Phylogenetic analysis of low pathogenicity H5N1 and H7N3 influenza A virus isolates recovered from sentinel, free flying, wild mallards at one study site during 2006

Abstract

From August 2-October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 and H7N3 avian influenza A viruses (AIV), and other subtypes, were recovered from free-flying, resident, wild mallards used as sentinels at one site. The antigenic subtypes, pathogenicity potential, and Sanger sequencing of the isolates determined the H5N1 and H7N3 isolates were only recovered from samples collected on 8/2/2006 and 9/8/2006, respectively. However, subsequent efforts using next-generation sequencing (NGS) and additional Sanger sequencing found partial H7 segments in other HA-NA virus combinations on 8/2/2006, 9/8/2006 and 10/11/2006. It is well established that over larger geographic areas and years AIVs form transient genomic constellations; this sequential sampling data revealed that over a short period of time the dynamics of AIVs can be active and newer sequencing platforms increase recognition of mixed infections. Both findings provide further insight into the natural history of AIVs in natural reservoirs.

Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

“…Earlier studies suggested that AIV exhibits a strongly spatially structured population in North America, with relatively infrequent gene flow among localities and especially between those that are spatially distant or belong to different flyways using phylogeographic analysis [27]. This hypothesis was supported by studies showed that AIV isolates from mallard were linked by migration between sites in central Canada and Maryland but limited reassortment occurred along the inter-migratory flyway routes [28]. However, more recently, the opposite was seen in a another study, which emphasized that the long-term persistence of the influenza A virus gene pool in North American wild birds may be independent of migratory flyways, and the short-term evolutionary consequences of these ecological barriers may be rapidly erased by East-West virus migration [29].…”

Pathogenesis, Transmissibility, and Ocular Tropism of a Highly Pathogenic Avian Influenza A (H7N3) Virus Associated with Human Conjunctivitis

“…The frequent reassortment and rapid movement of H7 influenza viruses within this population necessitate continued surveillance of this virus subtype in both wild and domestic birds (54). The continued assessment of H7 viruses detected during routine surveillance, poultry outbreaks, and human infections is critical to both assess the pandemic potential of these strains in humans and characterize laboratory mammalian models suited to examine the efficacy and cross-reactivity of candidate H7 vaccines against viruses within this subtype (34,(55)(56)(57).…”

Avian Influenza in wild birds from Chile, 2007–2009

“…KC703328 to KC703335), is in contrast with other viruses detected on Argentinian coasts, which have a diversity of segment similarities to other South American, North American and even Eurasian lineages (Pereda et al, 2008;Xu et al, 2012). These apparent differences among Pacific and Atlantic South American reports require more isolates for establishing distribution patterns, such as those described in North America where rapid temporal and geographical movements of AI viruses and virus gene segments have been seen across migratory flyways (Chen and Holmes, 2009;Dugan et al, 2011).…”