PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern

Abstract

With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses1–3, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa6 and P.1 (also 501Y.V3) recently detected in Brazil7. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern8. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.

Performance of vaccination with CoronaVac in a cohort of healthcare workers (HCW) - preliminary report

“…Part of the positive samples was evaluated for the presence of SARS-CoV-2 variants of concerns (VOC) using a screening protocol [8] that detects the deletion in the NSP6 gene that is common for the P1, B.1.1.7, and B.1.351 lineages. The samples were also studied using a protocol [9] that is able to distinguish B1.1.7 from P1 and B 1.351 lineages.…”

SARS-CoV-2 variants, spike mutations and immune escape

“…For example, viruses of lineage B.1.525, which has been observed in several countries, albeit at low frequency to date, have NTD deletions ΔH69–V70 and ΔY144 in common with viruses of the B.1.1.7 lineage; E484K in common with the B.1.351 and P.1 lineages; and spike amino acid substitutions Q52R, Q677H and F888L 73 . Repeated amino acid substitutions at position 677 and the independent emergence of Q677H in several lineages in the USA provides strong evidence of adaptation, potentially through an effect of this mutation on the proximal polybasic furin cleavage site, although further experiments are required to determine its impact 74 . Other novel variants have been identified spreading in California and New York, USA (B.1.427 and B.1.429, and B.1.526, respectively).…”

Immunogenicity and safety of an inactivated virus vaccine against SARS-CoV-2 in patients with autoimmune rheumatic diseases

“…Participants with positive samples collected at our hospital were further analyzed for variants of concern using the previously described protocol 53 , including the deletion in the NSP6 gene that is observed in the P1, B.1.1.7, and B.1.351 lineages. Distinction of B1.1.7 from P1 and B 1.351 lineages was performed as described 54 .…”