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Proficiency testing for SARS-CoV-2 whole genome sequencing.

Katherine A Lau1, Kristy Horan2, Anders Gonçalves da Silva2

  • 1RCPAQAP Biosecurity, St Leonards, NSW, Australia.

Pathology
|July 1, 2022
PubMed
Summary

A proficiency testing program (PTP) was developed to assess whole genome sequencing (WGS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Australian public health laboratories. The PTP demonstrated the critical role of WGS in surveillance and variant monitoring.

Keywords:
SARS-CoV-2bioinformatics analysisproficiency testingwhole genome sequencing

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Area of Science:

  • Genomics and Molecular Biology
  • Public Health Surveillance
  • Infectious Disease Epidemiology

Background:

  • Whole genome sequencing (WGS) is vital for tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, variants, and infection sources.
  • Disparities in SARS-CoV-2 genomics capacity exist across Australian public health laboratories.
  • External proficiency testing is recommended to ensure consistent and reliable WGS performance for public health.

Purpose of the Study:

  • To develop and describe a proficiency testing program (PTP) for SARS-CoV-2 whole genome sequencing (WGS).
  • To assess the performance and capacity of Australian public health laboratories in SARS-CoV-2 genomics.
  • To provide insights into the current state of SARS-CoV-2 genomic surveillance across Australia.

Main Methods:

  • The PTP comprised two parts: Part 1 assessed wet and dry laboratory capacity using simulated SARS-CoV-2 specimens.
  • Part 2 involved analyzing a genomic dataset of 70 SARS-CoV-2 consensus genomes, requiring raw data submission and independent analysis.
  • Laboratories submitted raw sequencing data and analyzed provided genomic datasets using their own bioinformatics pipelines.

Main Results:

  • Laboratory performance in SARS-CoV-2 WGS was generally commendable, with some variations attributed to different sequencing and bioinformatics approaches.
  • The PTP provided valuable insights into the current capabilities of SARS-CoV-2 genomics in Australian public health.
  • The study highlighted the importance of standardized quality control and performance benchmarking for genomic surveillance.

Conclusions:

  • The developed SARS-CoV-2 WGS PTP successfully supported the validation and implementation of genomic processes in public health laboratories.
  • Proficiency testing is crucial for ensuring the reliability and comparability of SARS-CoV-2 genomic data for public health decision-making.
  • Data from this PTP will aid in establishing bioinformatic quality control and performance benchmarks for accreditation.