Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022

Mircea Sofonea (1) , Bénédicte Roquebert (2) , Vincent Foulongne (3, 4) , David Morquin (5, 6) , Laura Verdurme (2) , Sabine Trombert-Paolantoni (2) , Mathilde Roussel (7, 2) , Jean-Christophe Bonetti (2) , Judith Zerah (2) , Stéphanie Haim-Boukobza (2) , Samuel Alizon (8)

1 MIVEGEC - Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle
2 Laboratoire CERBA [Saint Ouen l'Aumône]
3 PCCEI - Pathogenesis and Control of Chronic and Emerging Infections
4 Etablissement français du don du sang [Montpellier]
5 UM - Université de Monastir - University of Monastir
6 CHRU Montpellier - Centre Hospitalier Régional Universitaire [Montpellier]
7 UP8 - Université Paris 8 Vincennes-Saint-Denis
8 CIRB - Centre interdisciplinaire de recherche en biologie

We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021–February 28, 2022. Results showed the estimated growth advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%–114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%–52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.

Mots clés: BA.1; BA.2; COVID-19; France; Omicron; PCR; SARS-CoV-2; Coronavirus disease; Epidemiology; Genomics; Mass screening; Mutation; Respiratory infections; Severe acute respiratory syndrome coronavirus 2; Vaccine-preventable diseases; Variants; Viruses; Zoonoses

Domaines: Modélisation et simulation; Biodiversité et Ecologie; Santé publique et épidémiologie; Bio-Informatique, Biologie Systémique [q-bio.QM]; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie; Ecosystèmes; Interactions entre organismes; Santé; Génétique des populations [q-bio.PE]; Virologie

Mircea Sofonea, Bénédicte Roquebert, Vincent Foulongne, David Morquin, Laura Verdurme, et al.. Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022. Emerging Infectious Diseases, 2022, 28 (7), pp.1355-1365. ⟨10.3201/eid2807.220033⟩. ⟨hal-03714983⟩