Throughout 2020, as the SARS-CoV-2 virus spread globally the number of laboratories performing molecular testing to detect the virus increased dramatically. WHO has been active in the provision of External Quality Assessment (EQA) programmes, where an EQA provider prepares a panel of SARS-CoV-2 positive and negative specimens and sends them to participating laboratories to assess whether they are capable of producing the expected results. One such assessment programme was coordinated by the Public Health Laboratories Strengthening Unit (PHL) in the Lyon Office of the World Health Emergencies Programme (WHE), which allowed Member States to nominate any laboratory testing for SARS-CoV-2 in their country, whether at the national or the sub-national level.
Carried out in collaboration with Australian EQA provider the Royal College of Pathologists of Australasia Quality Assurance Program (RCPAQAP), a first round of EQA was executed in late 2020/early 2021, where over 97% of assessed results were reported correctly (i.e. correctly SARS-CoV-2 positive or negative) by participant laboratories. Results of this programme were used to allocate regional and national resources towards laboratory capacity building and also provided insights for Member States in reviewing their national laboratory network according to the ongoing developments of the pandemic, such as opening or allocating new laboratories to provide better sub-national testing coverage.
In August 2022, a second round of the program was commissioned that would allow newly designated sub-national laboratories testing for the virus a chance to participate in a global EQA programme, as well as to re-assess the quality of testing in a new phase of the pandemic where viral variants had begun to evolve. This new panel contained 6 specimens and included SARS-CoV-2 variants Omicron and Delta at various concentrations. In this round, 2,888 laboratories returned results, representing an increase of 60% participation from the first round of the programme. A total of 17,328 results were submitted, however those left blank or reported as “inconclusive” or “invalid” were not assessed. Of all assessed results 93.4% were reported correctly.
In both rounds of the EQA, a high and consistent level of performance was seen for specimens that were negative or contained moderate to high concentrations of SARS-CoV-2 nucleic acid. The specimens with the most incorrect results were those containing low concentrations of SARS-CoV-2 nucleic acid – an effect that was more pronounced in the second round indicating a slight decrease in the sensitivity of testing at low concentrations. The increase in the number of participating laboratories from less resourced sub-national locations, and a large number of methods, kits and platforms with limited validation data may be contributing factors.
The huge increase in participation in this programme from round one to round two helps to demonstrates that continued expansion of the COVID-19 pandemic actually enabled many countries to introduce new molecular testing methods and technologies into many sub-national laboratories who may otherwise have been unexposed to such methods. Furthermore, the overall performance of these laboratories remained consistently high globally across both rounds, providing health workers, the general public, and health authorities with confidence in the reliability of laboratories results. Individual laboratories could use the results of this EQA to identify problems in their laboratory practices, and in the case of an incorrectly reported results, investigate root causes and apply corrective actions. This included reevaluation of testing algorithms and operating procedure, review of the materials and equipment being used, and the identification of additional training needs for laboratory personnel. At national, regional and global level the outcomes of this EQA were used to identify countries or regions where additional resources could be allocated to implement essential actions such as the procurement of reliable testing kits, and support to Member States in setting up their own national EQA programs for the continuous quality monitoring of their national laboratory networks.