Abstract
To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April–7 May 2021 in France. In this period, contrarily to January–March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5–16.2) and Hauts-de-France (17.3%; 95% CI: 15.9–18.7) regions. This is consistent with VOC β’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.
Highlights
Since January 2021, the national guideline is to test all clinical samples that are positive for SARS-CoV-2 with an additional reverse-transcription (RT)-PCR to detect mutations indicative of certain variants [7,8]
Since April 2021, this variant-specific RT-PCR targets the N501Y mutation, which is shared by variants of concern (VOC) B.1.1.7, B.1.351 and P.1, and the E484K mutation, which is found in VOCs B.1.351 and P.1, as well as the variant of interest (VOI) B.1.525 (WHO: η; nextstrain clade: 20A/ S484K; GISAID clade/lineage: G/484K.V3) [1], but not in B.1.1.7
When analysing the results of variant-specific tests on samples obtained from January to March 2021, we found that the B.1.1.7’s (VOC α) transmission advantage relative to wild type lineages was larger than
Summary
This study has been approved by the Institutional Review Board of the CHU of Montpellier and is registered at ClinicalTrials.gov with identifier NCT04738331. The explanatory variables were the individual’s age (type of variable: integer), origin of the sample (hospital or community; Figure 1 Raw daily cumulative frequencies of variant-specific reverse-transcription PCR test results for SARS-CoV-2 in eight French regions, 12 April–7 May 2021 (n = 33,583)a. D Characterisation as B.1.525 lineage (VOI η) is based on the simultaneous absence of N501Y and presence of E484K mutation. E Characterisation as B.1.1.7 lineage (VOC α) is based on the simultaneous presence of N501Y and absence of E484K mutation. CI: confidence interval, NS: non-significant; VOC: variant of concern; VOI: variant of interest, RRR: relative risk ratios; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2. To investigate the temporal trends, we used the method described in [11] and, for each region of interest, fitted a logistic growth model to the fitted values of a generalised linear model (GLM) with three factors on the data sampled outside hospitals. In Nouvelle-Aquitaine, the logistic growth model was not significant, which could be due to the fact that this region was less affected by the third epidemic wave than the other two [13]
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