FUNCTIONAL GENOMICS CORE
COBRE CENTER FOR TARGETED THERAPEUTICS
University of South Carolina, College of Pharmacy
From the beginning of SARS-CoV 2 (COVID 19) pandemic, Functional Genomics Core and Prisma Health Department of Internal Medicine (Chair Dr. Albreht) start testing Prisma Health Care Professionals, to monitor the epidemiological situation and improve personal wellbeing. The COre purified viral RNA from nasopharyngeal swab and spit (saliva and sputum) samples and determined the virus load in the samples by RT-qPCR and LAMP isothermal amplification. To determine virus evolution and transmission routes, we are sequencing virus genomes from positive samples. Now, to support research and community projects, FGC offers services to fight the pandemic:
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Purification of viral RNA from body fluids, tissues, and cell cultures.
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Sequencing of virus genome by Oxford Nanopore and Illumina technologies
The FGC lab is not CLIA certified. The tests are for research projects only.
RT-qPCR: Virus determined by One Step RT-qPCR of SARS-CoV 2 with the detection limit ~5-10 copies per uL of RNA.
Assays:
CDC qPCR detection assay: Assay includes primers and internal probes for virus Gene N (N1 and N2 primer sets) and control set for RNAse P
WHO detection set (2019-nCoV Primer Probe Panel in ratios set forth in Charité/Berlin Protocol): Assay includes primers and internal probes for virus gene E and ORF1a/b.
Luminex SARS-CoV-2 RT-PCR Assay: Assay includes two multiplexed sets of primers and probes. The assay 1 (China CDC) includes ORF1ab, Gene N and RNAse P primers and probes designed for multiplexed (1 tube) amplification. The assay 2 (USA CDC) includes Gene N (N1 and N3), and RNAse P primers and probes designed for multiplexed (1 tube) amplification.
RT-LAMP: Virus determined by one-step colorimetric RT-LAMP with the detection limit ~500 copies per ul of RNA. LAMP, Loop-mediated isothermal amplification, does not require PCR and detection systems. The reaction performed in constant temperature and detected by color discrimination of positive (yellow) and negative (purple) samples.
SARS-COV-2 (COVID 19) detection by RT-QPCR and RT-LAMP
Sequencing of SARS-CoV 2 genomes
FGC performs the sequencing of the virus genome and bioinformatics analysis of the results.
Pipeline:
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Virus amplification with amplicon panels: ARCTIC NETWORK panel, V3 or Paragon Genomics Clean Plex SARS-CoV 2
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Oxford Nanopore (multiplexing up to 24 samples) or Illumina (multiplexing up to 384 samples) sequencing
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SARS-CoV-2 genome assembly and detection of the variants.
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Submission of SARS-CoV 2 genomes to GISAID
