Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting

TL;DR

This study shows a cost-effective way to test for SARS-CoV-2 using a simplified RT–qPCR method without sample extraction, suitable for resource-limited settings like Ghana.

Contribution

The study introduces an affordable, extraction-free RT–qPCR protocol using low-cost reagents and wooden swabs for SARS-CoV-2 detection.

Findings

Extraction-free RT–qPCR using 0.1× PBS or water after heat inactivation gave comparable Cq values to traditional methods.

Wooden shaft swabs can be used if sample incubation is limited to under 6 hours.

The proposed method reduces costs by eliminating the need for expensive extraction kits and equipment.

Abstract

The COVID-19 epidemic had a profound impact on global health and the economy and Ghana was no exception to its far-reaching consequences. Regarding detection of the causative agent—the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse-transcription–qPCR (RT–qPCR) is widely recognized as a very sensitive and reliable diagnostic technique used globally. There are, however, high operational costs in acquiring test kits, equipment, and accessories for RT–qPCR testing, which pose significant challenges in resource-limited settings. Hence, this proof-of-concept study set out to develop a more affordable COVID-19 protocol for use in low or lower-middle-income settings, such as Ghana, that would bypass the traditional extraction process using inexpensive reagents and evaluate the possibility of processing samples collected using wooden shaft swabs. Several less expensive media were used for the extraction-free process. Results demonstrated that direct RT–qPCR assay after 5 min heat inactivation of virus at 95 °C in 0.1× PBS or molecular grade water resulted in viral detection with quantification cycle (Cq) values that are comparable to results obtained following the extraction process. Also, wooden shaft swabs could be used for sampling if incubation times are kept to less than 6 h. The study demonstrates that extraction-free protocols are one way to minimize the cost of COVID-19 testing by RT–qPCR.

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