseases, https://www.ijidonline.com/article/S1201-9712(25)00354-6/fulltext

____