Surveillance for highly pathogenic influenza A viruses in California during 2014–2015 provides insights into viral evolutionary pathways and the spatiotemporal extent of viruses in the Pacific Americas Flyway

Abstract

We used surveillance data collected in California before, concurrent with, and subsequent to an outbreak of highly pathogenic (HP) clade 2.3.4.4 influenza A viruses (IAVs) in 2014–2015 to (i) evaluate IAV prevalence in waterfowl, (ii) assess the evidence for spill-over infections in marine mammals and (iii) genetically characterize low-pathogenic (LP) and HP IAVs to refine inference on the spatiotemporal extent of HP genome constellations and to evaluate possible evolutionary pathways. We screened samples from 1496 waterfowl and 1142 marine mammals collected from April 2014 to August 2015 and detected IAV RNA in 159 samples collected from birds (n=157) and pinnipeds (n=2). HP IAV RNA was identified in three samples originating from American wigeon (Anas americana). Genetic sequence data were generated for a clade 2.3.4.4 HP IAV-positive diagnostic sample and 57 LP IAV isolates. Phylogenetic analyses revealed that the HP IAV was a reassortant H5N8 virus with gene segments closely related to LP IAVs detected in mallards (Anas platyrhynchos) sampled in California and other IAVs detected in wild birds sampled within the Pacific Americas Flyway. In addition, our analysis provided support for common ancestry between LP IAVs recovered from waterfowl sampled in California and gene segments of reassortant HP H5N1 IAVs detected in British Columbia, Canada and Washington, USA. Our investigation provides evidence that waterfowl are likely to have played a role in the evolution of reassortant HP IAVs in the Pacific Americas Flyway during 2014–2015, whereas we did not find support for spill-over infections in potential pinniped hosts.

Respiratory tract explant infection dynamics of influenza A virus in California sea lions, northern elephant seals, and rhesus macaques

“…An ELX808 BioTek Spectrophotometer (BioTek Instruments, Winooski, VT) was used to measure absorbance. Sera was considered positive for IAV antibody when the ratio of the absorbance of the test sample to the negative control was less than 0.45, as previously established (21, 22). Marine mammals were also tested for IAV RNA by reverse transcription polymerase chain reaction (RT-PCR).…”

“…Viral RNAs were extracted using the Magmax-96 AI/ND Viral RNA isolation kit (Applied Biosystems). Viral RNA extracts were used as a template for multi-segment RT-PCR reactions to generate all 8 genomic segments of IAV using procedures described previously (22, 34). Consensus sequences were generated at the Icahn School of Medicine at Mount Sinai, as described previously (35).…”

“…Since then, IAV infection and sometimes disease has been identified in several marine mammal species, including mass mortalities in harbor seals near Cape Cod, Massachusetts, USA, attributed to H7N7, H4N5, or H4N6, and detection of antibody to multiple H and N subtypes in several seal species (13)(14)(15)(16)(17)(18)(19)(20). On the West Coast, surveillance from 2009 to 2015 (4,21,22), and from 2016 to present (unpublished) in multiple marine mammal species from California shows variable IAV exposure. Seroprevalence in sea otters and Northern elephant seals is higher than in sympatric harbor seals and California sea lions, and sea otters are exposed to avian-and human-origin IAV, including pandemic H1N1 (4,21).…”

High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface

“…While these studies collect valuable pathogen detection and identification data, most do not assess prevalence, ecological risk factors, or infection dynamics using multi-pathogen methods (Bodewes, 2018). Collecting concurrent data on host movements at interfaces across seasons could allow researchers to understand spatial, temporal, or host-specific attributes that contribute to pathogen diversity, especially in investigations of viral evolution and transmission pathways following outbreaks (e.g., Ramey et al, 2017). For example, one recent study used metabarcoding to determine feeding patterns and population structure of vampire bats that could be used to inform projections of rabies transmission across interfaces (Bohmann et al, 2018).…”

Predicting the initial spread of novel Asian origin influenza A viruses in the continental USA by wild waterfowl

“…Presumably, reassortant H5N1, H5N2, and H5N8 likely emerged in North America after introduction of a high‐pathogenic clade 2.3.4.4 H5N8 from Asia (Lee et al., ). The high‐pathogenic H5N2 and H5N8 reassortants (collectively referred to as clade 2.3.4.4 H5 viruses hereafter) subsequently spread through the Pacific Northwest and Midwestern USA (Hill et al., ; Lee et al., ; Ramey et al., ), where they caused devastating outbreaks for the poultry industry with economic losses of over $3 billion (Greene, ).…”