Five-Year (2017-2022) Evolutionary Dynamics of Human Coronavirus OC43 in Southern France Based on Whole Genome Next-Generation Sequencing

Abstract

HCoV-OC43 genomes and their evolution are scarcely studied worldwide and in France, with only 361 genomes available as of October 2023. Here, an in-house PCR amplification system was implemented to obtain retrospectively by next-generation sequencing, then analyze HCoV-OC43 genomes for infections diagnosed with this virus in southern France between February 2017 and October 2022. Multiplex PCR amplification using a set of in-house primers designed with the Gemi software was carried out on residuals of HCoV-OC43 RNA-positive nasopharyngeal samples, before next-generation sequencing (NGS) using Illumina technology on a NovaSeq. 6000 instrument. HCoV-OC43 genome assembly, bioinformatic analyses, and phylogeny reconstruction were then carried out using CLC Genomics, Mafft, BioEdit, Nextstrain, Nextclade, MEGA, iTOL, RDP4, and HyPhy softwares. Spike structural predictions used AlphaFold and HyperChem. A total of 34 PCR primer pairs were designed for amplification, before NGS of amplicons generated from HCoV-OC43 genomes. A total of 185 genomes were obtained, 17, 79, and 89 belonging to Genotypes G, J, and K, respectively. These three genotypes circulated exclusively or co-circulated according to the year. A total of 303, 940, and 1300 amino acid substitutions were detected in genomes of genotypes G, J, and K, respectively, compared with reference genomes of the same genotype dating back to 2017-2018. Possible recombinations were detected for five HCoV-OC43 genomes and involved genomes classified in genotypes J or K. HCoV-OC43 genes encoding the hemagglutinin esterase, the spike, and the Nsp14 protein harbored the greatest number of sites under positive selection. Signature amino acid mutations F467V and S507G in the spike protein of genotypes J and G, respectively, were predicted to decrease the binding of 43E6 neutralizing antibody. Overall, the present study more than doubled the set of HCoV-OC43 genomes available worldwide for the 2017-2022 period and contributed to the monitoring of the HCoV-OC43 evolutionary dynamics.

Keywords: genomics; human coronavirus OC43; lineages; mutations; recombination; respiratory infections.