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

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.

Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains

“…Extraction of viral dsRNAs was performed as described previously [14, 16, 33]. Briefly, viral dsRNAs were extracted from stool suspensions using a QIAamp Viral RNA Mini Kit (Qiagen).…”

“…Building of a cDNA library and Illumina MiSeq sequencing were performed as described previously [14, 16, 30, 33, 34]. Briefly, a 200 bp fragment library ligated with bar-coded adapters was constructed for the 14 strains using an NEBNext Ultra RNA Library Prep Kit for Illumina v1.2 (New England Biolabs), and NEBNext Multiplex Oligos for Illumina (New England Biolabs) according to the manufacturer’s instructions.…”

“…Sequence comparisons were performed as described previously [14, 16, 33]. Briefly, multiple alignment of each viral segment was carried out using CLUSTAL W. Phylogenetic trees were constructed using the maximum likelihood method and the Tamura-Nei substitution model using MEGA6.06 [36].…”

High Prevalence of G12 Human Rotaviruses in Children with Gastroenteritis in Myanmar

“…G12 was first detected in the Philippines in 1987 (10). More than 10 years later, the prevalence of G12 strains has been reported in various countries, implying their possible emergence worldwide (11)(12)(13)(14). In particular, the detection rate of G12 is high in Southeast Asia.…”

“…In our previous study (14), the 6 Myanmar G12 human rotavirus strains employed in this study were characterized by whole genome analysis. Five of them were found to have the constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, and 1 strain had that of G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1.…”