Genomic Evidence for Sequestration of Influenza A Virus Lineages in Sea Duck Host Species

Dillon S Mcbride,Sarah E Lauterbach,Mary Lea Killian,Jacqueline M Nolting,Andrew S Bowman,Gavin J D Smith,Yvonne C F Su,Yao-Tsun Li

doi:10.3390/v13020172

Abstract

Wild birds are considered the natural reservoir of influenza A viruses (IAVs) making them critical for IAV surveillance efforts. While sea ducks have played a role in novel IAV emergence events that threatened food security and public health, very few surveillance samples have been collected from sea duck hosts. From 2014–2018, we conducted surveillance focused in the Mississippi flyway, USA at locations where sea duck harvest has been relatively successful compared to our other sampling locations. Our surveillance yielded 1662 samples from sea ducks, from which we recovered 77 IAV isolates. Our analyses identified persistence of sea duck specific IAV lineages across multiple years. We also recovered sea duck origin IAVs containing an H4 gene highly divergent from the majority of North American H4-HA with clade node age of over 65 years. Identification of IAVs with long branch lengths is indicative of substantial genomic change consistent with persistence without detection by surveillance efforts. Sea ducks play a role in the movement and long-term persistence of IAVs and are likely harboring more undetected IAV diversity. Sea ducks should be a point of emphasis for future North American wild bird IAV surveillance efforts.

Highlights

IntroductionShorebirds, and gulls are recognized as the natural reservoir for influenza A viruses (IAVs) [1]
Published: 24 January 2021Wild birds including waterfowl, shorebirds, and gulls are recognized as the natural reservoir for influenza A viruses (IAVs) [1]
Based on virus isolation results, estimated prevalence of IAV in sea ducks was 4.63% (77/1662)

Summary

Introduction

Shorebirds, and gulls are recognized as the natural reservoir for influenza A viruses (IAVs) [1]. Because many populations of wild waterfowl migrate, they have been implicated in long distance dispersal and inter-hemispheric movement of IAV [2,3]. A result of this mobility coupled with high natural IAV diversity, wild bird populations have contributed to movement and emergence of economically devastating high pathogenic avian influenza (HPAI) outbreaks [4,5,6]. In addition to agricultural impact, avian-origin IAVs have contributed directly or indirectly to all of the modern influenza pandemics [7,8,9]. Due to the implications of avian-origin IAV, wild bird populations, especially waterfowl, have historically been a focus for influenza surveillance efforts. In 2010, H14-HA was isolated in North American sea ducks in Wisconsin, which was the first detection since its initial description in 1982 near

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Conclusion