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

From: An implementation science approach to evaluating pathogen whole genome sequencing in public health

  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