Molecular Diagnostic Tools for the Detection of SARS-CoV-2

References

• Fielding BC. Human coronavirus NL63: a clinically important virus. Future Microbiol 2011;6(2):153–159. doi:10.2217/fmb.10.166.
   PubMed Web of Science ®Google Scholar
• Lau SK, Lee P, Tsang AK, et al. Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. J Virol 2011;85(21):11325–11337. doi:10.1128/JVI.05512-11.
   PubMed Web of Science ®Google Scholar
• Boni MF, Lemey P, Jiang X, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020;5(11):1408–1417. doi:10.1038/s41564-020-0771-4.
   PubMed Web of Science ®Google Scholar
• Lau SK, Woo PC, Yip CC, et al. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J Clin Microbiol 2006;44(6):2063–2071. doi:10.1128/JCM.02614-05.
   PubMed Web of Science ®Google Scholar
• Cherry JD. The chronology of the 2002–2003 SARS mini pandemic. Paediatr Respir Rev 2004;5(4):262–269. doi:10.1016/j.prrv.2004.07.009.
   PubMedGoogle Scholar
• Raj VS, Osterhaus AD, Fouchier RA, et al. MERS: emergence of a novel human coronavirus. Curr Opin Virol 2014;5:58–62. doi:10.1016/j.coviro.2014.01.010.
   PubMed Web of Science ®Google Scholar
• Zheng J. SARS-CoV-2: an emerging coronavirus that causes a global threat. Int J Biol Sci 2020;16(10):1678–1685. doi:10.7150/ijbs.45053.
   PubMed Web of Science ®Google Scholar
• Kimball A, Hatfield KM, Arons M, et al. Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility – King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep 2020;69(13):377–381. doi:10.15585/mmwr.mm6913e1.
   PubMed Web of Science ®Google Scholar
• Xu X, Chen P, Wang J, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci 2020;63(3):457–460. doi:10.1007/s11427-020-1637-5.
   PubMed Web of Science ®Google Scholar
• Kliger Y, Levanon EY. Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy. BMC Microbiol 2003;3(1):20. doi:10.1186/1471-2180-3-20.
   PubMedGoogle Scholar
• Paraskevis D, Kostaki EG, Magiorkinis G, et al. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infect Genet Evol 2020;79:104212. doi:10.1016/j.meegid.2020.104212.
   PubMed Web of Science ®Google Scholar
• “WHO Director-General’s opening remarks at the media briefing on COVID-19”. World Health Organization (WHO) (Press release) 11 March 2020. Retrieved 12 March, 2020.
   Google Scholar
• Gordon CJ, Tchesnokov EP, Feng JY, et al. The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. J Biol Chem 2020;295(15):4773–4779. doi:10.1074/jbc.AC120.013056.
   PubMed Web of Science ®Google Scholar
• Ferron F, Subissi L, De Morais ATS, et al. Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA. PNAS 2018;115(2):162–171.
   PubMed Web of Science ®Google Scholar
• Báez-Santos YM, John SE, Mesecar AD. The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiv Res 2015;115:21–38. doi:10.1016/j.antiviral.2014.12.015.
   PubMed Web of Science ®Google Scholar
• Torres R, Rinder HM. Double-edged spike-are SARS-CoV-2 serologic tests safe right now?. Lab Med 2020;51(3):236–238. doi:10.1093/labmed/lmaa025.
   PubMed Web of Science ®Google Scholar
• Rahmani AR, Leili M, Azarian G, et al. Sampling and detection of corona viruses in air: a mini review. Sci Total Environ 2020;20:740. doi:10.1016/j.scitotenv.2020.140207
   Google Scholar
• Naqvi HR, Datta M, Mutreja G, et al. Improved air quality and associated mortalities in India under COVID-19 lockdown. Environ Pol 2021;268:115691. doi:10.1016/j.envpol.2020.115691
   Web of Science ®Google Scholar
• Liu Y, Ning Z, Chen Y, et al. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature 2020;582(7813):557–560. doi:10.1038/s41586-020-2271-3.
   PubMed Web of Science ®Google Scholar
• Guo ZD, Wang ZY, Zhang SF, et al. Aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in Hospital Wards, Wuhan, China 2020. Emerg Infect Dis 2020;26(7):1583-1591. doi:10.3201/eid2607.200885
   Web of Science ®Google Scholar
• Chia PY, Coleman KK, Tan YK, et al. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat Commun 2020;11(1):2800. doi:10.1038/s41467-020-16670-2.
   PubMed Web of Science ®Google Scholar
• Verreault D, Moineau S, Duchaine C. Methods for sampling of airborne viruses. Microbiology and molecular biology reviews. Microbiol Mol Biol Rev 2008;72(3):413–444. doi:10.1128/MMBR.00002-08.
   PubMed Web of Science ®Google Scholar
• Booth TF, Kournikakis B, Bastien N, et al. Detection of airborne severe acute respiratory syndrome (SARS) coronavirus and environmental contamination in SARS outbreak units. J Infect Dis 2005;191(9):1472–1477. doi:10.1086/429634.
   PubMed Web of Science ®Google Scholar
• Larsen DA, Wigginton KR. Tracking COVID-19 with wastewater. Nat Biotechnol 2020;38(10):1151–1153. doi:10.1038/s41587-020-0690-1.
   PubMed Web of Science ®Google Scholar
• Peccia J, Zulli A, Brackney DE, et al. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat Biotechnol 2020;38(10):1164–1167. doi:10.1038/s41587-020-0684-z.
   PubMed Web of Science ®Google Scholar
• Ishikawa FN, Chang HK, Curreli M, et al. Label-free, electrical detection of the SARS virus N-protein with nanowire biosensors utilizing antibody mimics as capture probes. ACS Nano 2009;3(5):1219–1224. doi:10.1021/nn900086c.
   PubMed Web of Science ®Google Scholar
• 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):386–389. doi:10.1080/22221751.2020.1729071.
   PubMed Web of Science ®Google Scholar
• Yu F, Du L, Ojcius DM, et al. Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China. Microbes Infect 2020; 22(2):74–79. doi:10.1016/j.micinf.2020.01.003.
   PubMed Web of Science ®Google Scholar
• Blanco JL, Ambrosioni J, Garcia F, et al. COVID-19 in patients with HIV: clinical case series. Lancet HIV 2020;7(5):e314–e316. doi:10.1016/S2352-3018(20)30111-9.
   PubMed Web of Science ®Google Scholar
• Yu L, Wu S, Hao X, et al. Rapid detection of COVID-19 coronavirus using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform. Clin Chem 2020; 66(7):975–977. doi:10.1093/clinchem/hvaa102.
   PubMed Web of Science ®Google Scholar
• Taylor SC, Laperriere G, Germain H. Droplet digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep 2017;7(1):2409. doi:10.1038/s41598-017-02217-x.
   PubMed Web of Science ®Google Scholar
• Falzone L, Musso N, Gattuso G, et al. Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection. Int J Mol Med 2020;46(3):957–964. doi:10.3892/ijmm.2020.4673.
   PubMed Web of Science ®Google Scholar
• Thi VLD, Herbst K, Boerner K, et al. A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci Transl Med 2020;12(556):eabc7075. doi:10.1126/scitranslmed.abc7075.
   PubMed Web of Science ®Google Scholar
• Jiang M, Pan W, Arastehfar A, et al. Development and validation of a rapid single-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) system potentially to be used for reliable and high-throughput screening of COVID-19. Front Cell Infect Microbiol 2020;10:331. doi:10.3389/fcimb.2020.00331.
   Web of Science ®Google Scholar
• EDI™ Novel Coronavirus COVID-19 ELISA Kits. http://www.epitopediagnostics.com/covid-19-elisa. Retrieved 28 March, 2020.
   Google Scholar
• Ortiz-Prado E, Simbaña-Rivera K, et al. Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review. Diagn Microbiol Infect Dis 2020;98(1):115094. doi:10.1016/j.diagmicrobio.2020.115094.
   PubMed Web of Science ®Google Scholar
• Huang JC, Chang YF, Chen KH, et al. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic biosensor. Biosens Bioelectron 2009;25(2):320–325. doi:10.1016/j.bios.2009.07.012.
   PubMed Web of Science ®Google Scholar
• Qi C, Duan JZ, Wang ZH, et al. Investigation of interaction between two neutralizing monoclonal antibodies and SARS virus using biosensor based on imaging ellipsometry. Biomed Microdev 2006;8(3):247–253. doi:10.1007/s10544-006-8305-2.
   PubMed Web of Science ®Google Scholar
• Promega Launches COVID-19 Serology Test: Lumit™ Dx SARS-CoV-2 Immunoassay Workflow is Quick, Simple and Scalable for High-Throughput Antibody Detection. https://www.promega.in/aboutus/press-releases/global/2020/aug-11-2020-promega-launches-covid-19-serology-test/.
   Google Scholar
• Datta M, Desai D, Kumar A. Gene specific DNA sensors for diagnosis of pathogenic infections. Indian J Microbiol 2017;57(2):139–147. doi:10.1007/s12088-017-0650-8.
   PubMed Web of Science ®Google Scholar
• Qiu G, Gai Z, Tao Y, et al. Dual-functional plasmonic photothermal biosensors for highly accurate severe acute respiratory syndrome coronavirus 2 detection. ACS Nano 2020;14(5):5268–5277. doi:10.1021/acsnano.0c02439.
   PubMed Web of Science ®Google Scholar
• Peng X, Zhou Y, Nie K, Zhou, et al. Promising near-infrared plasmonic biosensor employed for specific detection of SARS-CoV-2 and its spike glycoprotein. New J Phys 2020;22(10):103046. doi:10.1088/1367-2630/abbe53.
   Web of Science ®Google Scholar
• A 30-Second High-Sensitivity Covid-19 Antigen Test. https://pinpointscience.com/covid-19-test. Accessed October 24, 2020
   Google Scholar
• Ali MA, Hu C, Jahan S, et al. Sensing of COVID-19 antibodies in seconds via aerosol jet printed three dimensional electrodes. Adv Mater. 2020:e2006647. doi:10.1101/2020.09.13.20193722.
   Google Scholar
• Park TJ, Lee SY, Lee SJ, Park, et al. Protein nanopatterns and biosensors using gold binding polypeptide as a fusion partner. Anal Chem 2006;78(20):7197–7205. doi:10.1021/ac060976f.
   PubMed Web of Science ®Google Scholar
• 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):5135–5142. doi:10.1021/acsnano.0c02823.
   PubMed Web of Science ®Google Scholar
• Yanik AA, Huang M, Kamohara O, et al. An optofluidic nanoplasmonic biosensor for direct detection of live viruses from biological media. Nano Lett 2010;10(12):4962–4969. doi:10.1021/nl103025u.
   PubMed Web of Science ®Google Scholar
• Lin C, Nangreave JK, Li Z, Liu Y, et al. Signal amplification on a DNA-tile-based biosensor with enhanced sensitivity. Nanomedicine (Lond) 2008;3(4):521–528. doi:10.2217/17435889.3.4.521.
   PubMed Web of Science ®Google Scholar
• Kilianski A, Mielech A, Deng X, et al. Assessing activity and inhibition of MERS-CoV papain-like and 3C-like proteases using luciferase-based biosensors. J Virol 2013;87(21):11955–62. doi:10.1128/JVI.02105-13
   Google Scholar
• Teengam P, Siangproh W, Tuantranont A, et al. Multiplex paper-based colorimetric DNA sensor using pyrrolidinyl peptide nucleic acid-induced AgNPs aggregation for detecting MERS-CoV, MTB, and HPV oligonucleotides. Anal Chem 2017;89(10):5428–5435. doi:10.1021/acs.analchem.7b00255.
   PubMed Web of Science ®Google Scholar
• Kim H, Park M, Hwang J, et al. Development of label-free colorimetric assay for MERS-CoV using gold nanoparticles. ACS Sens 2019;4(5):1306–1312. doi:10.1021/acssensors.9b00175.
   PubMed Web of Science ®Google Scholar
• CONVAT. https://www.nanbiosis.es/tag/convat/. Accessed October 24, 2020
   Google Scholar
• Rahman S, Datta M, Kim J, Jan AT. CRISPR/Cas: an intriguing genomic editing tool with prospects in treating neurodegenerative diseases. Sem Cell Develop Biol 2019;96:22–31. doi:10.1016/j.semcdb.2019.05.014.
   PubMed Web of Science ®Google Scholar
• Azhar M, Phutela R, Ansari AH, et al. Rapid, field-deployable nucleobase detection and identification using FnCas9. bioRxiv 2020. 10.1101/2020.04.07.028167
   Google Scholar
• Broughton JP, Deng X, Yu G, et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat Biotech 2020;16:1–5.
   Google Scholar
• Kellner MJ, Koob JG, Gootenberg JS, et al. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 2019;14(10):2986–3012. doi:10.1038/s41596-019-0210-2.
   PubMed Web of Science ®Google Scholar
• Jayamohan H, Lambert CJ, Sant HJ, et al. SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations. Anal Bioanal Chem 2020:1–23. doi:10.1007/s00216-020-02958-1
   Web of Science ®Google Scholar
• In vitro diagnostics EUAs: Coronavirus Disease 2019 (Covid-19) Emergency use authorizations for medical devices. www.fda.gov. Retrieved Dec 6, 2020
   Google Scholar
• Xu M, Wang D, Wang H, et al. COVID-19 diagnostic testing: technology perspective. Clin Transl Med 2020;10(4):e158 2020doi:10.1002/ctm2.158.
   PubMed Web of Science ®Google Scholar
• Coronavirus (SARS-CoV-2): Test Kits to Detect the Causative Agent of COVID-19. https://www.rapidmicrobiology.com/test-method/testing-for-the-wuhan-coronavirus-a-k-a-covid-19-sars-cov-2-and-2019-ncov. Accessed June 4, 2020
   Google Scholar
• Sarma P, Prajapat M, Avti P, et al. Therapeutic options for the treatment of 2019-novel coronavirus: an evidence-based approach. Ind J Pharmacol 2020;52(1):1–5. 10.4103/ijp.IJP_119_20.
   Google Scholar
• Arabi YM, Mandourah Y, Al-Hameed F, et al. Corticosteroid therapy for critically ill patients with Middle East respiratory syndrome. Am J Respir Crit Care Med 2018;197(6):757–767. doi:10.1164/rccm.201706-1172OC.
   PubMed Web of Science ®Google Scholar
• Vincent MJ, Bergeron E, Benjannet S, et al. Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Virol J 2005;2(1):69. doi:10.1186/1743-422X-2-69.
   PubMed Web of Science ®Google Scholar
• GISAID: In Focus. https://www.gisaid.org/. Accessed June 4, 2020.
   Google Scholar
• Draft landscape of COVID-19 candidate vaccines. https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines. Accessed December 12, 2020.
   Google Scholar
• COVID-19 vaccine tracker. https://www.raps.org/news-and-articles/news-articles/2020/3/covid-19-vaccine-tracker. Accessed December 16, 2020.
   Google Scholar
• Lucia C, Federico PB, Alejandra GC. An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12. bioRxiv 2020. doi:10.1101/2020.02.29.971127.
   Google Scholar
• Emergency Use Authorizations. www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations#covid19ivd. Accessed June 4, 2020.
   Google Scholar