Comparative performances of seven quantitative Reverse-Transcription Polymerase Chain Reaction assays (RT-qPCR) for detecting SARS-CoV-2 infection in samples from individuals suspected of COVID-19 in São Paulo, Brazil

•Brazil ranks second in the number of COVID-19 cases worldwide, with the highest number in the state of São Paulo.•Rapid SARS-CoV-2 virus detection in São Paulo, Brazil requires a critical evaluation of performance and cost of commercial assays/kits.•Multiplex RT-qPCR assays employing E- and/or N-gene targets showed the best performance.•The RdRP-gene target had minor sensitivity in detecting SARS-CoV-2 circulating in this geographic region.•The in-house duplex IAL assay is ideal for COVID-19 testing in São Paulo, Brazil.