High throughput diagnostics and dynamic risk assessment of SARS-CoV-2 variants of concern

BACKGROUND: The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies to support public health control. Early detection and evaluation of their associated risk of spreading within the population are pivotal. METHODS: Between April 2020 and February 2021, the UK Lighthouse Labs Network at Alderley Park tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2, via PCR. The assay targeted three genomic regions of the virus: N, Orf1ab and S. Whole-genome next-generation sequencing was used to confirm positive PCR results. Positive results were mapped using the postal district origin of samples to allow real-time tracking of the spread of a new variant through the UK. FINDINGS: In mid-November 2020, the assay identified an increasing number of S gene negative, N and Orf1ab positive samples. Whole-genome sequencing demonstrated that the loss of S gene detection was due to the appearance of a SARS-CoV-2 lineage (B.1.1.7) designated as Variant of concern (VOC) 202012/01. By the beginning of January 2021, the new SARS-CoV-2 VOC comprised 70% of daily positive samples tested at Alderley Park and ∼98% by the end of February 2021. INTERPRETATION: The timeline view identified the rapid spread of the new SARS-CoV-2 variant across England during the first three weeks of December. Coupling high-throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant. The availability of real-time tracking of an emerging variant is an important new tool to inform decision-making authorities for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital, even more so when a variant is associated with the enhanced transmission, as has occurred with VOC 202012/01.