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

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  1 , Kim Steegen  2 , Irene Ketseoglou  3 , Zukiswa Mahlumba  4 , Naseem Cassim  2 , Tracey Wiggill  2 , W D Francois Venter  5 , Wendy Stevens  2
Affiliations

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 et al. Int J Infect Dis. 2021 Sep.

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.

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Figures

Figure 1
Figure 1
The comparative HIV Viral load (HIVVL) volumes for 2019, 2020 and 2021 and SARS-CoV-2 volumes for 2020 and 2021. Percentages within turnaround time (TAT) for SARS-CoV-2 and HIV viral load (HIVVL) displayed an upward trend from June 2021 and after July 2021, respectively. The drop in HIVVL percentage within TAT in November 2021 was due to instrument breakdowns. The second COVID-19 wave started during mid-December, with the January 2021 volumes comparable to the July 2021 peak. HIVVL was significantly impacted by supplier reagent and consumable shortages in January 2021.
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