key: cord-337220-yv7qdvzi authors: Demeke, Addis; Samaddar, Manalee; Alharbi, Mona G.; Al-Hindi, Rashad R.; Bhunia, Arun K. title: Biosensor and molecular-based methods for the detection of human coronaviruses: A review date: 2020-09-08 journal: Mol Cell Probes DOI: 10.1016/j.mcp.2020.101662 sha: doc_id: 337220 cord_uid: yv7qdvzi The ongoing crisis due to the global pandemic caused by a highly contagious coronavirus (Coronavirus disease – 2019; COVID-19) and the lack of either proven effective therapy or a vaccine has made diagnostic a valuable tool in disease tracking and prevention. The complex nature of this newly emerging virus calls for scientists’ attention to find the most reliable, highly sensitive, and selective detection techniques for better control or spread of the disease. Reverse transcriptase-polymerase chain reaction (RT-PCR) and serology-based tests are currently being used. However, the speed and accuracy of these tests may not meet the current demand; thus, alternative technology platforms are being developed. Nano biosensor technology platforms have been established as a promising diagnostic tool for rapid and accurate detection of viruses as well as other life-threatening diseases even in resource-limited settings. This review aims to provide a short overview of recent advancements in molecular and biosensor-based diagnosis of viruses, including the human coronaviruses, and highlight the challenges and future perspectives of these detection technologies. Another reverse transcription loop-mediated isothermal amplification (RT-LAMP) was 126 developed to detect the ORF1ab and S genes of SARS-CoV-2 in 18 to 20 min. In this point-of-127 care testing platform, positive results could be judged by the naked eye with a color change from 128 orange to green [19] . DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR) is a 129 comparatively new method of SARS-Cov-2 detection [20] . This assay involves simultaneous 130 reverse transcription and isothermal amplification using loop-mediated amplification (RT-131 LAMP) for RNA, followed by Cas12 detection of predefined coronavirus sequences, after which 132 cleavage of a reporter molecule confirms detection of the E and N genes of SARS-CoV-2. Cas12 133 fluorescent signals can be visualized by lateral flow assay within 5 min [21] . 134 Serological tests can play a critical role in the fight against COVID-19 by helping 136 healthcare professionals to identify individuals who have overcome infection in the past and 137 have developed an immune response. COVID-19 disease is reported to induce acute antibody 138 (IgM, IgG) response in all patients and the levels of anti-viral antibodies are plateaued within 6-139 days after seroconversion [22] . Therefore, a "serology" test can be performed to measure anti-140 viral antibodies in the blood and can potentially be used in patients with negative RT-PCR or 141 asymptomatic patients [23] . Serological/antibody-based assays are rapid and efficient for the 142 screening of many pathogenic infections, as pathogen-specific IgM and IgG antibodies can be 143 detected with various immunoassays [24] , which has relatively high throughput capacity and less 144 stringent specimen requirements (uniformity in serum collection) than viral RNA-based assays 145 [14] . Detecting IgM and IgG against the SERS-CoV-2 offers an alternate means to diagnose a 146 patient. Rapid lateral flow-based assays for anti-COVID-19 antibodies (IgM and IgG) are under 147 development which will play an important role in the epidemiological investigation of the 148 disease [9] . This method can be used to quickly screen all febrile patients effectively, as large-149 scale confirmation or exclusion of patients is essential for preventing the spread of disease and 150 for an epidemiological survey. However, there is a concern if the serology test could be useful 151 for the diagnosis of asymptomatic or symptomatic patients who may not mount a detectable 152 immune response. Interestingly, anti-SARS-CoV-2 antibodies (seroconversion requires at least 7 153 days of infection in a patient) have the potentials to neutralize the virus and to protect people 154 from developing future infections [25] . Therefore, the convalescent plasma has been used as 155 therapy for the treatment of critically ill COVID-19 patients [26, 27] The biosensor was developed by using a spike protein of SARS-CoV-2 immobilized onto the 237 FET graphene sheet (a two-dimensional sheet of hexagonal oriented carbon atom) with 1-pyrene 238 butyric acid N-hydroxy succinimide ester (PBASE) (Figure 1) . The team used the spike protein 239 of the virus due to its sequence diversity among the coronaviruses and they have evaluated its 240 performance by enzyme-linked immunosorbent assay (ELISA) before immobilizing onto the 241 FET surface. The sensor was designed to detect the SARS-CoV-2 virus in clinical samples with a 242 1 fg/mL detection limit. Most importantly, the device showed no significant cross-reactivity with 243 the MERS-CoV antigen. Hence, the sensor developed by this research group provides fast, 244 highly sensitive, and specific detection of the SARS-CoV-2 virus in clinical samples. 245 Disease caused by coronaviruses became the major public health threat worldwide [1]. It 359 is highly contagious thus there is a great demand for diagnostic/detection tool that is rapid, 360 accurate, user-friendly to support the healthcare industry. RT-PCR has been the key diagnostic 361 tool to combat the COVD-19 pandemic and is considered a major diagnostic tool for several 362 other viral diseases. However, this method is labor-intensive and often requires several days to 363 obtain results, which is counter-productive for tracing/tracking since the SARS-CoV-2 spreads 364 rapidly. The application of nano biosensors (using nanoparticles and nanomaterials) has the 365 potential to deliver results quickly with high accuracy. However, biosensors may encounter 366 many challenges in the clinical settings, such as biofouling which restricts the widespread 367 utilization of biosensors [107] . It has been investigated that the durability or functionality of 368 immobilized sensors is diminished by particle buildup i.e., biofouling can considerably impede 369 the influx of analyte to the detector. Another challenge is that some of the immunosensors are -nCoV) Causing an Outbreak of Pneumonia Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients Comparative performance of SARS-CoV-2 detection 444 assays using seven different primer-probe sets and one assay kit Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 449 of the Coronavirus Disease 2019 (COVID-19) 452 Evaluation of Nucleocapsid and Spike Protein-based ELISAs for detecting antibodies against 453 SARS-CoV-2 Stability issues of RT-PCR 456 testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19 Real-time RT-PCR in COVID-19 detection: issues affecting 460 the results Early diagnosis of SARS coronavirus infection by real time RT-PCR Multiple-centre clinical evaluation of an ultrafast single-tube 469 assay for SARS-CoV-2 RNA Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription 473 loop-mediated isothermal amplification assay Rapid and sensitive detection of COVID-19 using CRISPR/Cas12a-based detection with naked 477 eye readout, CRISPR/Cas12a-NER CRISPR-Cas12-based detection of 482 SARS-CoV-2 Antibody responses to SARS-490 CoV-2 in patients with COVID-19 A serological assay to detect SARS-CoV-2 497 seroconversion in humans 500 Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-501 reactivity with SARS-CoV Potent neutralizing antibodies in the sera of convalescent 505 COVID-19 patients are directed against conserved linear epitopes on the SARS-CoV-2 spike 506 protein 509 Treatment of 5 critically ill patients with COVID-19 with convalescent plasma Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals Potential rapid diagnostics, vaccine and therapeutics for 519 2019 novel coronavirus (2019-nCoV): a systematic review Performance of radiologists in differentiating COVID-19 from viral pneumonia on 523 chest CT CT features of coronavirus disease 2019 (COVID-19) 526 pneumonia in 62 patients in Wuhan, China Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-575 CoV-2 infection diagnosis Correlation of 578 chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 579 1014 cases Biosensors and bio-based methods for the separation and detection of 582 foodborne pathogens One day to one hour: how quickly can foodborne pathogens be detected? High throughput screening strategies and technology 588 platforms for detection of pathogens: an introduction Hyperspectral Imaging and Practical Applications2015 Recent trends in antibody based sensors Simulation and fabrication 596 of a new novel 3D injectable biosensor for high throughput genomics and proteomics in a lab-597 on-a-chip device Encyclopedia of Industrial Biotechnology Antibodies, enzymes, and 604 nucleic acid sensors for high throughput screening of microbes and toxins in food, High 605 throughput screening for food safety assessment New biorecognition molecules in biosensors 608 for the detection of toxins A multiplex nanoparticle-based bio-barcoded 611 DNA sensor for the simultaneous detection of multiple pathogens Multiplex Biosensor Using Gold Nanorods A review on viral biosensors to detect human 618 pathogens A novel and rapid assay for HIV-1 protease detection 621 using magnetic bead mediation Nanostructured optical photonic crystal biosensor for 625 HIV viral load measurement Beads-628 based electrochemical assay for the detection of influenza hemagglutinin labeled with CdTe 629 quantum dots Novel graphene-based biosensor for early detection of Zika 633 virus infection Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of 637 avian influenza A (H7N9) virus Detection of swine-origin influenza A (H1N1) viruses using a 641 localized surface plasmon coupled fluorescence fiber-optic biosensor Electrochemical impedance spectroscopy characterization of nanoporous alumina dengue virus 646 biosensor Surface plasmon resonance sensing of Ebola virus: a biological 650 threat Diagnostic methods and potential portable biosensors for coronavirus 653 disease Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 657 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 658 biosensor Label-free, electrical detection of the SARS virus N-protein 662 with nanowire biosensors utilizing antibody mimics as capture probes Investigation of interaction between two neutralizing monoclonal antibodies and 667 SARS virus using biosensor based on imaging ellipsometry Immunofluorescence assay for serologic diagnosis of SARS A 676 Rapid and Specific Assay for the Detection of MERS-CoV One-Pot Reverse 680 Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting Multiplex paper-based colorimetric DNA sensor using pyrrolidinyl peptide nucleic acid-induced 685 AgNPs aggregation for detecting MERS-CoV, MTB, and HPV oligonucleotides Real-689 time sequence-validated loop-mediated isothermal amplification assays for detection of Middle 690 East respiratory syndrome coronavirus (MERS-CoV) Assessing activity and inhibition of 694 MERS-CoV papain-like and 3C-like proteases using luciferase-based biosensors Dual-functional 698 plasmonic photothermal biosensors for highly accurate severe acute respiratory syndrome 699 coronavirus 2 detection Rapid 702 and Sensitive Detection of anti-SARS-CoV-2 IgG, Using Lanthanide-Doped Nanoparticles-703 Based Lateral Flow Immunoassay Causative Virus (SARS-CoV-2) in Human Nasopharyngeal Swab Specimens Using Field-Effect 708 Transistor-Based Biosensor Multiplex reverse transcription loop-mediated isothermal amplification 712 combined with nanoparticle-based lateral flow biosensor for the diagnosis of COVID-19 Rapid detection of novel 716 coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse 717 transcription-loop-mediated isothermal amplification Current trends in nanomaterial embedded field effect transistor-721 based biosensor InP Nanowire Biosensor with Tailored Biofunctionalization: 726 Ultrasensitive and Highly Selective Disease Biomarker Detection The rise of graphene Label-free graphene biosensor targeting cancer molecules based on non-covalent 733 modification Field-736 effect transistor biosensor for rapid detection of Ebola antigen Localized surface plasmon coupled fluorescence fiber-optic biosensor with gold nanoparticles Sensitive Detection of Dengue Virus Type 2 E-Proteins Signals 744 Using Self-Assembled Monolayers/Reduced Graphene Oxide-PAMAM Dendrimer Thin Film-745 SPR Optical Sensor An alternative medical diagnosis method: 748 Biosensors for virus detection A multi-virus detectable microfluidic 751 electrochemical immunosensor for simultaneous detection of H1N1, H5N1, and H7N9 virus 752 using ZnO nanorods for sensitivity enhancement Label-free detection of influenza viruses using a reduced 755 graphene oxide-based electrochemical immunosensor integrated with a microfluidic platform A highly sensitive electrochemical immunosensor for 759 hepatitis B virus surface antigen detection based on Hemin/G-quadruplex horseradish 760 peroxidase-mimicking DNAzyme-signal amplification A sensitive electrochemical immunosensor for label-free detection of Zika-virus protein Development of a portable 767 and disposable NS1 based electrochemical immunosensor for early diagnosis of dengue virus, 768 Anal Chim An electrochemical immunosensor for the corona virus associated 771 with the Middle East respiratory syndrome using an array of gold nanoparticle-modified carbon 772 electrodes Paper-based microfluidic point-of-care diagnostic 775 devices Recent developments in paper-778 based microfluidic devices Electrochemistry on paper-based analytical devices: a review Sensing approaches on paper-based devices: a review Recent advances in paper-based sensors The challenge of emerging and re-emerging 791 infectious diseases Emerging infectious diseases: threats to human health and 794 global stability Emerging viral diseases Bushmeat and emerging 800 infectious diseases: lessons from Africa, Problematic Wildlife Introduction to Foodborne Pathogens One Health, emerging infectious diseases 807 and wildlife: two decades of progress? Infectious disease management through point-of-care 810 personalized medicine molecular diagnostic technologies Development of rapid, automated diagnostics for infectious disease: 814 advances and challenges Rapid infectious diseases diagnostics using Smartphones Emerging infectious diseases: public 820 health issues for the 21st century Methods for reducing biosensor membrane biofouling Kinetic screening of antibodies from crude 826 hybridoma samples using Biacore