Table 3.

Widely used diagnostics approaches for SARS-CoV-2 detection.

Method	Principle	Advantage	Duration	Disadvantage
Next-generation sequencing (NGS)	Whole-genome sequencing	Highly sensitive and specific provides all related information. Can identify a novel strain	1–2 day	High expertise, Equipment dependency and high-cost Highly sophisticated Lab required
RT-PCR	Specific primer-probe based detection	Fast results, higher sensitivity, need small amount of DNA, can be performed in a single step. Well-established methodology in viral diagnostics	3–4 h	Higher costs due to the use of expensive consumables. Expensive lab equipment. Detection is also complex and time-consuming. May be affected by novel mutations in emerging variants. US FDA listed some molecular assays expected to fail to detect the SARS-CoV-2 omicron variants (https://www.fda.gov).
RT-LAMP	More than two sets of specific primers pair-based detection	Highly repeatable and accurate. Single working temperature	1 h	Too sensitive, highly prone to false positives due to carry-over or cross-contamination
Antigen detection assay	Lateral Flow Immunoassay (LFA)	POCT, Samples does not need to be transported to the laboratory, saving time and cost	15–30 min	Testing comes after 3–4 days of infection. Lower sensitivity and specificity
	CLIA, ELISA	Laboratory setting	4–6 h	Testing comes after 3–4 days of infection. Lower sensitive and specificity
Serological assays	Lateral Flow Immunoassay (LFA	POCT	15–30 min	Detected 1–2 weeks after vaccination or infection based on the type of antibody to be detected
Antibodies (IgG/IgM)	ELISA, CLIA	Laboratory setting	4–6 h	Detected 1–2 weeks after vaccination or infection.
CT scan	Chest images	Enhance sensitivity of detection if findings combined with RT-PCR results	1 h	Indistinguishability from other viral pneumonia and the hysteresis of abnormal CT
Virus culture and isolation	In vitro live virus isolation and propagation	Highly (100%) specific gold standard	5–15 days	Low sensitivity as isolation is not 100%