Metagenomic Detection and Genetic Characterization of Human Sapoviruses among Children with Acute Flaccid Paralysis in Nigeria

• Published in: Pathogens (Basel) Vol. 13; no. 3; p. 264
• Main Authors: George, Uwem Etop, Faleye, Temitope O C, De Coninck, Lander, Agbaje, Sheriff Tunde, Ifeorah, Ijeoma Maryjoy, Onoja, Bernard Anyebe, Oni, Elijah Igbekele, Olayinka, Adebowale Oluseyi, Ajileye, Toluwani Goodnews, Oragwa, Arthur Obinna, Akinleye, Toluwanimi Emmanuel, Popoola, Bolutife Olubukola, Osasona, Oluwadamilola Gideon, Olayinka, Olaitan Titilola, George, Oluwadamilola Adefunke, Muhammad, Ahmed Iluoreh, Komolafe, Isaac, Adeniji, Adekunle Johnson, Matthijnssens, Jelle, Adewumi, Moses Olubusuyi
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.03.2024; MDPI
• Subjects: Acute Flaccid Paralysis; Acute Gastroenteritis; Amino acid sequence; Amino acids; Causes of; Children; Communicable diseases in children; DNA sequencing; Epidemics; Evolution; Feces; Gastroenteritis; Gene sequencing; Genetic aspects; Genetic diversity; Genomes; Genotypes; Identification and classification; Infections; Metagenomics; Methods; Nigeria; Nonstructural proteins; Nucleotide sequencing; Paralysis; Phylogenetics; Phylogeny; Population studies; Proteins; RNA viruses; sapovirus; Strains (organisms); Viral infections; Viruses; Nigeria; United States > US; Germany; Africa; Acute Gastroenteritis; sapovirus; Nigeria; metagenomics; Acute Flaccid Paralysis
• ISSN: 2076-0817; 2076-0817
• DOI: 10.3390/pathogens13030264

Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six complete genome sequences and two partial genome sequences. Several SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1), and GI (GI.2 and GI.7). To our knowledge, this is the first description of SaV infections and complete genomes from Nigeria. Pairwise identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks with associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were seen in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria. Future studies in different populations are, therefore, recommended.