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

Juliana Maira Watanabe Pinhata,Angela Pires Brandao,Daniela Leite,Rosangela Siqueira de Oliveira,Lucila Okuyama Fukasawa,Maria Gisele Goncalves,Juliana Mariotti Guerra,Leonardo Jose Tadeu de Araujo, Gina Ploeger Mansueli, Lilian Beserra Santos, Tarcilla Corrente Borghesan,Lidia Midori Kimura,Juliana Possatto Fernandes Takahashi, Juliana Alves Garcia, Ana Rita de Toledo Piza, Camila Santos da Silva Ferreira, Ricardo Polatto, Maria Luiza Leopoldo e Silva Guerra, Raquel dos Anjos Fazioli,Rosemeire Cobo Zanella,Roberta Morozetti Blanco

JOURNAL OF MEDICAL MICROBIOLOGY(2023)

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摘要
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.
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关键词
COVID-19,laboratories,public health,real-time polymerase chain reaction,reverse transcriptase polymerase chain reaction,SARS-CoV-2
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