Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes.

Meriadeg Gouilh,Wei Lin,Epicorem Consortium,Astrid Vabret,Nathalie Kin,Fabien Miszczak

doi:10.3390/v7052358

Meriadeg Gouilh, Wei Lin + Show 4 more

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https://doi.org/10.3390/v7052358

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Abstract

Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.

Highlights

Coronaviruses belong to the Coronaviridae family in Nidovirales order [1]
This study focuses on the sequences of the nsp12, S, and N genes of 15 human coronaviruses (HCoVs)-OC43s detected in respiratory specimens sampled from 2001 to 2013
Of the 15 HCoV-OC43s and the prototype strain VR759, six, eight, and three overlapping sequences were obtained for the nsp12, S, and N genes, respectively

Summary

Introduction

Coronaviruses belong to the Coronaviridae family in Nidovirales order [1]. Six human coronaviruses (HCoVs) have been identified of which four are in circulation: HCoV-229E, HCoV-NL63 (genus Alphacoronavirus), and HCoV-OC43 and HCoV-HKU1 (genus Betacoronavirus clade A). These four viruses are responsible for mild upper-respiratory tract infections, yet cause more severe respiratory pathologies in infants, immunocompromised patients and elderly people [11,12,13,14,15,16,17,18,19,20,21,22]. The other two human coronaviruses, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle-East Respiratory Syndrome coronavirus (MERS-CoV), belonging to Betacoronavirus genus, clades B and C respectively, cause severe respiratory pathologies

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