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. 2015 May 4;10(5):e0124965.
doi: 10.1371/journal.pone.0124965. eCollection 2015.

Whole Genomic Analysis of Human G12P[6] and G12P[8] Rotavirus Strains that Have Emerged in Myanmar

Tomihiko Ide  1 , Satoshi Komoto  1 , Kyoko Higo-Moriguchi  1 , Khaing Win Htun  2 , Yi Yi Myint  3 , Theingi Win Myat  4 , Kyaw Zin Thant  4 , Hlaing Myat Thu  4 , Mo Mo Win  4 , Htun Naing Oo  5 , Than Htut  6 , Mitsutaka Wakuda  1 , Francis Ekow Dennis  7 , Kei Haga  8 , Yoshiki Fujii  8 , Kazuhiko Katayama  8 , Shofiqur Rahman  9 , Sa Van Nguyen  9 , Kouji Umeda  9 , Keiji Oguma  10 , Takao Tsuji  11 , Koki Taniguchi  1
Affiliations

Whole Genomic Analysis of Human G12P[6] and G12P[8] Rotavirus Strains that Have Emerged in Myanmar

Tomihiko Ide et al. PLoS One. .

Abstract

G12 rotaviruses are emerging rotavirus strains causing severe diarrhea in infants and young children worldwide. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed. In this study, we sequenced and characterized the complete genomes of six G12 strains (RVA/Human-tc/MMR/A14/2011/G12P[8], RVA/Human-tc/MMR/A23/2011/G12P[6], RVA/Human-tc/MMR/A25/2011/G12P[8], RVA/Human-tc/MMR/P02/2011/G12P[8], RVA/Human-tc/MMR/P39/2011/G12P[8], and RVA/Human-tc/MMR/P43/2011/G12P[8]) detected in six stool samples from children with acute gastroenteritis in Myanmar. On whole genomic analysis, all six Myanmarese G12 strains were found to have a Wa-like genetic backbone: G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strains A14, A25, P02, P39, and P43, and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strain A23. Phylogenetic analysis showed that most genes of the six strains examined in this study were genetically related to globally circulating human G1, G3, G9, and G12 strains. Of note is that the NSP4 gene of strain A23 exhibited the closest relationship with the cognate genes of human-like bovine strains as well as human strains, suggesting the occurrence of reassortment between human and bovine strains. Furthermore, strains A14, A25, P02, P39, and P43 were very closely related to one another in all the 11 gene segments, indicating derivation of the five strains from a common origin. On the other hand, strain A23 consistently formed distinct clusters as to all the 11 gene segments, indicating a distinct origin of strain A23 from that of strains A14, A25, P02, P39, and P43. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Myanmar. Our observations will provide important insights into the evolutionary dynamics of spreading G12 rotaviruses in Asia.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Genomic dsRNA profiles of strains A14, A23, A25, P02, P39, and P43.
Lane 1, dsRNAs of strain KU (G1P[8]) extracted from a cell culture; lanes 2–7, dsRNAs of strains A14 (lane 2), A23 (lane 3), A25 (lane 4), P02 (lane 5), P39 (lane 6), and P43 (lane 7) extracted from cell cultures. The numbers on the left indicate the order of the genomic dsRNA segments of strain KU.
Fig 2
Fig 2. Genotype natures of the 11 gene segments of six Myanmarese G12 strains, A14, A23, A25, P02, P39, and P43, with those of selected human and animal strains.
Strains A14, A23, A25, P02, P39, and P43 are shown in red. Gray shading indicates the 10 gene segments (VP7, VP6, VP1-3, and NSP1-5) with genotypes identical to those of strains A14, A23, A25, P02, P39, and P43. Green shading indicates the VP4 gene segments with a P[8] genotype identical to those of strains A14, A25, P02, P39, and P43. Blue shading indicates the VP4 gene segments with a P[6] genotype identical to that of strain A23. “−” 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 A14. bThe gene segments that are most similar to those of strain A23. cThe gene segments that are most similar to those of strain A25. dThe gene segments that are most similar to those of strain P02. eThe gene segments that are most similar to those of strain P39. fThe gene segments that are most similar to those of strain P43.
Fig 3
Fig 3. Phylogenetic tree constructed from the nucleotide sequences of the VP7 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
In the tree, the positions of strains A14, A23, A25, P02, P39, and P43 are shown in red. Bootstrap values of <75% are not shown. Scale bars, 0.05 substitutions per nucleotide.
Fig 4
Fig 4. Phylogenetic tree constructed from the nucleotide sequences of the VP4 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 5
Fig 5. Phylogenetic tree constructed from the nucleotide sequences of the VP6 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.02 substitutions per nucleotide.
Fig 6
Fig 6. Phylogenetic tree constructed from the nucleotide sequences of the VP1 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 7
Fig 7. Phylogenetic tree constructed from the nucleotide sequences of the VP2 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 8
Fig 8. Phylogenetic tree constructed from the nucleotide sequences of the VP3 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 9
Fig 9. Phylogenetic tree constructed from the nucleotide sequences of the NSP1 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 10
Fig 10. Phylogenetic tree constructed from the nucleotide sequences of the NSP2 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.02 substitutions per nucleotide.
Fig 11
Fig 11. Phylogenetic tree constructed from the nucleotide sequences of the NSP3 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.05 substitutions per nucleotide.
Fig 12
Fig 12. Phylogenetic tree constructed from the nucleotide sequences of the NSP4 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.02 substitutions per nucleotide.
Fig 13
Fig 13. Phylogenetic tree constructed from the nucleotide sequences of the NSP5 genes of strains A14, A23, A25, P02, P39, and P43, and representative RVA strains.
See legend of Fig 3. Scale bars, 0.02 substitutions per nucleotide.
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Grants and funding

This study was supported in part by the MEXT-Supported Program for the Strategic Research Foundation at Private Universities, 2010-2014 (KT), and Grants-in-Aid for Research on Emerging and Re-emerging Infectious Diseases from the Ministry of Health, Labor, and Welfare of Japan (KT). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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