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

Ide T, Komoto S, Higo-Moriguchi K, Htun KW, Myint YY, Myat TW, Thant KZ, Thu HM, Win MM, Oo HN, Htut T, Wakuda M, Dennis FE, Haga K, Fujii Y, Katayama K, Rahman S, Nguyen SV, Umeda K, Oguma K, Tsuji T, Taniguchi K - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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pone.0124965.g002: 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.

Mentions: The 11 genes of strains A14, A23, A25, P02, P39, and P43 were assigned as G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains A14, A25, P02, P39, and P43), and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain A23) (Fig 2). Strains A14, A23, A25, P02, P39, and P43 were confirmed to have the G12P[8], G12P[6], G12P[8], G12P[8], G12P[8], and G12P[8] genotypes, respectively, as determined by PCR-based genotyping (Ide et al., in preparation). Comparison of the complete genotype constellations of strains A14, A23, A25, P02, P39, and P43 with those of other G12 and non-G12 strains is shown in Fig 2. All the six Myanmarese G12 strains exhibited typical Wa-like genotype constellations, which are commonly found in the G12 strains recently detected worldwide (Rahman et al., 2007). Furthermore, as suggested by the genomic dsRNA profiles observed on PAGE analysis (Fig 1), strains A14, A25, P02, P39, and P43 exhibited extremely high nucleotide sequence identities (99.1–100%) to one another for all the 11 gene segments. On the other hand, the nucleotide sequence similarities of the VP4 and other 10 gene segments (VP7, VP6, VP1-3, and NSP1-5) of strain A23 to those of strains A14, A25, P02, P39, and P43 were comparatively low (75.3 and 93.1–98.7%, respectively).


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

Ide T, Komoto S, Higo-Moriguchi K, Htun KW, Myint YY, Myat TW, Thant KZ, Thu HM, Win MM, Oo HN, Htut T, Wakuda M, Dennis FE, Haga K, Fujii Y, Katayama K, Rahman S, Nguyen SV, Umeda K, Oguma K, Tsuji T, Taniguchi K - PLoS ONE (2015)

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.
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pone.0124965.g002: 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.
Mentions: The 11 genes of strains A14, A23, A25, P02, P39, and P43 were assigned as G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains A14, A25, P02, P39, and P43), and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain A23) (Fig 2). Strains A14, A23, A25, P02, P39, and P43 were confirmed to have the G12P[8], G12P[6], G12P[8], G12P[8], G12P[8], and G12P[8] genotypes, respectively, as determined by PCR-based genotyping (Ide et al., in preparation). Comparison of the complete genotype constellations of strains A14, A23, A25, P02, P39, and P43 with those of other G12 and non-G12 strains is shown in Fig 2. All the six Myanmarese G12 strains exhibited typical Wa-like genotype constellations, which are commonly found in the G12 strains recently detected worldwide (Rahman et al., 2007). Furthermore, as suggested by the genomic dsRNA profiles observed on PAGE analysis (Fig 1), strains A14, A25, P02, P39, and P43 exhibited extremely high nucleotide sequence identities (99.1–100%) to one another for all the 11 gene segments. On the other hand, the nucleotide sequence similarities of the VP4 and other 10 gene segments (VP7, VP6, VP1-3, and NSP1-5) of strain A23 to those of strains A14, A25, P02, P39, and P43 were comparatively low (75.3 and 93.1–98.7%, respectively).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.

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.

No MeSH data available.


Related in: MedlinePlus