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The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule.
Colson, Philippe; Gautret, Philippe; Delerce, Jeremy; Chaudet, Hervé; Pontarotti, Pierre; Forterre, Patrick; Tola, Raphael; Bedotto, Marielle; Delorme, Léa; Bader, Wahiba; Levasseur, Anthony; Lagier, Jean-Christophe; Million, Matthieu; Yahi, Nouara; Fantini, Jacques; La Scola, Bernard; Fournier, Pierre-Edouard; Raoult, Didier.
  • Colson P; IHU Méditerranée Infection, Marseille, France.
  • Gautret P; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
  • Delerce J; Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Marseille, France.
  • Chaudet H; IHU Méditerranée Infection, Marseille, France.
  • Pontarotti P; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
  • Forterre P; Institut de Recherche pour le Développement (IRD), Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille University, Marseille, France.
  • Tola R; IHU Méditerranée Infection, Marseille, France.
  • Bedotto M; IHU Méditerranée Infection, Marseille, France.
  • Delorme L; Institut de Recherche pour le Développement (IRD), Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille University, Marseille, France.
  • Bader W; French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte Marthe, Marseille, France.
  • Levasseur A; IHU Méditerranée Infection, Marseille, France.
  • Lagier JC; Centre national de la recherche scientifique (CNRS), Marseille, France.
  • Million M; Département de Microbiologie, Institut Pasteur, Paris, France.
  • Yahi N; Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
  • Fantini J; IHU Méditerranée Infection, Marseille, France.
  • La Scola B; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
  • Fournier PE; IHU Méditerranée Infection, Marseille, France.
  • Raoult D; IHU Méditerranée Infection, Marseille, France.
J Med Virol ; 2022 Aug 28.
Article in English | MEDLINE | ID: covidwho-2229042
ABSTRACT
The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Variants Language: English Year: 2022 Document Type: Article Affiliation country: Jmv.28102

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Variants Language: English Year: 2022 Document Type: Article Affiliation country: Jmv.28102