Molecular detection of SARS‐CoV‐2 strains and differentiation of Delta variant strains

• DOI: 10.1111/tbed.14443
• Publication Date: 2021-12-29T12:51:23Z
• Authors: Vaughn Hamill; Lance Noll; Nanyan Lu; Wai Ning Tiffany ...; Elizabeth Poulsen...; Mark Gray; Tesfaalem Sebhatu; Kyle Goerl; Susan Brown; Rachel Palinski; Sasha Thomason; Kelli Almes; Jamie Retallick; Jianfa Bai
• Keywords: 0301 basic medicine; 03 medical and health sciences; SARS-CoV-2; Animals; COVID-19; Humans; RNA, Viral; Amino Acids; Pandemics; 3. Good health

The Delta variant of SARS-CoV-2 has now become the predominant strain in global COVID-19 pandemic. Strain coverage some detection assays developed during early pandemic stages declined due to periodic mutations viral genome. We have a real-time RT-PCR (RT-qPCR) for that provides nearly 100% coverage, and differentiation highly transmissible strains. All full or (≥28 kb) genomes (n = 403,812), including 6422 280 Omicron strains, were collected from public databases at time analysis used assay design. two amino acid deletions spike gene (S-gene, Δ156-157) is characteristic targeted Although was very high (99.7%), non-Delta wild-type strains 93.9%, mainly confined region To increase assay, design CDC N1 target added assay. In silico 403,812 indicated 95.4% target, however, combination with our new S-gene total increased 99.8%. A human 18S rRNA also analyzed as an internal control. final four-plex RT-qPCR generated PCR amplification efficiencies between 102.0% correlation coefficients (R2 ) >0.99 cloned positive controls; clinical samples 93.4%-97.0% R2 > 0.99. detects 98.6% sequences. Assay primers probes no match other closely related coronaviruses, did not produce signal selected animal coronaviruses. Genotypes identified by confirmed Sanger sequencing.