Viral Genomics: A Pillar in Infectious Disease Prevention and Control
Keywords:
Viral genomics, Viral diseases, SARS-CoV-2, Human Papillomavirus, Influenza Virus, Viral DatabasesAbstract
Viral genomics has become a crucial tool for understanding the complex dynamics of viral infections, significantly advancing the methods for controlling and preventing infectious diseases. Genomic sequencing gives scientists new perspectives on virus evolution, mutation patterns, transmission dynamics, and interactions between hosts and viruses. Advancement of diagnostic tools, vaccinations, and antiviral therapies depends on the information shown, impacting public health policies. Viral genomic databases, including the Influenza Database, HPV Database, and SARS-CoV-2 Database, have greatly enhanced our ability to monitor and track viral diseases worldwide. These databases improve real-time genomic surveillance so researchers can predict viral behavior and change their response using control measures. This review clarifies the importance of these databases in studying the genetic makeup of SARS-CoV-2, HPV, and influenza viruses. It investigates their contributions to world health, particularly regarding pandemic response, vaccine development, and viral mutation monitoring. Addressing the disparities in genomic surveillance capabilities and ensuring the equitable utilization of genomic data are persistent challenges. Developments in next-generation sequencing technology offer great possibilities to improve our knowledge of viral genomes and guide disease preventive measures.
References
[1] Suryasa IW, Rodríguez-Gámez M, Koldoris T. The COVID-19 Pandemic. International Journal of Health Sciences. 2021, 5(2): 6-9. DOI: 10.53730/ijhs.v5n2.2937
[2] Spreeuwenberg P, Kroneman M, Paget J. Reassessing the Global Mortality Burden of the 1918 Influenza Pandemic. American Journal of Epidemiology. 2018, 187(12): 2561-2567. DOI: 10.1093/aje/kwy191
[3] Myoung J. Two Years of COVID-19 Pandemic: Where Are We Now? Journal of Microbiology. 2022, 60(3): 235-237. DOI: 10.1007/s12275-022-1679-x
[4] Carroll SP, Jørgensen PS, Kinnison MT, Bergstrom CT, Denison RF, et al. Applying Evolutionary Biology to Address Global Challenges. Science. 2014, 346(6207): 1245993. DOI: 10.1126/science.1245993
[5] Mahmoud SH, Khalil AA. Viral Genomics, in Microbial Genomics: Clinical, Pharmaceutical, and Industrial Applications. Elsevier. 2024, 31-70.
[6] Omersel J, Karas Kuželički N. Vaccinomics and Adversomics in the Era of Precision Medicine: A Review Based on HBV, MMR, HPV, and COVID-19 Vaccines. Journal of Clinical Medicine. 2020, 9(11): 3561. DOI: 10.3390/jcm9113561
[7] Chenchula S, Anitha K, Prakash S, Sharma JP, Aggarwal S. Multiomics in Human Viral Infections, in Biological Insights of Multi-Omics Technologies in Human Diseases. Elsevier. 2024, 145-166.
[8] Rahimian M, Panahi B. Next Generation Sequencing-Based Transcriptome Data Mining for Virus Identification and Characterization: Review on Recent Progress and Prospect. Journal of Clinical Virology Plus. 2024: 100194. DOI: 10.1016/j.jcvp.2024.100194
[9] Gangopadhayya A, Bhukya PL. Factors Contributing to the Emergence of Viral Diseases, in Emerging Human Viral Diseases, Volume I: Respiratory and Haemorrhagic Fever. Springer. 2023, 3-69.
[10] Løvestad AH. Viral Genomics by Next-generation Sequencing–Investigating Intra-Host Genomic Events in Human Papillomavirus and Improving Intra-hospital Outbreak Investigations of SARS-CoV-2. Oslomet - storbyuniversitetet. 2023.
[11] Swaminathan A, Ravi V, Gupta R, Singh S, Goswami S, et al., Interactions Shaping the Interactome: Genome Surveillance Inclusive of Host–Pathogen, in Genomic Surveillance and Pandemic Preparedness. Elsevier. 2023, 301-347. DOI: 110.1016/B978-0-443-18769-8.00001-5
[12] AlKhazindar M, El-Senousy WM, Abuhadema Y. Multi-omics in Viral Microbiome, in Multi-Omics Analysis of the Human Microbiome: From Technology to Clinical Applications. Springer. 2024, 275-294.
[13] Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq Methods to Interrogate Virus-host Interactions. Seminars Immunopathology. 2023, 45(1):71-89. DOI: 10.1007/s00281-022-00972-2
[14] Nguyen MH, Wong G, Gane E, Kao J-H, Dusheiko G. Hepatitis B Virus: Advances in Prevention, Diagnosis, and Therapy. Clinical Microbiology Reviews. 2020, 33(2): 10. DOI: 10.1128/CMR.00046-19
[15] Arisan ED, Dart A, Grant GH, Arisan S, Cuhadaroglu S, et al. The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities. Viruses. 2020, 12(6): 614. DOI: 10.3390/v12060614
[16] Vashisht V, Vashisht A, Mondal AK, Farmaha J, Alptekin A, et al. Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles. BioMedInformatics. 2023, 3(4): 1145-1177. DOI:
[17] Jain S, Nehra M, Kumar R, Dilbaghi N, Hu T, et al. Internet of Medical Things (IoMT)-Integrated Biosensors for Point-of-Care Testing of Infectious Diseases. Biosensors and Bioelectronics. 2021, 179: 113074. DOI: 10.1016/j.bios.2021.113074
[18] Gaurav A, Agrawal N, Al-Nema M, Gautam V. Computational Approaches in the Discovery and Development of Therapeutic and Prophylactic Agents for Viral Diseases. Current Topics in Medicinal Chemistry. 2022, 22(26): 2190-2206. DOI: 10.2174/1568026623666221019110334
[19] Tonk M, Růžek D, Vilcinskas A. Compelling Evidence for the Activity of Antiviral Peptides Against SARS-CoV-2. Viruses. 2021, 13(5): 912. DOI: 10.3390/v13050912
[20] Rahimi A, Mirzazadeh A, Tavakolpour S. Genetics and Genomics of SARS-CoV-2: A Review of the Literature with the Special Focus on Genetic Diversity and SARS-CoV-2 Genome Detection. Genomics. 2021, 113(1): 1221-1232. DOI: 10.1016/j.ygeno.2020.09.059
[21] Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, et al. The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the Covid-19 Pandemic and the Future Evolutionary Paths of Sars-Cov-2. Viruses. 2022, 14(1): 78. DOI: 10.3390/v14010078
[22] Domingo E, García-Crespo C, Lobo-Vega R, Perales C. Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in Rna Virus Genetics. Viruses. 2021, 13(9): 1882. DOI: 10.3390/v13091882
[23] Sarkar M, Madabhavi I. COVID-19 Mutations: An Overview. World Journal of Methodology. 2024, 14(3): 89761. DOI: 10.5662/wjm.v14.i3.89761
[24] Khairnar P, Soni M, Handa M, Riadi Y, Kesharwani P, et al. Recent Highlights on Omicron as a New SARS-COVID-19 Variant: Evolution, Genetic Mutation, and Future Perspectives. Journal of Drug Targeting. 2022, 30(6): 603-613. DOI: 10.1080/1061186X.2022.2056187
[25] Wang R, Hozumi Y, Yin C, Wei GW. Mutations on COVID-19 Diagnostic Targets. Genomics. 2020, 112(6): 5204-5213. DOI: 10.1016/j.ygeno.2020.09.028
[26] Oette M, Kaiser R, Däumer M, Petch R, Fätkenheuer G, et al. Primary HIV Drug Resistance and Efficacy of First-Line Antiretroviral Therapy Guided By Resistance Testing. JAIDS Journal of Acquired Immune Deficiency Syndromes. 2006, 41(5): 573-581. DOI: 10.1097/01.qai.0000214805.52723.c1
[27] Nastri BM, Pagliano P, Zannella C, Folliero V, Masullo A, et al. HIV and Drug-Resistant Subtypes. Microorganisms. 2023, 11(1): 221. DOI: 10.3390/microorganisms11010221
[28] Zanini F, Puller V, Brodin J, Albert J, Neher RA. In vivo Mutation Rates and the Landscape Of Fitness Costs of HIV-1. Virus Evolution. 2017, 3(1): vex003. DOI: 10.1093/ve/vex003
[29] Hie B, Zhong ED, Berger B, Bryson B. Learning the Language of Viral Evolution and Escape. Science. 2021, 371(6526): 284-288. DOI: 10.1126/science.abd7331
[30] Magazine N, Zhang T, Wu Y, McGee MC, Veggiani G, et al. Mutations and Evolution of the SARS-CoV-2 Spike Protein. Viruses. 2022, 14(3): 640. DOI: 10.3390/v14030640
[31] Onomoto K, Onoguchi K, Yoneyama M. Regulation of RIG-I-Like Receptor-Mediated Signaling: Interaction Between Host and Viral Factors. Cellular & Molecular Immunology. 2021, 18(3): 539-555. DOI: 10.1038/s41423-020-00602-7
[32] Abdullah D. Human Papillomavirus (HPV). Qeios. 2023. DOI: 10.32388/MY0H33
[33] Piret J, Boivin G. Viral Interference Between Respiratory Viruses. Emerging Infectious Diseases. 2022, 28(2): 273. DOI: 10.3201/eid2802.211727
[34] Duerkop BA, Hooper LV. Resident Viruses and Their Interactions with the Immune System. Nature Immunology. 2013, 14(7): 654-659. DOI: 10.1038/ni.2614
[35] Payne S. Viruses: from Understanding to Investigation. Elsevier. 2022.
[36] Rebensburg SV, Wei G, Larue RC, Lindenberger J, Francis AC, et al. Sec24C Is an HIV-1 Host Dependency Factor Crucial for Virus Replication. Nature Microbiology. 2021, 6(4): 435-444. DOI: 10.1038/s41564-021-00868-1
[37] Hendricks CM, Cordeiro T, Gomes AP, Stevenson M. The Interplay of HIV-1 and Macrophages in Viral Persistence. Frontiers in Microbiology. 2021, 12: 646447. DOI: 10.3389/fmicb.2021.646447
[38] Rossi E, Meuser ME, Cunanan CJ, Cocklin S. Structure, Function, and Interactions of the HIV-1 Capsid Protein. Life. 2021, 11(2): 100. DOI: 10.3390/life11020100
[39] Leung NH. Transmissibility and Transmission of Respiratory Viruses. Nature Reviews Microbiology. 2021, 19(8): 528-545. DOI: 10.1038/s41579-021-00535-6
[40] Wang Y, Chen R, Hu F, Lan Y, Yang Z, et al. Transmission, Viral Kinetics and Clinical Characteristics of the Emergent SARS-CoV-2 Delta VOC in Guangzhou, China. EClinicalMedicine. 2021, 40. DOI: 10.1016/j.eclinm.2021.101129
[41] Cevik M, Kuppalli K, Kindrachuk J, Peiris M. Virology, Transmission, and Pathogenesis of SARS-CoV-2. The British Medical Journal. 2020, 371. DOI: 10.1136/bmj.m3862
[42] Wang D, Zhou M, Nie X, Qiu W, Yang M, et al. Epidemiological Characteristics and Transmission Model of Corona Virus Disease 2019 in China. The Journal of Infection. 2020, 80(5): e25. DOI: 10.1016/j.jinf.2020.03.008
[43] Sahu KK, Mishra AK, Lal A. COVID-2019: Update on Epidemiology, Disease Spread and Management. Monaldi Archives for Chest Disease. 2020, 90(1). DOI:10.4081/monaldi.2020.1292
[44] Fiallo-Olivé E, Pan LL, Liu SS, Navas-Castillo J. Transmission of Begomoviruses and other Whitefly-Borne Viruses: Dependence on the Vector Species. Phytopathology. 2020, 110(1): 10-17. DOI: 10.1094/PHYTO-07-19-0273-FI
[45] Ryu S, Cowling BJ. Human Influenza Epidemiology. Cold Spring Harbor Perspectives in Medicine. 2021, 11(12): a038356. DOI: 10.1101/cshperspect.a038356
[46] Wille M, Holmes EC. The Ecology and Evolution of Influenza Viruses. Cold Spring Harbor Perspectives in Medicine. 2020, 10(7): a038489. DOI: 10.1101/cshperspect.a038489
[47] Hill S, Perkins M, von Eije KJ, Benschop K, Faria NR, et al. Genomic Sequencing of SARS-CoV-2: a Guide to Implementation for Maximum Impact on Public Health. World Health Organization. 2021.
[48] Banho CA, de Carvalho Marques B, Sacchetto L, Lima AKS, Parra MCP, et al. Dynamic Clade Transitions and the Influence of vaccination on the Spatiotemporal Circulation of SARS-CoV-2 Variants. NPJ Vaccines. 2024, 9(1): 145. DOI: 10.1038/s41541-024-00933-w
[49] Giovanetti M, Branda F, Cella E, Scarpa F, Bazzani L, et al. Epidemic History and Evolution of an Emerging Threat of International Concern, the Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Medical Virology. 2023, 95(8): e29012. DOI: 10.1002/jmv.29012
[50] Barbara JA, Dow BC. Retroviruses and Other Viruses. Rossi's Principles of Transfusion Medicine. 2009: 746-759. DOI: 10.1002/9781444303513.ch47
[51] Eniola Oaa. Epidemiology of HIV/AIDS. Eastern Mediterranean University. 2017.
[52] Basu P, Brisson M, Campos N, Clarke E, Drolet M, et al. Review of the Current Published Evidence on Single-Dose HPV Vaccination 3rd Edition. London School of Hygiene & Tropical Medicine. 2020. DOI:10.17037/PUBS.04661079
[53] Bryan S. Circulating HPV DNA as a Biomarker for Early Invasive Cervical Cancer. University College London. 2022.
[54] Moa A. The Epidemiology of Influenza B-evidence to Inform the Use of Quadrivalent Influenza Vaccines and Predict Seasonal Severity. UNSW Sydney. 2018.
[55] Suntronwong N. Identification of Genetic and Antigenic Variation and Evolution Pattern Among Influenza A and B Viruses in Thailand. Chulalongkorn University. 2020. DOI: 10.58837/CHULA.THE.2020.325
[56] Matiur TB. Prevalence of Zika Virus Infection in Patients with Guillain-Barre Syndrome in Bangladesh. Brac University. 2019.
[57] Tin YCH. Investigating Determinants of Immunogenicity and Safety in Zika Live Attenuated Vaccines. National University of Singapore. 2021.
[58] Rickett NY. Determinants of Patient Survival Following Acute Ebola Virus Infection. The University of Liverpool. 2019.
[59] Sellu EF. Ebola Virus Disease and COVID-19: A Critical Analysis of the Healthcare Response Strategies & Capacities in Sierra Leone. Oklahoma State University. 2023.
[60] Lakshmi V. A Study on Clinical Profile in Correlation with Laboratory Investigations and Radiological Findings in Dengue Fever. Rajiv Gandhi University of Health Sciences. 2013.
[61] Hantoushzadeh S, Shamshirsaz AA, Aleyasin A, Seferovic MD, Aski SK, et al. Maternal Death Due to COVID-19. American Journal of Obstetrics and Gynecology. 2020, 223(1): 109. e101-109. e116. DOI: 10.1016/j.ajog.2020.04.030
[62] Ewer KJ, Barrett JR, Belij-Rammerstorfer S, Sharpe H, Makinson R, et al. T Cell and Antibody Responses Induced by a Single Dose of ChAdOx1 nCoV-19 (AZD1222) Vaccine in a Phase 1/2 Clinical Trial. Nature Medicine. 2021, 27(2): 270-278. DOI: 10.1038/s41591-020-01194-5
[63] Perrott PE. Detection of Bacteriophage and Respiratory Viruses in Droplets. Queensland University of Technology. 2011.
[64] Jones AC. Elucidation of the Immunoinflammatory Mechanisms Underlying Severe Virus-Induced Respiratory Disease in Early Childhood. The University of Western Australia. 2018. DOI: 10.26182/5b90cf6557411
[65] Manish Da. Molecular Characterization of Chikungunya and Dengue Virus and Their Association with Liver and Renal Profiles. International Journal of Advanced Research. 2021.
[66] Otieno CW. Chikungunya Virus Characterization and Development of Enzyme Linked Immunosorbent Assays as Detection Tools for Human and Mosquito Samples. JOMO Kenyatta University of Agriculture and Technology. 2017.
[67] Rubin SA, Kennedy RB. Paramyxoviruses: Mumps, in Viral Infections of Humans: Epidemiology and Control. Springer. 2023, 1-57. DOI: 10.1007/978-1-4939-9544-8_24-1
[68] Wilson MR, Ludlow M, Duprex WP. Human Paramyxoviruses and Infections of the Central Nervous System. CRC Press. 2013.
[69] Huang YJ. Identification and Characterization of the Genetic Determinants for Yellow Fever Virus Infection and Dissemination in Aedes Aegypti. Kansas State University. 2014.
[70] Santos del Peral A, Effect of Prior Flavivirus Immunity on the Adaptive Response to the Yellow Fever 17D Vaccine. Ludwig-Maximilians-Universität München. 2024. DOI: 10.5282/edoc.33548
[71] Antoine TE. Herpes Simplex Virus Infectivity and the Development of Therapeutics Against Viral Invasion. University of Illinois at Chicago. 2014.
[72] Yap SH. The Role of Human Herpesvirus (HHV) Infections and Persistent Immune Activation in Antiretroviral Therapy-Treated HIV Infected Individuals/Yap Siew Hwei. University of Malaya. 2018.
[73] Oliveira OR. Risk Factors Associated with Multidrug-Resistant Tuberculosis Transmission in Portugal. Universidade do Minho. 2021. DOI: 10.4236/jtr.2014.23014
[74] Lim KL. A Study of Norovirus: Molecular Epidemiology, Pathogenesis and Antiviral Development. UNSW Sydney. 2015.
[75] Chan PK, Kwan HS, Chan MC, The Norovirus: Features, Detection, and Prevention of Foodborne Disease. Academic Press. 2016.
[76] Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, et al. Influenza Research Database: an Integrated Bioinformatics Resource for Influenza Virus Research. Nucleic Acids Research. 2017, 45(D1): D466-D474. DOI: 10.1093/nar/gkw857
[77] Shu Y, McCauley J. GISAID: Global Initiative on Sharing All Influenza Data–from Vision to Reality. Eurosurveillance. 2017, 22(13): 30494. DOI: 10.2807/1560-7917.ES.2017.22.13.30494
[78] Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Le Mercier P, et al. OpenFluDB, a Database for Human and Animal Influenza Virus. Database. 2010, 2010: baq004. DOI: 10.1093/database/baq004
[79] Squires RB, Noronha J, Hunt V, García‐Sastre A, Macken C, et al. Influenza Research Database: an Integrated Bioinformatics Resource for Influenza Research and Surveillance. Influenza and Other Respiratory Viruses. 2012, 6(6): 404-416. DOI: 10.1111/j.1750-2659.2011.00331.x
[80] Fernandes-Matano L, Monroy-Munoz I, de León MB, Leal-Herrera Y, Palomec-Nava I, et al. Analysis of Influenza Data Generated by Four Epidemiological Surveillance Laboratories in Mexico, 2010–2016. Epidemiology & Infection. 2019, 147: e183. DOI: 10.1017/S0950268819000694
[81] Chang S, Zhang J, Liao X, Zhu X, Wang D, et al. Influenza Virus Database (IVDB): an Integrated Information Resource and Analysis Platform for Influenza Virus Research. Nucleic Acids Research. 2007, 35(suppl_1): D376-D380. DOI: 10.1093/nar/gkl779
[82] Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, et al. The Influenza Virus Resource at the National Center for Biotechnology Information. Journal of Virology. 2008, 82(2): 596-601. DOI: 10.1128/JVI.02005-07
[83] Yang S, Lee J-Y, Lee JS, Mitchell WP, Oh H-B, et al. Influenza Sequence and Epitope Database. Nucleic Acids Research. 2009, 37(suppl_1): D423-D430. DOI: 10.1093/nar/gkn881
[84] Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, et al. Detecting Influenza Epidemics Using Search Engine Query Data. Nature. 2009, 457(7232): 1012-1014. DOI: 10.1038/nature07634
[85] Mühr LSA, Eklund C, Dillner J. Misclassifications in Human Papillomavirus Databases. Virology. 2021, 558: 57-66. DOI: 10.1016/j.virol.2021.03.002
[86] Van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D, et al. The Papillomavirus Episteme: a Major Update to the Papillomavirus Sequence Database. Nucleic Acids Research. 2017, 45(D1): D499-D506. DOI: 10.1093/nar/gkw879
[87] Yang Z, Yi W, Tao J, Liu X, Zhang MQ, et al. HPVMD-C: a Disease-Based Mutation Database of Human Papillomavirus in China. Database. 2022, baac018. DOI: 10.1093/database/baac018
[88] Van Doorslaer K, Tan Q, Xirasagar S, Bandaru S, Gopalan V, et al. The Papillomavirus Episteme: a Central Resource for Papillomavirus Sequence Data and Analysis. Nucleic Acids Research. 2012, 41(D1): D571-D578. DOI: 10.1093/database/baac018
[89] Rodriguez AM, Zeybek B, Vaughn M, Westra J, Kaul S, et al. Comparison of the Long‐Term Impact and Clinical Outcomes of Fewer Doses and Standard Doses of Human Papillomavirus Vaccine in the United States: a Database Study. Cancer. 2020, 126(8): 1656-1667. DOI: 10.1002/cncr.32700
[90] Rettig EM, Zaidi M, Faraji F, Eisele DW, El Asmar M, et al. Oropharyngeal Cancer is no Longer a Disease of Younger Patients and the Prognostic Advantage of Human Papillomavirus is Attenuated Among Older Patients: Analysis of the National Cancer Database. Oral Oncology. 2018, 83: 147-153. DOI: 10.1016/j.oraloncology.2018.06.013
[91] Syrjänen K, Syrjänen S. Detection of Human Papillomavirus in Sinonasal Papillomas: Systematic Review and Meta‐Analysis. The Laryngoscope. 2013, 123(1): 181-192. DOI: 10.1002/lary.23688
[92] Fang S, Li K, Shen J, Liu S, Liu J, et al. GESS: a Database of Global Evaluation of SARS-CoV-2/hCoV-19 Sequences. Nucleic Acids Research. 2021, 49(D1): D706-D714. DOI: 10.1093/nar/gkaa808
[93] Chen TF, Chang YC, Hsiao Y, Lee KH, Hsiao YC, et al. DockCoV2: a Drug Database Against SARS-CoV-2. Nucleic Acids Research. 2021, 49(D1): D1152-D1159. DOI: 10.1093/nar/gkaa861
[94] McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, et al. A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees. Molecular Biology and Evolution. 2021, 38(12): 5819-5824. DOI: 10.1093/molbev/msab264
[95] Patil S. Indian Publications on SARS-CoV-2: A Bibliometric Study of WHO COVID-19 Database. Diabetes & Metabolic Syndrome: Clinical Research & Reviews. 2020, 14(5): 1171-1178. DOI: 10.1016/j.dsx.2020.07.007
[96] Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T, et al. SCoV2-MD: a Database for the Dynamics of the SARS-CoV-2 Proteome and Variant Impact Predictions. Nucleic Acids Research. 2022, 50(D1): D858-D866. DOI: 10.1093/nar/gkab977
[97] Feng Y, Yi J, Yang L, Wang Y, Wen J, et al. COV2Var, a Function Annotation Database of SARS-CoV-2 Genetic Variation. Nucleic Acids Research. 2024, 52(D1): D701-D713. DOI: 10.1093/nar/gkad958
[98] Cheng Y, Ji C, Zhou HY, Zheng H, Wu A. Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking. Viruses. 2023, 15(5): 1158. DOI: 10.3390/v15051158
[99] Lundy L, Fatta-Kassinos D, Slobodnik J, Karaolia P, Cirka L, et al. Making Waves: Collaboration in the Time of SARS-CoV-2-Rapid Development of an International Co-Operation and Wastewater Surveillance Database to Support Public Health Decision-Making. Water Research. 2021, 199: 117167. DOI: 10.1016/j.watres.2021.117167
[100] Robishaw JD, Alter SM, Solano JJ, Shih RD, DeMets DL, et al. Genomic Surveillance to Combat COVID-19: Challenges and Opportunities. The Lancet Microbe. 2021, 2(9): e481-e484. DOI: 10.1016/S2666-5247(21)00121-X
[101] Uddin M, Mustafa F, Rizvi TA, Loney T, Al Suwaidi H, et al. SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions. Viruses. 2020, 12(5): 526. DOI: 10.3390/v12050526
[102] Saravanan K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, et al. Role of Genomics in Combating COVID-19 Pandemic. Gene. 2022, 823: 146387. DOI: 10.1016/j.gene.2022.146387
[103] Helmy YA, Fawzy M, Elaswad A, Sobieh A, Kenney SP, et al. The COVID-19 Pandemic: a Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control. Journal of Clinical Medicine. 2020, 9(4): 1225. DOI: 10.3390/jcm9041225
[104] Hoque MN, Chaudhury A, Akanda MAM, Hossain MA, Islam MT. Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease. PeerJ. 2020, 8: e9689. DOI: 10.7717/peerj.9689
[105] Jolly B, Scaria V, Genomics and Infectious Diseases: Lessons Learnt from the COVID-19 Pandemic, in Genomics, Populations, and Society. Elsevier. 2025. 183-206.
[106] Chen Y, Liang W, Yang S, Wu N, Gao H, et al. Human Infections with the Emerging Avian Influenza A H7N9 Virus from Wet Market Poultry: Clinical Analysis and Characterisation of Viral Genome. The Lancet. 2013, 381(9881): 1916-1925. DOI: 10.1016/S0140-6736(13)60903-4
[107] Yu X, Jin T, Cui Y, Pu X, Li J, et al. Influenza H7N9 and H9N2 Viruses: Coexistence in Poultry Linked to Human H7N9 Infection and Genome Characteristics. Journal of Virology. 2014, 88(6): 3423-3431. DOI: 10.1128/JVI.02059-13
[108] Tanner W, Toth D, Gundlapalli A. The Pandemic Potential of Avian Influenza A (H7N9) Virus: a Review. Epidemiology & Infection. 2015, 143(16): 3359-3374. DOI: 10.1017/S0950268815001570
[109] Belser JA, Gustin KM, Pearce MB, Maines TR, Zeng H, et al. Pathogenesis and Transmission of Avian Influenza A (H7N9) Virus in Ferrets and Mice. Nature. 2013, 501(7468): 556-559. DOI: 10.1038/nature12391
[110] Watanabe T, Watanabe S, Maher EA, Neumann G, Kawaoka Y. Pandemic Potential of Avian Influenza A (H7N9) Viruses. Trends in Microbiology. 2014, 22(11): 623-631. DOI: 10.1016/j.tim.2014.08.008
[111] Morrison J, Josset L, Tchitchek N, Chang J, Belser JA, et al. H7N9 and Other Pathogenic Avian Influenza Viruses Elicit a Three-Pronged Transcriptomic Signature that is Reminiscent of 1918 Influenza Virus and is Associated with Lethal Outcome in Mice. Journal of Virology. 2014, 88(18): 10556-10568. DOI: 10.1128/JVI.00570-14
[112] Yu H, Cowling BJ, Feng L, Lau EH, Liao Q, et al. Human Infection with Avian Influenza A H7N9 Virus: an Assessment of Clinical Severity. The Lancet. 2013, 382(9887): 138-145. DOI: 10.1016/S0140-6736(13)61207-6
[113] Yin X, Deng G, Zeng X, Cui P, Hou Y, et al. Genetic and Biological Properties of H7N9 Avian Influenza Viruses Detected After Application of the H7N9 Poultry Vaccine in China. PLoS Pathogens. 2021, 17(4): e1009561. DOI: 10.1371/journal.ppat.1009561
[114] Yiu LK, Wing YNG, Fai WK, Fan NHI, Kam FHJ, et al. Human H7N9 Avian Influenza Virus Infection: a Review and Pandemic Risk Assessment. Emerging Microbes & Infections. 2013, 2(1): 1-5. DOI: 10.1038/emi.2013.48
[115] Bock C, Lengauer T. Managing Drug Resistance in Cancer: Lessons from HIV Therapy. Nature Reviews Cancer. 2012, 12(7): 494-501. DOI: 10.1038/nrc3297
[116] Lengauer T, Pfeifer N, Kaiser R. Personalized HIV Therapy to Control Drug Resistance. Drug Discovery Today: Technologies. 2014, 11: 57-64. DOI: 10.1016/j.ddtec.2014.02.004
[117] Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, et al. A Genome-to-Genome Analysis of Associations Between Human Genetic Variation, HIV-1 Sequence Diversity, and Viral Control. Elife. 2013, 2: e01123. DOI: 10.7554/eLife.01123
[118] Tough RH, McLaren PJ. Interaction of the Host and Viral Genome and Their Influence on HIV Disease. Frontiers in Genetics. 2019, 9: 720. DOI: 10.3389/fgene.2018.00720
[119] Gilbert RK, Petersen LR, Honein MA, Moore CA, Rasmussen SA. Zika Virus As a Cause of Birth Defects: Were the Teratogenic Effects of Zika Virus Missed for Decades? Birth Defects Research. 2023, 115(3): 265-274. DOI: 10.1002/bdr2.2134
[120] Wang A, Thurmond S, Islas L, Hui K, Hai R. Zika Virus Genome Biology and Molecular Pathogenesis. Emerging Microbes & Infections. 2017, 6(1): 1-6. DOI: 10.1038/emi.2016.141
[121] Bullerdiek J, Dotzauer A, Bauer I. The Mitotic Spindle: Linking Teratogenic Effects of Zika Virus with Human Genetics? Molecular Cytogenetics. 2016, 9: 1-3. DOI: 10.1186/s13039-016-0240-1
[122] de Oliveira Melo AS, Aguiar RS, Amorim MMR, Arruda MB, de Oliveira Melo F, et al. Congenital Zika Virus Infection: Beyond Neonatal Microcephaly. Jama Neurology. 2016, 73(12): 1407-1416. DOI: 10.1001/jamaneurol.2016.3720
[123] Karcioglu O. New COVID-19 Variants-Diagnosis and Management in the Post-Pandemic Era: Diagnosis and Management in the Post-Pandemic Era. BoD–Books on Demand. 2024. DOI: 10.5772/intechopen.111256
[124] Andre M, Lau L-S, Pokharel MD, Ramelow J, Owens F, et al. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. Biology. 2023, 12(9): 1267. DOI: 10.3390/biology12091267
[125] Alexakis AF, Kuiken T, Mirinavičiūtė G, Ståhl K, Staubach C, et al. Avian Influenza Overview March–June 2024. EFSA J. 2024, 22(7):e8930. DOI: 10.2903/j.efsa.2024.8930
[126] Jernigan DB, Cox NJ. Human Influenza: One Health, One World. Textbook Of Influenza. 2013. 1-19. DOI: 10.1002/9781118636817.ch1
[127] Cheng L, Wang Y, Du J. Human Papillomavirus Vaccines: an Updated Review. Vaccines. 2020, 8(3): 391. DOI: 10.3390/vaccines8030391
[128] Zhou JZ, Jou J, Cohen E. Vaccine Strategies for Human Papillomavirus-Associated Head and Neck Cancers. Cancers. 2021, 14(1): 33. DOI: 10.3390/cancers14010033
[129] Fels JM. Mechanistic Insights into Ebola Virus Entry through Mutational Dissection of the Spike Glycoprotein. Albert Einstein College of Medicine. 2020.
[130] Kebenei CK, Okoth P. Ebola Virus Disease, Diagnostics and Therapeutics: Where Is the Consensus in Over Three Decades of Clinical Research? Scientific African. 2021, 13: e00862. DOI: 10.1016/j.ijid.2016.10.010
[131] Annamalai AS, Pattnaik A, Sahoo BR, Muthukrishnan E, Natarajan SK, et al. Zika Virus Encoding Nonglycosylated Envelope Protein Is Attenuated and Defective in Neuroinvasion. Journal of Virology. 2017, 91(23): 10.1128/jvi. 01348-01317. DOI: 10.1128/JVI.01348-17
[132] Hobman T, Kumar A, Limonta D, Zika Virus and Host Interactions. Multidisciplinary Digital Publishing Institute. 2021. DOI: 10.3390/books978-3-03943-950-8
[133] Zheng D-P, Rodrigues M, Bile E, Nguyen DB, Diallo K, et al. Molecular Characterization of Ambiguous Mutations in HIV-1 Polymerase Gene: Implications for Monitoring HIV Infection Status and Drug Resistance. PLoS One. 2013, 8(10): e77649. DOI: 10.1371/journal.pone.0077649
[134] Rhee S-Y, Blanco JL, Jordan MR, Taylor J, Lemey P, et al. Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: an Individual-Patient-and Sequence-Level Meta-Analysis. PloS Medicine. 2015, 12(4): e1001810. DOI: 10.1371/journal.pmed.1001810
[135] Sallam M, Khalil R. Contemporary Insights into Hepatitis C Virus: A Comprehensive Review. Microorganisms. 2024, 12(6): 1035. DOI: 10.3390/microorganisms12061035
[136] Maqsood Q, Hussain M, Sumrin A, Host Versus Virus: The Genetics in HCV Infection Leading to Treatment, in Hepatitis C-Recent Advances. IntechOpen. 2023. DOI: 10.5772/intechopen.1001050
[137] Connell AR, Connell J, Leahy TR, Hassan J. Mumps Outbreaks in Vaccinated Populations—Is It Time to Re-assess the Clinical Efficacy of Vaccines? Frontiers in Immunology. 2020, 11: 2089. DOI: 10.3389/fimmu.2020.02089
[138] Offit PA, DeStefano F. Vaccine Safety. Vaccines. 2012, 1464-1480. DOI: 10.1016/B978-1-4557-0090-5.00076-8
[139] Jorgensen D, Pons-Salort M, Shaw AG, Grassly NC. The Role of Genetic Sequencing and Analysis in the Polio Eradication Programme. Virus Evolution. 2020, 6(2): veaa040. DOI: 10.1093/ve/veaa040
[140] Dedepsidis E, Karakasiliotis I, Paximadi E, Kyriakopoulou Z, Komiotis D, et al. Detection of Unusual Mutation within the VP1 Region of Different Re-Isolates of Poliovirus Sabin Vaccine. Virus Genes. 2006, 33: 183-191. DOI: 10.1007/s11262-005-0055-3
[141] Esposito JJ, Sammons SA, Frace AM, Osborne JD, Olsen-Rasmussen M, et al. Genome Sequence Diversity and Clues to the Evolution of Variola (Smallpox) Virus. Science. 2006, 313(5788): 807-812. DOI: 10.1126/science.1125134
[142] Souza AR, Brinkmann A, Esparza J, Nitsche A, Damaso CR. Gene Duplication, Gene Loss, and Recombination Events with Variola Virus Shaped the Complex Evolutionary Path of Historical American Horsepox-Based Smallpox Vaccines. Mbio. 2023, 14(5): e01887-01823. DOI: 10.1128/mbio.01887-23
[143] Sahoo D. Molecular Epidemiology of Indian Isolates of Rabies Virus of Diverse Origin and Pathology of Spontaneous Brain Affections in Animals. Indian Veterinary Research Institute. 2022.
[144] Bibi A, Ahmed I, Safdar M, Ahmad T, Imtiaz A, et al. Guarding Against Rabies: The Power of Vaccination in Rabies Disease Management. Journal of Women Medical and Dental College. 2023, 2(2). DOI: 10.56600/jwmdc.v2i2.71
[145] Poovorawan Y, Pyungporn S, Prachayangprecha S, Makkoch J. Global Alert to Avian Influenza Virus Infection: from H5N1 to H7N9. Pathogens and Global Health. 2013, 107(5): 217-223. DOI: 10.1179/2047773213Y.0000000103
[146] Duan C, Li C, Ren R, Bai W, Zhou L. An Overview of Avian Influenza Surveillance Strategies and Modes. Science in One Health. 2023: 100043. DOI: 10.1016/j.soh.2023.100043
[147] Revill PA, Tu T, Netter HJ, Yuen LK, Locarnini SA, et al. The Evolution and Clinical Impact of Hepatitis B Virus Genome Diversity. Nature Reviews Gastroenterology & Hepatology. 2020, 17(10): 618-634. DOI: 10.1038/s41575-020-0296-6
[148] Zhang ZH, Wu CC, Chen XW, Li X, Li J, et al. Genetic Variation of Hepatitis B Virus and Its Significance for Pathogenesis. World Journal of Gastroenterology. 2016, 22(1): 126. DOI: 10.3748/wjg.v22.i1.126
[149] Pramod MS. Serological & Molecular Characterization of Dengue Virus in a Tertiary Care Hospital of North Karnataka. Deemed to be University. 2020.
[150] Mishra G, Jain A, Prakash O, Prakash S, Kumar R, et al. Molecular Characterization of Dengue Viruses Circulating During 2009-2012 in Uttar Pradesh, India. Journal of Medical Virology. 2015, 87(1): 68-75. DOI: 10.1002/jmv.23981
[151] Domingo C, Niedrig M. Safety of 17D Derived Yellow Fever Vaccines. Expert Opinion on Drug Safety. 2009, 8(2): 211-221. DOI: 10.1517/14740330902808086
[152] da Silva Antunes R, Babor M, Carpenter C, Khalil N, Cortese M, et al. Th1/Th17 Polarization Persists Following Whole-Cell Pertussis Vaccination Despite Repeated Acellular Boosters. The Journal of Clinical Investigation. 2018, 128(9): 3853-3865. DOI: 10.1172/JCI121309
[153] Maggi F, Pistello M, Antonelli G. Future Management of Viral Diseases: Role of New Technologies and New Approaches in Microbial Interactions. Clinical Microbiology and Infection. 2019, 25(2): 136-141. DOI: 10.1016/j.cmi.2018.11.015
[154] Organization WH, Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022–2032: Progress Report on the First Year of Implementation. World Health Organization. 2023.
[155] Hill V, Ruis C, Bajaj S, Pybus OG, Kraemer MU. Progress and Challenges in Virus Genomic Epidemiology. Trends in Parasitology. 2021, 37(12): 1038-1049. DOI: 10.1016/j.pt.2021.08.007
[156] Sanna S, Kurilshikov A, Van der Graaf A, Fu J, Zhernakova A. Challenges and Future Directions for Studying Effects of Host Genetics on the Gut Microbiome. Nature Genetics. 2022, 54(2): 100-106. DOI: 10.1038/s41588-021-00983-z
[157] Wang X, Stelzer‐Braid S, Scotch M, Rawlinson WD. Detection of Respiratory Viruses Directly from Clinical Samples Using Next‐Generation Sequencing: A Literature Review of Recent Advances and Potential for Routine Clinical Use. Reviews in Medical Virology. 2022, 32(5): e2375. DOI: 10.1002/rmv.2375
[158] Tay BQ, Wright Q, Ladwa R, Perry C, Leggatt G, et al. Evolution of Cancer Vaccines—Challenges, Achievements, and Future Directions. Vaccines. 2021, 9(5): 535. DOI: 10.3390/vaccines9050535
[159] Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From Biological Mechanisms to Future Directions. Cell. 2023, 186(1): 17-31. DOI: 10.3390/vaccines9050535
[160] Lauber C, Seitz S. Opportunities and Challenges of Data-Driven Virus Discovery. Biomolecules. 2022, 12(8): 1073. DOI: 10.3390/biom12081073
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Advances in Modern Biomedicine

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.