SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time

Abstract

Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants.

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022

“…P681H was the dominant heterogeneous SNP observed during the tail-end of the 3 rd COVID-19 wave, but sequencing confirmed that this position had the wild type or mutant at position 681, but not both. Amino acid mutations that usually occur adjacent to each other in the SARS-CoV-2 genome, including P681H and P681R, make genotyping analysis challenging since the probes in the assay for one mutation failed to bind to viral sequence with the adjacent mutations [ 25 ]. Mutations at this position appear as mixed (wild type/mutant) and moved away from wild type/wild type or mutant/mutant assignment as a result of weak amplification due to non-specific probe activity was evident.…”

Building-Level Detection Threshold of SARS-CoV-2 in Wastewater

“…RNA from samples collected and stored at −80°C between January 2021 and April 2021 was reanalyzed for presence of the B.1.1.7 α variant. For PCR testing, we used primers specific for either the wild-type sequence of SARS-CoV-2 or the Δ69/Δ70 spike protein deletion as packaged in the S.delH69V70 TaqMan SARS-CoV-2 mutation panel assay (Thermo Fisher Scientific, Waltham, MA) ( 26 ). We used 0.5 μL of the 40× stock solution per 20-μL reaction mixture in our adaptation of the CDC PCR assay ( 25 ).…”

Multicenter Diagnostic Evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among Symptomatic Individuals in Brazil and the United Kingdom

“…The RT-qPCR mixture was prepared, and samples were tested for the presence of each S-gene mutation. The mutation panel was customized to detect each variant as follows: Alpha (P681H[+], E484K[−], K417N[−], L452R[−], T20N[−], P681R[−], L452Q[−]), Beta (E484K[+], K417N[+], P681H[−], L452R[−], T20N[−], P681R[−], L452Q[−]), Gamma (E484K[+], T20N[+], K417N[−], L452R[−], P681H[−], P681R[−], L452Q[−]), Delta and Kappa (L452R[+], P681R[+], E484K[−], K417N[−], T20N[−], P681H[−], L452Q[−]), Zeta (E484K[+], K417N[−], L452R[−], T20N[−], P681H[−], P681R[−], L452Q[−]), and Lambda (L452Q[+], E484K[−], K417N[−], P681H[−], L452R[−], T20N[−], P681R[−]) ( 28 – 30 ). Data were analyzed by QuantStudio design and analysis software v2.5.1.…”