Medically Important Virus Families

Medically Important Virus Families

Virus Family	ICTV Classification	Baltimore Classification	Characteristics	Notable Examples	Diseases	Replication Cycle	Size (nm)	Cell Receptor
Herpesviridae	Kappa (Herpesvirales)	Group I (dsDNA)	Double-stranded DNA; latency in host	HSV-1, HSV-2, VZV, EBV, CMV	Cold sores, genital herpes, chickenpox, shingles, mononucleosis	Enters host cell, viral DNA is transported to the nucleus, transcription occurs, new virions assemble and bud off from the cell. Can remain latent in neurons.	120-300	Heparan sulfate, nectin-1
Retroviridae	Retrovirales	Group VI (ssRNA-RT)	Single-stranded RNA; reverse transcriptase	HIV, HTLV	AIDS, various leukemias	Enters host cell, reverse transcription to DNA, integrates into host genome, transcribes and translates, new virions assemble and bud off.	80-100	CD4, CCR5/CXCR4
Orthomyxoviridae	Articulavirales	Group V (ssRNA)	Single-stranded RNA; segmented genome	Influenza A, B, C	Influenza (seasonal flu, pandemics)	Enters cell via endocytosis, RNA segments are released into the nucleus for replication, new virions assemble at the membrane and bud off.	80-120	Sialic acid
Picornaviridae	Picornavirales	Group IV (ssRNA)	Single-stranded RNA; non-enveloped	Poliovirus, Coxsackievirus, Rhinovirus	Poliomyelitis, hand-foot-and-mouth disease, common cold	Enters host cell, RNA is released and translated immediately, viral replication occurs in the cytoplasm, new virions are released via cell lysis.	22-30	CD155 (poliovirus), ICAM-1 (rhinovirus)
Flaviviridae	Amarillovirales	Group IV (ssRNA)	Single-stranded RNA; enveloped	Hepatitis C, Dengue virus, Zika virus	Hepatitis C, dengue fever, Zika virus infection	Enters cell via receptor-mediated endocytosis, RNA is translated, replicated in the cytoplasm, new virions bud off from the endoplasmic reticulum.	40-100	CD81 (HCV), AXL (Dengue)
Arenaviridae	Arenavirales	Group V (ssRNA)	Single-stranded RNA; enveloped	Lassa fever virus, Machupo virus	Lassa fever, other viral hemorrhagic fevers	Enters cell via endocytosis, RNA is released, viral proteins are translated, new virions assemble in the cytoplasm and bud off.	110-130	Alpha-dystroglycan
Paramyxoviridae	Mononegavirales	Group V (ssRNA)	Single-stranded RNA; enveloped	Measles virus, Mumps virus, RSV	Measles, mumps, respiratory syncytial virus (RSV)	Enters cell via fusion or endocytosis, RNA is released and replicated, new virions assemble and bud off from the cell membrane.	150-300	CD46, SLAM (measles); sialic acid (RSV)
Togaviridae	Amarillovirales	Group IV (ssRNA)	Single-stranded RNA; enveloped	Rubella virus, Chikungunya virus	Rubella, Chikungunya fever	Enters cell via receptor-mediated endocytosis, RNA is translated and replicated in the cytoplasm, new virions bud off from the plasma membrane.	60-100	CD16 (Chikungunya)
Bunyaviridae	Bunyavirales	Group V (ssRNA)	Single-stranded RNA; segmented	Hantavirus, Crimean-Congo hemorrhagic fever virus	Hantavirus pulmonary syndrome, viral hemorrhagic fevers	Enters cell via endocytosis, RNA segments are released, viral proteins are produced, new virions assemble and bud off from the cell membrane.	80-120	β3 integrin
Coronaviridae	Nidovirales	Group II (ssRNA)	Single-stranded RNA; enveloped	SARS-CoV, MERS-CoV, SARS-CoV-2	SARS, MERS, COVID-19	Enters cell via receptor-mediated endocytosis, RNA is released, translated, and replicated in the cytoplasm, new virions bud off from the endoplasmic reticulum.	80-160	ACE2 (SARS-CoV-2)

References

• ICTV: International Committee on Taxonomy of Viruses. (2021). Virus Taxonomy: 2020 Release. Retrieved from ICTV.
• Baltimore, D. (1971). "On the classifications and nomenclature of viruses." Virology, 49(2), 881-884. doi:10.1016/S0042-6822(71)80005-0.
• Roeder, A. H. K., & Kochetkova, I. (2020). "Herpesviruses." In Medical Microbiology (pp. 301-312). Elsevier.
• Coffin, J. M., & Hughes, S. H. (2010). "Retroviruses." In Viral Pathogenesis (pp. 189-218). Cold Spring Harbor Laboratory Press.
• Palese, P., & Shaw, M. L. (2007). "Orthomyxoviridae." In Fields Virology (pp. 1647-1689). Lippincott Williams & Wilkins.
• Stanway, G. (2014). "Picornaviridae." In Viral Pathogenesis (pp. 321-330). Cold Spring Harbor Laboratory Press.
• Lindenbach, B. D., & Rice, C. M. (2003). "Molecular biology of flaviviruses." Advances in Virus Research, 59, 23-61. doi:10.1016/S0065-3527(03)59002-4.
• Enria, D., et al. (2010). "Arenaviruses." In Infectious Diseases: A Clinical Approach (pp. 577-587). Wiley.
• Collins, P. L., & Mottet, A. (2009). "Paramyxoviruses." In Fields Virology (pp. 1777-1820). Lippincott Williams & Wilkins.
• Strauss, J. H., & Strauss, E. G. (2002). "Viruses and Human Disease." In Togaviruses (pp. 63-77). Academic Press.
• Elliott, R. M. (2014). "Bunyaviruses." In The Bunyaviridae (pp. 1-31). Springer.
• Wu, F., et al. (2020). "A new coronavirus associated with human respiratory disease in China." Nature, 579, 265-269. doi:10.1038/s41586-020-2008-3.

Use of Animal Models in Virology Research

Animal Model	Usage	Examples	Limitations	References
Mouse Models	Genetic studies, pathogenesis, vaccine and treatment evaluation	Knockout mice for gene function, studying viral infections like influenza and HIV	May not always represent human disease accurately, limited by size	- Taubenberger JK, Morens DM. 1918 Influenza: the mother of all pandemics. Emerg Infect Dis. 2006 Jan;12(1):15-22. doi: 10.3201/eid1201.050979. PMID: 16494711; PMCID: PMC3291398.
Rat Models	Studying organ-specific viral infections	Hepatitis research, respiratory viruses	Less genetically tractable, limitations in genetic manipulation compared to mice	- Jacobsen KH, Aguirre AA, Bailey CL, Baranova AV, Crooks AT, Croitoru A, Delamater PL, Gupta J, Kehn-Hall K, Narayanan A, Pierobon M, Rowan KE, Schwebach JR, Seshaiyer P, Sklarew DM, Stefanidis A, Agouris P. Lessons from the Ebola Outbreak: Action Items for Emerging Infectious Disease Preparedness and Response. Ecohealth. 2016 Mar;13(1):200-12. doi: 10.1007/s10393-016-1100-5. Epub 2016 Feb 25. PMID: 26915507; PMCID: PMC7087787.
Non-Human Primates (NHPs)	Studying closely related human pathogens	HIV pathogenesis, Ebola virus, SARS-CoV-2	Ethical concerns, high cost, complex biology	- Zaki, A.M., et al. (2012). Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia Original Article, N Engl J Med 2012;367:1814-1820. - WHO. (2022). Middle East Respiratory Syndrome Coronavirus (MERS-CoV).
Ferret Models	Studying respiratory viruses	Influenza virus transmission and pathogenesis	Less well-characterized, limited genetic manipulation	- Oh,Ding Y and Hurt,Aeron C. (2016). Using the Ferret as an Animal Model for Investigating Influenza Antiviral Effectiveness. Front. Microbiol.,2016 - Poulami Basu Thakur, Victoria J Mrotz, Taronna R Maines, Jessica A Belser, Ferrets as a Mammalian Model to Study Influenza Virus-Bacteria Interactions, The Journal of Infectious Diseases, Volume 229, Issue 2, 15 February 2024, Pages 608–615, https://doi.org/10.1093/infdis/jiad408.
Guinea Pig Models	Studying respiratory and some other viral infections	RSV, hantaviruses	Small size limits blood volume and procedure complexity	- Victoria K. Baxter, Diane E. Griffin, Chapter 10 - Animal Models: No Model Is Perfect, but Many Are Useful, Editor(s): Michael G. Katze, Marcus J. Korth, G. Lynn Law, Neal Nathanson, Viral Pathogenesis (Third Edition), Academic Press, 2016, Pages 125-138, ISBN 9780128009642, https://doi.org/10.1016/B978-0-12-800964-2.00010-0..
Zebrafish Models	Studying virus-host interactions at cellular and developmental levels	Early stages of viral infection, antiviral drug development	Limited to studies in aquatic environment, less complex than mammals	- Zebrafish as a model organism for virus disease research: Current status and future directions Sullivan, C., Jurcyzszak, D., Goody, M. F., Gabor, K. A., Longfellow, J. R., Millard, P. J., Kim, C. H. Using Zebrafish Models of Human Influenza A Virus Infections to Screen Antiviral Drugs and Characterize Host Immune Cell Responses. J. Vis. Exp. (119), e55235, doi:10.3791/55235 (2017).

Historical Viral Outbreaks

Outbreak	Virus	Impact	Spread	Control Measures	References
1918 Influenza Pandemic	H1N1 Influenza A	50-100 million deaths globally	Airborne droplets, global travel	Isolation, quarantine, masks, hygiene practices	- Johnson, N.P.A.S., & Mueller, J.E. (2002). The pandemic of 1918. Emerging Infectious Diseases, 8(1), 21-26. - Taubenberger, J.K., & Morens, D.M. (2006). 1918 Influenza: The Mother of All Pandemics. Emerging Infectious Diseases, 12(1), 15-22.
1980s HIV/AIDS Epidemic	HIV	Over 36 million deaths worldwide	Sexual contact, contaminated needles	Safe sex practices, needle exchange, antiretroviral therapy	- UNAIDS. (2020). Global HIV & AIDS statistics — Fact sheet. - Fauci, A.S., & Marston, H.D. (2014). HIV and AIDS — 30 years of progress. New England Journal of Medicine, 370, 2381-2388.
2003 SARS Outbreak	SARS-CoV	Over 8,000 cases, 774 deaths	Airborne droplets, close contact	Quarantine, isolation, travel restrictions, contact tracing	- WHO. (2003). Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003. - Peiris, J.S.M., et al. (2004). Clinical progression and viral load in a community outbreak of pneumonia due to SARS-CoV. The Lancet, 361(9371), 1765-1772.
2014-2016 Ebola Outbreak	Ebola Virus	Over 28,000 cases, 11,000 deaths	Direct contact with bodily fluids	Quarantine, safe burial practices, contact tracing, vaccination	- WHO. (2016). The WHO Ebola Response Team. New England Journal of Medicine, 374, 664-674. - Jacobsen, K.H. (2016). The Ebola outbreak and the future of public health preparedness. Journal of Global Health, 6(2).
2019-2024 COVID-19 Pandemic	SARS-CoV-2	Millions of cases and deaths worldwide	Airborne droplets, aerosols, surfaces	Testing, social distancing, masks, travel restrictions, vaccination	- WHO. (2024). COVID-19 Dashboard. - Andrews, N., et al. (2021). Effectiveness of COVID-19 vaccines against the B.1.617.2 variant. New England Journal of Medicine, 385, 585-594.
2009 H1N1 Influenza Pandemic	H1N1 Influenza A	Estimated 200,000-500,000 deaths worldwide	Airborne droplets, global travel	Vaccination, antiviral medications, public health campaigns	- Dawood, F.S., et al. (2012). Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus infection. PLoS ONE, 7(6), e48209. - WHO. (2010). H1N1 pandemic (2009) – update 112.
Zika Virus Outbreak (2015-2016)	Zika Virus	Associated with microcephaly and neurological disorders in infants	Vector-borne (mosquitoes), sexual contact	Mosquito control, travel advisories, public health campaigns	- WHO. (2016). Zika virus. - Petersen, E.E., et al. (2016). Association between Zika virus and microcephaly. The New England Journal of Medicine, 374, 951-959.
Smallpox Eradication (1960s-1980s)	Variola Virus	300-500 million deaths prior to eradication	Airborne droplets, direct contact	Worldwide vaccination campaign, isolation, and surveillance	- Fenner, F., et al. (1988). Smallpox and its eradication. World Health Organization. - Whalen, C.C., & Dawood, F.S. (2014). The eradication of smallpox: A historical review.
Marburg Virus Outbreak (1967, 2005-2006)	Marburg Virus	High mortality rates, up to 90%	Direct contact with bodily fluids, contaminated materials	Quarantine, supportive care, contact tracing	- WHO. (2005). Marburg haemorrhagic fever – Angola. - Towner, J.S., et al. (2009). Marburg virus infection detected in a healthcare worker during a large outbreak in Angola. Journal of Infectious Diseases, 199(12), 199-204.
MERS Outbreak (2012-present)	MERS-CoV	Over 2,500 cases, 858 deaths	Airborne droplets, close contact, camels	Isolation, travel restrictions, public health education	- WHO. (2020). Middle East Respiratory Syndrome Coronavirus (MERS-CoV). - Zaki, A.M., et al. (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. New England Journal of Medicine, 367, 1814-1820.

Virus Cultivation: Techniques and Methods

Virus cultivation is a fundamental aspect of virology, essential for the study of viral structure, replication, and pathogenesis, as well as for vaccine development and antiviral drug testing. The choice of cultivation method depends on the virus type, host range, and the purpose of the study.

1. Methods of Virus Cultivation

a. Cell Culture

• Primary Cell Culture:
  • Derived directly from animal tissues, primary cell cultures closely mimic the in vivo environment. Examples include primary human fibroblasts or monkey kidney cells.
  • Advantages: High biological relevance, supports the growth of a wide range of viruses.
  • Disadvantages: Limited lifespan, variability between preparations.
• Continuous Cell Lines:
  • Immortalized cell lines like HeLa, Vero, and MDCK cells are used extensively in virology.
  • Advantages: Easy to maintain, high reproducibility, supports high virus yields.
  • Disadvantages: Less physiological relevance compared to primary cells, some viruses may not grow well.
• Co-culture Systems:
  • Involves growing multiple cell types together to mimic the interaction between different tissues, aiding in the study of viruses with complex host tropisms.
• 3D Cell Culture:
  • Organoids or spheroids that provide a more in vivo-like environment for virus cultivation, useful for studying tissue-specific infections and pathogenesis.

b. Embryonated Chicken Eggs

• Historical and Current Use:
  • First used in the 1930s, embryonated chicken eggs are still widely used for cultivating viruses like Influenza, which grows in the allantoic cavity.
  • Advantages: High virus yield, relatively low cost, suitable for large-scale production (e.g., influenza vaccines).
  • Disadvantages: Limited to viruses that can replicate in avian cells, ethical considerations, and batch variability.
• Techniques:
  • Chorioallantoic Membrane (CAM) Inoculation: Used for poxvirus cultivation.
  • Allantoic Cavity Inoculation: Commonly used for Influenza virus.
  • Amniotic Cavity Inoculation: Used for isolating respiratory viruses.
  • Yolk Sac Inoculation: Used for certain arboviruses and rickettsiae.

c. Animal Inoculation

• Role in Virus Research:
  • Although largely replaced by in vitro methods, animal inoculation is still used for studying pathogenesis, immune responses, and for viruses that cannot be easily cultured in vitro.
• Commonly Used Animals:
  • Mice, guinea pigs, rabbits, and non-human primates are typically used.
  • Advantages: Provides a complete living system for studying virus-host interactions and immune responses.
  • Disadvantages: Ethical concerns, high cost, and limitations in translating results to humans.
• Applications:
  • Studying the neurotropism of rabies virus, oncogenesis of human papillomavirus, or the immune response to HIV.

2. Techniques for Virus Detection and Quantification

• Cytopathic Effect (CPE) Observation:
  • CPEs are visible changes in host cells due to viral infection, such as cell rounding, detachment, or lysis. It is a primary method for detecting viral growth in cell cultures.
• Plaque Assay:
  • A quantitative method where viruses are diluted and plated on a cell monolayer, followed by counting plaques (areas of infected cells) to determine the viral titer (PFU/mL).
• Hemagglutination Assay:
  • Measures the ability of certain viruses (e.g., Influenza) to agglutinate red blood cells. It’s a rapid, indirect method for virus quantification.
• TCID₅₀ (Tissue Culture Infectious Dose 50):
  • Measures the dilution of a virus required to infect 50% of the cell cultures. It's useful for viruses that don't form clear plaques.

3. Applications and Importance of Virus Cultivation

• Vaccine Production:
  • Cultivation of viruses in eggs or cell cultures is essential for producing live-attenuated or inactivated vaccines (e.g., measles, mumps, influenza).
• Antiviral Drug Testing:
  • Cultivated viruses are used in cell-based assays to screen and evaluate the efficacy of antiviral compounds.
• Research and Diagnostics:
  • Cultivation allows for the study of viral genetics, pathogenesis, and evolution. It's also crucial for isolating and identifying viruses from clinical samples.

4. Challenges in Virus Cultivation

• Host Specificity:
  • Some viruses have strict host cell requirements, making them difficult to culture in vitro. For example, hepatitis B virus requires primary human hepatocytes or specialized cell lines for cultivation.
• Latency and Persistence:
  • Certain viruses, like herpesviruses, can establish latent infections, complicating their study in cell culture.
• Safety Concerns:
  • Cultivating highly pathogenic viruses requires high-containment laboratories (BSL-3 or BSL-4), limiting access and increasing costs.

5. References

• Fields, B. N., Knipe, D. M., & Howley, P. M. (2007). Fields Virology (5th ed.). Philadelphia: Lippincott Williams & Wilkins.
• Freshney, R. I. (2015). Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications (7th ed.). Wiley-Blackwell.
• Murphy, F. A., Gibbs, E. P. J., Horzinek, M. C., & Studdert, M. J. (1999). Veterinary Virology (3rd ed.). Academic Press.
• World Health Organization (WHO). (2021). Manual for the Production and Control of Vaccines: Influenza Vaccines. WHO Press.
• Coombs, K. (2006). Animal Virus Cultivation and Assays. In D. R. Harper & R. M. McCauley (Eds.), Virology Methods Manual. Academic Press.

Bioinformatics and Virology

Chapter 1: Viral Genomics and Evolution Chapter 2: Structural Bioinformatics and Viral Proteins Chapter 3: Metagenomics and Viral Discovery Chapter 4: Vaccine Development Chapter 5: Bioinformatics in Antiviral Resistance

Chapter 1: Viral Genomics and Evolution

One of the primary applications of bioinformatics in virology is the analysis of viral genomes. With advances in high-throughput sequencing technologies, researchers can rapidly sequence entire viral genomes, providing insights into their genetic makeup, evolution, and spread.

Importance and Applications:

• Genome Assembly and Annotation: Bioinformatics tools help in assembling raw sequencing data into complete viral genomes and annotating genes, regulatory elements, and functional domains.
• Evolutionary Analysis: Bioinformatics allows researchers to trace the evolutionary history of viruses, including identifying mutations that contribute to virulence and drug resistance.
• Epidemiology and Surveillance: Phylogenetic analysis reveals how a virus spreads, informing public health interventions.

Go to Chapter 2: Structural Bioinformatics and Viral Proteins

Chapter 2: Structural Bioinformatics and Viral Proteins

Structural bioinformatics focuses on understanding the 3D structures of viral proteins, which is critical for elucidating their functions and interactions with host molecules.

Importance and Applications:

• Protein Structure Prediction: Tools like AlphaFold enable the prediction of viral protein structures, aiding in identifying potential drug targets.
• Drug Design and Screening: Bioinformatics facilitates the virtual screening of compounds to identify potential antivirals that can inhibit viral proteins.
• Antibody Design: Structural bioinformatics aids in designing monoclonal antibodies that can neutralize viruses.

Go to Chapter 3: Metagenomics and Viral Discovery

Chapter 3: Metagenomics and Viral Discovery

Metagenomics, the study of genetic material recovered directly from environmental samples, has expanded the scope of virology by allowing the discovery of new viruses from diverse ecosystems.

Importance and Applications:

• Viral Diversity: Bioinformatics tools enable the classification and characterization of viruses within complex microbial communities.
• Pathogen Surveillance: Metagenomic sequencing, combined with bioinformatics, allows for the detection of emerging viral pathogens in real-time.
• Ecological Impact: Understanding the roles of viruses in ecosystems helps elucidate their impact on global biogeochemical cycles.

Go to Chapter 4: Vaccine Development

Chapter 4: Vaccine Development

Bioinformatics plays a crucial role in the design and development of vaccines, particularly in identifying viral antigens that can elicit protective immune responses.

Importance and Applications:

• Epitope Mapping: Bioinformatics tools predict B-cell and T-cell epitopes, which are critical for designing vaccines that can induce a robust immune response.
• Reverse Vaccinology: Genomic data is used to identify potential vaccine candidates, aiding in the rapid development of vaccines against emerging infectious diseases.
• Vaccine Optimization: Bioinformatics assists in optimizing vaccine formulations by predicting potential cross-reactivity with human proteins.

Go to Chapter 5: Bioinformatics in Antiviral Resistance

Chapter 5: Bioinformatics in Antiviral Resistance

The emergence of antiviral resistance is a significant challenge in the treatment of viral infections. Bioinformatics helps in understanding the mechanisms of resistance and in developing strategies to counteract it.

Importance and Applications:

• Resistance Mutation Analysis: By analyzing viral genomes, bioinformatics identifies mutations associated with resistance to antiviral drugs.
• Combination Therapy Design: Bioinformatics models simulate the effects of combining different antiviral drugs, helping to design therapies that are less likely to induce resistance.
• Surveillance Networks: Global bioinformatics networks collect and analyze data on resistance mutations, enabling the tracking of resistance trends.

Go to References

References

• Holmes, E. C. (2010). "The Evolution and Emergence of RNA Viruses." Oxford University Press.
• Jumper, J., et al. (2021). "Highly accurate protein structure prediction with AlphaFold." Nature, 596(7873), 583-589.
• Rappuoli, R., et al. (2016). "Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design." Journal of Experimental Medicine, 213(4), 469-481.
• Paez-Espino, D., et al. (2016). "Uncovering Earth's virome." Nature, 536(7617), 425-430.
• Gotte, M., & Feld, J. J. (2016). "Direct-acting antiviral agents for hepatitis C: structural and mechanistic insights." Nature Reviews Gastroenterology & Hepatology, 13(6), 338-351.

Back to Chapter 1: Viral Genomics and Evolution