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

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

doi:10.3389/fmicb.2021.786233

Abstract

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.

Highlights

Following its emergence in December 2019 in Wuhan, China, SARS-CoV-2 was declared to be a pandemic in March 2020 and its incidence since has shown different epidemic patterns according to the country1,2 (Cucinotta and Vanelli, 2020)
We describe our classification and naming system of SARS-CoV-2 lineages and the history and characteristics of the major lineages detected among patients diagnosed at our institute, which sharply highlights the role of travel and globalization in the current pandemic
The incidence of SARS-CoV-2-associated deaths evolved elsewhere with multiple epidemic patterns according to time and geographic location

Summary

Introduction

Following its emergence in December 2019 in Wuhan, China, SARS-CoV-2 was declared to be a pandemic in March 2020 and its incidence since has shown different epidemic patterns according to the country (Cucinotta and Vanelli, 2020). In Marseille, France, after a first epidemic period characterized by a bellshaped curve of incidence followed by a period of almost zero incidence in May and June 2020, an epidemic burst of SARSCoV-2 cases occurred in July As this differed from the single bell-shaped curve typically observed for most respiratory viral infections, we suspected this corresponded to the introduction of new SARS-CoV-2 genotypes. In the summer of 2020 we expanded our assessment of viral genetic diversity using genome next-generation sequencing This allowed us to detect and report as early as 7 September 2020 several SARS-CoV2 lineages that occurred concurrently or successively, and were associated with different genetic, epidemiological and clinical features (Colson et al, 2020b, 2021c; Fournier et al, 2021)

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