key: cord-0851240-0g083ih8 authors: Ansil, B. R.; George, C. E.; Chandrasingh, S.; Viswanathan, A.; Thattai, M.; Raghu, P.; Devadiga, S.; Harikumar, A. G.; Harsha, P. K.; Nair, I.; Ramakrishnan, U.; Mayor, S. title: Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2 date: 2022-02-08 journal: nan DOI: 10.1101/2022.02.07.22269889 sha: 4840ab9945906bd928abedd87001b838a31e5435 doc_id: 851240 cord_uid: 0g083ih8 Purpose: Compared to nasopharyngeal/oropharyngeal swabs, non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we are investigating the efficacy of saliva samples relative to nasopharyngeal/oropharyngeal swabs for use as a direct source for the RT-PCR based SARS-CoV-2 detection. Methods: Paired nasopharyngeal/oropharyngeal swabs and saliva samples were collected from suspected positive SARS-CoV-2 patients and tested using RT-PCR. Generalised linear models were used to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. Results: We observed 75.4% overall result agreement. Prospective positive samples stored for three or more days showed a drastic reduction in the probability of result agreement. We observed 83% result agreement and 74.5% test sensitivity in samples processed and tested within two days of collection. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. Conclusion: These results suggest that saliva may be a viable sample source for SARS-CoV-2 surveillance if samples are processed immediately. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. The COVID-19 pandemic spread rapidly in India, infecting more than 30 million people in 52 two years [1] . Given this magnitude and speed, COVID-19 presents various diagnostic 53 challenges, in the context of massive population density and limited diagnostic and health 54 infrastructure capabilities. Viral diagnosis has progressed tremendously, and of the various 55 modalities for SARS-CoV-2 diagnosis, the most reliable test is the reverse transcription- In this study, we assessed the performance of saliva relative to N/OPS-VTM samples for use 74 as a direct source (without RNA extraction) for the RT-PCR based SARS-CoV-2 detection. 75 . CC-BY-NC 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. 55.5% (SE 45.7-64.9) when samples were stored for more than two days (p=0.025). 147 Concordance (83%) and the sensitivity (74.5%) of the saliva test improved when we 148 considered only the samples tested within two days of collection (Table 2) . This also resulted 149 in a significant improvement (decrease) in inconclusive test results (1.8% in saliva and 0.9% 150 . CC-BY-NC 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. Simulations reveal that saliva-based screening can limit infection spread 155 We track the probability that a single starting infection leads to a large cluster (of size 25 or 156 more) as the testing parameters are varied (Fig 3) . This model is not meant to replicate the 157 transmission dynamics of an actual workforce; rather, it is a proof of principle to identify key 158 factors that influence the success of screening. We focus on three key factors of the testing 159 protocol: (a) sensitivity, (b) daily testing capacity, (c) delay in reporting results. In our 160 simulations, in the absence of testing and isolation, the probability of a large cluster is 20% 161 under the assumed parameter values. However, by using a test with 75% sensitivity, at 200 162 tests per day with a one-day delay for results, we decrease the probability of a large cluster 163 ten-fold, to about 2%. Moreover, this protocol works better than a test with 100% sensitivity, 164 but with half the capacity or twice the delay. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. ; https://doi.org/10.1101/2022.02.07.22269889 doi: medRxiv preprint . CC-BY-NC 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted February 8, 2022. ; https://doi.org/10.1101/2022.02.07.22269889 doi: medRxiv preprint (2021) Ministry of Health and Family Welfare, Government 288 of India Nasopharyngeal Swabs Are More Sensitive Than 290 Oropharyngeal Swabs for COVID-19 Diagnosis and Monitoring the SARS-CoV-2 SalivaDirect: A simplified and 293 flexible platform to enhance SARS-CoV-2 testing capacity Screening for SARS-CoV-2 by 296 Saliva or nasopharyngeal swab? Rapid review and meta-analysis A Saliva-Based RNA Extraction-Free 299 Workflow Integrated With Cas13a for SARS-CoV-2 Detection Microbiol 11:632646 Saliva for diagnosis of SARS-CoV First report from India False Negative Tests for SARS-CoV-2 304 Infection -Challenges and Implications Nasopharyngeal Swab Nucleic Acid Amplification Testing for Detection of SARS-310 CoV-2: A Systematic Review and Meta-analysis Challenges in use of saliva for detection of 313 SARS CoV-2 RNA in symptomatic outpatients Saliva is a reliable, non-invasive 316 specimen for SARS-CoV-2 detection Comparison of SARS-CoV-2 detection 319 in nasopharyngeal swab and saliva Practical challenges to the clinical 322 implementation of saliva for SARS-CoV-2 detection Saliva sample 325 pooling for the detection of SARS-CoV-2 Swab Specimens for Detection of SARS-CoV-2 Accuracy and stability of saliva as a 331 sample for reverse transcription PCR detection of SARS-CoV-2 Equivalent SARS-CoV-2 viral loads by PCR 334 between nasopharyngeal swab and saliva in symptomatic patients Saliva 337 as a possible tool for the SARS-CoV-2 detection: A review Pooling of SARS-CoV-2 samples to 340 increase molecular testing throughput Pooling saliva to increase 343 SARS-CoV-2 testing capacity. Infectious Diseases (except HIV/AIDS) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted February 8, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted February 8, 2022. ; https://doi.org/10.1101/2022.02.07.22269889 doi: medRxiv preprint