Table 2.

Data collection in application of the PG-PHASE Framework to SARS-CoV-2 sequencing

	Data collected in relation to each phase
Phase 1	• Number of sequenced cases • Number of total cases • Proportion of total cases sequenced • Turnaround time for all samples • Turnaround time for priority samples • Interviews with laboratory personnel • Interviews with end users
Phase 2	• Number of sequences uploaded to AusTrakka • Number of sequences uploaded to GISAID • Interviews with bioinformaticians • Interviews with genomic epidemiologists • Interviews with end users • Routine and ad-hoc reports • Observation of reporting meetings
Phase 3 (part 1)	• Interviews with end users • Media and publicly available inquiry records
Phase 3 (part 2)	• Estimated changes to health care costs due to cases averted • Estimated changes to costs of epidemiological investigation due to cases averted and use of WGS to identify transmission links • Estimated changes to costs of infection control interventions due to cases averted and use of WGS to identify transmission links