Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa

• Published in: Pathogens (Basel) Vol. 9; no. 5; p. 391
• Main Authors: Mwangi, Peter N., Mogotsi, Milton T., Rasebotsa, Sebotsana P., Seheri, Mapaseka L., Mphahlele, M. Jeffrey, Ndze, Valantine N., Dennis, Francis E., Jere, Khuzwayo C., Nyaga, Martin M.
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 20.05.2020; MDPI
• Subjects: Amino acids; atypical strains; capsid; Constellations; Gene sequencing; Genes; genome constellation; Genomes; Genotype & phenotype; Immunization; monitoring; Nucleotides; pathogens; Phylogenetics; Proteins; reassortment; RNA polymerase; Rotavirus; Rotavirus A; sampling; sequence analysis; South Africa; strains; Surveillance; Vaccination; Vaccines; Viruses; Whole genome sequencing; whole-genome characterization; Vietnam; Malawi; Asia; Philippines; China; Japan; Africa; Brazil; South Africa; Thailand; India; reassortment; genome constellation; atypical strains; rotavirus; whole-genome characterization
• ISSN: 2076-0817; 2076-0817
• DOI: 10.3390/pathogens9050391

Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.