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

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.

Keywords: SARS-CoV-2; classification; epidemics; mutant; pandemics; travel; variant; zoonosis.

FIGURE 1

Patterns of incidence curves of SARS-CoV-2-associated deaths according to countries. (A) Hierarchical clustering of incidence curves of SARS-CoV-2-associated deaths per country. (B) Major patterns of incidence curves of SARS-CoV-2-associated deaths defined based on hierarchical clustering, and the example of one country for each pattern. Patterns of incidence curves of SARS-CoV-2-associated deaths are shown in 10 panels numbered from 1 to 10; these numbers correspond to those from the cladogram of panel (A). The example of one country is shown in a panel at the right of each of the ten patterns. X-axis indicates time in numbers of days, and Y-axis indicates normalized daily deaths. (C) Worldwide distribution of the 10 major patterns of incidence curves of SARS-CoV-2-associated deaths defined based on hierarchical clustering. Colors are as used for panel (A).

FIGURE 2

Chronological distribution of SARS-CoV-2 diagnoses by qPCR at IHU Méditerranée Infection institute (A), and of mean (± standard deviation) numbers of mutations in SARS-CoV-2 genomes obtained from patients sampled per month (B). (A) Chronological distribution of SARS-CoV-2 diagnoses is the mean number of diagnoses by qPCR per sliding windows of 7 days and steps of 1 day. (B) Numbers of mutations in SARS-CoV-2 genomes were calculated in reference to the genome of the Wuhan-Hu-1 isolate (GenBank Accession no. NC_045512.2). Whiskers indicate 10–90 percentiles. *p < 10^–1; ***p < 10^–3.

FIGURE 3

Chronological distribution of mean (± standard deviation) pairwise genetic distances according to time periods for SARS-CoV-2 genomes obtained from patients SARS-CoV-2-diagnosed at IHU Méditerranée Infection, Marseille. ***p < 10^–3.

FIGURE 4

Phylogenetic tree of 10,773 genomic sequences of SARS-CoV-2 obtained from patients SARS-CoV-2-diagnosed at IHU Méditerranée Infection, Marseille, France. Phylogeny reconstruction was performed using the nextstrain/ncov tool (https://github.com/nextstrain/ncov) then visualized with Auspice (https://docs.nextstrain.org/projects/auspice/en/stable/). The genome of the original Wuhan-Hu-1 coronavirus isolate (GenBank accession no. NC_045512.2) was added as outgroup. Major (most prevalent) variants are labeled. Marseille variants or WHO clades, and Pangolin, or Nextstrain clades are indicated. X-axis shows the number of mutations compared to the genome of the Wuhan-Hu-1 isolate (GenBank accession no. NC_045512.2).

FIGURE 5

Three-dimensional plot of weekly proportions accounted by each SARS-CoV-2 variants among patients SARS-CoV-2-diagnosed at IHU Méditerranée Infection institute. See also IHU Méditerranée Infection (2021a; https://doi.org/10.35081/ffd4-1y77).

FIGURE 6

Weekly incidence of each SARS-CoV-2 mutants and variants extrapolated to the total number of cases, based on their proportions of genotyped cases, among patients SARS-CoV-2-diagnosed at IHU Méditerranée Infection institute.

FIGURE 7

Demonstrated or likely sources and origins of SARS-CoV-2 mutants or variants detected among patients SARS-CoV-2-diagnosed in our institute. See also IHU Méditerranée Infection (2021b; https://doi.org/10.35081/nz2g-f980).