Backyard production systems (BPS) are highly distributed in central Chile. Poultry BPS have been previously characterized; however, swine BPS have not yet been deeply characterized in central Chile. In addition, there is evidence that zoonotic pathogens, such as influenza A virus and Salmonella spp., are circulating in both poultry and pigs kept these production systems. A total of 358 BPS located in central Chile were evaluated between 2013 and 2015 by interviewing farm owners. Severe deficiencies in biosecurity measures were observed. The value chain of swine backyard production identified feeding, products and veterinary visits, and replacement or breeding animals as the main inputs to the backyard. The most common origin of swine replacements was from outside the BPS (63%). Meat and live animals (piglets and breeding animals) were identified as the main outputs of the system. In 16% of BPS, breeding animals were lent to other BPS, indicating the existence of animal and animal products movement in and out of backyard farms. Results from this study suggest that swine BPS in central Chile represent an animal-human interphase that need special attention to direct preventive measures aimed at avoiding the introduction and dissemination of animal pathogens and the emergence of zoonotic pathogens.

The Lluta River is the northernmost coastal wetland in Chile, representing a unique ecosystem and an important source of water in the extremely arid Atacama Desert. During peak season, the wetland is home to more than 150 species of wild birds and is the first stopover point for many migratory species that arrive in the country along the Pacific migratory route, representing a priority site for avian influenza virus (AIV) surveillance in Chile. The aim of this study was to determine the prevalence of influenza A virus (IAV) in the Lluta River wetland, to identify subtype diversity and to evaluate ecological and environmental factors that drive the prevalence at the study site. The wetland was studied and sampled from September 2015 to October 2020. In each visit, fresh fecal environmental samples (n = 178) of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index - NDVI) and water body size were determined. A generalized linear mixed model (GLMM) was built to assess the association between AIV prevalence and explanatory variables. Influenza positive samples were sequenced, and the host species was determined by barcoding. Of the 4,349 samples screened during the study period, overall prevalence in the wetland was 2.07% (95% CI: 1.68 to 2.55) and monthly prevalence of AIV ranged widely from 0% to 8.6%. A great diversity of hemagglutinin (HA) and neuraminidase (NA) subtypes were identified, and 10 viruses were isolated and sequenced, including low pathogenic H5, H7 and H9 strains. In addition, several reservoir species were recognized (both migratory and resident birds), including the newly identified host Chilean flamingo (Phoenicopterus chilensis). Regarding environmental variables, prevalence of AIV was positively associated with NDVI (OR=3.65, p<0.05) and with the abundance of migratory birds (OR=3.57, p<0.05). These results emphasize the importance of the Lluta wetland as a gateway to Chile for viruses that come from the Northern Hemisphere and contribute to the understanding of AIV ecological drivers.