Reassortment of Human and Animal Rotavirus Gene Segments in Emerging DS-1-Like G1P[8] Rotavirus Strains

Abstract

The emergence and rapid spread of novel DS-1-like G1P[8] human rotaviruses in Japan were recently reported. More recently, such intergenogroup reassortant strains were identified in Thailand, implying the ongoing spread of unusual rotavirus strains in Asia. During rotavirus surveillance in Thailand, three DS-1-like intergenogroup reassortant strains having G3P[8] (RVA/Human-wt/THA/SKT-281/2013/G3P[8] and RVA/Human-wt/THA/SKT-289/2013/G3P[8]) and G2P[8] (RVA/Human-wt/THA/LS-04/2013/G2P[8]) genotypes were identified in fecal samples from hospitalized children with acute gastroenteritis. In this study, we sequenced and characterized the complete genomes of strains SKT-281, SKT-289, and LS-04. On whole genomic analysis, all three strains exhibited unique genotype constellations including both genogroup 1 and 2 genes: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strains SKT-281 and SKT-289, and G2-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strain LS-04. Except for the G genotype, the unique genotype constellation of the three strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) is commonly shared with DS-1-like G1P[8] strains. On phylogenetic analysis, nine of the 11 genes of strains SKT-281 and SKT-289 (VP4, VP6, VP1-3, NSP1-3, and NSP5) appeared to have originated from DS-1-like G1P[8] strains, while the remaining VP7 and NSP4 genes appeared to be of equine and bovine origin, respectively. Thus, strains SKT-281 and SKT-289 appeared to be reassortant strains as to DS-1-like G1P[8], animal-derived human, and/or animal rotaviruses. On the other hand, seven of the 11 genes of strain LS-04 (VP7, VP6, VP1, VP3, and NSP3-5) appeared to have originated from locally circulating DS-1-like G2P[4] human rotaviruses, while three genes (VP4, VP2, and NSP1) were assumed to be derived from DS-1-like G1P[8] strains. Notably, the remaining NSP2 gene of strain LS-04 appeared to be of bovine origin. Thus, strain LS-04 was assumed to be a multiple reassortment strain as to DS-1-like G1P[8], locally circulating DS-1-like G2P[4], bovine-like human, and/or bovine rotaviruses. Overall, the great genomic diversity among the DS-1-like G1P[8] strains seemed to have been generated through reassortment involving human and animal strains. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like intergenogroup reassortant strains having G3P[8] and G2P[8] genotypes that have emerged in Thailand. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] strains and related reassortant ones.

Fig 1. Genomic dsRNA profiles of strains SKT-281, SKT-289, and LS-04.

Strains SKT-281, SKT-289, and LS-04 are shown in red, while DS-1-like G1P[8] strain SKT-109 is shown in blue. Lanes 1–2, dsRNAs of strains KU (G1P[8]) (lane 1) and DS-1 (G2P[4]) (lane 2) extracted from the cell cultures; lanes 3–6, dsRNAs of strains SKT-109 (lane 3), SKT-281 (lane 4), SKT-289 (lane 5), and LS-04 (lane 6) extracted from stool samples; and lanes 7–12, dsRNAs of co-circulating strains PCB-118 (lane 7), SKT-98 (lane 8), BD-20 (lane 9), NP-M51 (lane 10), SKT-138 (lane 11), and SSKT-133 (lane 12) extracted from fecal specimens. 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 three Thai DS-1-like intergenogroup reassortant strains, SKT-281, SKT-289, and LS-04, compared with those of selected human and animal strains.

Strains SKT-281, SKT-289, and LS-04 are shown in red, while DS-1-like G1P[8] strains are shown in blue. Asterisks indicate co-circulating strains PCB-118, SKT-98, BD-20, NP-M51, SKT-138, and SSKT-133. Gray shading indicates the 10 gene segments (VP4, VP6, VP1-3, and NSP1-5) with genotypes identical to those of strains SKT-281, SKT-289, and LS-04. Green shading indicates the VP7 gene segments with a G3 genotype identical to those of strains SKT-281 and SKT-289. Blue shading indicates the VP7 gene segments with a G2 genotype identical to that of strain LS-04. “−” indicates that no sequence data were available in the DDBJ and EMBL/GenBank data libraries. ^aThe gene segments that are most similar to those of strain SKT-281. ^bThe gene segments that are most similar to those of strain SKT-289. ^cThe gene segments that are most similar to those of strain LS-04.

Fig 3. Phylogenetic tree constructed from the nucleotide sequences of the G3-VP7 genes of strains SKT-281 and SKT-289, and representative RVA strains.

In the tree, the positions of strains SKT-281 and SKT-289 are shown in red. 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 G2-VP7 genes of strain LS-04 and representative RVA strains.

In the tree, the position of strain LS-04 is shown in red. Asterisks indicate co-circulating strains BD-20, NP-M51, SKT-138, and SSKT-133. Bootstrap values of <75% are not shown. Scale bars: 0.05 substitutions per nucleotide.

Fig 5. Phylogenetic tree constructed from the nucleotide sequences of the G1-VP7 genes of co-circulating strains PCB-118 and SKT-98, and representative RVA strains.

In the tree, the positions of DS-1-like G1P[8] strains are shown in blue. Asterisks indicate co-circulating strains PCB-118 and SKT-98. Bootstrap values of <75% are not shown. Scale bars: 0.05 substitutions per nucleotide.

Fig 6. Phylogenetic tree constructed from the nucleotide sequences of the P[8]-VP4 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

In the tree, the positions of strains SKT-281, SKT-289, and LS-04 are shown in red, while those of DS-1-like G1P[8] strains are shown in blue. Asterisks indicate co-circulating strains PCB-118 and SKT-98. Bootstrap values of <75% are not shown. Scale bars: 0.02 substitutions per nucleotide.

Fig 7. Phylogenetic tree constructed from the nucleotide sequences of the P[4]-VP4 genes of co-circulating strains BD-20, NP-M51, SKT-138, and SSKT-133, and representative RVA strains.

In the tree, asterisks indicate co-circulating strains BD-20, NP-M51, SKT-138, and SSKT-133. Bootstrap values of <75% are not shown. Scale bars: 0.02 substitutions per nucleotide.

Fig 8. Phylogenetic tree constructed from the nucleotide sequences of the I2-VP6 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

In the tree, the positions of strains SKT-281, SKT-289, and LS-04 are shown in red, while those of DS-1-like G1P[8] strains are shown in blue. Asterisks indicate co-circulating strains BD-20, NP-M51, SKT-138, and SSKT-133. Bootstrap values of <75% are not shown. Scale bars: 0.05 substitutions per nucleotide.

Fig 9. Phylogenetic tree constructed from the nucleotide sequences of the R2-VP1 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.05 substitutions per nucleotide.

Fig 10. Phylogenetic tree constructed from the nucleotide sequences of the C2-VP2 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.05 substitutions per nucleotide.

Fig 11. Phylogenetic tree constructed from the nucleotide sequences of the M2-VP3 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.05 substitutions per nucleotide.

Fig 12. Phylogenetic tree constructed from the nucleotide sequences of the A2-NSP1 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.05 substitutions per nucleotide.

Fig 13. Phylogenetic tree constructed from the nucleotide sequences of the N2-NSP2 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.02 substitutions per nucleotide.

Fig 14. Phylogenetic tree constructed from the nucleotide sequences of the T2-NSP3 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.02 substitutions per nucleotide.

Fig 15. Phylogenetic tree constructed from the nucleotide sequences of the E2-NSP4 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.02 substitutions per nucleotide.

Fig 16. Phylogenetic tree constructed from the nucleotide sequences of the H2-NSP5 genes of strains SKT-281, SKT-289, and LS-04, and representative RVA strains.

See legend of Fig 8. Scale bars: 0.02 substitutions per nucleotide.