Variant Surveillance


MUSC Health Molecular Pathology Lab in Charleston has validated a massively parallel sequencing assay (Illumina) to supplement the efforts of DHEC and the CDC to identify and track SARS-CoV-2 variants of interest and variants of concern as defined by CDC. We plan to collect all patient samples who test positive for SARS-CoV-2 RNA by the Cepheid or Abbott m2000/Alinity m tests with Ct values ≤28. Samples with higher Ct values (lower viral burdens) give poor quality sequences. Samples for variant analysis will be batched and run weekly. It is important to note that this test is not orderable in EPIC or reported in EPIC. This results will not be released for individual patients since it does not currently impact patient management. 
 
SARS-CoV-2 sequencing allows detection of variants. The clinical extension laboratory, supervised by Dr. Dariusz Pytel is performing whole genome sequencing of the virus from positive patients using the Illumina COVIDSeq (EUA) assay as a laboratory developed test to obtain the consensus sequence from patients positive for COVID-19. The sequencing is performed using the Illumina NextSeq550 Dx or the NovaSeq instrument. The assay is validated as a laboratory developed test currently for surveillance purposes only.

The clinical extension laboratory was an effort early in the pandemic to increase and contribute to COVID-19 testing at MUSC. It is an extension of the CLIA-certified molecular pathology laboratory that is staffed by MUSC reasearchers. 

Viral genome data will be collected and submitted to public databases and the appropriate health authorities when requested. 

The CDC is currently increasing efforts to track variants in the United States (see figure below, link). According to the CDC website, a US government interagency group has developed a classification scheme that defines 3 classes of variants:

1. Variants of Interest

2. Variants of Concern

3. Variants of HIgh Consequence

Variants Detected by MUSC Sequencing of COVID-19 Positives from December 2020 - March 10, 2021

As part of our the MUSC surveillance plan, we will be monitoring both lineages and variants. Since December 2020, the overwhelming majority of the samples sequenced show B.1.2 as the prominant lineage, until recently. There was an increase in the VOCs present in the sequenced positive population in March (almost 40% of cases). A variant of concern is defined by the CDC as "a variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures." MUSC is tracking the number of cases sequenced with variants of concern and will continue to follow CDC guidance for the identification and reporting of variant strains. 

“Although vaccination coverage is increasing and COVID-19 incidence is currently decreasing, it is important to perform Next Generation Sequencing (NGS) studies and continue surveillance to determine the spread of viral variants. These studies may provide critical new insight into understanding COVID-19 variant strains on transmissibility, symptom severity, therapeutics, and vaccine failure possibly due to emerging variants and their effect on public health” said Dariusz Pytel, Ph.D.

DHEC is currently requesting all potential vaccine breakthrough cases be sent to them for sequencing. MUSC is also attempting to sequence those cases that meet the sequencing criteria established by the laboratory. 
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