key: cord-0730997-5n1847is authors: ANNAMALAI, PAZHANIMUTHU; KANTA, MADHU; RAMU, PAZHANIVEL; RAVI, BASKAR; VEERAPANDIAN, KOKILAVANI; SRINIVASAN, RENGARAJAN title: A SIMPLE COLORIMETRIC MOLECULAR DETECTION OF NOVEL CORONAVIRUS (COVID-19), AN ESSENTIAL DIAGNOSTIC TOOL FOR PANDEMIC SCREENING date: 2020-04-14 journal: nan DOI: 10.1101/2020.04.10.20060293 sha: 4de2ed1a2bde308480b79b8003dbfb582e57236d doc_id: 730997 cord_uid: 5n1847is The recent outbreak of the newly emerged novel coronavirus (SARS-CoV-2) presents a big challenge for public health laboratories as virus isolates are not available while there is an increasing evidence that the epidemic is more widespread than initially thought, as well as spreading internationally across borders through travellers does already happen warranting a methodology for the rapid detection of the infection to control SARS-CoV-2. Aim: We intended to develop and deploy a robust and rapid diagnostic methodology using LAMP assay for use in point of care settings to detect SARS-COV-2 infection. Methodology: In the present study, we have developed a validated rapid diagnostic procedure to detect SARS-CoV-2 using LAMP assay, its design relying on isothermal amplification of the nucleic acids of the SARS-CoV-2. Results: The LAMP assay developed detects SARS-CoV-2 infection rapidly with high sensitivity and reliability. The data generated by LAMP assay were comparable and at par with the data generated by real-time PCR method. Conclusion: The present study demonstrates that the LAMP assay developed was a rapid, reliable, sensitive and cost effective method to detect SARS-CoV-2 infection in a point of care as well as in laboratory settings. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the is of great concern as is always the case for emerging infections. Most of the 107 infected patients had a high fever and some had dyspnoea, with chest 108 radiographs revealing invasive lesions in both lungs. 1, 16 Non-pharmaceutical 109 All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the The LAMP primers ( Table 1) author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint different copy numbers (10 -6 -10 0 ) of the N and ORF target RNAs as well as for 197 internal control RNaseP RNA were given in Table 2 . (Fig. 1A, 1B, 1C) . The sensitivity was found to be high the viral RNA is detected 211 even up to 10 copy number with good specificity. The present study was aimed at developing a LAMP assay specifically for the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint from the amplifications curves generated in the assay, it is observed that the 219 amplicons generated were respective to each of N, ORF and RNaseP genes 220 from the LAMP reaction mix that contained the respective target DNAs and In the current study, at the end of the LAMP assay, we observed a dilution-233 dependent colour difference (i.e., pink to yellow) in the reactions mixes that author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint To conclude, the present study has demonstrated that SARS-CoV-2 infection in 241 humans can be detected by LAMP and RT-LAMP assays by targeting the N and 242 ORF genes of SARS-CoV-2 with high sensitivity and specificity. In addition, our 243 study has also confirmed that LAMP assay is a potential, suitable, cost effective author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint 1: 10 7 copies of ORF gene; 2: 341 4: 10 4 copies of ORF gene; 5. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.20060293 doi: medRxiv preprint GISAID: Genomic epidemiology of BetaCoV A familial cluster of pneumonia 255 associated with the 2019 novel coronavirus indicating person-to-person 256 transmission: a study of a family cluster The severe acute respiratory 259 syndrome European Centre for Disease Prevention and Control. Severe acute 261 respiratory syndrome-Annual Epidemiological Report The SARS epidemic in Hong Kong Epidemiology, genetic recombination, and 268 pathogenesis of coronaviruses Coronavirus avian infectious bronchitis virus All rights reserved. No reuse allowed without permission author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the Pathogenicity of turkey coronavirus in 272 turkeys and chickens Fatal swine acute diarrhoea syndrome caused 274 by an HKU2-related coronavirus of bat origin Severe acute respiratory syndrome SARS: epidemiology A dynamic compartmental model for the Middle 283 East respiratory syndrome outbreak in the Republic of Korea: a 284 retrospective analysis on control interventions and superspreading events The clinical and virological features of 287 the first imported case causing MERS-CoV outbreak in South Korea A novel coronavirus genome identified in a 290 cluster of pneumonia cases-Wuhan All rights reserved. No reuse allowed without permission author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is the