Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2

Abstract

Background: This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes.

Method: It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested.

Result: Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%.

Conclusion: These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.

Keywords: COVID-19 RDT; Genomic surveillance; Molecular diagnostics.

Fig. 1

Implementation of the viral RNA extraction protocol from the rapid diagnostic test for SARS-CoV-2. (1) Quality of the PCR curves made from the sample placement area. The CT values were: Gene N = 24.19; Gene ORF1ab = 30.29 and Internal Control (C. Int) Cy5 = 29.64. (2) Quality of the PCR curves made from the reading area of the RDT, with CT values of: Gene N = 28.12; ORF1ab gene = 32.24 and C. Int Cy5 = 32.53. (3) Quality of the PCR curves made from the distal end of the RDT, with CT values of: Gene N = 30.45; ORF1ab gene = 33.34 and C. Int Cy5 = 34.55. (4) Positive control curves. N gene = 19.09; ORF1ab gene = 21.49 and C. Int Cy5 = 22.25. This result indicates that the sample placement zone curves closely resemble those of the positive control

Fig. 2

The sample distribution flowchart for PCR conducted using COVID-19 RDT extract is called PCR using RDT strip and PCR conducted with nasopharyngeal samples contained in a viral transport medium is called PCR using VTM (PCR). The macroscopic results of the COVID-19 antigen RDT are simply called the RDT

Fig. 3

Ct value distribution for PCR_VTM and PCR_Strip. a Designates the distribution of forty-six (46) samples positive for the COVID-19 RDT, PCR using VTM (PCR_VTM) and PCR DRT strip (PCR_Strip). b Represents the distribution of sixty-four PCR_Strip and PCR_VTM positive samples. c Designates the distribution of Ct values of eighteen samples positive for PCR_VTM and PCR_Strip and negative for the COVID-19 RDT. d Represent the eight samples negative for PCR_Strip and RDT COVID-19 tests