{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T15:06:52Z","timestamp":1768403212811,"version":"3.49.0"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,7,15]],"date-time":"2020-07-15T00:00:00Z","timestamp":1594771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,7,15]],"date-time":"2020-07-15T00:00:00Z","timestamp":1594771200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The molecular detection system has evolved over last two decades and is rapidly replacing the conventional confirmatory techniques in diagnostic virology. However the major limitation in implementation of available molecular detection assays is the non availability of field deployable nucleic acid isolation platform coupled with gene amplification technique. The rapid and early molecular detection is crucial for employing effective measure against many viral infections. The re-emergence of chikungunya virus (CHIKV) has led to epidemics since 2004 in several parts of the world including India. The main association of CHIKV with severe arthritis and long-lasting arthralgia and closely mimics symptoms of Dengue and Zika virus infection requiring laboratory confirmation. In this study, a simple magnetic bead based ribonucleic acid extraction method was optimized, which was coupled with isothermal polymerase spiral reaction (PSR) technique for early and rapid detection. Subsequently, the polymerase spiral reaction reagents were converted to dry down format that led to a rapid user friendly field compatible sample processing to answer method for rapid and onsite detection of Chikungunya virus. Both the methods were evaluated with a panel of clinical samples. The sensitivity of the assays were compared with available commercial viral RNA extraction platform and qRT-PCR. The in-house nucleic acid extraction system based on magnetic bead followed by dry down RT-Polymerase Spiral Reaction assay was found to be highly sensitive with 10 copies of RNA as limit of detection in CHIKV clinical specimens. With respect to other closely related viruses no cross reactivity was observed. This novel methodology has the potential to revolutionize the diagnosis of infectious agents in resource limited settings around the world.<\/jats:p>","DOI":"10.1038\/s41598-020-68469-2","type":"journal-article","created":{"date-parts":[[2020,7,15]],"date-time":"2020-07-15T10:04:02Z","timestamp":1594807442000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Development of magnetic bead based sample extraction coupled polymerase spiral reaction for rapid on-site detection of Chikungunya virus"],"prefix":"10.1038","volume":"10","author":[{"given":"Shashi","family":"Sharma","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deepak","family":"Pardasani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paban Kumar","family":"Dash","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manmohan","family":"Parida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Devendra Kumar","family":"Dubey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,7,15]]},"reference":[{"key":"68469_CR1","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/j.0042-9007.2004.00379.x","volume":"86","author":"DA Marshall","year":"2004","unstructured":"Marshall, D. A. et al. Cost-effectiveness of nucleic acid test screening of volunteer blood donations for hepatitis B, hepatitis C and human immunodeficiency virus in the United States. Vox. Sang. 86, 28\u201340 (2004).","journal-title":"Vox. Sang."},{"key":"68469_CR2","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nrmicro841","volume":"2","author":"D Mabey","year":"2004","unstructured":"Mabey, D. et al. Diagnostics for the developing world. Nat. Rev. Microbiol. 2, 231\u2013240 (2004).","journal-title":"Nat. Rev. Microbiol."},{"key":"68469_CR3","doi-asserted-by":"publisher","first-page":"5294","DOI":"10.1021\/bi00591a005","volume":"18","author":"JM Chirgwin","year":"1979","unstructured":"Chirgwin, J. M. et al. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18, 5294\u20135299 (1979).","journal-title":"Biochemistry"},{"key":"68469_CR4","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1128\/JCM.28.3.495-503.1990","volume":"28","author":"R Boom","year":"1990","unstructured":"Boom, R. et al. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495\u2013503 (1990).","journal-title":"J. Clin. Microbiol."},{"key":"68469_CR5","doi-asserted-by":"publisher","first-page":"E63","DOI":"10.1093\/nar\/28.12.e63","volume":"28","author":"T Notomi","year":"2000","unstructured":"Notomi, T. et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28, E63. https:\/\/doi.org\/10.1093\/nar\/28.12.e63 (2000).","journal-title":"Nucleic Acids Res."},{"key":"68469_CR6","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1002\/rmv.593","volume":"18","author":"MM Parida","year":"2008","unstructured":"Parida, M. M. et al. Loop mediated isothermal amplification (LAMP): A new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev. Med. Virol. 18, 407\u2013421 (2008).","journal-title":"Rev. Med. Virol."},{"key":"68469_CR7","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1101\/gr.1.1.25","volume":"1","author":"E Fahy","year":"1991","unstructured":"Fahy, E. et al. Self-sustained sequence replication (3SR): An isothermal transcription-based amplification system alternative to PCR. PCR Methods Appl. 1, 25\u201333. https:\/\/doi.org\/10.1101\/gr.1.1.25 (1991).","journal-title":"PCR Methods Appl."},{"key":"68469_CR8","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1038\/sj.embor.7400200","volume":"5","author":"M Vincent","year":"2004","unstructured":"Vincent, M. et al. Helicase-dependent isothermal DNA amplification. EMBO Rep. 5, 795\u2013800. https:\/\/doi.org\/10.1038\/sj.embor.7400200 (2004).","journal-title":"EMBO Rep."},{"key":"68469_CR9","doi-asserted-by":"publisher","first-page":"12723","DOI":"10.1038\/srep12723","volume":"5","author":"W Liu","year":"2015","unstructured":"Liu, W. et al. Polymerase spiral reaction (PSR): A novel isothermal nucleic acid amplification method. Sci. Rep. 5, 12723\u201312730 (2015).","journal-title":"Sci. Rep."},{"key":"68469_CR10","first-page":"916","volume":"7","author":"X Jiang","year":"2016","unstructured":"Jiang, X. et al. Rapid detection of Candida albicans by polymerase spiral reaction assay in clinical blood samples. Front. Microbiol. 7, 916 (2016).","journal-title":"Front. Microbiol."},{"key":"68469_CR11","first-page":"1100","volume":"6","author":"D Dong","year":"2016","unstructured":"Dong, D. et al. Rapid detection of Pseudomonas aeruginosa targeting the toxA gene in intensive care unit patients from Beijing, China. Front Microbiol. 6, 1100 (2016).","journal-title":"Front Microbiol."},{"issue":"7","key":"68469_CR12","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.1007\/s00705-017-3321-5","volume":"162","author":"V Gupta","year":"2017","unstructured":"Gupta, V. et al. Polymerase spiral reaction (PSR): A novel, visual isothermal amplification method for detection of canine parvovirus 2 genomic DNA. Arch. Virol. 162(7), 1995\u20132001 (2017).","journal-title":"Arch. Virol."},{"key":"68469_CR13","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.gene.2017.11.004","volume":"644","author":"JA Malla","year":"2018","unstructured":"Malla, J. A. et al. Novel polymerase spiral reaction (PSR) for rapid visual detection of Bovine Herpesvirus 1 genomic DNA from aborted bovine fetus and semen. Gene 644, 107\u2013112 (2018).","journal-title":"Gene"},{"issue":"1","key":"68469_CR14","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1080\/22221751.2018.1559708","volume":"8","author":"BMCR Wimalasiri-Yapa","year":"2019","unstructured":"Wimalasiri-Yapa, B. M. C. R. et al. Chikungunya virus in Asia\u2013Pacific: a systematic review. Emerg Microbes Infect. 8(1), 70\u201379. https:\/\/doi.org\/10.1080\/22221751.2018.1559708 (2019).","journal-title":"Emerg Microbes Infect."},{"key":"68469_CR15","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1089\/vbz.2006.0648","volume":"7","author":"PK Dash","year":"2007","unstructured":"Dash, P. K. et al. East Central South african Genotype as causative agent inreemergence of Chikungunya out break in India. Vector Borne Zoonotic Dis. 7, 719\u2013727 (2007).","journal-title":"Vector Borne Zoonotic Dis."},{"key":"68469_CR16","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00350-19","author":"S Muktha","year":"2019","unstructured":"Muktha, S. et al. Beyond fever and pain: diagnostic methods for Chikungunya virus. J. Clin. Microbiol. https:\/\/doi.org\/10.1128\/JCM.00350-19 (2019).","journal-title":"J. Clin. Microbiol."},{"key":"68469_CR17","doi-asserted-by":"publisher","DOI":"10.1007\/82_2018_147","author":"MK McCarthy","year":"2019","unstructured":"McCarthy, M. K. et al. Chronic Chikungunya virus disease. Curr. Top. Microbiol. Immunol. https:\/\/doi.org\/10.1007\/82_2018_147 (2019).","journal-title":"Curr. Top. Microbiol. Immunol."},{"issue":"2","key":"68469_CR18","doi-asserted-by":"publisher","first-page":"179","DOI":"10.2217\/17460794.3.2.179","volume":"3","author":"MM Parida","year":"2008","unstructured":"Parida, M. M. et al. Rapid and real-time assays for detection and quantification of Chikungunya virus. Fut. Virol. 3(2), 179\u2013192 (2008).","journal-title":"Fut. Virol."},{"key":"68469_CR19","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.jviromet.2013.07.004","volume":"193","author":"A Agarwal","year":"2013","unstructured":"Agarwal, A. et al. Application of Real-Time RT-PCR in vector surveillance and assessment of replication kinetics of an emerging Novel ECSA genotype of Chikungunya virus in Aedes aegypti. J. Virol. Methods 193, 419\u2013425 (2013).","journal-title":"J. Virol. Methods"},{"key":"68469_CR20","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/s12033-009-9238-9","volume":"45","author":"S Sharma","year":"2010","unstructured":"Sharma, S. et al. Development of a quantitative competitive reverse transcription polymerase chain reaction (QC-RT-PCR) for detection and quantitation of Chikungunya virus. Mol. Biotechnol. 45, 49\u201355 (2010).","journal-title":"Mol. Biotechnol."},{"key":"68469_CR21","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.jcv.2007.04.015","volume":"39","author":"SR Santhosh","year":"2007","unstructured":"Santhosh, S. R. et al. Development and evaluation of SYBR Green I based one step real time RT-PCR assay for detection and quantification of Chikungunya virus. J. Clin. Virol. 39, 188\u2013193 (2007).","journal-title":"J. Clin. Virol."},{"issue":"2","key":"68469_CR22","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1128\/JCM.01734-06","volume":"45","author":"MM Parida","year":"2007","unstructured":"Parida, M. M. et al. Rapid and real-time detection of chikungunya virus by reverse transcription loop mediated isothermal amplification assay. J. Clin. Microbiol. 45(2), 351\u2013357 (2007).","journal-title":"J. Clin. Microbiol."},{"key":"68469_CR23","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.actatropica.2018.09.003","volume":"188","author":"JVJJ Silva","year":"2018","unstructured":"Silva, J. V. J. J. et al. A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control. Acta Trop. 188, 213\u2013224. https:\/\/doi.org\/10.1016\/j.actatropica.2018.09.003 (2018).","journal-title":"Acta Trop."},{"issue":"8","key":"68469_CR24","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1590\/0074-02760170044","volume":"112","author":"RVD Cunha","year":"2017","unstructured":"Cunha, R. V. D. & Trinta, K. S. Chikungunya virus: Clinical aspects and treatment\u2014a review. Mem Inst Oswaldo Cruz. 112(8), 523\u2013531. https:\/\/doi.org\/10.1590\/0074-02760170044 (2017).","journal-title":"Mem Inst Oswaldo Cruz."},{"key":"68469_CR25","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/367382","author":"M Soni","year":"2013","unstructured":"Soni, M. et al. Molecular and virological investigation of a focal Chikungunya outbreak in northern India. Sci. World J. https:\/\/doi.org\/10.1155\/2013\/367382 (2013).","journal-title":"Sci. World J."},{"issue":"2","key":"68469_CR26","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.diagmicrobio.2009.06.017","volume":"65","author":"J Shukla","year":"2009","unstructured":"Shukla, J. et al. Development and evaluation of antigen capture ELISA for early clinical diagnosis of chikungunya. Diagn. Microbiol. Infect Dis 65(2), 142\u2013149 (2009).","journal-title":"Diagn. Microbiol. Infect Dis"},{"issue":"1","key":"68469_CR27","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1002\/smll.200700456","volume":"4","author":"J Lee","year":"2008","unstructured":"Lee, J. et al. Simple synthesis of functionalized superparamagnetic magnetite\/silica core\/shell nanoparticles and their application as magnetically separable high-performance biocatalysts. Small 4(1), 143\u2013152 (2008).","journal-title":"Small"},{"issue":"6","key":"68469_CR28","doi-asserted-by":"publisher","first-page":"709","DOI":"10.4269\/ajtmh.1997.57.709","volume":"57","author":"M Pfeffer","year":"1997","unstructured":"Pfeffer, M. et al. Genus-specific detection of alphaviruses by a semi-nested reverse transcription-polymerase chain reaction. Am. J. Trop. Med. Hygiene 57(6), 709\u2013718 (1997).","journal-title":"Am. J. Trop. Med. Hygiene"},{"issue":"1","key":"68469_CR29","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1007\/s13337-018-0423-y","volume":"29","author":"S Sharma","year":"2018","unstructured":"Sharma, S. et al. Simultaneous detection and serotyping of dengue infection using single tube multiplex CDC Dengue Real-Time RT-PCR from India. Virus dis 29(1), 40\u201345. https:\/\/doi.org\/10.1007\/s13337-018-0423-y (2018).","journal-title":"Virus dis"},{"issue":"1","key":"68469_CR30","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.jviromet.2007.02.011","volume":"143","author":"SR Santhosh","year":"2007","unstructured":"Santhosh, S. R. et al. Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantitation of Japanese encephalitis virus. J. Virol. Methods 143(1), 73\u201380. https:\/\/doi.org\/10.1016\/j.jviromet.2007.02.011 (2007).","journal-title":"J. Virol. Methods"},{"issue":"11","key":"68469_CR31","doi-asserted-by":"publisher","first-page":"4066","DOI":"10.1128\/JCM.38.11.4066-4071.2000","volume":"38","author":"RS Lanciotti","year":"2000","unstructured":"Lanciotti, R. S. et al. Rapid detection of west nile virus from human clinical specimens, field-collected mosquitoes, and avian samples by a TaqMan reverse transcriptase-PCR assay. J. Clin. Microbiol. 38(11), 4066\u20134071 (2000).","journal-title":"J. Clin. Microbiol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68469-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68469-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68469-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,6]],"date-time":"2022-12-06T13:58:03Z","timestamp":1670335083000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68469-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,15]]},"references-count":31,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["68469"],"URL":"https:\/\/doi.org\/10.1038\/s41598-020-68469-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,15]]},"assertion":[{"value":"2 November 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 June 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 July 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"11651"}}