Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic

Abstract

Objective Rotavirus A (RVA) remains the main causative agent of gastroenteritis in young children and the young of many mammalian and avian species. In this study we describe a RVA strain detected from a 6-month-old child from Central African Republic (CAR). Results We report the 11 open reading frame sequences of a G29-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 rotavirus strain, RVA/Human-wt/CAR/CAR91/2014/G29P[6]. Nine genes (VP1–VP3, VP6, NSP1–NSP5) shared 90–100% sequence similarities with genogroup 2 rotaviruses. Phylogenetically, backbone genes, except for VP3 and NSP4 genes, were linked with cognate gene sequences of human DS-1-like genogroup 2, hence their genetic origin. The VP3 and NSP4 genes, clustered genetically with both human and animal strains, an indication genetic reassortment human and animal RVA strains has taken place. The VP7 gene shared nucleotide (93–94%) and amino acid (95.5–96.7%) identities with Kenyan and Belgian human G29 strains, as well as to buffalo G29 strain from South Africa, while the VP4 gene most closely resembled P[6]-lineage I strains from Africa and Bangladesh (97%).

Differentiation between Wild-Type Group A Rotaviruses and Vaccine Strains in Cases of Suspected Horizontal Transmission and Adverse Events Following Vaccination

“…The determined detection limit was 600 RNA copies/reaction (1.3 × 10 6 copies/g stool) of wild-type virus and 60 RNA copies/reaction (1.3 × 10 5 copies/g stool) of RV5. Additionally, 100% reproducibility was found via intraand inter-assay comparison of samples with the RV5 and a G1P [8] wild-type strain. The specificity of the assay was tested with samples from patients with AGE which were known to be positive for human norovirus (3 samples) or positive for sapovirus (3 samples) or positive for three enteroviruses (echovirus 18, coxsackie B5 virus, and coxsackie A9 virus).…”

“…In order to distinguish between wild-type P [8]-and vaccine-derived strains more reliably, especially in mixed infections, capillary fragment-length analysis was used to increase the overall specificity of amplicon size calling (ABI 3500xL Dx device and GeneMapper 5.0 software: Applied Biosystems, Forster City, CA, USA) [26]. Fragments of 246 bp for RV1-like strain and 224 bp for RVA wild-type strains could be distinguished reliably by two sharply distinct peaks.…”

“…Classification of RVA is standardized for all 11 genome segments, including a binary G+P-genotyping system based on VP7 (G type) and VP4 (P type) [6]. Currently, 42 different VP7 G types and 58 different VP4 P-types have been accepted by the Rotavirus Classification Working Group, and at least 16 G-types and 19 VP4 P-types have been identified for RVA strains infecting humans [7,8]. A small number of RVA genotype combinations circulate globally in the human population at higher frequencies, including combinations of G1, G3, G4, G9, G12 with P [8], and G2 with P [4].…”

“…Currently, 42 different VP7 G types and 58 different VP4 P-types have been accepted by the Rotavirus Classification Working Group, and at least 16 G-types and 19 VP4 P-types have been identified for RVA strains infecting humans [7,8]. A small number of RVA genotype combinations circulate globally in the human population at higher frequencies, including combinations of G1, G3, G4, G9, G12 with P [8], and G2 with P [4]. Additionally, in some regions, P [6] is relevant in different genotype constellations [9].…”

“…The monovalent Rotarix ® vaccine (RV1) contains a live attenuated human G1P1A [8] RVA strain. RotaTeq ® (RV5) is a pentavalent bovinehuman vaccine of five reassortant bovine strains containing genes that express outer capsid proteins of five common circulating human RVA strains (G1, G2, G3, G4, and P [8]), together with the antigens originating from the bovine RVA strain used as a vector (G6 and P7 [5]). The vaccines RV5 and RV1 are administered orally to infants in two or three doses, respectively [10].…”