{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T02:45:57Z","timestamp":1791945957146,"version":"4.3.4"},"reference-count":20,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2025,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Coronaviruses rapidly evolve and are prone to new virus emergence. Human coronavirus (HCoV)\u2212229E is one of the seven coronaviruses (aside HCoV\u2010OC43, HCoV\u2010HKU1, HCoV\u2010NL63, SARS\u2010CoV, MERS\u2010CoV, SARS\u2010CoV\u20102) causing respiratory infections in humans. Genomic data are very scarce for this virus. We implemented an in\u2010house multiplex PCR strategy to amplify HCoV\u2010229E genomes from nasopharyngeal samples, before next\u2010generation sequencing using Nanopore or Illumina technologies. HCoV\u2010229E genomes were assembled and analyzed using MAFFT, MEGA, Itol, Nexstrain, and Nextclade softwares. Thirty\u2010one PCR primer pairs designed to amplify HCoV\u2010229E genome overlapping fragments allowed obtaining 123 genomes classified in an emerging HCoV\u2010229E lineage first reported in China, with two sublineages being delineated. Relatively to genome NC_002645.1 (2001), regarding nucleotide mutations, 1167 substitutions, 72 insertions, and 34 deletions were detected, while regarding amino acid mutations, 415 susbstitutions, 39 deletions, and 14 amino acid insertions were detected. Genes with the greatest diversity were the spike protein\u2010encoding gene, then Nsp3. The two sublineages harbored signature mutations. We almost doubled the HCoV\u2010229E genome set available worldwide and provided the first French genomes. Further studies are needed to strengthen knowledge about this virus\u2032 phylogenomics and evolutionary dynamics, which may purvey clues to contribute improving coronavirus knowledge.<\/jats:p>","DOI":"10.1002\/jmv.70653","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T13:27:53Z","timestamp":1761226073000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Implementation of a Multiplex PCR Amplification System Combined With Next\u2010Generation Genome Sequencing to Decipher the Circulation of Human Coronavirus 229E Lineages in Southern France"],"prefix":"10.1002","volume":"97","author":[{"given":"Houmadi","family":"Hikmat","sequence":"first","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Microbes Evolution Phylogeny and Infections (MEPHI), Aix\u2010Marseille Univ. (AMU) Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justine","family":"Py","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Microbes Evolution Phylogeny and Infections (MEPHI), Aix\u2010Marseille Univ. (AMU) Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9line","family":"Boschi","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Microbes Evolution Phylogeny and Infections (MEPHI), Aix\u2010Marseille Univ. 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(AMU) Marseille France"},{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucile","family":"Lesage","sequence":"additional","affiliation":[{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"},{"name":"Service de P\u00e9diatrie g\u00e9n\u00e9rale, h\u00f4pital Timone, AP\u2010HM Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aur\u00e9lie","family":"Morand","sequence":"additional","affiliation":[{"name":"Assistance Publique\u2010H\u00f4pitaux de Marseille (AP\u2010HM) Marseille France"},{"name":"Service de P\u00e9diatrie g\u00e9n\u00e9rale, h\u00f4pital Timone, AP\u2010HM Marseille France"},{"name":"Service d\u2032accueil des Urgences P\u00e9diatriques, h\u00f4pital Nord, AP\u2010HM Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8006-7704","authenticated-orcid":false,"given":"Bernard","family":"La Scola","sequence":"additional","affiliation":[{"name":"IHU M\u00e9diterran\u00e9e Infection Marseille France"},{"name":"Microbes Evolution Phylogeny and Infections (MEPHI), Aix\u2010Marseille Univ. 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