Abstract
Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.
Highlights
Astroviruses (AstVs) are emerging pathogens, belonging to members of the family Astroviridae
Considering the high prevalence and worldwide distribution of the AstV and Porcine Astrovirus (PoAstV), the suspected zoonotic potential, and the lack of information regarding these viruses in a regional context, this study aims to determine the presence and genetic diversity of PoAstV circulating in Chilean intensive pig farms
Reads that belong to other families, such as Caliciviridae, Parvoviridae, and Reoviridae, were found at lower rates and were not considered for further analysis as they are beyond the aim of this study
Summary
Astroviruses (AstVs) are emerging pathogens, belonging to members of the family Astroviridae. AstV infections cause a wide range of clinical signs from gastroenteric (e.g., human, turkey, sheep, and pig) to neurologic (e.g., human, mink, cattle, sheep, and pig) disease [2,3,4,5,6,7,8,9,10]. They are non-enveloped small viruses (30 nm) with a positive-sense single-stranded RNA genome of 6.4–7.9 kb [11].
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