ABSTRACT
Background: SARS-CoV-2 highlighted worldwide, the need of enhance testing capacity. Government of India, under Atmanirbhar Bharat provided platform to private/public companies to develop and manufacture diagnostic reagents /kits for SARS CoV 2 testing. Objective(s): * Performance evaluation of commercial kits. * Handholding of private/public companies to improve the kits quality for its diagnostic accuracy to use for Covid 19 diagnosis Material(s) and Method(s): The SOP for the validation of diagnostic kits were prepared and approved by ICMR technical committee. The ICMR NIV single tube assay was used as gold slandered. The panels of known positives and negatives were prepared. Validation of commercially developed RT-PCRs, RNA extraction kits and virus transport medium were undertaken. The sensitivity and specificity of the kit were calculated and reported as per ICMR's acceptance. Result(s): Real time RT-PCR kits evaluation: Total 165 kits were evaluated, which includes 12 LAMP assay. Among domestic kits, 31 kits were satisfactory while 83 were not satisfactory. Among the imported kits, 25 kits were satisfactory while 26 were not satisfactory. RNA extraction kits evaluation:- Total 157 kits were evaluated, Among domestic kits, 57 kits were satisfactory while 53 were not satisfactory. Among the imported kits, 31 kits were satisfactory and 17 were not satisfactory. VTM kits evaluated = Total 89 kits were evaluated among which nine kits were imported while 80 kits were of domestic origin. Performance of 10 kits was not satisfactory. Conclusion(s): Kit validation is important to access the quality of commercial kits and to enhanced the testing capacity exponentially in country.
ABSTRACT
SARS-CoV-2 infected cases diagnosis is based on the count of realtime reverse transcription-polymerase chain reaction (RT-PCR). The widely used reverse transcription-polymerase chain reaction (RTPCR) method has some limitations for clinical diagnosis and treatment. However, there are only few reports on the detection of the viral load in the stool and urine samples. While information about other modes of transmission is relatively less, some published literature supporting the possibility of a faecal-oral mode of transmission has been accumulating. Objective(s): The current study's objective was to assess the performance of real-time RT-qPCR assay and a droplet digital RT-PCR (dd RT-PCR) for detecting SARS-CoV-2 in stool and urine specimens. Methodology: One hundred and seven paired samples from 107 COVID-19-confirmed patients were analysed by dd RT-PCR and RTPCR based target gene (N1 and N2). Stool and urine were collected from COVID Care Centers of Pune Region. RNA was isolated using MagMax magnetic beads base procedure for further analysis. Real Time RT-PCR and DD PCR was performed from all the patients. Result(s): In 107 patients, all the stool samples showed 100% positive concordance by both methods, the average of 28.88 cycle threshold (Ct) of RT-PCR was highly correlated with the average copy number of 327.10 copies/mul analyzed in ddPCR. Whereas 27.1% urine samples were tested positive in ddPCR & 1.86% were positive with the average of 36.41 cycle threshold (Ct) in RT-PCR. Using Pangolin COVID-19 Lineage Assigner variants were analyzed and found to be delta prevalent. Conclusion(s): In the context of the COVID-19 pandemic, environmental surveillance for the detection of SARS-CoV-2 has become increasingly important. The findings of this study not only show that SARS-CoV-2 is present in urine and faeces, but they also raise the possibility that low concentrations of the viral target may make it easier to identify positive samples and help resolve situations of inconclusive diagnosis.