Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018.

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.

Molecular characteristics of rotavirus genotypes circulating in the south of Benin, 2016-2018.

OBJECTIVE: Rotavirus remains the main causative agent of gastroenteritis in young children in countries that have not yet introduced the vaccine. In Benin, rotavirus vaccine was introduced late December 2019 into the EPI. This study aims to provide pre-vaccination era rotavirus genotyping data in Benin. These data can supplement data from the surveillance system of Ministry of Health of Benin which is supported by the World Health Organization (WHO). RESULTS: Of the 420 diarrheal stool samples, actively collected in southern Benin from July 2016 through November 2018 from children under 5 years old and suffering from gastroenteritis, 167 (39.8%) samples were rotavirus EIA positive. 186 (44.3%) samples contained amplifiable rotavirus RNA detected by qRT-PCR method and were genotyped using one-step RT-PCR multiplex genotyping method. G1P[8] represents the predominant genotype (32%) followed by the G2P[4] (26%), G3P[6] (16%), G12P[8] (13%) and mixed G and P types (1%). Four samples (2%) could not be assigned both G and P type specificity.

Epidemiological Survey of Rotaviruses Responsible for Infantile Diarrhea by the Immunomolecular Technique in Cotonou (Benin, West Africa).

Rotavirus remains the main causative agent of gastroenteritis in young children, in countries that have not yet introduced the vaccine. Benin, in order to implement the WHO recommendations, projects to introduce the rotavirus vaccine in 2018 as part of its Expanded Program on Immunization. But before the introduction of this vaccine, epidemiological data on rotavirus infections and rotavirus genotypes circulating in Benin should be available. The aim of this study is to generate epidemiological data on infantile rotavirus diarrhea in Benin. In order to determine the epidemiological characteristics and electrophoretypes of rotavirus responsible for gastroenteritis in diarrheic children aged 0 to 5 years, 186 stool samples were collected according to the WHO Rotavirus Laboratory Manual from March 2014 to February 2015 at Suru-Lere University Hospital Center. Detection of rotavirus antigen was performed by the ELISA test, followed by molecular characterization using polyacrylamide gel electrophoresis. 186 stool samples were analyzed for rotavirus, and seventy-three (39.2%) were found to be positive for rotavirus antigen by ELISA. Children aged 3 to 24 months were the most affected by rotavirus diarrhea in this study. Of the seventy-three children affected with rotavirus diarrhea, 27 (37%) had vomiting accompanied by dehydration and fever. Results based on electrophoresis showed that, among the 73 samples tested, 38 yielded typical rotavirus electrophoretic migration profiles.