Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Carlos Flores; Naomi Ariyama; Benjamín Bennett; Juan Mena; Claudio Verdugo; Sunil Mor; Barbara Brito; Galia Ramírez-Toloza; Victor Neira

doi:10.3389/fvets.2021.764837

Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Carlos Flores, Naomi Ariyama, Benjamín Bennett, Juan Mena, Claudio Verdugo, Sunil Mor, Barbara Brito, Galia Ramírez-Toloza, Victor Neira

Veterinary Population Medicine

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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.

Original language	English (US)
Article number	764837
Journal	Frontiers in Veterinary Science
Volume	8
DOIs	https://doi.org/10.3389/fvets.2021.764837
State	Published - Nov 25 2021

Bibliographical note

Funding Information:
Animal Virology Laboratory, Faculty of Veterinary and Animal Sciences, Universidad de Chile and Programa Fondecyt 11170877 and 1211517.

Funding Information:
We are grateful to the staff of Animal Virology Lab, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile for all their support in sampling processing, specially to Dr. Felipe Berrios and Valentina Valdes. This study was partially funded by the Animal Virology Laboratory, Faculty of Veterinary and Animal Sciences, Universidad de Chile, and Programa Fondecyt N◦ 11170877 and N◦ 1211517 to VN.

Publisher Copyright:
Copyright © 2021 Flores, Ariyama, Bennett, Mena, Verdugo, Mor, Brito, Ramírez-Toloza and Neira.

Keywords

next-generating sequencing
phylogenetic analysis
poAstV
porcine astrovirus
swine intensive farm

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title = "Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile",

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 Valpara{\'i}so, Metropolitana, O'Higgins, {\~N}uble and Araucan{\'i}a 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.",

keywords = "next-generating sequencing, phylogenetic analysis, poAstV, porcine astrovirus, swine intensive farm",

author = "Carlos Flores and Naomi Ariyama and Benjam{\'i}n Bennett and Juan Mena and Claudio Verdugo and Sunil Mor and Barbara Brito and Galia Ram{\'i}rez-Toloza and Victor Neira",

note = "Funding Information: Animal Virology Laboratory, Faculty of Veterinary and Animal Sciences, Universidad de Chile and Programa Fondecyt 11170877 and 1211517. Funding Information: We are grateful to the staff of Animal Virology Lab, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile for all their support in sampling processing, specially to Dr. Felipe Berrios and Valentina Valdes. This study was partially funded by the Animal Virology Laboratory, Faculty of Veterinary and Animal Sciences, Universidad de Chile, and Programa Fondecyt N◦ 11170877 and N◦ 1211517 to VN. Publisher Copyright: Copyright {\textcopyright} 2021 Flores, Ariyama, Bennett, Mena, Verdugo, Mor, Brito, Ram{\'i}rez-Toloza and Neira.",

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AU - Mor, Sunil

AU - Brito, Barbara

AU - Ramírez-Toloza, Galia

AU - Neira, Victor

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Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Abstract

Bibliographical note

Keywords

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