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Fig. 1 | BMC Infectious Diseases

Fig. 1

From: Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program

Fig. 1

CDC tracking of emerging variants through the pipeline for genomic surveillance (https://www.cdc.gov/coronavirus/2019-ncov/variants/cdc-role-surveillance.html). As part of the CDC National SARS-CoV-2 Strain Surveillance (NS3) System, contracted laboratories select for sequencing a set of deidentified specimens that were previously subjected to SARS-CoV-2 RT-PCR testing and determined to be positive. Generally, the samples then undergo a three-step process for generating sequence data. Specimen preparation and sequencing: SARS-CoV-2 RNA is extracted and converted to complimentary DNA, enriched, and loaded into the next-generation sequencers. Sequence reads are aligned to SARS-COV-2 reference strain using the k-mer detection method. Aligned reads are then used to generate the consensus sequence, call variants and lineage determination. The information along with sequencing quality control statistics are transferred to the CDC repository electronically. Published data are made available to scientists around the world through public repositories

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