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Updated: Oct 1, 2025
Assays for the Specific Growth Rate and Cell-binding Ability of Rotavirus
Published on: January 28, 2019
Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018
Jijoho Michel Agbla1, Mathew D Esona2, Jose Jaimes2
1National Health Laboratory, Ministry of Public Health, 01 P.O. Box 418, Cotonou, Benin; Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 P.O. Box 2009, Cotonou, Benin.
Insights
This study characterized 72 rotavirus A strains in Benin, revealing genetic diversity and identifying novel alleles for VP7 and VP4 genes. These findings provide a baseline for post-vaccination rotavirus surveillance.
Area of Science:
- Virology
- Genetics
- Public Health
Background:
- Species A rotaviruses (RVA) are a leading cause of severe diarrhea in young children globally.
- An 11-gene system classifies RVA strains, crucial for understanding viral evolution and vaccine impact.
- Benin introduced the ROTAVAC® vaccine in December 2019, necessitating pre-vaccination RVA strain characterization.
Purpose of the Study:
- To perform whole-genome characterization of RVA strains circulating in Benin before vaccine introduction.
- To identify genetic diversity, including common and unusual genotypes, and novel alleles.
- To establish a baseline for future RVA surveillance in the post-vaccination era.
Main Methods:
- Whole-genome sequencing of 72 randomly selected RVA strains collected in Benin between 2016-2018.
- Genotyping based on the 11-gene classification system (Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx).
- Comparative analysis of identified alleles against reference and vaccine strains.
Main Results:
- Characterization of diverse RVA strains, including G1P[8], G2P[4], G9P[8], G12P[8], G3P[6], and others.
- Identification of two main genetic constellations: Wa-like and DS-1-like.
- Discovery of 3 new alleles for VP7 (G3, G12) and VP4 (P[4], P[6]) genes, along with novel alleles in other genes.
Conclusions:
- The study provides comprehensive whole-genome data for RVA strains circulating in Benin prior to vaccination.
- Genetic diversity, including novel alleles and evidence of reassortment, was observed.
- The findings establish a crucial baseline for monitoring RVA evolution and vaccine effectiveness in Benin.
Abstract:
Species A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016 to 2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3 = 1 new allele and G12 = 2 new alleles) and VP4 (P[4] = 1 new allele and P[6] = 2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.
