Rapid response of a public health reference laboratory to the COVID-19 pandemic

Introduction. Brazil was one of the most affected countries by the COVID- 19 pandemic. Instituto Adolfo Lutz (IAL) is the refer-ence laboratory for COVID- 19 in Sao Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL- 2 was created to enhance IAL's capacity for COVID- 19 diagnosis. Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics. Aim. To describe the design of IAL- 2 and correlate the results of RT- qPCR tests for COVID- 19 with secondary data on suspected cases of SARS- CoV- 2 infection in the Sao Paulo state.Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS- CoV- 2 whose clinical samples were submitted to real -time PCR after reverse transcription (RT- qPCR) at IAL- 2, between 1 April 2020 and 8 March 2022. RT- qPCR Ct results of the different kits used were also analysed.Results. IAL- 2 was implemented in April 2020, just over a month after the detection of the first COVID- 19 case in Brazil. The laboratory performed 304,250 RT- qPCR tests during the study period, of which 98 319 (32.3 %) were positive, 205827 (67.7 %) negative, and 104 (0.03 %) inconclusive for SARS-CoV- 2. RT- qPCR Ct values <= 30 for E/N genes of SARS- CoV- 2 were presented by 79.7 % of all the samples included in the study.Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID- 19, outlining strategies to carry out work with quality, using different RT- qPCR protocols.