Emerging SARS-CoV-2 Genotypes Show Different Replication Patterns in Human Pulmonary and Intestinal Epithelial Cells

Gabriel Augusto Pires de Souza (1, 2) , Marion Le Bideau (2) , Celine Boschi (1, 2) , Lorène Ferreira (1, 2) , Nathalie Wurtz (1, 2) , Christian Devaux (1, 2, 3) , Philippe Colson (1, 2) , Bernard La Scola (1, 2)

1 MEPHI - Microbes évolution phylogénie et infections
2 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
3 CNRS - Centre National de la Recherche Scientifique

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) quickly spread worldwide following its emergence in Wuhan, China, and hit pandemic levels. Its tremendous incidence favoured the emergence of viral variants. The current genome diversity of SARS-CoV-2 has a clear impact on epidemiology and clinical practice, especially regarding transmission rates and the effectiveness of vaccines. In this study, we evaluated the replication of different SARS-CoV-2 isolates representing different virus genotypes which have been isolated throughout the pandemic. We used three distinct cell lines, including Vero E6 cells originating from monkeys; Caco-2 cells, an intestinal epithelium cell line originating from humans; and Calu-3 cells, a pulmonary epithelium cell line also originating from humans. We used RT-qPCR to replicate different SARS-CoV-2 genotypes by quantifying the virus released in the culture supernatant of infected cells. We found that the different viral isolates replicate similarly in Caco-2 cells, but show very different replicative capacities in Calu-3 cells. This was especially highlighted for the lineages B.1.1.7, B.1.351 and P.1, which are considered to be variants of concern. These results underscore the importance of the evaluation and characterisation of each SARS-CoV-2 isolate in order to establish the replication patterns before performing tests, and of the consideration of the ideal SARS-CoV-2 genotype–cell type pair for each assay.

Mots clés: SARS-CoV-2; COVID-19; viral culture; isolate; genotype; variants; Vero E6 cells; Caco-2 cells; Calu-3 cells

Domaines: Bactériologie; Cardiologie et système cardiovasculaire; Maladies émergentes; Maladies infectieuses; Parasitologie; Virologie

Gabriel Augusto Pires de Souza, Marion Le Bideau, Celine Boschi, Lorène Ferreira, Nathalie Wurtz, et al.. Emerging SARS-CoV-2 Genotypes Show Different Replication Patterns in Human Pulmonary and Intestinal Epithelial Cells. Viruses, 2022, 14 (1), pp.23. ⟨10.3390/v14010023⟩. ⟨hal-03663691⟩