![]() It is therefore essential to evaluate the alternative methods for SARS-CoV-2 testing that are simple, cost-effective, and produce high throughput results in a short period of time in a laboratory within a resource-limited setting. Of note, high-income countries (HICs) test more samples daily to control the spread of the SARS-CoV-2 virus, whereas LMICs test fewer samples due to financial constraints. As a result, mass testing for SARS-CoV-2 infection in LMICs poses a challenge. This is partly due to a lack of local capacity in these countries to produce their analytical instrument and reagents for RT-PCR-based SARS-CoV-2 testing. The RT-PCR assay has superior sensitivity and specificity in comparison to antigen and antibody rapid tests, however, it is highly specialized and expensive, especially for LMICs. The N gene, S gene, E gene, and ORF1ab gene are the most tested target genes for SARS-CoV-2 infection using the RT-PCR assay. The RT-PCR assay is the most accurate test for detecting SARS-CoV-2, hence it is regarded as a gold standard diagnostic procedure for diagnosing SARS-CoV-2 infection. Furthermore, antigen rapid testing was found to have a higher risk of false negatives than molecular RT-PCR tests, with some evidence indicating false negative rates as high as 50%, therefore, a confirmatory RT-PCR test is still recommended. According to a Cochrane systematic review of 22 antigen rapid test trials for detecting SARS-CoV-2 infection, the antigen rapid test showed an average sensitivity of 56.2%. ![]() However, antigen rapid tests, on the other hand, are less accurate in detecting SARS-CoV-2 infection, especially in asymptomatic individuals and those with low SARS-CoV-2 viral load. Antigen rapid tests are less expensive and provide results faster than RT-PCR. ![]() SARS-CoV-2 infection can be detected using two different types of tests: real-time reverse transcription polymerase chain reaction (RT-PCR) and antigen rapid tests. It also contains four structural proteins, namely, the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins that contribute to the SARS-CoV-2 overall structure. Furthermore, the SARS-CoV-2 genome contains non-structural open reading frames (ORF1ab), which are polypeptide coding genes that are translated from genomic RNA. SARS-CoV-2 is an enveloped virus with a single positive-sense RNA genome. The implementation of alternative methods will be the most cost-effective option for testing SARS-CoV-2 infection in LMICs. The above-mentioned cost-effective, fast, and accurate evaluated alternative methods can be used in routine diagnostic laboratories with limited resources for mass testing for SARS-CoV-2 because these were comparable to the internationally approved kits, Thermo Fisher PureLink™ Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit. When compared to the Thermo Fisher PureLink™ Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit, the alternative methods had a faster turnaround time, indicating that laboratories with limited resources may be able to process more samples in a day. The cost per sample was reduced by more than 50% when compared to internationally approved kits. ![]() In terms of performance, all of the alternative RNA extraction methods evaluated were comparable to the internationally approved kits but were more cost-effective (Lucigen QuickExtract™ RNA Extraction Kit, Bosphore EX-Tract Dry Swab RNA Solution and Sonicator method) and four commercial SARS-CoV-2 RT-PCR assay kits (Nucleic Acid COVID-19 Test Kit (SARS-CoV-2), abTES TM COVID-19 qPCR I Kit, PCL COVID19 Speedy RT-PCR Kit, and PCLMD nCoV One-Step RT-PCR Kit) with a sensitivity range of 76–100% and specificity of 96–100%. ![]() A total of 50 residual nasopharyngeal swab samples were used for evaluation and comparison between internationally approved kits (Thermo Fisher PureLink™ RNA Isolation Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit) and alternative methods (three RNA extraction and four commercial SARS-CoV-2 RT-PCR assay kits) in terms of the cost analysis, diagnostic accuracy, and turnaround time. Hence, this study aimed to compare and evaluate alternative methods for the mass testing of SARS-CoV-2 infection in laboratories with limited resources to identify cost-effective, faster, and accurate alternatives to the internationally approved kits. However, the challenge with this method is that it is expensive, which has resulted in under-testing for SARS-CoV-2 infection in many LMICs. The polymerase chain reaction (PCR) is the gold standard method for detecting SARS-CoV-2 infection. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak posed a challenge for diagnostic laboratories worldwide, with low-middle income countries (LMICs) being the most affected. ![]()
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