A novel approach to minimize the false negative COVID-19 diagnosis by inclusion of specific cell markers and multiple sample collection

Abstract

The SARS-CoV-2 pandemic has caused unpredictable mortality and economic losses globally. With no approved drug for the treatment, the accurate diagnosis of COVID-19 becomes essential. RNA based test takes several hours and require extensive human intervention for RNA extraction and RT-PCR, but it is preferred over the antibody-based detection as the latter does not detect the early stage infections. The RT-PCR being a gold standard of COVID-19 diagnosis offers highly standardized detection of the SARS-CoV-2 RNA, still vulnerable for false-negative diagnosis due to absence of infected cells in the sample or inaccurate RNA extraction. Hence there is a need to develop alternative protocols and methods for the accurate COVID-19 diagnosis. Here we propose two additional steps in RT-PCR based COVID-19 diagnosis to minimize false-negative detection. The first step involves collection of four samples from an individual. Each sample should be collected from nasopharyngeal and oropharyngeal regions on day 01, mixed together followed by RNA extraction and then repeating the same exercise on day 03. The RNA extracted on day 01 and day 03 must be pooled together to be used in the RT-PCR. Second, we propose the inclusion of the control marker genes specific to nasal goblet cell, type-II pneumocyte and absorptive enterocytes to ensure the specificity of the RNA source. Overall, these additional steps in the proposed method would increase the chances of SARS-CoV-2 detection in the infected population and would limit the false-negative diagnosis of COVID-19 and hence the spread of this disease.•RT-PCR based COVID-19 diagnosis is vulnerable to the false-negative results due to inaccurate sample isolation or RNA extraction.•RNA pool of multiple samples from an individual improves the chances of detection of SARS-CoV-2 by RT-PCR.•Inclusion of specific marker genes would ensure the right RNA source from the desired cell.

Keywords: COVID-19; COVID-19, Coronavirus disease 2019; RT-PCR; RT-PCR, Reverse Transcriptase PCR; RdRp, RNA dependent RNA polymerase; SARS-CoV-2; SARS-CoV-2, Human Coronavirus-2.

Graphical abstract

Fig. 1

Overview of multiple swab method of sample collection from potential COVID-19 patients. The RNA pool prepared from multiple samples (isolated from NP and OP regions on Day-1 and Day-3) of same patients should be used in RT-PCR along with inclusion of specific cell markers as internal controls to minimize the false negative diagnosis of SARS-CoV-2 infected indivuduals.