In this current COVID 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS COV 2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer- Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS CoV 2 testing.
Background The current pandemic of SARS- COV- 2 virus, widely known as COVID-19 has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS- COV- 2 virus has provided the solution to mass screening of people. The pooled testing strategy can be very effective in testing with limited resources, yet it comes with its own limitations. These limitations need critical consideration when it comes to testing of highly infectious disease like COVID -19. Methods The study evaluated the pooled testing of nasopharyngeal swabs for SARS- COV- 2 by comparing sensitivity of individual sample testing with 4 and 8 pool sample testing. Median cycle threshold (Ct) values were compared. The precision of pooled testing was assessed by doing an inter and intra assay of pooled samples. Coefficient of variance was calculated for inter and intra assay variability. Results The sensitivity becomes considerably low when the samples are pooled, there is a higher percentage of false negatives with higher pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra and inter assay, especially in weak positive samples and larger pool size. Conclusion As COVID - 19 numbers are still high and testing capacity needs to be high, we have to meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to make a serious call on cost effective strategy of resource saving and risk/ cost of missing positive patients.
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