How COVID-19 Variants Are Traced Through Covid Sequencing

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    COVID sequencing is being employed by the Centers for Disease Control and Prevention or CDC in the United States in order to monitor developing SARS-CoV-2 mutations that cause COVID-19. The Centers for Disease Control and Prevention (CDC) established multiple transmission lines to connect COVID sequencing data from the CDC, public health laboratories, and commercial diagnostic laboratories to publicly accessible records managed by the National Center for Biotechnology Information (NCBI) and also the Global Initiative for Sharing Avian Influenza Data (GISAID).

    Public health facilities provide de-identified samples to CDC as an aspect of the CDC’s National SARS-CoV-2 Strain Surveillance (NS3) System to provide a representative group of viruses for sequencing. The method of producing SARS-CoV-2 genetic sequence data from all these specimens as well as making it publicly available consists of four major steps.

    COVID sequencing method is done through the following steps:

    1. Collection and initial processing of specimens: Specimens are collected and recorded into the laboratory information management system.
    2. Preparation and sequencing of the specimens: SARS-CoV-2 RNA is collected and converted to complementary DNA, enriched, and put into next-generation sequencing equipment.
    3. Generation and collection of sequence data: Specimens are sequenced while data is gathered from sequencers, as well as early quality control activities. The unprocessed data is transformed into sequence data. At this time, a parallel process of integrating sequencing data from commercial laboratories with CDC databases for processing begins.
    4. Submit sequence data to public repositories: Scientists do quality control checks. Sequences that were initially rejected by public repositories are evaluated and may be re-sequenced in preparation for resubmission. Public repositories make published data available to scientists worldwide.

    Analyses of Genomic Sequence Data Using Bioinformatics

    Publicly available data are accessible to scientists worldwide via public repositories and the CDC obtains genomic sequence data from a variety of sources on a regular basis to aid in national monitoring. At step 3, commercial laboratories provide genetic sequence data to the CDC, which processes it and submits it for publication. Data are submitted directly to public repositories by public health laboratories, research institutions, and universities. CDC scientists undertake in-depth studies of the sequencing data to discover variations and actively monitor their prevalence in order to assess the possible impact on crucial SARS-CoV-2 countermeasures, such as vaccinations, treatments, and diagnostics.

    The Centers for Disease Control and Prevention (CDC) urges state public health laboratories to “tag” the sequences they create and post in public databases in order for their output to be included in CDC analysis. The inclusion of uniform and standardized tagging information on submitted sequences enhances our capacity to search for, analyze, and exchange data created across the United States.

    Spearheading the National SARS-CoV-2 Strain Surveillance System (NS3)

    The NS3 program collects, analyzes, and disseminates data on SARS-CoV-2, the virus that produces COVID-19. The program establishes a comprehensive and population-based surveillance system for the United States, with the goal of tracking virus evolution over time and identifying emerging variants that may impair the performance of diagnostics, therapeutics, or vaccines or have an effect on the transmissibility of SARS-CoV-2 or the severity of COVID-19. A distinguishing feature of NS3 is the routine collecting of specimens from across the United States to assist variant characterization efforts, which offers critical data to aid public health decision-making.

    CDC wants up to 750 total samples a week from all states as well as jurisdictions for COVID sequencing as well as further characterization of sample viruses through cooperation with state and local public health organizations. The NS3 initiative has three primary objectives:

    1. National viral surveillance: Each week or biweekly, US public health laboratories transmit sample SARS-CoV-2–positive clinical specimens to CDC to aid federal efforts to decode, genetically analyze, and phenotypically define the viruses circulating in our population over time. Additionally, this enables a public repository of SARS-CoV-2 sequencing data and specimens.
    2. Increased Surveillance: Since the advent of SARS-CoV-2, national and international sequencing efforts have detected alterations in the SARS-CoV-2 genome caused by transmission as well as evolution in people and animals. These genetic modifications have the potential to have a significant impact on several elements of public health, including disease transmission, severity, diagnostics, treatments, and vaccinations. CDC may request extra specimens from public health laboratories as part of NS3 enhanced monitoring to study variants of interest, variations of concern, or other specific viral categories, or cases of vaccination breakthrough.
    3. Virus characterization: SARS-CoV-2 variants are isolated from positive specimens reported by US public health laboratories using genomic analysis. CDC laboratories assess these isolated viruses to determine their potential influence on currently available vaccinations, treatments, and diagnostics, as well as their overall danger to public health.

    As laboratories expand their sequencing capacity, the CDC seeks to improve and expand technological infrastructure and procedures to enable fast submission of sequence data to public repositories, which hold publicly available sequence data for scientists to analyze. COVID  sequencing is a multistep procedure requiring both laboratory and bioinformatics operations. It takes roughly ten days from the moment a specimen is received at the CDC until a sequence is constructed and suitable for submission to public databases. State, local, academic, and commercial partners frequently follow a similar timeframe.

    The CDC and state and municipal public health laboratories contribute genetic sequence data to publicly available databases managed by the National Center for Biotechnology Information (NCBI) and the Global Initiative for Sharing Avian Influenza Data (GISAID) (GISAID). By integrating monitoring across the United States, the sequencing capacity, knowledge, and data available to guide public health decision-making are maximized.

    How to Notify Public Health Departments with SARS-CoV-2 Sequencing Results

    There is a guideline that includes a SARS-CoV-2 genetic sequencing result into an existing electronic laboratory report in order to communicate that information to state, municipal, tribal, or territorial health authorities. SARS-CoV-2 sequencing findings should be submitted to the same public health agency as the first positive virus test result. The electronic reporting of the sequencing data should contain all of the patient’s initial demographic information, as well as the content of the viral test report and the second requested test with detected viral genetic lineage. 

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