High Throughput Diagnostics and Dynamic Risk Assessment of Variants of Concern

Background: The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies, in support of public health control. Early detection and evaluation of their risk of spreading within the population is pivotal. Methods: Between April 2020 and February 2021, the Lighthouse Laboratory at Alderley Park Network tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2. The PCR assay used, targets three genomic regions of the virus N, Orf1ab and S. Whole genome next-generation sequencing was used to confirm PCR positive results. Positive sample results were mapped to postal code origin of samples to allow real-time tracking of the spread of the 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 had risen to comprise 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 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 for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital especially when a variant is associated with enhanced transmission, as has occurred with VOC 202012/01. Funding Statement: The Lighthouse laboratory network was generated using funding from DHSC. Declaration of Interests: None to declare. Ethics Approval Statement: The manuscript was reviewed by the Head of Approvals Support, NHS Health Research Authority (HRA-NHS, UK), who confirmed that the study, which used unlinked and anonymised data was health surveillance and did not require NHS Research ethics review.