qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples.

The protocols herein outline the use of qRT-PCR to detect the presence of SARS-CoV-2 genomic RNA in patient samples. In order to cope with potential fluctuations in supply chain and testing demands and to enable expedient adaptation of reagents and assays on hand, we include details for three parallel methodologies (one- and two-step singleplex and one-step multiplex assays). The diagnostic platforms described can be easily adapted by basic science research laboratories for SARS-CoV-2 diagnostic testing with relatively short turnaround time. For complete details on the use and execution of this protocol, please refer to Vanuytsel et al. (2020).

Rapid Implementation of a SARS-CoV-2 Diagnostic Quantitative Real-Time PCR Test with Emergency Use Authorization at a Large Academic Safety Net Hospital.

BACKGROUND: Significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 (COVID-19) infection have prevented adequate public health management of the disease, impacting the timely mapping of viral spread and the conservation of personal protective equipment. Furthermore, vulnerable populations, such as those served by the Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. METHODS: We developed a SARS-CoV-2 diagnostic medium-throughput qRT-PCR assay with rapid turnaround time and utilized this Clinical Laboratory Improvement Amendments (CLIA)-certified assay for testing nasopharyngeal swab samples from BMC patients, with emergency authorization from the Food and Drug Administration (FDA) and the Massachusetts Department of Public Health. FINDINGS: The in-house testing platform displayed robust accuracy and reliability in validation studies and reduced institutional sample turnaround time from 5-7 days to less than 24 h. Of over 1,000 unique patient samples tested, 44.1% were positive for SARS-CoV-2 infection. CONCLUSIONS: This work provides a blueprint for academic centers and community hospitals lacking automated laboratory machinery to implement rapid in-house testing. FUNDING: This study was supported by funding from the Boston University School of Medicine, the National Institutes of Health, Boston Medical Center, and the Massachusetts Consortium on Pathogen Readiness (MASS CPR).