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Current Molecular Medicine

Author(s): Akansha Bhatt, Zeeshan Fatima*, Munindra Ruwali* and Saif Hameed*

DOI: 10.2174/1566524021666210910113714

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An Inventory of Diagnostic Tools for Detection of COVID-19

Page: [608 - 620] Pages: 13

  • * (Excluding Mailing and Handling)

Abstract

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has afflicted millions of lives globally and disrupted almost all the activities of mankind. Under such pressing circumstances when no effective therapeutics are available, a fast and accurate diagnosis of the coronavirus is the only way out to limit the transmission. Since the inception of COVID-19, the demand for diagnostic tests has increased day by day and RT-PCR is the commonly used screening test that is not only time-consuming but requires sophisticated resources. To address the increasing rate of spread of COVID-19, there is an urgent need for more diagnostic tools as the research on vaccines is still at a rudimentary level. This review summarizes an inventory of the diverse and currently available diagnostic methods based on nucleic acid and serology along with some of those working on novel principles viz. CRISPR, biosensors, and NGS. Additionally, accessible diagnostic kits that are already approved by the US and European authorities for the diagnosis of COVID-19 are also suggested that will help in selecting the most effective tests under the given scenario. Taken together, this review will pave way for further strengthening the research on the rapid and safer diagnostics of SARS-COV-2.

Keywords: COVID-19, SARS-COV-2, diagnostics, nucleic acid, serology, biosensors, NGS, CRISPR.

[1]
Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet 2020; 395(10223): 470-3.
[http://dx.doi.org/10.1016/S0140-6736(20)30185-9] [PMID: 31986257]
[2]
Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382(8): 727-33.
[http://dx.doi.org/10.1056/NEJMoa2001017] [PMID: 31978945]
[3]
Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020; 395(10223): 497-506.
[http://dx.doi.org/10.1016/S0140-6736(20)30183-5] [PMID: 31986264]
[4]
Li Q, Guan X, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Engl J Med 2020; 382(13): 1199-207.
[http://dx.doi.org/10.1056/NEJMoa2001316] [PMID: 31995857]
[5]
Han Y, Yang H. The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID-19): A Chinese perspective. J Med Virol 2020; 92(6): 639-44.
[http://dx.doi.org/10.1002/jmv.25749] [PMID: 32141619]
[6]
Gopal C. Kundu,Srinivas Patnaik,Amit S Yadav,NNV Radharani,Ipsita G Kundu: SARS-CoV-2: Origin, patho-genesis and Therapeutic Interventions. Coronaviruses 2020; 2(7): e160721188927.
[http://dx.doi.org/10.2174/2666796701999201209144207]
[7]
Therapeutic Measures for the Novel Coronavirus A Review of Current Status and Future Perspective. Curr Mol Med 2021; 21(7): 562-72.
[http://dx.doi.org/10.2174/1566524020666201203170230]
[8]
Ali N, Rampazzo RCP, Costa ADT, Krieger MA. Current nucleic acid extraction mehods and their implications to point-of-care diagnostics. BioMed Res Int 2017; 2017: 9306564.
[http://dx.doi.org/10.1155/2017/9306564] [PMID: 28785592]
[9]
Mlcochova Petra, Collier Dami, Ritchie Allyson, et al. The Cambridge institute of therapeutic immunology and infectious disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration.
[10]
Kilic T, Weissleder R, Lee H. Molecular and immunological diagnostic tests of COVID-19–current status and challenges. iScience 2020; 23(8): 101406.
[http://dx.doi.org/10.1016/j.isci.2020.101406] [PMID: 32771976]
[11]
Corman V, Bleicker T, Brünink S, Drosten C, Zambon M. Diagnostic detection of Wuhan coronavirus 2019 by real-time RT-PCR. Geneva: World Health Organization 2020.
[12]
Bustin SA, Ed. AZ of quantitative PCR. La Jolla, CA: International University Lin 2004; pp. 439-92.
[13]
Wong ML, Medrano JF. Real-time PCR for mRNA quantitation. Biotechniques 2005; 39(1): 75-85.
[http://dx.doi.org/10.2144/05391RV01] [PMID: 16060372]
[14]
Zhang W, Du RH, Li B, et al. Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect 2020; 9(1): 386-9.
[http://dx.doi.org/10.1080/22221751.2020.1729071] [PMID: 32065057]
[15]
Sexton NR, Smith EC, Blanc H, Vignuzzi M, Peersen OB, Denison MR. Homology-based identification of a mutation in the coronavirus RNA-dependent RNA polymerase that confers resistance to multiple mutagens. J Virol 2016; 90(16): 7415-28.
[http://dx.doi.org/10.1128/JVI.00080-16] [PMID: 27279608]
[16]
Mizumoto K, Kagaya K, Zarebski A, Chowell G. Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020. Euro Surveill 2020; 25(10): 2000180.
[http://dx.doi.org/10.2807/1560-7917.ES.2020.25.10.2000180] [PMID: 32183930]
[17]
Mori Y, Notomi T. Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother 2009; 15(2): 62-9.
[http://dx.doi.org/10.1007/s10156-009-0669-9] [PMID: 19396514]
[18]
Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 2000; 28(12): E63.
[http://dx.doi.org/10.1093/nar/28.12.e63] [PMID: 10871386]
[19]
Chou PH, Lin YC, Teng PH, Chen CL, Lee PY. Real-time target-specific detection of loop-mediated isothermal amplification for white spot syndrome virus using fluorescence energy transfer-based probes. J Virol Methods 2011; 173(1): 67-74.
[http://dx.doi.org/10.1016/j.jviromet.2011.01.009] [PMID: 21256868]
[20]
Nagai K, Horita N, Yamamoto M, et al. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep 2016; 6: 39090.
[http://dx.doi.org/10.1038/srep39090] [PMID: 27958360]
[21]
Qian C, Wang R, Wu H, Ji F, Wu J. Nicking enzyme-assisted amplification (NEAA) technology and its applications: A review. Anal Chim Acta 2019; 1050: 1-15.
[http://dx.doi.org/10.1016/j.aca.2018.10.054] [PMID: 30661576]
[22]
Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M. Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis. Malar J 2014; 13(1): 99.
[http://dx.doi.org/10.1186/1475-2875-13-99] [PMID: 24629133]
[23]
Faye O, Faye O, Soropogui B, et al. Development and deployment of a rapid recombinase polymerase amplification Ebola virus detection assay in Guinea in 2015. Euro Surveill 2015; 20(44): 30053.
[http://dx.doi.org/10.2807/1560-7917.ES.2015.20.44.30053] [PMID: 26558690]
[24]
Yehia N, Arafa AS, Abd El Wahed A, El-Sanousi AA, Weidmann M, Shalaby MA. Development of reverse transcription recombinase polymerase amplification assay for avian influenza H5N1 HA gene detection. J Virol Methods 2015; 223: 45-9.
[http://dx.doi.org/10.1016/j.jviromet.2015.07.011] [PMID: 26225482]
[25]
Piepenburg O, Williams CH, Stemple DL, Armes NA. DNA detection using recombination proteins. PLoS Biol 2006; 4(7): e204.
[http://dx.doi.org/10.1371/journal.pbio.0040204] [PMID: 16756388]
[26]
Krõlov K, Frolova J, Tudoran O, et al. Sensitive and rapid detection of Chlamydia trachomatis by recombinase polymerase amplification directly from urine samples. J Mol Diagn 2014; 16(1): 127-35.
[http://dx.doi.org/10.1016/j.jmoldx.2013.08.003] [PMID: 24331366]
[27]
Crannell ZA, Rohrman B, Richards-Kortum R. Equipment-free incubation of recombinase polymerase amplification reactions using body heat. PLoS One 2014; 9(11): e112146.
[http://dx.doi.org/10.1371/journal.pone.0112146] [PMID: 25372030]
[28]
Xia S, Chen X. Single-copy sensitive, field-deployable, and simultaneous dual-gene detection of SARS-CoV-2 RNA via modified RT-RPA. Cell Discov 2020; 6(1): 37.
[http://dx.doi.org/10.1038/s41421-020-0175-x] [PMID: 34045433]
[29]
Makarova KS, Wolf YI, Iranzo J, et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 2020; 18(2): 67-83.
[http://dx.doi.org/10.1038/s41579-019-0299-x] [PMID: 31857715]
[30]
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337(6096): 816-21.
[31]
Chen JS, Ma E, Harrington LB, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 2018; 360(6387): 436-9.
[http://dx.doi.org/10.1126/science.aar6245] [PMID: 29449511]
[32]
Chiu C. Cutting-edge infectious disease diagnostics with CRISPR. Cell Host Microbe 2018; 23(6): 702-4.
[http://dx.doi.org/10.1016/j.chom.2018.05.016] [PMID: 29902435]
[33]
Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017; 356(6336): 438-42.
[http://dx.doi.org/10.1126/science.aam9321] [PMID: 28408723]
[34]
Myhrvold C, Freije CA, Gootenberg JS, et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 2018; 360(6387): 444-8.
[http://dx.doi.org/10.1126/science.aas8836] [PMID: 29700266]
[35]
Li SY, Cheng QX, Wang JM, et al. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov 2018; 4(1): 20.
[http://dx.doi.org/10.1038/s41421-018-0028-z] [PMID: 29707234]
[36]
Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38(7): 870-4.
[http://dx.doi.org/10.1038/s41587-020-0513-4] [PMID: 32300245]
[37]
Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 2019; 14(10): 2986-3012.
[http://dx.doi.org/10.1038/s41596-019-0210-2] [PMID: 31548639]
[38]
Peeling RW, Wedderburn CJ, Garcia PJ, et al. Serology testing in the COVID-19 pandemic response. Lancet Infect Dis 2020; 20(9): e245-9.
[http://dx.doi.org/10.1016/S1473-3099(20)30517-X] [PMID: 32687805]
[39]
Zhao J, Yuan Q, Wang H, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin Infect Dis 2020; 71(16): 2027-34.
[http://dx.doi.org/10.1093/cid/ciaa344] [PMID: 32221519]
[40]
Mahmoudi T, de la Guardia M, Baradaran B. Lateral flow assays towards point-of-care cancer detection: A review of current progress and future trends. Trends Analyt Chem 2020; 125: 115842.
[http://dx.doi.org/10.1016/j.trac.2020.115842]
[41]
Jääskeläinen AJ, Kekäläinen E, Kallio-Kokko H, et al. Evaluation of commercial and automated SARS-CoV-2 IgG and IgA ELISAs using coronavirus disease (COVID-19) patient samples. Euro Surveill 2020; 25(18): 2000603.
[http://dx.doi.org/10.2807/1560-7917.ES.2020.25.18.2000603] [PMID: 32400364]
[42]
Woo PC, Lau SK, Wong BH, et al. False-positive results in a recombinant severe acute respiratory syndrome-associated coronavirus (SARS-CoV) nucleocapsid enzyme-linked immunosorbent assay due to HCoV-OC43 and HCoV-229E rectified by Western blotting with recombinant SARS-CoV spike polypeptide. J Clin Microbiol 2004; 42(12): 5885-8.
[http://dx.doi.org/10.1128/JCM.42.12.5885-5888.2004] [PMID: 15583332]
[43]
Tan CW, Chia WN, Chen MI, Hu Z, Young BE, Tan YJA. SARS-CoV-2 surrogate virus neutralization test (sVNT) based on antibody-mediated blockage of ACE2-spike (RBD) protein-protein interaction. Nat Biotechnol 2020; 38(9): 1073-8.
[http://dx.doi.org/10.21203/rs.3.rs-24574/v1]
[44]
Xiong H, Wu Y, Cao J, et al. Robust neutralization assay based on SARS-CoV-2 S-bearing vesicular stomatitis virus (VSV) pseudovirus and ACE2-overexpressed BHK21 cells. Emerg Microbes Infect 2020; 9(1): 2105-13.
[http://dx.doi.org/10.1101/2020.04.08.026948]
[45]
Lijia S, Lihong S, Huabin W, et al. Serological chemiluminescence immunoassay for the diagnosis of SARS-CoV-2 infection. J Clin Lab Anal 2020; 34(10): e23466.
[http://dx.doi.org/10.1002/jcla.23466] [PMID: 32671890]
[46]
Bhunia AK. Biosensors and bio‐based methods for the separation and detection of foodborne pathogens. In: advances in food and nutrition research. Academic Press 2008; Vol. 54: pp. 1-44.
[http://dx.doi.org/10.1016/S1043-4526(07)00001-0]
[47]
Demeke A, Samaddar M, Alharbi MG, Al-Hindi RR, Bhunia AK. Biosensor and molecular-based methods for the detection of human coronaviruses: A review. Mol Cell Probes 2020; 101662.
[http://dx.doi.org/10.1016/j.mcp.2020.101662]
[48]
Holford TR, Davis F, Higson SP. Recent trends in antibody based sensors. Biosens Bioelectron 2012; 34(1): 12-24.
[http://dx.doi.org/10.1016/j.bios.2011.10.023] [PMID: 22387037]
[49]
Nehra A, Pal Singh K. Current trends in nanomaterial embedded field effect transistor-based biosensor. Biosens Bioelectron 2015; 74: 731-43.
[http://dx.doi.org/10.1016/j.bios.2015.07.030] [PMID: 26210471]
[50]
Janissen R, Sahoo PK, Santos CA, et al. InP nanowire biosensor with tailored biofunctionalization: ultrasensitive and highly selective disease biomarker detection. Nano Lett 2017; 17(10): 5938-49.
[http://dx.doi.org/10.1021/acs.nanolett.7b01803] [PMID: 28895736]
[51]
Seo G, Lee G, Kim MJ, et al. Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor. ACS Nano 2020; 14(4): 5135-42.
[http://dx.doi.org/10.1021/acsnano.0c02823] [PMID: 32293168]
[52]
Qiu G, Gai Z, Tao Y, Schmitt J, Kullak-Ublick GA, Wang J. Dual-functional plasmonic photothermal biosensors for highly accurate severe acute respiratory syndrome coronavirus 2 detection. ACS Nano 2020; 14(5): 5268-77.
[http://dx.doi.org/10.1021/acsnano.0c02439] [PMID: 32281785]
[53]
Hui Q, Pan Y, Yang Z. based devices for rapid diagnostics and testing sewage for early warning of COVID-19 outbreak. Case Studies in Chemical and Environmental Engineering 2020; 100064.
[http://dx.doi.org/10.1016/j.cscee.2020.100064]
[54]
Sheridan C. Fast, portable tests come online to curb coronavirus pandemic. Nat Biotechnol 2020; 38(5): 515-8.
[http://dx.doi.org/10.1038/d41587-020-00010-2] [PMID: 32203294]