Prevalence and Genetic Characterization of Rotavirus Infections among Children under Five Years in Mutaho Health District, Gitega Province and Bujumbura Municipality, Burundi.

Abstract

Rotavirus is the leading cause of severe diarrhea in children under five years worldwide. In Burundi, rotavirus took the lives of more than 3,500 children under 5 years, each year, in the pre-rotavirus vaccine era. In 2013, the rotavirus vaccine was implemented in Burundi. Nonetheless, persistent diarrhea in Mutaho health district raised questions of whether uncommon rotavirus strains were circulating and challenging the efficacy of rotavirus vaccine in that part of Burundi. In Burundi, no study has been carried out to document the genetic diversity of circulating rotavirus strains. This cross-sectional study aimed at determining the prevalence and genetic characteristics of rotavirus infections among children under five years of age in Mutaho Health District and the Municipality of Bujumbura, in Burundi. Stool specimens were collected from 646 children presenting with acute diarrhea. In addition, data on the socio-demographic characteristics and the vaccination status of the study subjects were collected using a questionnaire. These specimens were screened for rotavirus antigen using Diagnostar® rapid test kit and confirmed by ELISA. Samples positive by ELISA underwent Polyacrylamide Gel Electrophoresis (PAGE), RT-PCR, G and P genotyping by multiplex semi-nested PCR using a cocktail of type specific primers or by sequencing. The difference between different proportions or the significance of the association between rotavirus prevalence, G and P type prevalence and exposure variables including socio-demographic characteristics and vaccination status of the study participants as well as the season were tested using Chi-square test or estimated as Odds-ratio. Furthermore, the VP4 and VP7 sequences from this study were subjected to molecular evolutionary analysis and phylogenetic analysis using p-distance nucleotide substitution model and maximum likelihood method respectively. The overall prevalence of rotavirus was 6.2% (40/646). Rotavirus detection rate increased as the amount of rainfall went down, showing a significant negative association between the two variables (r = - 0.875; P = 0.0001). The prevalence of the genotype G1 was significantly higher in Bujumbura Municipality than Mutaho health district while G12 predominated in Mutaho health district (OR = 7.33; P = 0.026). Three different P types were identified; P [8] the most common, followed by P [6] and P [4]. The most common G/P combination genotype was G1P [8] (45.5%), followed by G12 P [8] (41.0%), G1P [6] (4.5%), G12 P [6] (4.5%) and G12 P [4] (4.5%). The emergence of G12 rotavirus strains with potential to challenge the efficacy of rotavirus vaccines was highlighted. Furthermore, the high degree of divergence between the VP7 and VP4 amino acid sequences of G1P [8] rotavirus strains from this study and the rotavirus vaccine stain, Rotarix, showed their potential to escape from the protection conferred by vaccination. It is recommended that strain surveillance for rotavirus in Burundi should be continuous to monitor trends in the occurrence of these prevailing and potentially emerging new rotavirus strains.