ABSTRACT
In South America little is known regarding influenza virus circulating in backyard poultry and swine populations. Backyard productive systems (BPS) that breed swine and poultry are widely distributed throughout Chile with high density in the central zone, and several BPS are located within the "El Yali" (EY) ecosystem, which is one of the most important wetlands in South America. Here, 130 different wild bird species have been described, of them, at least 22 species migrate yearly from North America for nesting. For this reason, EY is considered as a high-risk zone for avian influenza virus. This study aims to identify if backyard poultry and swine bred in the EY ecosystem have been exposed to influenza A virus and if so, to identify influenza virus subtypes. A biosecurity and handling survey was applied and samples were collected from BPS in two seasons (spring 2013 and fall 2014) for influenza seroprevalence, and in one season (fall 2014) for virus presence. Seroprevalence at BPS level was 42% (95% CI:22-49) during spring 2013 and 60% (95% CI 43-72) in fall 2014. rRT-PCR for the influenza A matrix gene indicated a viral prevalence of 27% (95% CI:14-39) at BPS level in fall 2014. Eight farms (73% of rRT-PCR positive farms) were also positive to the Elisa test at the same time. One BPS was simultaneously positive (rRT-PCR) in multiple species (poultry, swine and geese) and a H1N2 virus was identified from swine, exemplifying the risk that these BPS may pose for generation of novel influenza viruses.