External quality assessment of nucleic acid testing in provincial or municipal CDC laboratories in the COVID-19 surveillance network in China

  Objective  To understand the RNA detection performance of SARS-CoV-2 Variants of Concern (VOCs) in 32 provincial or municipal CDC laboratories in COVID-19 surveillance network in China through an external quality assessment (EQA), and evaluate the clinical performance of the current SARS-CoV-2 nucleic acids detection kits used and provided by the participating laboratories.

  Methods  The viral RNA extractions of SARS-CoV-2 Wuhan strain, four VOCs (Alpha, Beta, Gamma, and Delta), human coronavirus OC43 (HCoV-OC43), and influenza A virus (H3N2) was conducted. The viral RNA was used to prepare EQA panel samples with high (～35) and low (～30) Ct values. The EQA panel included 10 RNA samples (two Ct sets) from three SARS-CoV-2 strains (Wuhan strain, Beta variant, and Delta variant or Wuhan strain, Alpha variant, and Gamma variant), HCoV-OC43 strain, and influenza virus strain. Each participating laboratory was given a random panel of samples for assessment. According to the feedback results, the detection coincidence rate was calculated, and the results were analyzed comprehensively. Furthermore, SARS-CoV-2 nucleic acid detection kits used by the participating laboratories were collected to verify the detection limit and specificity.

  Results  In the EQA, all the participating laboratories met the assessment standard and there were 72% (23/32) laboratories with excellent performance. The overall coincidence rate was 99.7% (319/320) in SARS-CoV-2 RNA detection and 89% (57/64) in HCoV-OC43 RNA detection in the EQA. Among the rRT-PCR-based SARS-CoV-2 nucleic acid detection kits provided by 32 participating laboratories, 66% (33/50) of the kits met limit of detection, and 92% (11/12) of the kits met the specificity standard.

  Conclusion   All the participating laboratories were capable of detecting SARS-CoV-2 RNA, including prototype Wuhan strain and VOCs of Alpha, Beta, Gamma, and Delta. Some SARS-CoV-2 detection kits provided by participating laboratories didn’t meet the limit of detection, and the specificity needs improvement.