Table 1 |.

Glossary of key terms.

WT virus	Ancestral SARS-CoV-2 (Isolate USA-WA1/2020)
Viral variant or lineage	Virus that harbors fixed, characteristic genomic mutations compared to WT (e.g. Alpha, Delta, Omicron)
RNA variant	Any base alteration from the WT genomic RNA sequence (e.g. G>A)
Clonal variants	Fixed RNA alterations present at a given loci across sequenced observations (clonality > .9)
Subclonal variants	RNA alterations present in <90% of consensus sequences but >5%
De novo variants	A new RNA variant that arises from RNAP errors, RNA modification or damage and not from propagation of an existing variant during replication (clonality < 0.05)