Whole genome analyses of African G2, G8, G9, and G12 rotavirus strains using sequence-independent amplification and 454® pyrosequencing

Khuzwayo C. Jere, Luwanika Mlera, Hester G. O'Neill, A. Christiaan Potgieter, Nicola A. Page, Mapaseka L. Seheri, Alberdina A. van Dijk*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

53 Citations (Scopus)

Abstract

High mortality rates caused by rotaviruses are associated with several strains such as G2, G8, G9, and G12 rotaviruses. Rotaviruses with G9 and G12 genotypes emerged worldwide in the past two decades. G2 and G8 rotaviruses are however also characterized frequently across Africa. To understand the genetic constellation of African G2, G8, G9, and G12 rotavirus strains and their possible origin, sequence-independent cDNA synthesis, amplification, and 454 ® pyrosequencing of the whole genomes of five human African rotavirus strains were performed. RotaC and phylogenetic analysis were used to assign and confirm the genotypes of the strains. Strains RVA/Human-wt/MWI/1473/2001/G8P[4], RVA/Human-wt/ZAF/3203WC/2009/G2P[4], RVA/Human-wt/ZAF/3133WC/2009/G12P[4], RVA/Human-wt/ZAF/3176WC/2009/G12P[6], and RVA/Human-wt/ZAF/GR10924/1999/G9P[6] were assigned G8-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2, G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2, G12-P[4]-I1-R1-C1-M1-A1-N1-T1-E1-H1, G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, and G9-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotypes, respectively. The detection of both Wa- and DS-1-like genotypes in strain RVA/Human-wt/ZAF/3133WC/2009/G12P[4] and Wa-like, DS-1-like and P[6] genotypes in strain RVA/Human-wt/ZAF/GR10924/1999/G9P[6] implies that these two strains were generated through intergenogroup genome reassortment. The close similarity of the genome segments of strain RVA/Human-wt/MWI/1473/2001/G8P[4] to artiodactyl-like, human-bovine reassortant strains and human rotavirus strains suggests that it originated from or shares a common origin with bovine strains. It is therefore possible that this strain might have emerged through interspecies genome reassortment between human and artiodactyl rotaviruses. This study illustrates the swift characterization of all the 11 rotavirus genome segments by using a single set of universal primers for cDNA synthesis followed by 454 ® pyrosequencing and RotaC analysis.

Original languageEnglish
Pages (from-to)2018-2042
Number of pages25
JournalJournal of Medical Virology
Volume83
Issue number11
DOIs
Publication statusPublished - Nov 2011
Externally publishedYes

Keywords

  • 454® pyrosequencing
  • Emerging strains
  • Genogroup
  • Rotavirus

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