6,081
Views
9
CrossRef citations to date
0
Altmetric
review

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

, , , , , , , ORCID Icon, & show all
Pages 8594-8613 | Received 10 Aug 2021, Accepted 28 Sep 2021, Published online: 18 Oct 2021

References

  • Worldometers. COVID-19 Coronavirus Pandemic. 2021.
  • Rebecca MN, Sutter KM, Sutherland MD. Global economic effects of COVID-19. Congressional Research Service; 2021. https://fas.org/sgp/crs/row/R46270.pdf
  • Gheblawi M, Wang K, Viveiros A, et al. Angiotensin-converting enzyme 2: SARS-CoV-2 receptor and regulator of the renin-angiotensin system: celebrating the 20th anniversary of the discovery of ACE2. Circ Res. 2020;126(10):1456–1474.
  • Sharma A, Tiwari S, Deb MK, et al. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): a global pandemic and treatment strategies. Int J Antimicrob Agents. 2020;56(2):106054.
  • Shaffaf T, Ghafar-Zadeh E. COVID-19 Diagnostic Strategies. In: Part I: nucleic Acid-Based Technologies. Bioengineering (Basel). 2021. p. 8.
  • Mahbub MH, Khan M, Yamaguchi N, et al. Japans public health and culture, and the ongoing fight against COVID-19. J Adv Biotechnol Exp Ther. 2020;3(3):42–48.
  • Mina F, Billah M, Rahman M, et al. COVID-19: transmission, diagnosis, policy intervention, potential broader perspective on the rapidly evolving situation in Bangladesh. J Adv Biotechnol Exp Ther. 2020;3(4):18–29.
  • Rahman M, Sajib E, Chowdhury I, et al. Present scenario of COVID-19 in Bangladesh and government preparedness for facing challenges. J Adv Biotechnol Exp Ther. 2021;4(2):187–199.
  • Sheam M, Syed S, Barman S, et al. COVID-19: the catastrophe of our time. J Adv Biotechnol Exp Ther. 2020;3(4):1–13.
  • Sohel M, Hossain M, Hasan M, et al. Management of mental health during COVID 19 pandemic: possible strategies. J Adv Biotechnol Exp Ther. 2021;4(3):276–289.
  • Zhao H, Lu X, Deng Y, et al. COVID-19: asymptomatic carrier transmission is an underestimated problem. Epidemiol Infect. 2020;148:e116.
  • Harapan H, Itoh N, Yufika A, et al. Coronavirus disease 2019 (COVID-19): a literature review. J Infect Public Health. 2020;13(5):667–673.
  • Sironi M, Hasnain SE, Rosenthal B, et al. SARS-CoV-2 and COVID-19: a genetic, epidemiological, and evolutionary perspective. Infect Genet Evol. 2020;84:104384.
  • BCC Research. COVID-19 diagnostic services: global markets. https://www.bccresearch.com/market-research/medical-devices-and-surgical/covid-19-diagnostics-market-report.html. 2021.
  • Song YJ, Yang JS, Yoon HJ, et al. Asymptomatic middle east respiratory syndrome coronavirus infection using a serologic survey in Korea. Epidemiol Health. 2018;40:e2018014.
  • Wan Y, Shang J, Sun S, et al. Molecular mechanism for antibody-dependent enhancement of coronavirus entry. J Virol. 2020;94.
  • Cockrell AS, Yount BL, Scobey T, et al. A mouse model for MERS coronavirus-induced acute respiratory distress syndrome. Nat Microbiol. 2016;2(2):16226.
  • Fukushi S, Fukuma A, Kurosu T, et al. Characterization of novel monoclonal antibodies against the MERS-coronavirus spike protein and their application in species-independent antibody detection by competitive ELISA. J Virol Methods. 2018;251:22–29.
  • Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273.
  • Kashir J, Yaqinuddin A. Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19. Med Hypotheses. 2020;141:109786.
  • Gootenberg JS, Abudayyeh OO, Kellner MJ, et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 2018;360(6387):439–444.
  • Tang R, Yang H, Gong Y, et al. Improved analytical sensitivity of lateral flow assay using sponge for HBV nucleic acid detection. Sci Rep. 2017;7(1):1360.
  • Ding X, Yin K, Li Z, et al., CRISPR-Cas12a (AIOD-CRISPR) assay: a case for rapid, ultrasensitive and visual detection of novel coronavirus SARS-CoV-2 and HIV virus, bioRxiv, 2020; 2020.03.19.998724
  • Islam KU, Iqbal J. An update on molecular diagnostics for COVID-19. Front Cell Infect Microbiol. 2020;10:560616.
  • To KK, Tsang OT, Leung WS, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 2020;20(5):565–574.
  • Zhao J, Yuan Q, Wang H, et al. Antibody responses to SARS-CoV-2 in patients with novel coronavirus disease 2019. Clin Infect Dis. 2020;71(16):2027–2034.
  • Tan W, Lu Y, Zhang J, et al. Viral kinetics and antibody responses in patients with COVID-19. medRxiv. 2020.
  • Amanat F, Stadlbauer D, Strohmeier S, et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat Med. 2020;26(7):1033–1036.
  • Peterhoff D, Gluck V, Vogel M, et al. A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization. Infection. 2021;49(1):75–82.
  • Indenbaum V, Koren R, Katz-Likvornik S, et al. Testing IgG antibodies against the RBD of SARS-CoV-2 is sufficient and necessary for COVID-19 diagnosis. PLoS One. 2020;15(11):e0241164.
  • Tre-Hardy M, Wilmet A, Beukinga I, et al. Analytical and clinical validation of an ELISA for specific SARS-CoV-2 IgG, IgA, and IgM antibodies. J Med Virol. 2021;93(2):803–811.
  • Risch M, Weber M, Thiel S, et al. Temporal course of SARS-CoV-2 antibody positivity in patients with COVID-19 following the first clinical presentation. Biomed Res Int. 2020;2020:9878453.
  • Van Elslande J, Houben E, Depypere M, et al. Diagnostic performance of seven rapid IgG/IgM antibody tests and the Euroimmun IgA/IgG ELISA in COVID-19 patients. Clin Microbiol Infect. 2020;26(8):1082–1087.
  • Kyosei Y, Namba M, Yamura S, et al. Proposal of De novo antigen test for COVID-19: ultrasensitive detection of spike proteins of SARS-CoV-2. Diagnostics (Basel). 2020;10(8):594.
  • Mendoza R, Silver M, Zuretti AR, et al. Correlation of automated chemiluminescent method with enzyme-linked immunosorbent assay (ELISA) antibody titers in convalescent COVID-19 plasma samples: development of rapid, cost-effective semi-quantitative diagnostic methods. J Blood Med. 2021;12:157–164.
  • Tre-Hardy M, Wilmet A, Beukinga I, et al. Validation of a chemiluminescent assay for specific SARS-CoV-2 antibody. Clin Chem Lab Med. 2020;58(8):1357–1364.
  • Ma H, Zeng W, He H, et al. Serum IgA, IgM, and IgG responses in COVID-19. Cell Mol Immunol. 2020;17(7):773–775.
  • Suhandynata RT, Hoffman MA, Kelner MJ, et al. Multi-platform comparison of SARS-CoV-2 serology assays for the detection of COVID-19. J Appl Lab Med. 2020;5(6):1324–1336.
  • Soleimani R, Khourssaji M, Gruson D, et al. Clinical usefulness of fully automated chemiluminescent immunoassay for quantitative antibody measurements in COVID-19 patients. J Med Virol. 2021;93(3):1465–1477.
  • Swadzba J, Bednarczyk M, Anyszek T, et al. The real life performance of 7 automated anti-SARS-CoV-2 IgG and IgM/IgA immunoassays. Practical Laboratory Medicine. 2021;25:e00212.
  • GeurtsvanKessel CH, Okba NMA, Igloi Z, et al. An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment. Nat Commun. 2020;11(1):3436.
  • Trabaud MA, Icard V, Milon MP, et al. Comparison of eight commercial, high-throughput, automated or ELISA assays detecting SARS-CoV-2 IgG or total antibody. J Clin Virol. 2020;132:104613.
  • Vauloup-Fellous C, Maylin S, Perillaud-Dubois C, et al. Performance of 30 commercial SARS-CoV-2 serology assays in testing symptomatic COVID-19 patients. Eur J Clin Microbiol Infect Dis. 2021;40(10):2235–2241.
  • Lee SM, Kim IS, Lim S, et al. Comparison of serologic response of hospitalized COVID-19 patients using 8 immunoassays. J Korean Med Sci. 2021;36(9):e64.
  • Wu HS, Hsieh YC, Su IJ, et al. Early detection of antibodies against various structural proteins of the SARS-associated coronavirus in SARS patients. J Biomed Sci. 2004;11(1):117–126.
  • Cosgun Y, Altas AB, Kuzucu EA, et al. Role of rapid antibody and ELISA tests in the evaluation of serological response in patients with SARS-CoV-2 PCR positivity. Folia Microbiol (Praha). 2021;66(4):579–586.
  • Ghaffari A, Meurant R, Ardakani A. COVID-19 serological tests: how well do they actually perform? Diagnostics. 2020;10(7):453.
  • Lisboa Bastos M, Tavaziva G, Abidi SK, et al. Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis. BMJ. 2020;370:m2516.
  • Bendavid E, Mulaney B, Sood N, et al. COVID-19 antibody seroprevalence in Santa Clara County, California. Int J Epidemiol. 2021;50(2):410–419.
  • Boum Y, Fai KN, Nikolay B, et al. Performance and operational feasibility of antigen and antibody rapid diagnostic tests for COVID-19 in symptomatic and asymptomatic patients in Cameroon: a clinical, prospective, diagnostic accuracy study. Lancet Infect Dis. 2021;21(8):1089–1096.
  • Mak GC, Cheng PK, Lau SS, et al. Evaluation of rapid antigen test for detection of SARS-CoV-2 virus. J Clin Virol. 2020;129:104500.
  • Bruzzone B, De Pace V, Caligiuri P, et al. Comparative diagnostic performance of rapid antigen detection tests for COVID-19 in a hospital setting. Int J Infect Dis. 2021;107:215–218.
  • Scohy A, Anantharajah A, Bodeus M, et al. Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis. J Clin Virol. 2020;129:104455.
  • Scheiblauer H, Filomena A, Nitsche A, et al. Comparative sensitivity evaluation for 122 CE-marked SARS-CoV-2 antigen rapid tests. medRxiv. 2021. 2021.05.11.21257016.
  • Torres I, Poujois S, Albert E, et al. Evaluation of a rapid antigen test (Panbio COVID-19 Ag rapid test device) for SARS-CoV-2 detection in asymptomatic close contacts of COVID-19 patients. Clin Microbiol Infect. 2021;27(4):636 e1- e4.
  • Pena M, Ampuero M, Garces C, et al. Performance of SARS-CoV-2 rapid antigen test compared with real-time RT-PCR in asymptomatic individuals. Int J Infect Dis. 2021;107:201–204.
  • McKay SL, Tobolowsky FA, Moritz ED, et al. Performance evaluation of serial SARS-CoV-2 rapid antigen testing during a nursing home outbreak. Ann Intern Med. 2021;174(7):945–951.
  • Smith RL, Gibson LL, Martinez PP, et al. Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. J Infect Dis. 2021;224(6):976–982.
  • Linares M, Perez-Tanoira R, Carrero A, et al. Panbio antigen rapid test is reliable to diagnose SARS-CoV-2 infection in the first 7 days after the onset of symptoms. J Clin Virol. 2020;133:104659.
  • Jaafar R, Aherfi S, Wurtz N, et al. Correlation between 3790 quantitative polymerase chain reaction–positives samples and positive cell cultures, including 1941 severe acute respiratory syndrome coronavirus 2 isolates. Clinl Infect Dis. 2020;72(11):e921–e.
  • Hiroi S, Kubota-Koketsu R, Sasaki T, et al. Infectivity assay for detection of SARS-CoV-2 in samples from patients with COVID-19. J Med Virol. 2021;93(10):5917–5923.
  • Larremore DB, Wilder B, Lester E, et al. Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening. Sci Adv. 2021;7.
  • WHO. A compile of RT-PCR protocols for the detection of SARS-CoV-2. 2019.
  • Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045.
  • Nalla AK, Casto AM, Huang MW, et al. Comparative performance of SARS-CoV-2 detection assays using seven different primer-probe sets and one assay kit. J Clin Microbiol. 2020;58(6):e00557–20.
  • Penarrubia L, Ruiz M, Porco R, et al. Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak. Int J Infect Dis. 2020;97:225–229.
  • Rana DR, Pokhrel N. Sequence mismatch in PCR probes may mask the COVID-19 detection in Nepal. Mol Cell Probes. 2020;53:101599.
  • Alvarez-Diaz DA, Franco-Munoz C, Laiton-Donato K, et al. Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia. Infect Genet Evol. 2020;84:104390.
  • Khan KA, Cheung P. Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome. R Soc Open Sci. 2020;7(6):200636.
  • Wang R, Hozumi Y, Yin C, et al. Mutations on COVID-19 diagnostic targets. Genomics. 2020;112(6):5204–5213.
  • Artesi M, Bontems S, Gobbels P, et al. A recurrent mutation at position 26340 of SARS-CoV-2 is associated with failure of the E gene quantitative reverse transcription-PCR utilized in a commercial dual-target diagnostic assay. J Clin Microbiol. 2020;58(10):e01598–20.
  • Ziegler K, Steininger P, Ziegler R, et al. SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene. Euro Surveill. 2020;25(39):2001650.
  • Hasan MR, Sundararaju S, Manickam C, et al. A novel point mutation in the N gene of SARS-CoV-2 may affect the detection of the virus by reverse transcription-quantitative PCR. J Clin Microbiol. 2021;59(4):e03278–20.
  • Liu R, Wu P, Ogrodzki P, et al. Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response. Sci Rep. 2021;11(1):13971.
  • Mourier T, Sadykov M, Carr MJ, et al. Host-directed editing of the SARS-CoV-2 genome. Biochem Biophys Res Commun. 2021;538:35–39.
  • Visseaux B, Le Hingrat Q, Collin G, et al. Evaluation of the QIAstat-Dx respiratory SARS-CoV-2 panel, the first rapid multiplex PCR commercial assay for SARS-CoV-2 detection. J Clin Microbiol. 2020;58(8):e00630–20.
  • Storey N, Brown JR, Pereira RPA, et al. Single base mutations in the nucleocapsid gene of SARS-CoV-2 affects amplification efficiency of sequence variants and may lead to assay failure. J Clin Virol Plus. 2021;1(3):100037.
  • Alosaimi B, Naeem A, Hamed ME, et al. Influenza co-infection associated with severity and mortality in COVID-19 patients. Virol J. 2021;18(1):127.
  • Pabbaraju K, Wong AA, Ma R, et al. Development and validation of a multiplex reverse transcriptase-PCR assay for simultaneous testing of influenza A, influenza B and SARS-CoV-2. J Virol Methods. 2021;293:114151.
  • Norz D, Hoffmann A, Aepfelbacher M, et al. Clinical evaluation of a fully automated, laboratory-developed multiplex RT-PCR assay integrating dual-target SARS-CoV-2 and influenza A/B detection on a high-throughput platform. J Med Microbiol. 2021;70(2):001295.
  • Yang Y, Yang M, Yuan J, et al. Laboratory diagnosis and monitoring the viral shedding of SARS-CoV-2 infection. Innovation (N Y). 2020;1:100061.
  • Wang X, Tan L, Wang X, et al. Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously. Int J Infect Dis. 2020;94:107–109.
  • Wu J, Liu J, Li S, et al. Detection and analysis of nucleic acid in various biological samples of COVID-19 patients. Travel Med Infect Dis. 2020;37:101673.
  • Casagrande M, Fitzek A, Puschel K, et al. Detection of SARS-CoV-2 in human retinal biopsies of deceased COVID-19 patients. Ocul Immunol Inflamm. 2020;28(5):721–725.
  • Meinhardt J, Radke J, Dittmayer C, et al. Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19. Nat Neurosci. 2021;24(2):168–175.
  • Song E, Zhang C, Israelow B, et al. Neuroinvasion of SARS-CoV-2 in human and mouse brain. J Exp Med. 2021;218.
  • Green DA, Zucker J, Westblade LF, et al. Clinical Performance of SARS-CoV-2 Molecular Tests. J Clin Microbiol. 2020;58(8):e00995–20.
  • Lin C, Xiang J, Yan M, et al. Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2)-infected pneumonia (COVID-19). Clin Chem Lab Med. 2020;58(7):1089–1094.
  • Koskinen A, Tolvi M, Jauhiainen M, et al. Complications of COVID-19 nasopharyngeal swab test. JAMA Otolaryngol Head Neck Surg. 2021;147(7):672–674.
  • Tsang NNY, So HC, Ip DKM. Is oropharyngeal sampling a reliable test to detect SARS-CoV-2? – authors’ reply. Lancet Infect Dis. 2021;21(10):1348–1349.
  • Hanege FM, Kocoglu E, Kalcioglu MT, et al. SARS-CoV-2 presence in the saliva, tears, and cerumen of COVID −19 patients. Laryngoscope. 2021;131(5):E1677–E82.
  • Fougere Y, Schwob JM, Miauton A, et al. Performance of RT-PCR on saliva specimens compared with nasopharyngeal swabs for the detection of SARS-CoV-2 in children: a prospective comparative clinical trial. Pediatr Infect Dis J. 2021;40(8):e300–e4.
  • Pasomsub E, Watcharananan SP, Boonyawat K, et al. Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study. Clin Microbiol Infect. 2021;27(2):285 e1- e4.
  • Teo AKJ, Choudhury Y, Tan IB, et al. Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection. Sci Rep. 2021;11(1):3134.
  • Dogan OA, Kose B, Agaoglu NB, et al. Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs. J Virol Methods. 2021;290:114049.
  • Tan SH, Allicock O, Armstrong-Hough M, et al. Saliva as a gold-standard sample for SARS-CoV-2 detection. Lancet Respir Med. 2021;9(6):562–564.
  • Nacher M, Mergeay-Fabre M, Blanchet D, et al. Diagnostic accuracy and acceptability of molecular diagnosis of COVID-19 on saliva samples relative to nasopharyngeal swabs in tropical hospital and extra-hospital contexts: the COVISAL study. PLoS One. 2021;16(9):e0257169.
  • Lippi G, Simundic AM, Plebani M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med. 2020;58(7):1070–1076.
  • Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn. 2020;20(5):453–454.
  • Fang Y, Zhang H, Xie J, et al. Sensitivity of chest CT for COVID-19: comparison to RT-PCR. Radiology. 2020;296(2):E115–E7.
  • He JL, Luo L, Luo ZD, et al. Diagnostic performance between CT and initial real-time RT-PCR for clinically suspected 2019 coronavirus disease (COVID-19) patients outside Wuhan, China. Respir Med. 2020;168:105980.
  • Ren X, Liu Y, Chen H, et al. Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection. medRxiv. 2020.
  • Williams TC, Wastnedge E, McAllister G, et al. Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study. Wellcome Open Res. 2020;5:254.
  • Munblit D, Nekliudov NA, Bugaeva P, et al. Stop COVID Cohort: an Observational Study of 3480 Patients Admitted to the Sechenov University Hospital Network in Moscow City for Suspected Coronavirus Disease 2019 (COVID-19) Infection. Clinl Infect Dis. 2020;73(1):1–11.
  • Kortela E, Kirjavainen V, Ahava MJ, et al. Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients. PLoS One. 2021;16(5):e0251661.
  • Bergmans BJM, Reusken C, van Oudheusden AJG, et al. Test, trace, isolate: evidence for declining SARS-CoV-2 PCR sensitivity in a clinical cohort. Diagn Microbiol Infect Dis. 2021;101(2):115392.
  • LeBlanc JJ, Pettipas J, Di Quinzio M, et al. Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: a three-headed comparison on multiple molecular platforms. J Virol Methods. 2021;295:114184.
  • Braz-Silva PH, Mamana AC, Romano CM, et al. Performance of at-home self-collected saliva and nasal-oropharyngeal swabs in the surveillance of COVID-19. J Oral Microbiol. 2020;13(1):1858002.
  • SoRelle JA, Mahimainathan L, McCormick-Baw C, et al. Saliva for use with a point of care assay for the rapid diagnosis of COVID-19. Clin Chim Acta. 2020;510:685–686.
  • Smyrlaki I, Ekman M, Lentini A, Rufino de Sousa N, Papanicolaou N, Vondracek M, et al. Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun. 2020;11:4812.
  • Adams NM, Leelawong M, Benton A, et al. COVID-19 diagnostics for resource-limited settings: evaluation of “unextracted” qRT-PCR. J Med Virol. 2021;93(1):559–563.
  • Byrnes SA, Gallagher R, Steadman A, et al. Multiplexed and extraction-free amplification for simplified SARS-CoV-2 RT-PCR tests. Anal Chem. 2021;93(9):4160–4165.
  • Visseaux B, Collin G, Houhou-Fidouh N, et al. Evaluation of three extraction-free SARS-CoV-2 RT-PCR assays: a feasible alternative approach with low technical requirements. J Virol Methods. 2021;291:114086.
  • Lubke N, Senff T, Scherger S, et al. Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials. J Clin Virol. 2020;130:104579.
  • Renzoni A, Perez F, Ngo Nsoga MT, et al. Analytical evaluation of visby medical RT-PCR portable device for rapid detection of SARS-CoV-2. Diagnostics (Basel). 2021;11(5):813.
  • Gibani MM, Toumazou C, Sohbati M, et al. Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study. Lancet Microbe. 2020;1(7):e300–e7.
  • Wee SK, Sivalingam SP, Yap EPH. Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler. Genes (Basel). 2020;11(6):664.
  • Cuevas-Ferrando E, Randazzo W, Perez-Cataluna A, et al. Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples. Sci Rep. 2021;11(1):18120.
  • Libin PJK, Willem L, Verstraeten T, et al. Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics. PLoS Comput Biol. 2021;17(3):e1008688.
  • Lyng GD, Sheils NE, Kennedy CJ, et al. Identifying optimal COVID-19 testing strategies for schools and businesses: balancing testing frequency, individual test technology, and cost. PLoS One. 2021;16(3):e0248783.
  • Stohr JJ, Wennekes M, van der Ent M, et al. Clinical performance and sample freeze-thaw stability of the cobas® 6800 SARS-CoV-2 assay for the detection of SARS-CoV-2 in oro-/nasopharyngeal swabs and lower respiratory specimens. J Clin Virol. 2020;133:104686.
  • Hirschhorn JW, Kegl A, Dickerson T, et al. Verification and validation of SARS-CoV-2 assay performance on the abbott m 2000 and alinity m systems. J Clin Microbiol. 2021;59(5):e03119–20.
  • Goldenberger D, Leuzinger K, Sogaard KK, et al. Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay. J Virol Methods. 2020;284:113925.
  • Mostafa HH, Hardick J, Morehead E, et al. Comparison of the analytical sensitivity of seven commonly used commercial SARS-CoV-2 automated molecular assays. J Clin Virol. 2020;130:104578.
  • Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):E63.
  • Li J, Hu X, Wang X, et al. A novel One-pot rapid diagnostic technology for COVID-19. Anal Chim Acta. 2021;1154:338310.
  • Lamb LE, Bartolone SN, Ward E, et al. Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification. PLoS One. 2020;15(6):e0234682.
  • Baek YH, Um J, Antigua KJC, et al. Development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel SARS-CoV-2. Emerg Microbes Infect. 2020;9(1):998–1007.
  • 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.
  • Rodel J, Egerer R, Suleyman A, et al. Use of the variplex SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis. J Clin Virol. 2020;132:104616.
  • Dao Thi VL, 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.
  • Jiang M, Pan W, Arasthfer 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.
  • Chow FW, Chan TT, Tam AR, et al. A rapid, simple, inexpensive, and mobile colorimetric assay COVID-19-LAMP for mass on-site screening of COVID-19. Int J Mol Sci. 2020;21(15):5380.
  • Kitagawa Y, Orihara Y, Kawamura R, et al. Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification. J Clin Virol. 2020;129:104446.
  • Tran DH, Cuong HQ, Tran HT, et al. A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point-of-care. bioRxiv. 2021.
  • Carter C, Akrami K, Hall D, et al. Lyophilized visually readable loop-mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNA. J Virol Methods. 2017;244:32–38.
  • Chen HW, Ching WM. Evaluation of the stability of lyophilized loop-mediated isothermal amplification reagents for the detection of Coxiella burnetii. Heliyon. 2017;3(10):e00415.
  • Aoki MN, de Oliveira Coelho B, Goes LGB, et al. Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load. Sci Rep. 2021;11(1):9026.
  • Silva LDC, Dos Santos CA, Mendes GM, et al. Can a field molecular diagnosis be accurate? A performance evaluation of colorimetric RT-LAMP for the detection of SARS-CoV-2 in a hospital setting. Anal Methods: Adv Methods Appl. 2021;13(26):2898–2907.
  • Piepenburg O, Williams CH, Stemple DL, et al. DNA detection using recombination proteins. PLoS Biol. 2006;4(7):e204.
  • 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.
  • Lau YL, Ismail IB, Mustapa NIB, et al. Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). PLoS One. 2021;16(1):e0245164.
  • Van Ness J, Van Ness LK, Galas DJ. Isothermal reactions for the amplification of oligonucleotides. Proc Natl Acad Sci U S A. 2003;100(8):4504–4509.
  • Wang L, Qian C, Wu H, et al. Technical aspects of nicking enzyme assisted amplification. Analyst. 2018;143(6):1444–1453.
  • Serei VD, Cristelli R, Joho K, et al. Comparison of abbott ID NOW COVID-19 rapid molecular assay to cepheid xpert xpress SARS-CoV-2 assay in dry nasal swabs. Diagn Microbiol Infect Dis. 2021;99(4):115208.
  • Basu A, Zinger T, Inglima K, et al. Performance of Abbott ID Now COVID-19 rapid nucleic acid amplification test using nasopharyngeal swabs transported in viral transport media and dry nasal swabs in a New York city academic institution. J Clin Microbiol. 2020;58(8):e01136–20.
  • Harrington A, Cox B, Snowdon J, et al. Comparison of Abbott ID now and Abbott m2000 methods for the detection of SARS-CoV-2 from nasopharyngeal and nasal swabs from symptomatic patients. J Clin Microbiol. 2020;58(8):e00798–20.
  • Rhoads DD, Cherian SS, Roman K, et al. Comparison of Abbott ID now, diasorin simplexa, and CDC FDA emergency use authorization methods for the detection of SARS-CoV-2 from nasopharyngeal and nasal swabs from individuals diagnosed with COVID-19. J Clin Microbiol. 2020;58(8):e00760–20.
  • Smithgall MC, Scherberkova I, Whittier S, et al. Comparison of cepheid xpert Xpress and Abbott ID now to roche cobas for the rapid detection of SARS-CoV-2. J Clin Virol. 2020;128:104428.
  • Zhen W, Smith E, Manji R, et al. Clinical evaluation of three sample-to-answer platforms for detection of SARS-CoV-2. J Clin Microbiol. 2020;58(8):e00783–20.
  • Tu YP, Iqbal J, O’Leary T. Sensitivity of ID NOW and RT-PCR for detection of SARS-CoV-2 in an ambulatory population. Elife. 2021;10:e65726.
  • Naveen KP, Bhat AI. Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays for the detection of two novel viruses infecting ginger. J Virol Methods. 2020;282:113884.
  • Naveen KP, Bhat AI. Reverse transcriptase loop-mediated isothermal amplification and reverse transcriptase recombinase amplification assays for rapid and sensitive detection of cardamom vein clearing virus. 3 Biotech. 2020;10(6):250.
  • Kobayashi GS, Brito LA, Moreira DP, et al. A Novel Saliva RT-LAMP Workflow for Rapid Identification of COVID-19 Cases and Restraining Viral Spread. Diagnostics (Basel). 2021;11(8):1400.
  • Toppings NB, Mohon AN, Lee Y, et al. A rapid near-patient detection system for SARS-CoV-2 using saliva. Sci Rep. 2021;11(1):13378.
  • Soto F, Ozen MO, Guimaraes CF, et al. Wearable collector for noninvasive sampling of SARS-CoV-2 from exhaled breath for rapid detection. ACS Appl Mater Interfaces. 2021;13(35):41445–41453.
  • Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315(5819):1709–1712.
  • Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327(5962):167–170.
  • McGinn J, Marraffini LA. CRISPR-cas systems optimize their immune response by specifying the site of spacer integration. Mol Cell. 2016;64(3):616–623.
  • Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol. 2017;37:67–78.
  • Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–823.
  • Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–821.
  • Singh V, Braddick D, Dhar PK. Exploring the potential of genome editing CRISPR-Cas9 technology. Gene. 2017;599:1–18.
  • Singh V, Gohil N, Ramirez Garcia R, et al. Recent advances in CRISPR-Cas9 genome editing technology for biological and biomedical investigations. J Cell Biochem. 2018;119(1):81–94.
  • Bikard D, Euler CW, Jiang W, et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol. 2014;32(11):1146–1150.
  • Citorik RJ, Mimee M, Lu TK. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol. 2014;32(11):1141–1145.
  • Yosef I, Manor M, Kiro R, et al. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci U S A. 2015;112(23):7267–7272.
  • Ebina H, Misawa N, Kanemura Y, et al. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep. 2013;3(1):2510.
  • Zhu W, Lei R, Le Duff Y, et al. The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA. Retrovirology. 2015;12(1):22.
  • Kennedy EM, Bassit LC, Mueller H, et al. Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology. 2015;476:196–205.
  • Lin S, Yu Z, Chen D, et al. Progress in microfluidics-based exosome separation and detection technologies for diagnostic applications. Small. 2020;16(9):e1903916.
  • Abbott TR, Dhamdhere G, Liu Y, et al. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and Influenza. Cell. 2020;181(4):865–76 e12.
  • Chen JS, Ma E, Harrington LB, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436–439.
  • Shmakov S, Smargon A, Scott D, et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169–182.
  • Abudayyeh OO, Gootenberg JS, Essletzbichler P, et al. RNA targeting with CRISPR-Cas13. Nature. 2017;550(7675):280–284.
  • Cox DBT, Gootenberg JS, Abudayyeh OO, et al. RNA editing with CRISPR-Cas13. Science. 2017;358(6366):1019–1027.
  • Kellner MJ, Koob JG, Gootenberg JS, et al. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc. 2019;14(10):2986–3012.
  • Gootenberg JS, Abudayyeh OO, Kellner MJ, et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 2018;360:439–444.
  • Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–442.
  • de Puig H, Lee RA, Najjar D, et al. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci Adv. 2021;7(32):eabh2944.
  • Khambhati K, Bhattacharjee G, Singh V. Current progress in CRISPR-based diagnostic platforms. J Cell Biochem. 2019;120(3):2721–2725.
  • Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020;38(7):870–874.
  • Ding X, Yin K, Li Z, et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun. 2020;11(1):4711.
  • Huang Z, Tian D, Liu Y, et al. Ultra-sensitive and high-throughput CRISPR-p owered COVID-19 diagnosis. Biosens Bioelectron. 2020;164:112316.
  • Chen Y, Shi Y, Chen Y, et al. Contamination-free visual detection of SARS-CoV-2 with CRISPR/Cas12a: a promising method in the point-of-care detection. Biosens Bioelectron. 2020;169:112642.
  • Yang Y, Liu J, Zhou X. A CRISPR-based and post-amplification coupled SARS-CoV-2 detection with a portable evanescent wave biosensor. Biosens Bioelectron. 2021;190:113418.
  • Bhatia SN, Ingber DE. Microfluidic organs-on-chips. Nat Biotechnol. 2014;32(8):760–772.
  • Carrera J, Rodrigo G, Singh V, et al. Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnol J. 2011;6(7):773–783.
  • Kim JA, Lee JY, Seong S, et al. Fabrication and characterization of a PDMS–glass hybrid continuous-flow PCR chip. Biochem Eng J. 2006;29(1–2):91–97.
  • Wolf MP, Salieb-Beugelaar GB, Hunziker P. PDMS with designer functionalities—Properties, modifications strategies, and applications. Prog Polym Sci. 2018;83:97–134.
  • Mao K, Min X, Zhang H, et al. Paper-based microfluidics for rapid diagnostics and drug delivery. J Control Release. 2020;322:187–199.
  • Sackmann EK, Fulton AL, Beebe DJ. The present and future role of microfluidics in biomedical research. Nature. 2014;507(7491):181–189.
  • Taylor BJ, Howell A, Martin KA, et al. A lab-on-chip for malaria diagnosis and surveillance. Malar J. 2014;13(1):179.
  • Zhuang J, Yin J, Lv S, et al. Advanced “lab-on-a-chip” to detect viruses - Current challenges and future perspectives. Biosens Bioelectron. 2020;163:112291.
  • Basiri A, Heidari A, Nadi MF, et al. Microfluidic devices for detection of RNA viruses. Rev Med Virol. 2021;31(1):1–11.
  • Ferguson BS, Buchsbaum SF, Wu TT, et al. Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics. J Am Chem Soc. 2011;133(23):9129–9135.
  • Brassard D, Geissler M, Descarreaux M, et al. Extraction of nucleic acids from blood: unveiling the potential of active pneumatic pumping in centrifugal microfluidics for integration and automation of sample preparation processes. Lab Chip. 2019;19(11):1941–1952.
  • Geissler M, Brassard D, Clime L, et al. Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates. Analyst. 2020;145:6831–6845.
  • Sullivan BP, Bender AT, Ngyuen DN, et al. Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis. J Chromatogr B Analyt Technol Biomed Life Sci. 2021;1163:122494.
  • Qiu X, Zhang S, Xiang F, et al. Instrument-free point-of-care molecular diagnosis of H1N1 based on microfluidic convective PCR. Sens Actuators B Chem. 2017;243:738–744.
  • Rodriguez-Moncayo R, Cedillo-Alcantar DF, Guevara-Pantoja PE, et al. A high-throughput multiplexed microfluidic device for COVID-19 serology assays. Lab Chip. 2021;21(1):93–104.
  • Funari R, Chu KY, Shen AQ. Detection of antibodies against SARS-CoV-2 spike protein by gold nanospikes in an opto-microfluidic chip. Biosens Bioelectron. 2020;169:112578.
  • Lin Q, Wen D, Wu J, et al. Microfluidic immunoassays for sensitive and simultaneous detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min. Anal Chem. 2020;92(14):9454–9458.
  • Ramachandran A, Huyke DA, Sharma E, et al. Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. Proc Natl Acad Sci U S A. 2020;117(47):29518–29525.
  • Mavrikou S, Tsekouras V, Hatziagapiou K, et al. Clinical application of the novel cell-based biosensor for the ultra-rapid detection of the SARS-CoV-2 S1 spike protein antigen: a practical approach. Biosensors (Basel). 2021;11(7):224.
  • Agarwal DK, Nandwana V, Henrich SE, et al. Highly sensitive and ultra-rapid antigen-based detection of SARS-CoV-2 using nanomechanical sensor platform. Biosens Bioelectron. 2021;113647.
  • Raziq A, Kidakova A, Boroznjak R, et al. Development of a portable MIP-based electrochemical sensor for detection of SARS-CoV-2 antigen. Biosens Bioelectron. 2021;178:113029.
  • Nurputra DK, Kusumaatmadja A, Hakim MS, et al. Fast and noninvasive electronic nose for sniffing out COVID-19 based on exhaled breath-print recognition. Res Square. 2021.
  • De Lima LF, Ferreira AL, Torres MDT, et al. Minute-scale detection of SARS-CoV-2 using a low-cost biosensor composed of pencil graphite electrodes. PNAS. 2021;118(30):e2106724118.
  • Nguyen NHL, Kim S, Lindemann G, et al. COVID-19 spike protein induced phononic modification in antibody-coupled graphene for viral detection application. ACS Nano. 2021;15(7):11743–11752.
  • Hwang MT, Park I, Heiranian M, et al. Ultrasensitive detection of dopamine, IL‐6 and SARS‐CoV‐2 proteins on crumpled graphene FET biosensor. Adv Mater Technol. 2021;2100712:2100712.
  • Nguyen PQ, Soenksen LR, Donghia NM, et al. Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nat Biotechnol. 2021. DOI:10.1038/s41587-021-00950-3.
  • Ye Z, Zhang Y, Wang Y, et al. Chest CT manifestations of new coronavirus disease 2019 (COVID-19): a pictorial review. Eur Radiol. 2020;30(8):4381–4389.
  • Saeed GA, Gaba W, Shah A, et al. Correlation between Chest CT Severity Scores and the Clinical Parameters of Adult Patients with COVID-19 Pneumonia. Radiol Res Pract. 2021;2021:6697677.
  • Kovacs A, Palasti P, Vereb D, et al. The sensitivity and specificity of chest CT in the diagnosis of COVID-19. Eur Radiol. 2021;31(5):2819–2824.
  • Saba L, Agarwal M, Patrick A, et al. Six artificial intelligence paradigms for tissue characterisation and classification of non-COVID-19 pneumonia against COVID-19 pneumonia in computed tomography lungs. Int J Comput Assist Radiol Surg. 2021;16(3):423–434.
  • Song Y, Zheng S, Li L, et al. Deep learning enables accurate diagnosis of novel coronavirus (COVID-19) with CT images. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2021 1 10.1109/TCBB.2021.3065361
  • Jaiswal A, Gianchandani N, Singh D, et al. Classification of the COVID-19 infected patients using DenseNet201 based deep transfer learning. J Biomol Struct Dyn. 2021;39(15):5682–5689.
  • Wang S, Kang B, Ma J, et al. A deep learning algorithm using CT images to screen for Corona virus disease (COVID-19). Eur Radiol. 2021;31(8):6096–6104.
  • Abbas A, Abdelsamea MM, Gaber MM. Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network. Appl Intell. 2020;51(2):854–864.
  • Chen J, Wu L, Zhang J, et al. Deep learning-based model for detecting 2019 novel coronavirus pneumonia on high-resolution computed tomography. Sci Rep. 2020;10(1):19196.
  • Shan F, Gao Y, Wang J, et al. Lung infection quantification of COVID-19 in CT images with deep learning. arXiv Preprint. 2020.
  • Laguarta J, Hueto F, Subirana B. COVID-19 artificial intelligence diagnosis using only cough recordings. IEEE Open Journal of Engineering in Medicine and Biology. 2020;1:275–281.
  • Orlandic L, Teijeiro T, Atienza D. The COUGHVID crowdsourcing dataset, a corpus for the study of large-scale cough analysis algorithms. Sci Data. 2021;8(1):156.
  • Sharma N, PrashantKrishnan V, Kumar R, et al. Coswara - A Database of Breathing, Cough, and Voice Sounds for COVID-19 Diagnosis. In: INTERSPEECH. 2020.
  • FDA. Coronavirus (COVID-19) Update: July 23, 2021. 2021.