Abstract
BackgroundThe 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.MethodsBetween 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.FindingsIn 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.InterpretationThe 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.
Highlights
The numerous novel lineages of SARS-CoV-2 detected worldwide have mobilised global molecular surveillance actions [1À7]
At the end of 2020, the proportion of positive specimens tested in England using the ThermoFisher TaqPathTM COVID-19 assay with failure of S-gene target detection increased rapidly, rising to more than 70% of positive test results detected within the Alderley Park (AP) facility by the beginning of January 2021 (Fig. 1, five-day rolling rate)
Given that the sample distribution was richer in local (North West England) than distal sites, the spread at high infection rates that we observed at distal sites (e.g., London, see Table 2) was slightly underestimated rather than exaggerated
Summary
The numerous novel lineages of SARS-CoV-2 detected worldwide have mobilised global molecular surveillance actions [1À7]. The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies to support public health control. 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. 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. Coupling high-throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant.
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