Table 3.

Relationship of Pathogen Genome Identity (GENI) score derived from mutational difference from the index genome (Wuhan isolate of SARS-CoV-2 or cluster isolate reference from multiple outbreak regions outside of territory).

Equivalent Pathogen Genome Identity (GENI) score for SARS-CoV-2	Clinical interpretation and epidemiological inference	Note
0–2	No difference from index case isolate genome or reference, imported case if there is no prior report, indicative of acute transmission < 1 month	Reference genome is primarily earliest isolate available
3–4	Recent local transmission (average 1–2 months) if there are no prior report of cases	Subsequent outbreak clusters can serve as sources of introduction hence near neighbor reference has to be selected to generate an accurate GENI score
> 4	Sustained local transmission (greater than 2 months) if there is are no prior report of cases	Subsequent outbreak clusters can serve as sources of introduction hence near neighbor reference has to be selected to generate an accurate GENI score