Comparative Assessment of SARS-CoV-2 Diagnostics in Nigeria

Abstract

Viral pandemics are a major threat to public health, as they have the potential to overwhelm health systems and cause a significant loss of lives and economic meltdown. The COVID-19 pandemic highlighted not only the impact of pandemics but also the critical role of diagnostics in curbing their spread. Early and accurate diagnosis of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was very important in the effective management, control, and prevention of the pandemic. Several diagnostics tools were deployed during the COVID-19 pandemic, such as the gold standard, quantitative reverse transcription polymerase chain reaction (RT-qPCR), point-of-care (POC) Rapid Diagnostic Tests (RDTs), and enzyme-linked immunosorbent assay (ELISA). None of these diagnostics tools deployed in Africa were manufactured locally. Nigeria and other African countries relied on diagnostics donated from developed countries. Therefore, many commercially available diagnostic kits were utilized during the pandemic. This thesis evaluated the performance of the different commercial RT-qPCR diagnostic test kits (all one-step reverse transcriptase real-time PCR assays), CRISPR-based detection (mCARMEN) and viral RNA extraction methods (Qiagen and AviPure extraction kits, which are used for manual and automated extraction, respectively) that were deployed in a genomic reference lab in Nigeria. Nasopharyngeal (NP) swab samples from known positive SARS-CoV-2 cases with precise Ct values (divided into ranges Ct , 25-35 and 35-40) were used for the evaluation. The result showed that although both automated (AviPure) and manual (Qiagen) extractions were efficient for nucleic acid extraction for the RT-qPCR assays, Qiagen, a manual extraction kit, had better RNA concentration yield. All the RT-qPCR assays were specific to SARS-CoV-2. However, the best-performing RT- qPCR commercial test was the DaAn Gene kit, while the Allplex had the lowest performance rate. mCARMEN was also very sensitive (100%) and specific for SARS- CoV-2. For sequencing assay, only samples with low and moderate Ct had complete genomic sequence using Illumina short read sequencing, while with the Oxford Nanopore (ONT), the complete sequence was seen at low, 73.3% at mid and 6.7% at high Ct. Reviewing the performance of different diagnostics deployed during the pandemic will enable us to select the best-performing diagnostics for future pandemics.