Molecular characterization and genetic diversity of norovirus strains recovered from stool of Nigerian children

Noroviruses (NoVs) are the leading causes of viral acute gastroenteritis (AGE). However, there is limited information on the molecular characterization and genetic diversity of NoVs in Nigeria. Archived stool samples from children with acute flaccid paralysis were collected, purified, processed using the NetoVIR protocol and sequenced using a metagenomic approach. Samples with NoV Reads were assembled, and phylogenetic and recombination analyses were performed to characterize and determine NoV genetic diversity. Of the fifty-five pools sequenced, three had NoV reads of which three genome sequences were obtained. The norovirus genotyping tool and phylogenetic analysis revealed that two sequences correspond to genotype GII.P7-GII.6, while one sequence belonged to GII.P7-GII.14 genotype. The Recombination analysis indicated a recombination event with an intra-genotypic recombinant strain detected. In this study, we describe the use of a metagenomic technique in the detection of divergent NoVs in the faeces of children and report for the first time the complete NoV genome of GII.P7-GII.6 in Nigeria. Findings from this study will serve as a reference for other Norovirus epidemiology and diversity studies in Nigeria. • We describe the use of a metagenomic technique to detect NoVs in stool samples of children with AFP in Nigeria. • We document for the first time the complete NoV genome of GII.P7-GII.6 in Nigeria. • Characterizations of this complete genome showed evidence of GII.P7-GII.6/GII.P7-GII.6 intra-genotypic recombination. • This study's findings will serve as a baseline for comprehensive molecular epidemiology and evolutionary diversity of NoV in Nigeria and Africa.