Alliance for Pandemic Preparedness

May 11, 2021

A New SARS-CoV-2 Variant Poorly Detected by RT-PCR on Nasopharyngeal Samples with High Lethality

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  • [Pre-print, not peer-reviewed] Patients confirmed by viral sequencing to be infected with a novel SARS-CoV-2 variant first described in France (assigned lineage B.1.616) (n=34) were less likely to test positive on their first PCR test (15% vs 97%) and more likely to die within 28 days (44% vs 16%) compared to patients infected with variants of concern (VOC) B.1.1.7 and B.1.351. The B.1.616 variant was also associated with severe disease (HR=4.2) independent of baseline characteristics and comorbidities compared to other VOCs. Additionally, during the study period from January to March 2021, 32 nosocomial infections associated with the B.1.616 variant were identified among 108 exposed patients corresponding to an incidence of 41 cases per 1,000-patient days. The B.1.616 is characterized by 9 amino acid changes and one deletion in the S protein, with other mutations in structural and non-structural proteins relative to the parent strain from Wuhan. Notably, it possesses the amino acid substitution V483A in the receptor binding domain, close to the E484K change which is linked to reduced neutralization.

Fillatre et al. (May 10, 2021). A New SARS-CoV-2 Variant Poorly Detected by RT-PCR on Nasopharyngeal Samples with High Lethality. Pre-print downloaded May 11 from https://doi.org/10.1101/2021.05.05.21256690