Researchers propose new SNP-PCR for subtyping SARS-CoV-2 and its variants

CITF-funded researchers have published a short letter in Clinical Microbiology and Infection proposing a complementary approach, known as SNP-PCR, as a front-line diagnostic approach. SNP-PCR is based on the detection of minor targeted genomic variations among SARS-CoV-2 variants (also known as single nucleotide polymorphisms). This technology can be easily implemented and rolled out to rapidly detect and respond to the emergence of new variants across Canada. The study was conducted by Dr. Marc Romney in collaboration with Dr. Christopher Lowe and Dr. Nancy Matic (all University of British Columbia [UBC]).

Key findings:

• Single nucleotide polymorphisms–polymerase chain reaction (SNP-PCR) is complementary to whole-genome sequencing (WGS). While WGS involves reading the entire viral genome to identify a viral variant, SNP-PCR specifically targets variants via the amplification and detection of specific known mutations within the viral genome.
• Teams at UBC have been using SNP-PCR to subtype PCR-positive samples and have been validating their results with WGS since January 2021. The SNP-PCR algorithm used to classify viral variants has been constantly updated to incorporate new mutations that are reflected in the latest variants of concern (VOCs), such as Omicron XBB, XBB1.5, and B.Q.1.1.
• Researchers have validated their SNP-PCR with whole genome sequencing and demonstrated excellent concordance:
  • In September 2022, the percent agreement between SNP-PCR and WGS was 100% in detecting tested variants (20/20 (100%) BA.1 samples, 26/26 (100%) BA.2 samples, 7/7 (100%) BA.4 samples, and 20/20 (100%) BA.5 samples).
  • As the pandemic evolved, the research team updated their SNP-PCR algorithm in March 2023 and re-validated SNP-PCR with WGS, finding a high degree of consistency: 26/26 (100%) B.Q.1/B.Q.1.1 samples, 1/1 (100%) XBB sample, and 33/38 (86.8%) XBB.1.5 samples. The discordance in the 5 XBB.1.5 samples was confirmed by WGS to be due to uncommon strains outside the assay algorithm used to determine the variant identification.
• SNP-PCR is a single-well, multiplex PCR method allowing the detection of multiple variants in a single test (the authors have tested up to 7 variants). SNP-PCR presents other advantages such as high accuracy, flexibility, and scalability for SARS-CoV-2 subtyping. It can also be potentially used for the detection of variants in samples with low PCR cycle thresholds (extremely low numbers of viral copies), which may pose problems for WGS.
• Non-definitive SNP-PCR results may be indicative of uncommon strains which can then be identified and prioritized for WGS.

As SARS-CoV-2 evolves, it is important to utilize adaptive laboratory methodologies that can efficiently identify and characterize viral variants as an early detection strategy for emerging VOCs. SNP-PCR demonstrates a cost-effective, flexible, and scalable approach that can be followed by diagnostic laboratories across Canada for SARS-CoV-2 surveillance and clinical management.