Repeat Testing Outcomes of Inconclusive SARS-CoV-2 RT- PCR results in inpatients at Charlotte Maxeke Johannesburg Academic Hospital (CMJAH)

Abstract

Background With an analytical sensitivity of > 99% in samples harbouring viral loads between 500 – 5000 copies/ml, SARS-CoV-2 RT-PCR is regarded as the gold standard test method for the diagnosis of COVID-19. The reality of inconclusive results occurring, presents a laboratory diagnostic challenge that has an impact on patient management as well as infection and control preventative measures. Methods Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) Virology laboratory performed a total of 42790 SARS-CoV-2 RT PCR tests using the Allplex™ 2019-nCoV (Allplex; Seegene, Seoul, Korea) molecular assay on nasopharyngeal swabs collected from inpatients during the period of June 2020 to December 2020. Inpatient samples with initial inconclusive result outcomes, were subjected to repeat testing of the residual sample within 24 – 48 hours. Results Of the overall samples tested, 709 (1.7%) yielded inconclusive results. A finding of single gene target detection was observed in 98.4% (n=698) of inpatient samples, with the N gene predominance at 73.6% (n=514). Repeat testing provided negative and positive results in 47% (n=335) and 16% (n=112) respectively, with 28% (n=198) remaining persistently inconclusive. Inconclusive samples which subsequently tested positive detected 2 (56.3%) and 3 (47.3%) gene targets. Inpatients samples testing repeat inconclusive, whilst displaying a single gene target distribution, 66% detected the same gene target at initial and repeat testing (N-N, (n=131); RdRP-RdRP, n=19); with the initial gene target failing to detect the same gene target in 34%, displaying N- RdRP, n=12; N-E, n=6, RdRP-N, n=6; E-RdRP, n=3 and E-N, n=3. Conclusion Our relatively low prevalence rate of 1.7% is consistent with other studies. Although clinical history was not furnished, the finding of N gene predominance is explained by inpatients tested at either initial presentation or late stage of COVID-19 infection. Retesting of samples that are initially inconclusive, should be advocated for it allows for establishment of a definitive SARS-CoV-2 outcome.