Journal:Current approaches in laboratory testing for SARS-CoV-2

Full article title	Current approaches in laboratory testing for SARS-CoV-2
Journal	International Journal of Infectious Diseases
Author(s)	Xu, Yuzhong; Cheng, Minggang; Chen, Xinchun; Zhu, Jialou
Author affiliation(s)	Shenzhen Baoan Hospital, Shenzhen University
Primary contact	Email: zhujialou at szu dot edu dot cn
Year published	2020
Volume and issue	100
Page(s)	7–9
DOI	10.1016/j.ijid.2020.08.041
ISSN	1201-9712
Distribution license	Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Website	https://www.sciencedirect.com/science/article/pii/S1201971220306718
Download	https://www.sciencedirect.com/science/article/pii/S1201971220306718/pdfft (PDF)

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, which originated in Wuhan, Hubei Province, China, has rapidly spread to produce a global pandemic. It is now clear that person-to-person transmission of SARS-CoV-2 has been occurring and that the virus has been dramatically spreading in recent months. Early, rapid, and accurate diagnosis is of great significance for curtailing the spread of SARS-CoV-2. There are currently several diagnostic techniques (e.g., viral culture and nucleic acid amplification test) being used to detect the virus. However, the sensitivity and specificity of these methods are quite different, with the sample source and detection limit varying greatly. This study reviewed all types and characteristics of the currently available laboratory diagnostic assays for detecting SARS-CoV-2 infection and summarized the selection strategies of testing and sampling sites at different disease stages to improve the diagnostic accuracy of testing for the virus' associated disease, coronavirus disease 2019 (COVID-19).

Keywords: novel coronavirus, SARS-CoV-2, COVID-19, laboratory testing, laboratory diagnosis

Discussion

An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered in Wuhan, China, in December 2019. It then rapidly developed into a global pandemic. As of May 29, 2020 a total of 5,701,337 laboratory-confirmed COVID-19 cases had been reported worldwide, with 357,688 deaths confirmed. Among the effective control measures to reduce transmission in the community, early and reliable laboratory confirmation of SARS-CoV-2 infection is of crucial importance. This review summarizes the advances made in technologies for rapid diagnosis and confirmation of respiratory infections caused by SARS-CoV-2, as well as the selection strategies of testing and sampling sites in SARS-CoV-2 detection.

Since the initial cases of pneumonia of unknown cause were first reported, viral culture and genetic sequencing of isolates obtained from these patients in January 2020 identified within 10 days a novel coronavirus as the etiology. This benefitted understanding of the disease occurrence and transmission, as well as diagnostic test development. Although viral culture is relatively time-consuming and labor-intensive, it is much more useful in the initial phase of emerging epidemics before other diagnostic assays are clinically available. Besides, unbiased, high-throughput sequencing has been proven as a powerful tool for discovering pathogens (Table 1). A detection assay (BGI, Shenzhen, China), based on next-generation sequencing, was approved for emergency use authorization (EUA) by the National Medical Products Administration (NMPA) in China (see Table S1 in the Supplementary data). However, whole genome sequencing is time-consuming and requires specialized instruments with high technical thresholds, and thus is not recommended for widespread clinical use.

Table 1. Laboratory testing for detection of SARS-CoV-2. NAAT, nucleic acid amplification test; RT-PCR, reverse transcription polymerase chain reaction. Testing type Specimen type Characteristics Testing time Limitation Viral culture Respiratory sample Gold standard for virus diagnosis and useful in the initial phase of emerging epidemics 3–7 days Time- and labor-consuming, biosafety level 3 laboratory needed, cannot be widely used in clinical settings NAAT, whole genome sequencing Respiratory sample and blood Detects all pathogens in a given specimen, including SARS-CoV-2, as well as viral genome mutations 20 hours Time-consuming, specialized instruments with high technical thresholds, and high cost NAAT, real-time RT-PCR Respiratory sample, stool and blood Most widely used for laboratory confirmation of SARS-CoV-2 infection 1.5–3 hours Time-consuming procedure, requires biosafety conditions, expensive equipment, skilled personnel, and can have false negative results NAAT, isothermal amplification Respiratory sample, stool and blood Requires only a single temperature for amplification, takes less time yet has comparable performance with real-time RT-PCR, and does not require specialized laboratory equipment 0.5–2 hours False negative results, as real-time RT-PCR Serological testing Serum, plasma and blood Less time required, simple to operate, useful in disease surveillance and epidemiologic research 15–45 minutes Cross-reaction with other subtypes of coronaviruses Point-of-care test Respiratory sample Provides rapid actionable information with good sensitivity and specificity for patient care outside of the clinical diagnostic laboratory 5–30 minutes Risk of quality loss and lack of cost-effectiveness

Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used in acute respiratory infection to detect causative viruses from respiratory specimens. The World Health Organization (WHO) recommends that patients who meet the case definition for suspected SARS-CoV-2 should be screened for the virus using a nucleic acid amplification test (Table 1). Various real-time RT-PCR assays for detecting SARS-CoV-2 RNA have been developed worldwide, with different targeted viral genes or regions (Table S1, Supplementary data). To date, 13 and 52 commercial SARS-CoV-2 real-time RT-PCR diagnostic panels have been issued for EUA by China and the U.S., respectively, with the limit of detection varying from 100 to 1000 copies/mL (Table S1, Supplementary data). Although RT-PCR has relatively high sensitivity, there have been reports of multiple false negative tests for the same patients infected with SARS-CoV-2 in China, suggesting that negative results do not preclude the presence of SARS-CoV-2 in a clinical specimen. In addition, fluctuating RT-PCR results have been observed in several patients who first tested positive for SARS-CoV-2, then tested negative in the following test, and returned to being positive in a final test. False negative results may be due to the selection of sampling locations, poor sample quality, low viral load of the specimen, incorrect storage and transportation, as well as laboratory testing conditions and personnel operations. If a highly suspected patient is negative for the virus, the nucleic acid amplification test should be repeated or a more suitable sample should be collected.

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. Some grammar, punctuation, and repetition was cleaned up to improve readability. In some cases important information was missing from the references, and that information was added. Nothing else was changed in accordance with the NoDerivatives portion of the license.