New PCR Test Can Identify All COVID-19 Variants in a Positive Patient Sample
upstart writes:
New PCR Test Can Identify All COVID-19 Variants in a Positive Patient Sample:
[...] Identifying specific strains reveals important information such as the length of incubation period, length of contagious period, transmissibility, pathogenicity, and even changes in the predominant symptoms.
Information on strain types is generally reported by the international community or a few states with large populations that perform genetic sequencing. The deep sequencing needed to identify SARS-CoV-2 strains is accurate and can identify each mutation present in a sample, but it is costly, slow and requires specialized equipment. Yet knowledge of the strain type provides important information for public health professionals, policymakers, and individuals.
[...] Using real-time PCR probes designed by Rutgers University and already used around the world for many purposes, Rutgers designed the Rutgers-RP RT-PCR assay to detect mutations in SARS-CoV-2 that have been shown to increase immune escape, avoid neutralization, and increase transmissibility. They pioneered the use of molecular beacons to identify specific genetic mutations. Molecular beacons are hairpin-shaped molecules that can be designed to selectively bind to a specific mutant sequence, avoiding wild-type sequences that often differ by a single nucleotide.
Nine mutations were selected for testing, and the beacon for each has differently colored dyes. Every original variant of concern - alpha, beta, gamma, delta, and omicron - has a unique combination of these mutations. and when the beacon binds to its target molecule, its distinct color can be detected by the assay.
Journal Reference: "Multiplex PCR Assays for Identifying all Major Severe Acute Respiratory Syndrome Coronavirus 2 Variants" by Ryan J. Dikdan, Salvatore A.E. Marras, Amanda P. Field, Alicia Brownlee, Alexander Cironi, D. Ashley Hill and Sanjay Tyagi, 1 February 2022, Journal of Molecular Diagnostics.
DOI: 10.1016/j.jmoldx.2022.01.004
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