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. 2020 Dec 29;15(12):e0244498.
doi: 10.1371/journal.pone.0244498. eCollection 2020.

Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States

Jennifer J A Hull  1 , Mingpu Qi  2   3 , Anna M Montmayeur  1 , Deepak Kumar  3 , Daniel E Velasquez  1 , Sung-Sil Moon  1 , Laura Cristal Magaña  1   4 , Naga Betrapally  1   4 , Terry Fei Fan Ng  1 , Baoming Jiang  1 , Douglas Marthaler  3   5
Affiliations

Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States

Jennifer J A Hull et al. PLoS One. .

Abstract

The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogenetic trees of the RVA strains MN9.65 and OK5.68.
The RVA strains from this study are represented in bold. The strains from Asia, North America, South America, Europe, and Africa are colored in pink, blue, green, purple, and orange, respectively.
Fig 2
Fig 2. Phylogenetic trees of the RVC strain OK5.68.
The RVC strain from this study is represented in bold. The strains from Asia, North America, and South America are colored pink, blue, and green, respectively.
Fig 3
Fig 3. Phylogenetic trees of the RVH strains MN9.65 and OK5.68.
The RVH strains from this study are represented in bold. The strains from Asia, North America, South America, and Africa are colored pink, blue, green, and orange respectively.
See this image and copyright information in PMC

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