Epidemiological Investigation of New SARS-CoV-2 Variant of Concern 202012/01 in England

Abstract

Lighthouse Labs network tests for the presence of RNA of SARS-CoV-2, the causative agent of COVID-19. The Thermofisher TaqPath assay targets three regions of SARS-CoV-2; ORF1ab, N and S-genes. The assay identified a drop in S-gene target detection among positive samples due to the circulation of a new SARS-CoV-2 Variant of Concern (VOC) designated as 202012/01. By end of December 2020, 60% of daily positive test results at Alderley Park Lighthouse Labs, were linked to the new Variant of Concern. This timeline view identifies the rapid spread of the variant across the country.

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes

“…Previous work suggests that these factors will play a central role in shaping the future dynamics of COVID-19 cases (13). Future cases also create an environment for the selection of novel variants [e.g., (14)(15)(16)]. Of particular concern is the possibility of antigenic drift [e.g., for influenza (17) and for the seasonal human coronavirus 229E (18)] via immune escape from natural or vaccinal immunity.…”

Neutralising antibody escape of SARS‐CoV‐2 spike protein: Risk assessment for antibody‐based Covid‐19 therapeutics and vaccines

“…Δ H 69/Δ V 70 diminishes protrusion of the 69–76 loop, increasing Spike‐mediated infectivity by approximately twofold. Interestingly for screening purposes, the deletion causes false negativity in the Spike target (so called S‐dropout variant or S‐gene target failures [SGTF]) of a 3‐target TaqPath® RT‐PCR COVID19 assay (Thermo Fisher Scientific), 71–73 and is associated with higher viral loads 74 . While this lone mutation exists, it is commonly seen in association with the different RBD mutations N439K, Y453F and N501Y (separately discussed below) 36 .…”

The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies

“…ΔH69/ΔV70 diminishes protrusion of the 69-76 loop, increasing Spike-mediated infectivity by 2 folds. Interestingly for screening purposes, the deletion causes false negativity in the Spike target (so called S-dropout variant or S-gene target failures (SGTF)) of a 3-target TaqPath® RT-PCR COVID19 assay (Thermo Fischer Scientific) ( Bal et al, 2020 , Gravagnuolo et al, 2021 , Washington et al, 2020 ). The deletion can also be detected as a positive signal using a pair of molecular beacons paired with loop mediated isothermal amplification (LAMP) ( Sherrill-Mix et al, 2021 ).…”