Abstract
Over a hundred species of aquatic birds overwinter in Central America's wetlands, providing opportunities for the transmission of influenza A viruses (IAVs). To date, limited IAV surveillance in Central America hinders our understanding of the evolution and ecology of IAVs in migratory hosts within the Western Hemisphere. To address this gap, we sequenced the genomes of 68 virus isolates obtained from ducks overwintering along Guatemala's Pacific Coast during 2010 to 2013. High genetic diversity was observed, including 9 hemagglutinin (HA) subtypes, 7 neuraminidase (NA) subtypes, and multiple avian IAV lineages that have been detected at low levels (<1%) in North America. An unusually large number of viruses with the rare H14 subtype were identified (n = 14) over two consecutive seasons, the highest number of H14 viruses ever reported in a single location, providing evidence for a possible H14 source population located outside routinely sampled regions of North America. Viruses from Guatemala were positioned within minor clades divergent from the main North American lineage on phylogenies inferred for the H3, H4, N2, N8, PA, NP, and NS segments. A time-scaled phylogeny indicates that a Eurasian virus PA segment introduced into the Americas in the early 2000s disseminated to Guatemala during ~2007.1 to 2010.4 (95% highest posterior density [HPD]). Overall, the diversity detected in Guatemala in overwintering ducks highlights the potential role of Central America in the evolution of diverse IAV lineages in the Americas, including divergent variants rarely detected in the United States, and the importance of increasing IAV surveillance throughout Central America. IMPORTANCE Recent outbreaks of highly pathogenic H7N3, H5Nx, and H7N8 avian influenza viruses in North America were introduced by migratory birds, underscoring the importance of understanding how wild birds contribute to the dissemination and evolution of IAVs in nature. At least four of the main IAV duck host species in North America migrate through or overwinter within a narrow strip of Central America, providing opportunities for diverse IAV lineages to mix and exchange gene segments. By obtaining whole-genome sequences of 68 IAV isolates collected from migratory waterfowl in Guatemala (2010 to 2013), the largest data set available from Central America to date, we detected extensive viral diversity, including gene variants rarely found in North America and gene segments of Eurasian origin. Our findings highlight the need for increased IAV surveillance across the geographical span of bird migration flyways, including Neotropical regions that have been vastly undersampled to date.
Highlights
IMPORTANCE Recent outbreaks of highly pathogenic H7N3, H5Nx, and H7N8 avian influenza viruses in North America were introduced by migratory birds, underscoring the importance of understanding how wild birds contribute to the dissemination and evolution of Influenza A viruses (IAVs) in nature
Additional virus surveillance is important as low-pathogenicity avian influenza viruses (LPAIVs) carried by aquatic birds have been continually identified as the precursors of highly pathogenic avian influenza (HPAI) outbreaks in poultry, including most recently the 2012 outbreak of H7N3 in Mexico and the H5Nx and H7N8 outbreaks in North America during 2014 to 2016 [11,12,13]
Most LPAIVs found in dabbling ducks overwintering in Guatemala are positioned within the North American lineage
Summary
IMPORTANCE Recent outbreaks of highly pathogenic H7N3, H5Nx, and H7N8 avian influenza viruses in North America were introduced by migratory birds, underscoring the importance of understanding how wild birds contribute to the dissemination and evolution of IAVs in nature. 15 duck species (family Anatidae) have been reported, 10 of which are migratory and include several of the main North American reservoirs of IAV, such as northern shovelers (Anas clypeata), northern pintails (Anas acuta), blue-winged teals (Anas discors), and American wigeons (Anas americana) [15]. Among these species, blue-winged teals are abundant on the Pacific coast of Guatemala, with counts of Ͼ10,000 individuals, whereas the other species are less frequently reported (counts of Ͻ250) [14]. We found evidence of reassortment among viruses sourced from different locations and bird populations, including rarely detected lineages with source populations possibly located in Central America or other undersampled regions
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