Frontiers in Microbiology (Feb 2022)

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

  • Philippe Colson,
  • Philippe Colson,
  • Philippe Colson,
  • Pierre-Edouard Fournier,
  • Pierre-Edouard Fournier,
  • Pierre-Edouard Fournier,
  • Hervé Chaudet,
  • Hervé Chaudet,
  • Hervé Chaudet,
  • Jérémy Delerce,
  • Audrey Giraud-Gatineau,
  • Audrey Giraud-Gatineau,
  • Audrey Giraud-Gatineau,
  • Audrey Giraud-Gatineau,
  • Linda Houhamdi,
  • Claudia Andrieu,
  • Ludivine Brechard,
  • Marielle Bedotto,
  • Elsa Prudent,
  • Céline Gazin,
  • Mamadou Beye,
  • Emilie Burel,
  • Pierre Dudouet,
  • Pierre Dudouet,
  • Pierre Dudouet,
  • Hervé Tissot-Dupont,
  • Hervé Tissot-Dupont,
  • Hervé Tissot-Dupont,
  • Philippe Gautret,
  • Philippe Gautret,
  • Philippe Gautret,
  • Jean-Christophe Lagier,
  • Jean-Christophe Lagier,
  • Jean-Christophe Lagier,
  • Matthieu Million,
  • Matthieu Million,
  • Matthieu Million,
  • Philippe Brouqui,
  • Philippe Brouqui,
  • Philippe Brouqui,
  • Philippe Parola,
  • Philippe Parola,
  • Philippe Parola,
  • Florence Fenollar,
  • Florence Fenollar,
  • Florence Fenollar,
  • Michel Drancourt,
  • Michel Drancourt,
  • Michel Drancourt,
  • Bernard La Scola,
  • Bernard La Scola,
  • Bernard La Scola,
  • Anthony Levasseur,
  • Anthony Levasseur,
  • Anthony Levasseur,
  • Didier Raoult,
  • Didier Raoult,
  • Didier Raoult

DOI
https://doi.org/10.3389/fmicb.2021.786233
Journal volume & issue
Vol. 12

Abstract

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After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

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