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SARS-CoV-2 nucleocapsid and RT-PCR results

Citation

Kristiansen, Søren et al. (2022), SARS-CoV-2 nucleocapsid and RT-PCR results, Dryad, Dataset, https://doi.org/10.5061/dryad.2v6wwpzr3

Abstract

We collected blood samples from patients admitted to the hospital during a period with RT-PCR based-screening of patients for Severe Acute Respiratory Syndrome Cornavirus-2 (SARS-CoV-2). Retrospectively the SARS-CoV-2 nucleocapsid protein (NP) plasma concentrations were measured with an ELISA method and used for an initial time course study to find the optimal time-point for sampling blood. Next, we estimated the diagnostic accuracy i.e. the clinical sensitivity and specificity at different plasma NP cut-off concentrations.

The time course study revealed profiles with rapid or more slow declines in NP titers after the RT-PCR result. Nevertheless, in the time interval 0 – 7 days after the RT-PCR result, the NP concentration was always above the level of detection at 1.66 pg/ml suggesting that the diagnosis could be established in the time interval of 0 - 7 days.

The median time gap between the plasma NP and RT-PCR results was 0.0 days (n = 1957, interval: -26 to + 21 days). Reducing the time gap to seven days, the clinical sensitivity was 90.0% (n= 60, 95% CI, 82.4% to 97.6%) at a specificity of 95.9% (n=1876, 95% CI, 95.0% to 96.8%). Curve analysis by receiver operation characteristics identified a cut-off concentration of 1.87 pg/mL NP as optimal resulting in a positive predictive value of 41.2%, a negative predictive value of 99.7% and a prevalence of 3.1%.

In conclusion, the NP method is acceptable for making the laboratory diagnosis of SARS-CoV-2, and an intended use of plasma NP as a prospective nosocomial screening method is considered feasible.

Methods

In the period from 1st. - 30th November 2021 oro- and nasopharyngeal swab samples were obtained from patients admitted to the North Zealand Hospital, Hillerød, Denmark. To diagnose SARS-CoV-2 the samples were analyzed for the presence or absence of viral RNA with an RT-qPCR method. Routine blood samples were sent to the local Department of Clinical Biochemistry. After all the requested biochemical analyses were carried out, the centrifuged plasma samples were kept for one day at 4oC. The plasma samples were frozen at -20oC and later thawed batch-wise for NP analysis. Patients with paired results (<7 days apart) from RT-PCR - and NP analysis, respectively, were used to determine the diagnostic accuracy of the NP method.