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Direct amplification and sequencing of enterovirus genomes from clinical and wastewater samples reveals uncommon virus types in Cameroon
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Edité par CCSD ; Springer Verlag -
International audience. The knowledge about the genetic diversity of enteroviruses in sub-Saharan Africa remains biased by the fact that it has mainly been described through the characterization of specimens isolated in cell cultures. This study aimed to characterize enteroviruses that circulate among humans in Cameroon by focusing more specifically on respiratory enteroviruses and on enteroviruses that are noncultivable or non-cytopathogenic in standard cell lines. For this purpose, RNAs were extracted from nasopharyngeal swabs, stool suspensions and sewage concentrates collected in Cameroon from January 2018 to December 2019. RNA extracts were subjected to molecular screening to detect enterovirus genomes that were subsequently sequenced with the Illumina technology. Overall, 81 strains of 32 virus types were identified. Most strains (61.7%) belonged to the species Enterovirus coxsackiepol, followed by members of the species Enterovirus betacoxsackie (21%), Enterovirus alphacoxsackie (14.8%) and Enterovirus deconjuncti (2.5%). Almost all strains were found in sewage concentrates (79%) and stool suspensions (18.5%). Only two EV-D68s, were identified in nasopharyngeal swabs. Interestingly, several virus types that have been rarely reported were detected, including non-cultivable/non-cytopathogenic EV-Cs, among which a new virus type assigned as EV-C119. These results highlight the fact that virus isolation and unbiased cell culture-free approaches complement each other to provide a more complete view of the enterovirus landscape in humans.
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