SARS-CoV-2 variant identification and detection

Detect the presence and manage the impact of SARS-CoV-2 variants

Worrisome variants of SARS-CoV-2 have challenged health systems to add a new dimension to pandemic preparedness: genomic surveillance. Widespread, standardised efforts to screen for and sequence SARS-CoV-2 samples will enable fast, efficient identification and management of viral mutations.

 

SARS-CoV-2 is an RNA virus, which tends to have high mutation rates.1 These viral mutations, or variants, may influence viral characteristics such as pathogenicity, transmission rate, host range and more. As such, it is critical that we continue to closely monitor the emergence of these variants as well as track the known, dangerous mutations.

 

As labs prepare to add genomic surveillance to SARS-CoV-2 diagnostic workflows, it is important to understand the two basic methods to detect and identify known or novel SARS-CoV-2 variants:

RT-PCR WGS
Probe-based Reverse Transcription PCR (RT-PCR) genotyping
Confirm the presence of known variants

An RT-PCR-based assay can determine whether that viral sample contains the wild type or variant at that specific, previously identified location in the SARS-CoV-2 genome. This type of assay is comprised of:

Primers: Designed to the flanking regions of the known variation in the RNA genome sequence and used to amplify that target region from cDNA made from each viral RNA sample.

Fluorescently-labelled probe specific for wild type/reference SARS-CoV-2

Differentially-labelled fluorescent probe specific for known variant

 

Detect your desired variant with SARS-CoV-2 Variant ValuPanels™

Combine the gold-standard quenching power of the BHQ™ quencher with BHQplus™ probes engineered to provide the high-fidelity required for confident genotyping results. Our SARS-CoV-2 Variant ValuPanels consist of separately delivered probes and primers for qualitative detection of specific SARS-CoV-2 mutations by RT-PCR-based genotyping. For Research Use Only. Not for diagnostic procedures.

ValuPanel SARS-CoV-2 Mutation Variants containing specified SARS-CoV-2 mutation Availability
SARS-CoV-2 Variant ValuPanel [E484K] E484K B.1.351, B.1.1.28 (P.1) Coming soon
SARS-CoV-2 Variant ValuPanel [D614G] D614G B.1.1.7, B.1.351, B.1.1.28 (P.1)
SARS-CoV-2 Variant ValuPanel [N501Y] N501Y B.1.1.7, B.1.351, B.1.1.28 (P.1)
SARS-CoV-2 Variant ValuPanel [△H69/70V] △H69/70V B.1.1.7
SARS-CoV-2 Variant ValuPanel [L452R] L452R B.1.429 (CAL.20C)
SARS-CoV-2 Variant ValuPanel [K417N] K417N B.1.351
SARS-CoV-2 Variant ValuPanel [K417T] K417T B.1.1.28 (P.1)
Looking to add variant detection to your SARS-CoV-2 testing workflow?
Detect with confidence
Whole genome sequencing (WGS)
Identify novel variants and get the full picture

WGS converts the cDNA generated by reverse transcription of a viral RNA genome present in a sample to a sequenceable whole genome SARS-CoV-2 library (e.g. an Illumina-compatible library). In most cases, this method generates overlapping RT-PCR amplicons spanning the entire viral genome, which are converted into NGS library fragments. The key to this approach is to generate overlapping library fragments such that there are no gaps in the final viral genome sequence generated.

Drive your sequencing throughput with our service labs

Skip investing in sequencing instrumentation and necessary personnel, and get straight to reliable, actionable data. Our labs serve as an extension of yours when you outsource your WGS project to our global service teams. For Research Use Only. Not for diagnostic procedures. 

Identify the next COVID-19 variant
Starting is easy
A side-by-side comparison of the two methods

Specification

Probe-based RT-PCR genotyping

Whole genome sequencing

  • Variants detected

    Known only

    Known and UNKNOWN

  • Design requirements

    New design and testing for each new variant – slower

    None required once WGS method is established

  • Turnaround time/speed

    Fast

    Slow

  • Simplicity

    Standard, well-accepted method

    Greater expertise required

  • Cost

    +

    +++

  • Throughput

    High

    Low

1. Domingo E, Holland JJ. RNA virus mutations and fitness for survival. Annu Rev Microbiol. 1997;51:151-78. doi: 10.1146/annurev.micro.51.1.151. PMID: 9343347.