Table 4. Summary of Empirical Studies Referenced.

Sampling schema and results from empirical studies that reported the number of intra-host SNPs identified in patient samples. Note that all studies apart from Lythgoe et al. 2021 utilized serial sampling within at least one patient during their data collection; this did not impact their reported number of intra-host SNPs, but did allow for confirmation of SNPs as true positives.

Paper	Time to Sample	MAF Filter	Intra-host SNPs
Lythgoe et al. 2021	“symptomatic individuals on admission to the hospital”	3%	1.4 (mean)
Valesano et al. 2021	−7 to 20 days post symptom onset	2%	1 (median); 0–2 (IQR)
Wang et al. 2021	10 to 37 days post-symptom onset (18.09 days (mean))	5%	7.33 (mean); 1–23 (Range)
Bendall et al. 2023	Symptoms and positive test within 7 days	2%*	~0.82 (mean); 0–5 (Range)
Gu et al. 2023	With 5 days of symptom onset (2.3 days (mean))	2.50%	10.05 (mean); 5 (median)

^*Intra-host SNP had to clear MAF filter in two technical replicates