A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality (preprint)

ABSTRACT

Background: In early January 2021, an outbreak of nosocomial cases of COVID 19 emerged in Western France, with RT PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS CoV 2 lineage B.1.616. In March, WHO classified this variant as "under investigation" (VUI). We analyzed the characteristics and outcomes of COVID 19 cases related to this new variant. Methods: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled patients with at least one of the following i) positive SARS CoV 2 RT PCR on a respiratory sample; ii) seroconversion with anti SARS CoV 2 IgG/IgM; iii) suggestive symptoms and typical features of COVID 19 on chest CT scan. Cases were categorized as either i) B.1.616; ii) variant of concern (VOC); iii) unknown. Findings: From January 1st to March 24th, 2021, 114 patients fulfilled the inclusion criteria B.1.616 (n=34), VOC (n=32), and unknown (n=48). B.1.616 related cases were older than VOC related cases (81 years [73-88], vs 73 years [67-82], P<0.05) and their first RT PCR tests were less often positive (5/34, 15% vs 31/32, 97%, P<0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.2 [1.3 , 13.5], P=0.018), and increased lethality (logrank test P=0.01) 28day mortality 15/34 (44%) with B.1.616, vs. 5/32 (16%) for VOC, P=0.036. Interpretation: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT PCR on nasopharyngeal samples, with high lethality.