Molecular epidemiology and pathogenicity of H5N1 and H9N2 avian influenza viruses in clinically affected chickens on farms in Bangladesh

ABSTRACT

Avian influenza virus (AIV) subtypes H5N1 and H9N2 co-circulate in poultry in Bangladesh, causing significant bird morbidity and mortality. Despite their importance to the poultry value chain, the role of farms in spreading and maintaining AIV infections remains poorly understood in most disease-endemic settings. To address this crucial gap, we conducted a cross-sectional study between 2017 and 2019 in the Chattogram Division of Bangladesh in clinically affected and dead chickens in farms with suspected AIV infection. Viral prevalence of each subtype was approximately 10% among farms for which veterinary advice was sought, indicating high levels of virus circulation in chicken farms despite the low number of reported outbreaks. Co-circulation of both subtypes was common in farms, with our findings suggest that in the field, the co-circulation of H5N1 and H9N2 can modulate disease severity, which could facilitate an underestimated level of AIV transmission in the poultry value chain. Finally, using newly generated whole-genome sequences, we investigate the evolutionary history of a small subset of H5N1 and H9N2 viruses. Our analyses revealed that for both subtypes, the sampled viruses were genetically most closely related to other viruses isolated in Bangladesh and represented multiple independent incursions. However, due to lack of longitudinal surveillance in this region, it is difficult to ascertain whether these viruses emerged from endemic strains circulating in Bangladesh or from neighbouring countries. We also show that amino acids at putative antigenic residues underwent a distinct replacement during 2012 which coincides with the use of H5N1 vaccines.

KEYWORDS:

• Avian influenza
• virus evolution
• phylodynamics
• co-infection
• antigenicity
• H5N1
• H9N2

Acknowledgements

The authors are grateful to the farmers who gave the information and samples for the study. RNR, TD, MM, AKMS collected the samples, took interviews with the farmers to collect epidemiological data, tested the samples in the laboratory and developed the data. JES, JR, GF and PKB analysed the data, prepared figures and tables and wrote the manuscript. PKB, HB and RH conceived and designed the experiments, and assisted in supervising laboratory testing of samples and reviewed the manuscript. MIU tested samples in the laboratory and reviewed the manuscript. DF, MI supported data analysis and reviewed the manuscript. IB and NL generated sequencing data and reviewed the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was primarily funded by the Bangladesh Academy of Sciences – United States Department of Agriculture (BAS – USDA), with [grant number BAS-USDA PALS CVASU LS-21]. The work was also supported by additional projects: the BALZAC research programme “Behavioural Adaptations in Live Poultry Trading and Farming Systems and Zoonoses Control in Bangladesh” [grant number BB/L018993/1], one of 11 programmes funded under Zoonoses & Emerging Livestock Systems, ZELS, a joint research initiative between BBSRC, DSTL, DFID, ESRC, MRC and NERC, the UKRI GCRF One Health Poultry Hub [grant number BB/S011269/1], one of twelve interdisciplinary research hubs funded under the UK government’s Grand Challenge Research Fund Interdisciplinary Research Hub initiative, and BBSRC funded grants [BB/S013792/1, BBS/E/I/00007035].