One year of SARS-CoV-2 circulation in the Nouvelle-Aquitaine region, February 2021-2022, France

Abstract

Background: Since 2021, 3 variants of concern (VOC) have spread to France, causing successive epidemic waves.

Objectives: To describe the features of Alpha, Delta and Omicron VOC circulation in the Nouvelle-Aquitaine region, France, between February 2021 and February 2022.

Study design: Data from the three university hospitals (UH) of Nouvelle-Aquitaine were used to describe regional SARS-CoV-2 circulation (RT-PCR positive rates and identified VOC) as well as its consequences (total number of hospitalizations and admissions in intensive care unit). They were analyzed according to the predominant variant and compared with national data.

Results: A total of 611,106 SARS-CoV-2 RT-PCR tests were performed in the 3 Nouvelle-Aquitaine UH during the study period. The 37,750 positive samples were analyzed by variant-specific RT-PCR or whole-genome sequencing. In 2021, Alpha VOC was detected from week 5 until week 35. Delta became the most prevalent variant (77.3%) in week 26, reaching 100% in week 35. It was replaced by Omicron, which was initially detected week 48, represented 77% of positive samples in week 52 and was still predominant in February 2022. The RT-PCR positive rates were 4.3, 4.2, and 21.9% during the Alpha, Delta and Omicron waves, respectively. The ratio between intensive care unit admissions and total hospitalizations was lower during the Omicron wave than during the two previous waves due to the Alpha and Delta variants.

Conclusion: This study highlighted the need for strong regional cooperation to achieve effective SARS-CoV-2 epidemiological surveillance, in close association with the public health authorities.

Keywords: France; Nouvelle-Aquitaine; SARS-CoV-2; epidemiological survey; variant.

Figure 1

Percentage of VOCs detected for each hospital and cumulative data between W5/2021 and W4/2022. The VOCs were determined either by PCR detection of specific mutations harbored by VOCs (del69-70, N501Y, E484K/Q, L452R) or by sequencing. For Limoges Hospital, data were not available at Week 26.

Figure 2

Number of PCR tests analyzed (grey) and percentage of SARS-CoV-2 positive PCRs (red) for each hospital and cumulative data between W5/2021 and W4/2022. The vertical dashed lanes separate the 3 VOCs-induced epidemics waves (i.e. when a VOC is dominant).

Figure 3

Total Number of hospitalized patients and ICU hospitalized patients between W5/2021 and W4/2022 for each hospital and cumulative data. The vertical dashed lanes separate the 3 VOCs induced epidemics waves (i.e. when a VOC is dominant).