Clinical testing for COVID-19

Abstract

As the novel coronavirus severe acute respiratory syndrome coronavirus 2 caused coronavirus disease 2019 cases in the United States, the initial test was developed and performed at the Centers for Disease Control and Prevention. As the number of cases increased, the demand for tests multiplied, leading the Centers for Disease Control and Prevention to use the Emergency Utilization Authorization to allow clinical and commercial laboratories to develop tests to detect the presence of the virus. Many nucleic acid tests based on RT-PCR were developed, each with different techniques, specifications, and turnaround time. As the illnesses turned into a pandemic, testing became more crucial. The test supply became inadequate to meet the need and so it had to be prioritized according to guidance. For surveillance, the need for serologic tests emerged. Here, we review the timeline of test development, the turnaround times, and the various approved tests, and compare them as regards the genes they detect. We concentrate on the point-of-care tests and discuss the basis for new serologic tests. We discuss the testing guidance for prioritization and their application in a hospital setting.

Keywords: COVID-19; Centers for Disease Control and Prevention; E protein; Food and Drug Administration; M protein; N protein; RT-PCR; S protein; SARS-CoV-2; World Health Organization; coronavirus; guidance; nucleic acid test; point-of-care; prioritization; serologic test; test; viral genes.

Fig 1

SARS-CoV-2 genome and RT-PCR primer/amplicon sites: Schematic of SARS-CoV-2 genome with localization of various published RT-PCR amplicons in ORF1ab/b, S, E, and N genes. Primer/amplicon sequences aligned with 2 highly similar viral consensus sequences (EPI_ISL_412026 [BetaCoV/Hefei/2/2020] and MT106052.1 [2019-nCoV/USA-CA7/2020]) using NCBI BLAST program. E, Envelope; ORF, Open Reading Frame; RdRp, RNA-dependent RNA polymerase; UTR, untranslated region. Primer sequences from referenced publications., , US CDC primers (N1, N2, N3) as reported in Udugama et al.

Fig 2

COVID-19 testing uses and modalities by clinical phase: Diagnosis, treatment, infection control, and epidemiologic monitoring (A) are reliant on the thoughtful deployment and use of various clinical testing modalities (B), including NAT (primarily implemented via RT-PCR) and anti–SARS-CoV-2 serology (IgM and IgG). Each testing modality has maximal utility at a given clinical phase (C), with NATs being most useful during late incubation and symptomatic illness and serology being useful during resolution of illness/convalescence. Classically, antiviral IgM antibodies develop early in an acute infection before IgG antibodies, but recent reports suggest that IgM and IgG seroconversion occurs simultaneously in many subjects during the second week of infection. The persistence of protective humoral IgG-mediated immunity is not yet established for COVID-19 survivors. The natural history of asymptomatic carriers of SARS-CoV-2 is also not yet clear., , ,

Fig 3

Tracking of time to receipt of COVID-19 RT-PCR test results by date of test and change by testing site. For the X-bar portion of the X-bar and S control chart, each data point represents the average turnaround time of all tests collected that day. The center line is the average of the daily data points, subgrouped by preintervention and following system changes, when special cause is detected according to Western Electric methodology. Control limits on the X-bar are calculated, on the basis of average SD of the subgrouped points, multiplied by a factor for group size for each data point.