B.1.1.7 / V1 is currently the source of the majority of infections in Europe and North America, while B.1.351 / V2 is dominant in South Africa. The V3 variant of the P.1 line has become dominant in Brazil and South America. These variants are classified as variants of concern (VOCs).
According to the Centers for Disease Control and Prevention (CDC), a variant of concern is a variant for which there is evidence of increased transmissibility, more serious illness (for example, increased hospitalizations or deaths) , a significant reduction in neutralization by antibodies generated during a previous infection or vaccination, reduced efficacy of treatments or vaccines, or diagnostic detection failures ”.
Since January 2021, the national guideline is to test all positive samples in France with additional reverse transcription by real-time polymerase chain reaction (RT-PCR), for an early assessment of the diffusion and possible expansion of the SARS-CoV-2 line. This will help detect the rapid spread of the SARS-CoV-2 variant. More specifically, since April 2021, laboratories have been advised to test RT-PCRs specific to variants targeting the N501Y and E484K mutations.
In this study, the researchers analyzed 36,590 variant-specific RT-PCR tests performed on samples taken between April 12 and May 7, 2021, in 13 French regions. The data included individuals aged 5 to 80 years.
“17.3% of the tests could not be interpreted, due to a Ct value too high to keep an equal sensitivity for the N501Y and E484K targets, and were withdrawn from the analysis,” the researchers added. . Therefore, to avoid biasing the screening for variants, they skipped all tests with cycle cutoff (Ct) values greater than 30.
They found that unlike January to March 2021, the V2 variant had a significant transmission advantage over V1 in some regions (15.1 to 16.1% in Île-de-France and 16.1 to 18.8% in Hauts -of France).
Because the specificity of the variant-specific RT-PCR used in this study only targeted 2 mutations and was therefore limited, the researchers probed the sequencing profiles for additional information. They sequenced all the samples taken on March 30 and found 79.1% of the viruses of the B.1.1.7 / V1 line, in the 478 samples. They found that the other prevalent lineages were B.1.351 / V2 (7.9%), B.1.525 (4.4%) and B.1.214 (2.3%), and the remainder accounted for less than 2% of samples (P. 1 / V3 line being less than 1%).
In this study, the researchers noted that samples with only the N501Y mutation are treated as V1, samples with both mutations as V2, samples with only the E484K mutation as B.1.525, and samples without the mutation as wild types ( B.1.214 being rare).
While the researchers found that older patients were more infected with V1 than with V2 or B.1.525, in hospital settings V2 was overrepresented compared to V1.
In region-specific trends, they analyzed that infection with a wild type or B.1.525 / V2 virus was less likely than with V1. Conversely, in Île-de-France, and to a lesser extent in Hauts-de-France and Nouvelle-Aquitaine, the researchers found that the risk of being infected with V2 instead of V1 increases significantly over time. The V2 variant is said to have immune evasion properties.
Thus, Île-de-France being one of the French regions most affected to date by the epidemic, it makes sense that we detect the shift in the advantage of transmission because the proportion of natural immune individuals is high there.
As vaccination is added to the favorable selection of immune escape mutants, the researchers are asking for a more detailed analysis to understand the link between the transmission advantage of the V2 variant and the proportion of the population immunized in the different French regions.
Notably, most of the tests analyzed in this study are performed in a declining epidemic (during the third national lockdown). However, the researchers believe, “It is unlikely that the lockdown in itself would affect the transmission of variants differently. “
Given the high incidence of COVID-19 in France and the uncertainties surrounding the lifting of the lockdown, these results call for special attention to avoid a new epidemic wave in the country, the researchers write.
medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behavior, or be treated as established information.