Genomic Characteristics and Clinical Impact of the Emergent SARS-CoV-2 B.1.1.7 Lineage in North Central London, November to December 2020

Background: Emergence of variants with specific mutations in key epitopes in the spike protein of SARS-CoV-2 raise concerns pertinent to the current mass vaccination campaigns and use of monoclonal antibodies. We describe emergence of the variant of concern (VOC) B.1.1.7 in two North Central London (NCL) hospitals including virological characteristics and clinical severity in contemporaneous patients with and without the new variant. The strength of our study is the depth and granularity of clinical data. Methods: SARS-CoV-2 PCR positive samples collected from 9th November 2020 for patients acutely admitted to one of 2 NCL hospitals on or before 20th December 2020 were sequenced and analysed for the presence of VOC-defining mutations. We compared illness severity in those with variant of concern (VOC) and non-VOC infections and conducted supplementary genomic analyses in a cohort of chronically shedding immunocompromised/treated patients. Viral loads were compared by Ct value and sequencing read-depth. Findings: Of 341 successfully sequenced patients, 198 (58%) had VOC infections. There was no evidence of an association with severe disease by lineage (VOC vs non-VOC) in unadjusted analyses (PR 0.97, 95% CI 0.72-1.31), or analyses adjusted for sex, age, comorbidities and ethnicity (aPR 1.07, 95% CI 0.79-1.43). We detected no VOC-defining mutations in immunocompromised/treated patients; viral loads were higher in VOC samples. Interpretation: Despite emerging evidence of increased transmissibility of the VOC, we did not identify an association with severe disease, suggesting the surge in hospitalisations was more likely related to a significant increase in cases overall rather than virus characteristics. Funding Statement: UCLH APDU receives funding from the University College London Hospitals NHS Trust. DF was funded by the i-sense EPSRC IRC in Agile Early Warning Sensing Systems for Infectious Diseases and Antimicrobial Resistance (EP/R00529X/1). Declaration of Interests: We declare no competing interests. Ethics Approval Statement: The clinical information and SARS-CoV-2 PCR samples were collected as part of routine clinical care. Data were extracted and analysed using permission granted by the NHS REC (IRAS:284088, REC reference:20/HRA/2505).