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. 2015 May 7;7(5):2358-77.
doi: 10.3390/v7052358.

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

Nathalie Kin  1   2 , Fabien Miszczak  3   4   5 , Wei Lin  6 , Meriadeg Ar Gouilh  7   8   9 , Astrid Vabret  10   11   12 ; EPICOREM Consortium
Affiliations

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

Nathalie Kin et al. Viruses. .

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.

Keywords: HCoV-OC43; coronavirus; genotype; phylogeny; recombination; sequencing.

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Figures

Figure 1
Figure 1
Phylogenetic analysis of the complete nsp12, S, and N genes of the 36 HCoV-OC43 strains and 3 BCoV strains. The phylogenetic trees were constructed by the neighbor joining method [35]. Bootstrap values were calculated from 1000 replicates. Bootstrap values over 70% are shown [40]. The evolutionary distances were computed using the Kimura 2-parameter method (kimura) and units are the number of base substitutions per site. Evolutionary analyses were conducted in MEGA, version 6.06. [41]. Blue triangle, isolates from Caen; red circle, isolates from USA; green circle, isolates from Hong-Kong; black diamond, isolates from Belgium; purple square, ATCC-VR759 strains, empty black square, BCoV strains.
Figure 2
Figure 2
Results of Bayesian analysis based on S and N gene sequence data. Inferences were calculated with the one parametric coalescent model with a constant size, under the TN93+G substitution parameter, using the BEAST package (version 1.8.2) [42]. The length of MCMC was fixed at 108 states for S and N genes. The dates of emergence of mean clusters are indicated, associated with the 95% HPD.
Figure 3
Figure 3
Alignement of some of the S genes sequences. This aligment was made using Bioedit Software version 7.2.5 (Ibis Biosciences, Carlsbad, CA, USA).
See this image and copyright information in PMC

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