Advanced Biosensors for Virus Detection: Smart Diagnostics to Combat SARS-CoV-2

460 Pages·2022·26.639 MB·English

by  Raju Khan, Arpana Parihar, Ajeet Kumar Kaushik, Ashok Kumar

Advanced Biosensors for
Virus Detection
Smart Diagnostics to Combat
SARS-CoV-2
Advanced Biosensors for
Virus Detection
Smart Diagnostics to Combat
SARS-CoV-2
Edited by
Raju Khan
CSIR-Advanced Materials &
Processes Research Institute (AMPRI), Bhopal, India
Arpana Parihar
CSIR-Advanced Materials &
Processes Research Institute (AMPRI), Bhopal, India
Ajeet Kaushik
Assistant Professor of Chemistry, NanoBioTech Laboratory, Department of
Environmental Engineering, Florida Polytechnic University, Lakeland,
FL, United States
Ashok Kumar
Department of Biochemistry, All India Institute of Medical Sciences (AIIMS),
Bhopal, India
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Contents
List ofcontributors............................................................................................................................xvii
Preface..............................................................................................................................................xxiii
Acknowledgments.............................................................................................................................xxv
CHAPTER 1 The emergence of severe acute respiratory
syndrome-coronavirus 2 epidemic and pandemic..............................1
Tabassum Zafar
1.1 Introduction................................................................................................................1
1.2 Severe acute respiratorysyndrome-coronavirus 2:the memberof the
coronavirus family......................................................................................................1
1.2.1 SARS-CoV-2 inconnection with severe acute respiratorysyndrome-
coronavirus andMiddle East respiratory syndrome-coronavirus...................2
1.3 Virion structure ofsevere acute respiratorysyndrome-coronavirus 2......................3
1.4 Pathophysiology of severe acute respiratory syndrome-coronavirus2
infection......................................................................................................................4
1.5 Transmissibility ofsevere acute respiratorysyndrome-coronavirus 2.....................7
1.6 Origin andetiology ofsevereacute respiratorysyndrome-coronavirus 2................8
1.7 From epidemic topandemic....................................................................................10
1.8 Perspective................................................................................................................13
References.................................................................................................................14
CHAPTER 2 Lesson learned from coronaviruses (SARS-CoV, MERS-CoV,
and SARS-CoV-2) and socioeconomic impact of (SARS-CoV-2)
pandemic.............................................................................................19
M.K. Verma, Y.K. Verma, H.S. Mann, Thomas Briese and
Rashmi Chowdhary
2.1 Introduction..............................................................................................................19
2.2 Coronaviruses and family........................................................................................19
2.2.1 Coronaviruses and human diseases...............................................................20
2.2.2 Coronavirusoutbreaks inthe past.................................................................21
2.2.3 Severe acute respiratory syndrome-coronavirus...........................................21
2.2.4 Middle East respiratory syndrome-coronavirus............................................22
2.2.5 Severe acute respiratory syndrome-coronavirus2........................................22
2.3 Diagnostics...............................................................................................................23
2.4 Therapeutics.............................................................................................................24
2.5 Vaccines...................................................................................................................25
2.6 World health response tocoronavirus disease........................................................25
v
vi Contents
2.7 Public health response tocoronavirus disease........................................................26
2.8 Human(cid:1)animal nexus..............................................................................................27
2.9 What we learned from pandemic and future...........................................................28
2.10 Conclusion................................................................................................................29
Acknowledgment......................................................................................................30
Conflicts of interest..................................................................................................30
References.................................................................................................................30
CHAPTER 3 Structure, genomic analysis, and pathogenesis of SARS-CoV-2......37
Divya Gupta, OnkarAwadhiya, Saurabh Saigal and AshokKumar
3.1 Classification ofcoronaviruses................................................................................37
3.2 Morphology and structure ofSARS-CoV-2............................................................39
3.2.1 Spike (S) protein............................................................................................39
3.2.2 Membrane(M) protein...................................................................................41
3.2.3 Envelope (E) protein......................................................................................41
3.2.4 Nucleocapsid (N)protein...............................................................................42
3.3 Nonstructural proteins..............................................................................................42
3.3.1 RNA-dependentRNA polymerase................................................................42
3.3.2 Themain protease..........................................................................................42
3.4 Genomic analysis.....................................................................................................43
3.4.1 Phylogenetic analysis.....................................................................................44
3.4.2 Emergenceof newer variants ofSARS-CoV-2.............................................44
3.5 Pathogenesis ofcoronavirus 19...............................................................................46
3.5.1 Infection andviremia.....................................................................................47
3.5.2 Inflammation and cytokine storm..................................................................48
3.5.3 Postinflammatory pulmonaryfibrosis...........................................................52
3.6 Extrapulmonary manifestations of coronavirus 19..................................................53
3.6.1 Cardiac involvement......................................................................................53
3.6.2 Hematological manifestations........................................................................53
3.6.3 Renal manifestation.......................................................................................54
3.6.4 Gastrointestinal and Hepatobiliary manifestations........................................54
3.6.5 Endocrine manifestations...............................................................................54
3.6.6 Neurological manifestations..........................................................................54
3.7 Conclusion................................................................................................................55
Acknowledgment......................................................................................................55
References.................................................................................................................55
CHAPTER 4 COVID-19 diagnosis: approaches and challenges............................61
Divya Namdeo, Anirudh K.Singh, Adarsh Meher, AshviniKumar Yadav
andDebasis Biswas
4.1 Introduction..............................................................................................................61
Contents vii
4.2 Sample collection.....................................................................................................62
4.3 qRT-PCR for detectionofSARS-CoV-2 RNA.......................................................64
4.4 Cartridge-based nucleic acid amplification tests.....................................................67
4.5 Pooling ofspecimens for nucleic acid amplification test.......................................67
4.6 Isothermalassays......................................................................................................68
4.7 Rapid antigen detectiontest.....................................................................................69
4.8 Quality control ofCOVID-19 testing......................................................................70
4.9 Conclusion................................................................................................................71
References.................................................................................................................72
CHAPTER 5 Current therapeutic choices for coronavirus disease 2019:
a state-of-the-art review.....................................................................79
P. Aparna,SmritiPanda and RajnishJoshi
5.1 Introduction..............................................................................................................79
5.2 Pathophysiology of coronavirus disease..................................................................79
5.2.1 Stage ofinfection andviremia......................................................................80
5.2.2 Stage ofinflammation and cytokine storm...................................................80
5.2.3 Postinflammatory pulmonaryfibrosis and itscomplications........................80
5.3 Therapeutics ofproven utility, targetingstage ofinfectionand viremia...............81
5.3.1 Monoclonalantibodies...................................................................................81
5.4 Therapeutics oflimited orunprovenutility, targeting stage of
Infection andviremia...............................................................................................82
5.4.1 Remdesivir.....................................................................................................82
5.4.2 Hydroxychloroquine.......................................................................................83
5.4.3 Ivermectin......................................................................................................84
5.4.4 Lopinavir........................................................................................................84
5.5 Therapeutics ofproven utility, targetingcytokine storm........................................85
5.5.1 Glucocorticoids..............................................................................................85
5.5.2 Anticoagulants................................................................................................86
5.6 Therapeutics oflimited utility, targeting cytokine storm........................................86
5.6.1 Tocilizumab....................................................................................................86
5.6.2 Interferons......................................................................................................86
5.6.3 Baricitinib.......................................................................................................87
5.6.4 Bevacizumab..................................................................................................87
5.6.5 Infliximab.......................................................................................................87
5.6.6 Artesunate.......................................................................................................87
5.7 Therapeutics oflimited oruncertainutility, targeting post-coronavirus
disease complications...............................................................................................88
5.7.1 Drugstargetingpulmonary fibrosis: nintedaniband pirfenidone.................88
5.7.2 Colchicine......................................................................................................88
viii Contents
5.7.3 Drugs targeting pulmonary hypertension......................................................88
5.7.4 Long term anticoagulation therapy................................................................89
5.8 Conclusion................................................................................................................89
References.................................................................................................................90
CHAPTER 6 Genomic, proteomic biomarkers and risk factors associated
with COVID-19.....................................................................................95
HimadriSingh, Rajeev Nema and Ashok Kumar
6.1 Introduction..............................................................................................................95
6.2 Biomarkers...............................................................................................................96
6.3 Proteomic Biomarkers for COVID-19.....................................................................96
6.3.1 Cytokines........................................................................................................96
6.3.2 Acute-phase proteins......................................................................................97
6.3.3 Clinical biochemical parameters...................................................................99
6.3.4 Identification of novel proteomicsbiomarkers for COVID-19....................99
6.4 Genetic biomarkers................................................................................................102
6.4.1 Genetic predisposition biomarkers..............................................................102
6.4.2 Noncoding RNA..........................................................................................105
6.5 Conclusion and future perspective.........................................................................106
References...............................................................................................................106
CHAPTER 7 Biological/synthetic receptors (antibody, enzyme, and aptamer)
used for biosensors development for virus detection.....................113
Akanksha Roberts,Subhasis Mahariand Sonu Gandhi
7.1 Introduction............................................................................................................113
7.2 Types ofbioreceptors.............................................................................................114
7.2.1 Enzymes.......................................................................................................114
7.2.2 Antibody and antigen...................................................................................115
7.2.3 Nucleic acid.................................................................................................115
7.2.4 Whole cell....................................................................................................115
7.2.5 Aptamers......................................................................................................115
7.2.6 Peptides........................................................................................................116
7.2.7 Molecularlyimprinted polymers.................................................................116
7.2.8 Other sensorparadigms...............................................................................116
7.3 Properties of biosensors based on bioreceptors.....................................................116
7.4 Examples ofbiosensors for detectionofcoronavirus disease 2019 based on
different bioreceptors.............................................................................................117
7.4.1 Antibody receptorbased..............................................................................117
7.4.2 Antigen receptorbased................................................................................118
7.4.3 Nucleic acid receptor based.........................................................................121
Contents ix
7.4.4 Peptide receptorbased.................................................................................123
7.5 Future prospects.....................................................................................................125
7.6 Conclusion..............................................................................................................125
References...............................................................................................................125
CHAPTER 8 Potential electrochemical biosensors for early detection of
viral infection....................................................................................133
Annu Pandey, Priya Chauhan and AyushiSinghal
8.1 Introduction............................................................................................................133
8.2 Types ofviral infections and their detection.........................................................136
8.2.1 Respiratory viral infection...........................................................................136
8.2.2 Sexuallytransmitted viral infection.............................................................139
8.2.3 Food-borne viral infection...........................................................................142
8.2.4 Mosquito-borneviral infection....................................................................144
8.3 Conclusion..............................................................................................................147
References...............................................................................................................148
CHAPTER 9 Optical biosensors for SARS-CoV-2 detection.................................155
PriyankaPulugu, Akanksha Wakhare and Neha Arya
9.1 Introduction............................................................................................................155
9.2 Biosensors: an introduction to optical biosensors.................................................156
9.3 Surface-plasmonresonance-basedbiosensors.......................................................157
9.4 Localizedsurface plasmonresonance-based optical biosensors...........................158
9.5 Surface-enhanced Ramanscattering-based optical biosensors.............................161
9.6 Optical lateral flow assay for SARS-CoV-2-detection.........................................161
9.7 Challengesin developingopticalbiosensors.........................................................163
9.8 Conclusion andfuture perspectives.......................................................................163
Acknowledgments..................................................................................................164
References...............................................................................................................164
CHAPTER 10 Recent developments of molecular/biosensor diagnostics for
SARS-CoV-2 detection......................................................................167
Rupesh K.Mishra, Navin Pai,K. YugenderGoud, Ravi Ranjan Kumar Niraj,
DeepakKumar, GaurangPatel, Vinod Singh Gour, Amin Zareei,
Rahim Rahimi, Vinay Sharma, RogerNarayanand LiaStanciu
10.1 Introduction............................................................................................................167
10.2 Nucleic acid-based detection.................................................................................168
10.2.1 RT-qPCR-based detection........................................................................168
10.2.2 Alternate nucleic acid testing....................................................................168
x Contents
10.3 Serological testing..................................................................................................169
10.4 Biosensors for COVID-19 diagnostics..................................................................170
10.4.1 Electrochemical biosensors for SARS-CoV-2detection..........................171
10.4.2 Optical biosensors......................................................................................173
10.4.3 CRISPR-based biosensor for SARS-CoV-2..............................................175
10.5 Electrical and piezoelectric biosensors..................................................................176
10.5.1 COVID test based on antibody detection..................................................177
10.5.2 Detection of blocking antibodies...............................................................178
10.5.3 Harnessing wearable devices to detect SARS-CoV-2 infections.............179
10.5.4 Smart toilettechnology..............................................................................179
10.6 Futuredirections.....................................................................................................179
10.7 Conclusions............................................................................................................181
Acknowledgments..................................................................................................181
References...............................................................................................................181
CHAPTER 11 Role of magnetic nanoparticles in development of biosensors
for viral infection diagnostics..........................................................189
AtripanMukherjee,LukasRichtera,VojtechAdamandAmirmansoorAshrafi
11.1 Introduction............................................................................................................189
11.2 Capture,preconcentration,extraction....................................................................190
11.3 Multiple detections with immunomagnetic separation.........................................193
11.4 Labeling..................................................................................................................194
11.5 Magneticlabel........................................................................................................194
11.6 Fluorometric label..................................................................................................195
11.7 Labelingbased on the enzyme-like activityof magnetic nanoparticles...............198
11.8 Dualrole ofmagnetic nanoparticles and application inmicrofluidics.................199
11.9 Conclusion and perspective...................................................................................199
References...............................................................................................................200
CHAPTER 12 Advances in nanomaterials-based biosensors for the
development of virus detection........................................................203
AmilanD. Jose and Amrita Ghosh
12.1 Introduction............................................................................................................203
12.2 Fundamental principles..........................................................................................204
12.3 Gold nanoparticles-based biosensor.......................................................................205
12.3.1 Gold nanoparticles for the detection of Zika virus...................................205
12.3.2 Gold nanoparticles for the detection of SARS-CoV.................................205
12.4 Quantumdots-based nanomaterials.......................................................................208
12.5 Upconversionnanoparticles...................................................................................210