• New PCR test can identify all SARS-CoV-2

    From ScienceDaily@1:317/3 to All on Thu Mar 17 22:30:44 2022
    New PCR test can identify all SARS-CoV-2 variants in a positive patient
    sample

    Date:
    March 17, 2022
    Source:
    Elsevier
    Summary:
    As SARS-C0V-2 variants emerged, researchers developed a PCR test
    that uses molecular beacons not only to diagnose COVID-19 infection,
    but also to identify the specific variant causing that infection.



    FULL STORY ========================================================================== After the start of the SARS-C0V-2 pandemic, investigators from
    ResearchPath LLC and their collaborators at Rutgers University quickly dedicated resources to develop accurate and reliable COVID-19 testing. As variants emerged, they developed a PCR test that uses molecular beacons
    not only to diagnose COVID-19 infection, but also to identify the specific variant causing that infection.

    Their research appears in The Journal of Molecular Diagnostics, published
    by Elsevier. Their methodology is openly available so that it can be
    replicated by any facility that can run a PCR test.


    ==========================================================================
    "It is extraordinary to see that SARS-CoV-2 was not a monolithic
    infection with a predictable set of clinical features, but rather an ever-evolving disease for which the different strains produce unique
    clinical features that affect testing, symptoms, and even which organ
    systems can be attacked," explained lead investigator Sanjay Tyagi, PhD,
    Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA.

    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.

    "Knowing that a highly contagious and dangerous strain is emerging in a
    local community could inform policymakers to initiate safety measures to
    limit spread," said co-investigator Ashley Hill, MD, ResourcePath LLC, Sterling, VA, USA. "It can also serve as an early warning system for
    healthcare systems that need to plan for surges in ER visits and ICU
    care. Knowing which strain has infected a person can also help determine
    which treatments would be most beneficial." 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.

    Each beacon was tested individually to confirm its specificity to the
    assigned mutation. Then, the beacons were combined into a multiplex assay
    and tested by RT-PCR on 26 SARS-CoV2-positive patient samples that had previously been tested and identified with deep sequencing. Two samples
    were identified as the alpha variant, two as the epsilon variant, and
    eight as the delta variant. The multiplex assay was in full agreement with results from deep sequencing, with a sensitivity and specificity of 100%.

    Researchers report that the test is also very adaptable. When omicron
    emerged, the investigators were able to design a beacon in less than a
    month to identify a mutation that is unique to omicron and is important
    for immune evasion. The investigators identified the omicron variant
    in 17 of 33 additional patient samples that had been previously tested,
    and the results were 100% in agreement.

    "The tools we developed to track and identify new variants will be
    useful for this pandemic and for any unforeseen viruses or pathogens
    that may arise going forward," said lead author Ryan J. Dikdan, BS,
    Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA.

    "The SARS-CoV-2 virus is not done with us yet. We desperately need
    a worldwide monitoring system for the inevitable emerging strains
    that could be even more contagious or deadly," the investigators
    said. "The Rutgers-RP RT-PCR variant assay could be widely deployed
    in laboratories around the world right now to monitor all the known
    variants of concern. The assay will be updated with new primer/probe
    sets for each new important variant that emerges."

    ========================================================================== Story Source: Materials provided by Elsevier. Note: Content may be edited
    for style and length.


    ========================================================================== Journal Reference:
    1. Ryan J. Dikdan, Salvatore A.E. Marras, Amanda P. Field, Alicia
    Brownlee,
    Alexander Cironi, D. Ashley Hill, Sanjay Tyagi. Multiplex PCR
    Assays for Identifying all Major Severe Acute Respiratory Syndrome
    Coronavirus 2 Variants. The Journal of Molecular Diagnostics,
    2022; DOI: 10.1016/ j.jmoldx.2022.01.004 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/03/220317111845.htm

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