Search bioRxiv⌕ Search

Biology subjects

LESAGE, L.

Publications and source records attributed to LESAGE, L..

2 recordsLinked to original sources
bioRxiv2025

Five-year (2017-2022) evolutionary dynamics of human coronavirus OC43 in southern France based on whole genome next-generation sequencing

HCoV-OC43 genomes and their evolution are scarcely studied worldwide and in France with only 361 genomes available as of October 2023. Here we implemented an in-house PCR amplification system to obtain retrospectively by next-generation sequencing then analyze HCoV-OC43 genomes for infections diagnosed with this virus in southern France between 02/2017 and 10/2022. Multiplex PCR amplification using a set of in-house primers designed using the Gemi software was carried out on residues 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 and RDP4 softwares. A total of 34 PCR primer pairs were designed for amplification then NGS of 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 1,300 amino acid substitutions were detected in genotype G, J and K, respectively, compared with reference genomes of the same genotype dating back to 2017-2018. Possible recombinations were detected for 10 HCoV-OC43 genomes classified in genotypes K or J. 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.

microbiology↗
bioRxiv2025

Implementation of a multiplex PCR amplfication system combined with next-generation genome sequencing to decipher the circulation of Human coronavirus 229E lineages in Southern France

Coronaviruses are known to evolve rapidly and be prone to new virus emergence. Human coronavirus-229E is one of the seven coronaviruses currently known to cause respiratory symptoms in humans. Genomic data are very scarce for this virus. Here, we implemented an in-house multiplex PCR strategy to amplify HCoV-229E genomes from nasopharyngeal samples diagnosed as positive for this virus RNA in Southeastern France. Then, next-generation sequencing was performed using Nanopore or Illumina technologies on Gridion or Novaseq 6000 instruments, respectively. HCoV-229E genomes were assembled and analyzed using MAFFT, MEGA, Itol, Nexstrain and Nextclade softwares. Thirty-one PCR primer pairs were designed to amplify overlapping fragments of the HCoV-229E genome. They allowed obtaining 123 genomes, which were classified in an emerging HCoV-229E lineage first reported in China, with two sublineages being delineated. Relatively to genome NC_002645.1 dating back to 1962, regarding nucleotide mutations, 1,167 substitutions, 72 insertions and 34 deletions were detected in viral genomes obatined here, while regarding amino acid mutations, 415 susbstitutions, 39 deletions and 14 amino acid insertions were detected. The genes with the greatest diversity were S (that encodes the spike protein) then Nsp3. Signature mutations were identified for the two sublineages. In summary, we almost doubled the set of HCoV-229E genomes available worldwide and provided the first genomes from France. Further studies are needed to strengthen the knowledge about the phylogenomics and evolutionary dynamics of this neglected respiratory virus, and about their specificities, which may also purvey clues to contribute improving knowledge for all other human coronaviruses.

microbiology↗