Classic Human Astrovirus 4, 8, MLB-3 and likely new genotype 5 sub-lineage in stool samples of children with Acute Flaccid Paralysis (AFP) in Nigeria

Introduction: Acute viral gastroenteritis is a common illness especially in developing countries. Globally, the role of human astroviruses (HAstV) in gastroenteritis among children and elderly is well documented. But there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Method: Viral like particles (VLPs) were purified from stool samples from children diagnosed with acute flaccid paralysis (AFP) between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step, and subsequent random PCR amplification. Library preparation and Illumina sequencing were performed. Using the Virome Paired-End Reads (ViPER) pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Results : Six near complete genome sequences of HAstV were identified and classified as HAstV 4 (n=1), HAstV5 (n=1), HAstV8 (n=1) and MLB-3 (n=3). The HAstV5 belonged to a yet unclassified sub-lineage which we tentatively named HAstV-5d. Phylogenetic analysis of ORFs 1a, 1b and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. Conclusion: We report for the first time the circulation of HAstV genotypes 4, 8 and MLB-3 in Nigeria and present data suggestive for the existence of a new sub-lineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV increased research interest as well as robust HAstV surveillance in Nigeria is essential.