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

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

doi:10.1016/j.ijid.2021.06.019

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

Int J Infect Dis. 2021 Sep:110:1-3. doi: 10.1016/j.ijid.2021.06.019. Epub 2021 Jun 15.

Authors

Lucia Hans¹, Kim Steegen², Irene Ketseoglou³, Zukiswa Mahlumba⁴, Naseem Cassim², Tracey Wiggill², W D Francois Venter⁵, Wendy Stevens²

Affiliations

¹ National Health Laboratory Service, Johannesburg, South Africa; University of the Witwatersrand, Johannesburg, South Africa. Electronic address: lucia.hans@nhls.ac.za.
² National Health Laboratory Service, Johannesburg, South Africa; University of the Witwatersrand, Johannesburg, South Africa.
³ National Health Laboratory Service, Johannesburg, South Africa.
⁴ Wits Health Consortium, Johannesburg, South Africa.
⁵ University of the Witwatersrand, Johannesburg, South Africa; Ezintsha, University of the Witwatersrand, Johannesburg, South Africa.

Abstract

Africa's readiness to 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 NHLS HIV Molecular Laboratory in Johannesburg, South Africa, is one of the largest automated HIV molecular laboratories worldwide. 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 large scale SARS-CoV-2 testing. We describe the strategies employed to manage these challenges that resulted in a 30% improvement in SARS-CoV-2 test turn-around-time during the first wave peak during which approximately 25000 samples were tested per month, and further improvement during the second wave peak, with 81% within targeted turn-around-time.

Keywords: Automated; Diagnostics; Molecular; SARS-CoV-2; Scale-up.

MeSH terms

COVID-19 Testing
COVID-19*
HIV Infections* / diagnosis
HIV Infections* / epidemiology
HIV Infections* / prevention & control
Humans
Laboratories
Pandemics / prevention & control
SARS-CoV-2
South Africa / epidemiology