Whole Genomic Analysis of an Unusual Human G6P[14] Rotavirus Strain Isolated from a Child with Diarrhea in Thailand: Evidence for Bovine-To-Human Interspecies Transmission and Reassortment Events

Abstract

An unusual rotavirus strain, SKT-27, with the G6P[14] genotypes (RVA/Human-wt/THA/SKT-27/2012/G6P[14]), was identified in a stool specimen from a hospitalized child aged eight months with severe diarrhea. In this study, we sequenced and characterized the complete genome of strain SKT-27. On whole genomic analysis, strain SKT-27 was found to have a unique genotype constellation: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The non-G/P genotype constellation of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) is commonly shared with rotavirus strains from artiodactyls such as cattle. Phylogenetic analysis indicated that nine of the 11 genes of strain SKT-27 (VP7, VP4, VP6, VP2-3, NSP1, NSP3-5) appeared to be of artiodactyl (likely bovine) origin, while the remaining VP1 and NSP2 genes were assumed to be of human origin. Thus, strain SKT-27 was found to have a bovine rotavirus genetic backbone, and thus is likely to be of bovine origin. Furthermore, strain SKT-27 appeared to be derived through interspecies transmission and reassortment events involving bovine and human rotavirus strains. Of note is that the VP7 gene of strain SKT-27 was located in G6 lineage-5 together with those of bovine rotavirus strains, away from the clusters comprising other G6P[14] strains in G6 lineages-2/6, suggesting the occurrence of independent bovine-to-human interspecies transmission events. To our knowledge, this is the first report on full genome-based characterization of human G6P[14] strains that have emerged in Southeast Asia. Our observations will provide important insights into the origin of G6P[14] strains, and into dynamic interactions between human and bovine rotavirus strains.

Fig 1. Genomic dsRNA profile of strain SKT-27.

Lanes 1–2, dsRNAs of strains KU (G1P[8]) (lane 1) and DS-1 (G2P[4]) (lane 2), respectively, extracted from the cell cultures; lane 3, dsRNAs of strain SKT-27 extracted from a stool sample. The numbers on the left indicate the order of the genomic dsRNA segments of strain KU.

Fig 2. Genotype natures of the 11 gene segments of strain SKT-27 compared with those of selected human and animal strains.

Strain SKT-27 is shown in red, while other G6P[14] strains are shown in blue. Gray shading indicates the gene segments with a genotype identical to that of strain SKT-27. ^aThe gene segments that are most similar to those of strain SKT-27. “−” indicates that no sequence data were available in the DDBJ and EMBL/GenBank data libraries. ^bGenotype assignment of strain DK11601 based on a report by Midgley et al. (2012). To our knowledge, to date, nucleotide sequence accession numbers for the VP7 and VP4 genes of strain DK11601 are not available in the DDBJ and EMBL/GenBank data libraries.

Fig 3. Phylogenetic tree constructed from the nucleotide sequences of the VP7 genes of strain SKT-27 and representative RVA strains.

In the tree, the position of strain SKT-27 is shown in red, while other G6P[14] strains are shown in blue. Bootstrap values of <75% are not shown. Scale bars: 0.05 substitutions per nucleotide.

Fig 4. Phylogenetic tree constructed from the nucleotide sequences of the VP4 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.1 substitutions per nucleotide.

Fig 5. Phylogenetic tree constructed from the nucleotide sequences of the VP6 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 6. Phylogenetic tree constructed from the nucleotide sequences of the VP1 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 7. Phylogenetic tree constructed from the nucleotide sequences of the VP2 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 8. Phylogenetic tree constructed from the nucleotide sequences of the VP3 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 9. Phylogenetic tree constructed from the nucleotide sequences of the NSP1 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 10. Phylogenetic tree constructed from the nucleotide sequences of the NSP2 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.1 substitutions per nucleotide.

Fig 11. Phylogenetic tree constructed from the nucleotide sequences of the NSP3 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.02 substitutions per nucleotide.

Fig 12. Phylogenetic tree constructed from the nucleotide sequences of the NSP4 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.05 substitutions per nucleotide.

Fig 13. Phylogenetic tree constructed from the nucleotide sequences of the NSP5 genes of strain SKT-27 and representative RVA strains.

See legend of Fig 3. Scale bars: 0.02 substitutions per nucleotide.