Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America

Wild waterbirds, the natural reservoirs for avian influenza viruses, undergo migratory movements each year, connecting breeding and wintering grounds within broad corridors known as flyways. In a continental or global view, the study of virus movements within and across flyways is important to understanding virus diversity, evolution, and movement. From 2015 to 2017, we sampled waterfowl from breeding (Maine) and wintering (Maryland) areas within the Atlantic Flyway (AF) along the east coast of North America to investigate the spatio-temporal trends in persistence and spread of influenza A viruses (IAV). We isolated 109 IAVs from 1,821 cloacal / oropharyngeal samples targeting mallards (Anas platyrhynchos) and American black ducks (Anas rubripes), two species having ecological and conservation importance in the flyway that are also host reservoirs of IAV. Isolates with >99% nucleotide similarity at all gene segments were found between eight pairs of birds in the northern site across years, indicating some degree of stability among genome constellations and the possibility of environmental persistence. No movement of whole genome constellations were identified between the two parts of the flyway, however, virus gene flow between the northern and southern study locations was evident. Examination of banding records indicate direct migratory waterfowl movements between the two locations within an annual season, providing a mechanism for the inferred viral gene flow. Bayesian phylogenetic analyses provided evidence for virus dissemination from other North American wild birds to AF dabbling ducks (Anatinae), shorebirds (Charidriformes), and poultry (Galliformes). Evidence was found for virus dissemination from shorebirds to gulls (Laridae), and dabbling ducks to shorebirds and poultry. The findings from this study contribute to the understanding of IAV ecology in waterfowl within the AF.


PB1
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the PB1 gene segment.

PA
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the PA gene segment.

NP
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the NP gene segment.

M
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the M gene segment.

NS
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the NS gene segment.

H3
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the H3 gene segment.

H5
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the H5 gene segment. Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the N2 gene segment. 1940 1950 1960 1970 1980 1990 2000

N8
Bayesian phylogenetic tree (Panel A), heat map inferred number of Markov jumps among hosts groups (Panel B), plot of estimates for transitions from the other North American wild bird host group to northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel C), and plot of ratios of posterior odds versus prior odds to infer differences in migration rate estimates between the other North American wild bird host group and northern Atlantic Flyway host groups as compared to strictly among northern Atlantic Flyway host groups (Panel D) for the N8 gene segment.