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.