Table 1.

Comparison of Different Approaches to Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping

Comparisons	Allele-Specific RT-qPCR	Targeted/Sanger Sequencing	WGS
Costa	$	$$	$$$ (Depends on batch size)
Real-world TAT, d	0–2	2–7	3–10
Advantages	Rapid TAT to affect mAb choice; widely available; easy-to-define targets	Potentially shorter TAT than 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; higher cost; longer TAT

Abbreviations: mAb, monoclonal antibody; RT-qPCR, reverse-transcription quantitative polymerase chain reaction; TAT, turnaround time; WGS, whole-genome sequencing.

^aReagent costs for WGS can be as low as $30–$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.