title: 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.
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.
authors.affiliation: Normandie Université, 14032 Caen, France. nathalie.kin@unicaen.fr.|Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. nathalie.kin@unicaen.fr.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Kin
authors.affiliation: Normandie Université, 14032 Caen, France. fabienmzz@yahoo.fr.|Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. fabienmzz@yahoo.fr.|Department of Virology, University Hospital of Caen, F-14033 Caen, France. fabienmzz@yahoo.fr.
authors.forename: Fabien
authors.initials: F
authors.lastname: Miszczak
authors.affiliation: Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. wei.lin@hotmail.fr.
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.affiliation: Normandie Université, 14032 Caen, France. meriadeg.le-gouil@pasteur.fr.|Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. meriadeg.le-gouil@pasteur.fr.|Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France. meriadeg.le-gouil@pasteur.fr.
authors.forename: Meriadeg Ar
authors.initials: MA
authors.lastname: Gouilh
authors.affiliation: Normandie Université, 14032 Caen, France. a-vabret@chu-caen.fr.|Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. a-vabret@chu-caen.fr.|Department of Virology, University Hospital of Caen, F-14033 Caen, France. a-vabret@chu-caen.fr.
authors.forename: Astrid
authors.initials: A
authors.lastname: Vabret
mesh_terms: D000368:Aged; D002675:Child, Preschool; D016000:Cluster Analysis; D018352:Coronavirus Infections / Q000821:virology*; D028962:Coronavirus OC43, Human / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D005602:France; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D012141:Respiratory Tract Infections / Q000821:virology*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: HCoV-OC43; coronavirus; genotype; phylogeny; recombination; sequencing