Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya: Identification of porcine-like NSP4 genes

Satoshi Komoto, Ernest Wandera Apondi, Mohammad Shah, Erick Odoyo, James Nyangao, Mayuko Tomita, Mitsutaka Wakuda, Yoshimasa Maeno, Haruko Shirato, Takao Tsuji, Yoshio Ichinose, Koki Taniguchi

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Abstract

G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.

Original languageEnglish
Pages (from-to)277-293
Number of pages17
JournalInfection, Genetics and Evolution
Volume27
DOIs
Publication statusPublished - 01-01-2014

Fingerprint

Rotavirus
Kenya
genomics
Swine
swine
genome
gene
Genes
Genome
genes
Diarrhea
phylogenetics
analysis
Africa
diarrhea
childhood

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Microbiology (medical)
  • Infectious Diseases

Cite this

Komoto, Satoshi ; Wandera Apondi, Ernest ; Shah, Mohammad ; Odoyo, Erick ; Nyangao, James ; Tomita, Mayuko ; Wakuda, Mitsutaka ; Maeno, Yoshimasa ; Shirato, Haruko ; Tsuji, Takao ; Ichinose, Yoshio ; Taniguchi, Koki. / Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya : Identification of porcine-like NSP4 genes. In: Infection, Genetics and Evolution. 2014 ; Vol. 27. pp. 277-293.
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abstract = "G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.",
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Komoto, S, Wandera Apondi, E, Shah, M, Odoyo, E, Nyangao, J, Tomita, M, Wakuda, M, Maeno, Y, Shirato, H, Tsuji, T, Ichinose, Y & Taniguchi, K 2014, 'Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya: Identification of porcine-like NSP4 genes', Infection, Genetics and Evolution, vol. 27, pp. 277-293. https://doi.org/10.1016/j.meegid.2014.08.002

Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya : Identification of porcine-like NSP4 genes. / Komoto, Satoshi; Wandera Apondi, Ernest; Shah, Mohammad; Odoyo, Erick; Nyangao, James; Tomita, Mayuko; Wakuda, Mitsutaka; Maeno, Yoshimasa; Shirato, Haruko; Tsuji, Takao; Ichinose, Yoshio; Taniguchi, Koki.

In: Infection, Genetics and Evolution, Vol. 27, 01.01.2014, p. 277-293.

Research output: Contribution to journalArticle

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T1 - Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya

T2 - Identification of porcine-like NSP4 genes

AU - Komoto, Satoshi

AU - Wandera Apondi, Ernest

AU - Shah, Mohammad

AU - Odoyo, Erick

AU - Nyangao, James

AU - Tomita, Mayuko

AU - Wakuda, Mitsutaka

AU - Maeno, Yoshimasa

AU - Shirato, Haruko

AU - Tsuji, Takao

AU - Ichinose, Yoshio

AU - Taniguchi, Koki

PY - 2014/1/1

Y1 - 2014/1/1

N2 - G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.

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