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Development of a new method, Rapid Viability RT-PCR, for Detection of Live (Infectious) Coronavirus (SARS-CoV-2) that causes COVID-19 from swab.
There is a need for development of an analytical method for rapid detection of SARS-CoV-2 virus which is causing the COVID-19 pandemic. Currently available traditional tissue/cell culture-based analytical method is too laborious and takes several days to get the results on the presence/absence of viable/infectious virus in a sample. Such a delay in getting the sample analysis results can be a serious obstacle in rapidly determining the presence of infectious virus in environment which, in turn, can impact environmental epidemiological investigations and studies on surface transmission of this virus. In this manuscript, development of a Rapid Viability Reverse Transcriptase Polymerase Chain Reaction (RV-RT-PCR) method that can significantly reduce the time-to-results for sample analysis from several days to less than a day is described. The RV-RT-PCR method integrates cell-culture based enrichment of the virus with virus-specific RT-PCR analysis. The RTPCR analysis is conducted before and after the cell-culture-virus (sample) incubation. An optimum algorithm is established such that the resultant RT-PCR cycle threshold (CT) value difference between before and after cell-culture-virus incubation RT-PCR analyses determines the presence of viable/infectious virus in the sample. The data set included here is from this research work. A manuscript has also been included here along with the Supplemental Tables for additional data. The Data-Metadata file includes all the data and a glossary to explain the scientific terms used. This dataset is associated with the following publication: Shah, S., S. Kane, M. Elsheikh, and T. Alfaro. Development of a Rapid Viability RT-PCR (RV-RT-PCR) Method to Detect Infectious SARS-CoV-2 from Swabs. JOURNAL OF VIROLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 297: 114251, (2021).
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Examination of SARS-CoV-2 serological test results from multiple commercial and laboratory platforms with an in-house serum panel
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Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) is a novel human coronavirus that was identified in 2019. SARS-CoV-2 infection results in an acute, severe respiratory disease called coronavirus disease 2019 (COVID-19). The emergence and rapid spread of SARS-CoV-2 has led to a global public health crisis, which continues to affect populations across the globe. Real time reverse transcription polymerase chain reaction (rRT-PCR) is the reference standard test for COVID-19 diagnosis. Serological tests are valuable tools for serosurveillance programs and establishing correlates of protection from disease. This study evaluated the performance of one in-house enzyme linked immunosorbent assay (ELISA) utilizing the pre-fusion stabilized ectodomain of SARS-CoV-2 spike (S), two commercially available chemiluminescence assays Ortho VITROS Immunodiagnostic Products Anti-SARS-CoV-2 Total Reagent Pack and Abbott SARS-CoV-2 IgG assay and one commercially available Surrogate Virus Neutralization Test (sVNT), GenScript USA Inc., cPass SARS-CoV-2 Neutralization Antibody Detection Kit for the detection of SARS-CoV-2 specific antibodies. Using a panel of rRT-PCR confirmed COVID-19 patients’ sera and a negative control group as a reference standard, all three immunoassays demonstrated high comparable positivity rates and low discordant rates. All three immunoassays were highly sensitive with estimated sensitivities ranging from 95.4%-96.6%. ROC curve analysis indicated that all three immunoassays had high diagnostic accuracies with area under the curve (AUC) values ranging from 0.9698-0.9807. High positive correlation was demonstrated among the conventional microneutralization test (MNT) titers and the sVNT inhibition percent values. Our study indicates that independent evaluations are necessary to optimize the overall utility and the interpretation of the results of serological tests. Overall, we demonstrate that all serological tests evaluated in this study are suitable for the detection of SARS-CoV-2 antibodies.
Nationwide Commercial Laboratory Seroprevalence Survey
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CDC is working with commercial laboratories to conduct large-scale geographic seroprevalence surveys to estimate the percentage of people who were previously infected with SARS-CoV-2, the virus that causes COVID-19 disease. The strategy involves working with state, local, territorial, academic, and commercial partners to better understand COVID-19 in the United States using serology (antibody) testing for surveillance (“seroprevalence surveys” or “serosurveys”). For the surveys, de-identified clinical blood samples are tested for antibodies to SARS-CoV-2. This dataset contains the data used to by the Nationwide Commercial Laboratory Seroprevalence Survey interactive visualization available at https://covid.cdc.gov/covid-data-tracker/#national-lab. Additional information is available at https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/commercial-lab-surveys.html.
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