Preparing for the next pandemic: Lessons from rapid scale-up of SARS-CoV-2 testing in a South African high-throughput automated HIV molecular laboratory

Hans, Lucia; Steegen, Kim; Ketseoglou, Irene; Mahlumba, Zukiswa; Cassim, Naseem; Wiggill, Tracey; Venter, WD Francois; Stevens, Wendy

Africa’s readiness to the respond to the SARS-COV-2 pandemic was tested due to reliance on rapid turn-around-time of polymerase chain reaction results for clinical management, isolation and quarantine decisions. The HIV Molecular Laboratory in Johannesburg, South Africa is one of the largest automated HIV molecular laboratories worldwide, performing 1.2 million tests annually. Despite its extensive molecular capacity and experience in managing high volumes acquired from a large HIV program, significant challenges were encountered during its rapid transition to largescale SARS-CoV-2 testing. Here, we describe the strategies employed to manage challenges related to policy, staff, introduction of new assays and workflow efficiencies, and to mitigate the risks of reprioritization of resources on routine HIV tests, that resulted in a 50% improvement in SARS-COV-2 turn-around-time during the first wave peak during which approximately 25 000 samples were tested per month, and further improvement during the second wave, with 91% within targeted turn-around-time.