Phylogenetic analysis of avian influenza viruses from migratory waterfowl at Pacific wetlands

Abstract

The surveillance of influenza A viruses (IAV) in migratory waterfowl is of great importance, given the possibility of transmission to susceptible hosts and introduction of viral subtypes, including highly pathogenic strains, to new geographic regions. IAV were previously identified from migratory birds in two wetlands located in Mexico during two wintering seasons. Using next-generation sequencing, thirteen samples of RNA from the field sampled cloacal swabs were subjected to whole genome sequencing. Seven whole IAV ge-nomes were obtained, while remaining six samples provided partial results. Eight different hemagglutinin (HA) and neuraminidase (NA) combinations were identified in analyzed samples, while the analysis of the remaining genes in seven whole genome samples demonstrated four different combinations of viral segments, suggesting a diversity of circulating IAV. Phylogenetic analysis of samples whose whole genomes were sequenced showed that they are closely related to North American IAV, with some segments (NP, H6 and H11) related to the Eurasian virus. The use of high-throughput technologies enabled genetic characterization of field samples and contributed to fostering our knowledge of IAV genomics and virus circulation in Mexico, a lowly surveyed but biological and epidemiological relevant region, thus highlighting the need for future studies in Mexican wetlands.