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Virus Basics
Virus Basics
Louten, J. (2016). Virus replication. In Elsevier eBooks (pp. 49–70). https://doi.org/10.1016/b978-0-12-800947-5.00004-1
⬇️Viruses replicate themselves in multiple ways. Sometimes, like below, they go from DNA to RNA, and then back to DNA.
Simmonds, Peter & Adriaenssens, Evelien & Zerbini, Francisco & Abrescia, Nicola & Aiewsakun, Pakorn & Alfenas-Zerbini, Poliane & Bao, Yiming & Barylski, Jakub & Drosten, Christian & Duffy, Siobain & Duprex, W. & Dutilh, Bas & Elena, Santiago & Garcia, Maria Laura & Junglen, Sandra & Katzourakis, Aris & Koonin, Eugene & Krupovic, Mart & Kuhn, Jens. (2023). Four principles to establish a universal virus taxonomy. PLOS Biology. 21. e3001922. 10.1371/journal.pbio.3001922.
⬇️Like with living organisms, viruses are classified within different ranks.
MicrobeTV. (2014, February 14). RNA synthesis from dsRNA genomes [Video]. YouTube. https://www.youtube.com/watch?v=NKGy3xuEKQM
⬇️The life cycle of a dsRNA virus.
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). dsRNA replication/transcription ~ ViralZone. https://viralzone.expasy.org/1936
⬇️Closer look at how a dsRNA virus replicates within the cell.
GeeksforGeeks. (2025, July 23). Viroids structure, characteristics, features, and diseases. GeeksforGeeks. https://www.geeksforgeeks.org/biology/viroid-definition-structure/
Racaniello, V. (2021, March 3). Understanding virus isolates, variants, and strains. Virology Blog. https://virology.ws/2021/02/25/understanding-virus-isolates-variants-strains-and-more/
Varicellovirus - Group I: dsDNA viruses
Varicellovirus - Group I: dsDNA viruses
Zerboni, L., Sen, N., Oliver, S. L., & Arvin, A. M. (2014). Molecular mechanisms of varicella zoster virus pathogenesis. Nature Reviews Microbiology, 12(3), 197–210. https://doi.org/10.1038/nrmicro3215
⬇️Top: after initial infection (causes chickenpox), varicella remains dormant in neurons until reactivation (causes shingles)
Bottom: Replication cycle of varicella.
Johnson, J. (2023, April 25). What and where are dermatomes? https://www.medicalnewstoday.com/articles/what-are-dermatomes
⬇️Dermatomes are skin areas associated with a specific spinal nerve. When varicella reactivates to cause shingles, the affected skin area (dermatome) will reflect the spinal nerve in which it was hiding.
Taxon Details | ICTV. (n.d.). https://ictv.global/taxonomy/taxondetails?taxnode_id=202401454&taxon_name=Varicellovirus%20humanalpha3
Reichelt, M., Brady, J., & Arvin, A. M. (2009). The replication cycle of Varicella-Zoster virus: Analysis of the kinetics of viral protein expression, genome synthesis, and virion assembly at the Single-Cell level. Journal of Virology, 83(8), 3904–3918. https://doi.org/10.1128/jvi.02137-08
Oliver, S. L., Yang, E., & Arvin, A. M. (2016). Varicella-Zoster virus glycoproteins: entry, replication, and pathogenesis. Current Clinical Microbiology Reports, 3(4), 204–215. https://doi.org/10.1007/s40588-016-0044-4
Herpes simplex is taxonomically very similar to varicellovirus.
Taxon Details | ICTV. (n.d.). https://ictv.global/taxonomy/taxondetails?taxnode_id=202401428&taxon_name=Simplexvirus%20humanalpha1
Depledge, D. P., Sadaoka, T., & Ouwendijk, W. J. D. (2018). Molecular aspects of Varicella-Zoster virus latency. Viruses, 10(7), 349. https://doi.org/10.3390/v10070349
Laemmle, L., Goldstein, R. S., & Kinchington, P. R. (2019). Modeling varicella zoster virus persistence and reactivation – closer to resolving a perplexing persistent state. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.01634
Rotavirus - Group II: dsRNA viruses
Rotavirus - Group II: dsRNA viruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Rotavirus ~ ViralZone. https://viralzone.expasy.org/107?outline=all_by_species
⬇️Structure of a rotavirus, which has a genome split into 11different segments of dsRNA.
Lundgren, O., & Svensson, L. (2001). Pathogenesis of diarrhea. Microbes and Infection, 3(13), 1145–1156. https://doi.org/10.1016/s1286-4579(01)01475-7
Amimo, J. O., Raev, S. A., Chepngeno, J., Mainga, A. O., Guo, Y., Saif, L., & Vlasova, A. N. (2021). Rotavirus interactions with host intestinal epithelial cells. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.793841
Arias, C. F., Silva-Ayala, D., & López, S. (2014). Rotavirus Entry: a Deep Journey into the Cell with Several Exits. Journal of Virology, 89(2), 890–893. https://doi.org/10.1128/jvi.01787-14
Group IV: (+)ssRNA viruses
Group IV: (+)ssRNA viruses
Polioviruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Enterovirus ~ ViralZone. https://viralzone.expasy.org/97?outline=all_by_species
⬇️Polioviruses are grouped within the genus Enterovirus. Their structure involves a single strand of positive-sense RNA.
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Poliovirus replication cycle ~ ViralZone. https://viralzone.expasy.org/3276
⬇️Replication cycle of polioviruses.
Betacoronaviruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Poliovirus replication cycle ~ ViralZone. https://viralzone.expasy.org/3276
⬇️SARS-CoV-2, the cause of the pandemic, is in the genus Betacoronavirus. Like polioviruses, they have positive-sense RNA genomes.
Taxon Details | ICTV. (n.d.). https://ictv.global/taxonomy/taxondetails?taxnode_id=202401868&taxon_name=Betacoronavirus%20pandemicum
Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-COV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271-280.e8. https://doi.org/10.1016/j.cell.2020.02.052
Jackson, C. B., Farzan, M., Chen, B., & Choe, H. (2021). Mechanisms of SARS-CoV-2 entry into cells. Nature Reviews Molecular Cell Biology, 23(1), 3–20. https://doi.org/10.1038/s41580-021-00418-x
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Coronavirus life-cycle ~ ViralZone. https://viralzone.expasy.org/9096
⬇️Replication cycle of coronaviruses.
Koyou, H. L., Salleh, M. N., Jelemie, C. S., Badrin, M. J. Q., Prastiyanto, M. E., & Ramachandran, V. (2025). TMPRSS2: a key host factor in SARS-COV-2 infection and potential therapeutic target. Medeniyet Medical Journal, 40(2), 101–109. https://doi.org/10.4274/mmj.galenos.2025.40460
Pilz, S., Theiler-Schwetz, V., Trummer, C., Krause, R., & Ioannidis, J. P. (2022). SARS-CoV-2 reinfections: Overview of efficacy and duration of natural and hybrid immunity. Environmental Research, 209, 112911. https://doi.org/10.1016/j.envres.2022.112911
Influenza A Virus - Group V: (-)ssRNA viruses
Influenza A Virus - Group V: (-)ssRNA viruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Alphainfluenzavirus ~ ViralZone. https://viralzone.expasy.org/6
⬇️There are many subtypes in the Influenza A virus species, but they all have a segmented, negative-sense RNA genome.
Dou, D., Revol, R., Östbye, H., Wang, H., & Daniels, R. (2018). Influenza A virus cell entry, replication, virion assembly and movement. Frontiers in Immunology, 9. https://doi.org/10.3389/fimmu.2018.01581
⬇️During transcription, viral proteins "snatch" the 5' cap from a host mRNA and put it on the viral mRNA.
Influenza: A case study. (n.d.). Open Learning. https://www.open.edu/openlearn/science-maths-technology/biology/influenza-a-case-study/content-section-2.4
HIV - Group VI: ssRNA-RT viruses
HIV - Group VI: ssRNA-RT viruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Human immunodeficiency virus 1 ~ ViralZone. https://viralzone.expasy.org/7
⬇️ Top: HIV has a single stranded RNA genome.
Bottom: Replication cycle of HIV. The RNA genome gets reverse transcribed into DNA.
biointeractive. (2016, October 5). HIV Life Cycle | HHMI BioInteractive Video [Video]. YouTube. https://www.youtube.com/watch?v=PlSvywlLuNw
⬇️ great video with animations that show the molecular aspects of HIV replication.
Hep B Virus - Group VII: dsDNA-RT viruses
Hep B Virus - Group VII: dsDNA-RT viruses
Philippe Le Mercier, Chantal Hulo, Patrick Masson (content); Yann Haefliger (front-end styling), Edouard de Castro (software). (n.d.). Orthohepadnavirus ~ ViralZone. https://viralzone.expasy.org/101
⬇️ Top: The Hep B virus has a relaxed DNA structure with parts that are double, and parts that are single stranded.
Bottom: Hep B gets transcribed into RNA, and then eventually reverse transcribed back into DNA. Along with virions, empty particles also get released.
Tsukuda, S., & Watashi, K. (2020). Hepatitis B virus biology and life cycle. Antiviral Research, 182, 104925. https://doi.org/10.1016/j.antiviral.2020.104925
⬇️ Similar to the image on the right, but has a better view of the empty particles being released (labeled "SVP" for subviral particle).
Vaccines
Vaccines
World Health Organization: WHO. (2021, January 12). The different types of COVID-19 vaccines. https://www.who.int/news-room/feature-stories/detail/the-race-for-a-covid-19-vaccine-explained
⬇️ Different approaches to making various types of vaccinations.
Measles cases and outbreaks. (2025, August 20). Measles (Rubeola). https://www.cdc.gov/measles/data-research/index.html
Kurlander, C., & Juhl, R. P. (2020, September 16). Lessons from how the polio vaccine went from the lab to the public that Americans can learn from today. Medical Xpress. https://medicalxpress.com/news/2020-09-lessons-polio-vaccine-lab-americans.html
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