TABLE 1.

Comparison of different approaches to SARS-CoV-2 genotyping^a

Parameter	Allele-specific RT-qPCR	Targeted/Sanger sequencing	WGS
Cost	$	$$	$$$ (depends on batch size)
Real-world TAT	0−2 days	2–7 days	3−10 days
Advantages	Rapid TAT to impact MAb choice; widely available; easy to define targets	Potentially faster TAT than that of WGS; potentially more widely available	Outbreak investigation; novel mutation identification; no need to redevelop assay to identify new variants
Disadvantages	Limited targets; need for continuous updates to include new variants	Limited targets	Greater informatics expertise, cost, TAT

^aTAT, turnaround time; MAb, monoclonal antibody. Reagent costs for WGS can be as low as $30 to $40 per sample if sufficient batch size is obtained. Given that none of these tests are highly automated, labor costs comprise a significant proportion of the total cost.