Virus

t-Virus under a microscope

A virus is a submicroscopic pathogen capable of infecting the cells of any organism, be they archaea, bacteria, plant, fungus or animal. They are considered to be non-living, as their primitive nature and inability to self-replicate separate them the aforementioned organisms. Instead, they replicate by inserting genetic material into a cell, which hijacks its functions to instead produce more virions.

Introduction

What makes up a virion?

The make-up of a virion (an individual virus) is that of a protein shell, known as a capsid, which protects the genome itself - a single or double strand of DNA or RNA - any may also include certain enzymes called polymerase. In some viruses, this capsid is itself covered by the remains of cell membrane, dubbed the viral envelope. This envelope may include glycoproteins, which play a part in forcing the virion's entry into a cell.

How do viruses affect cells?

Viruses can enter cells in different ways depending on what kind of virus is involved. In some cases a virion will attach itself to the cell membrane and inject the contents of the capsid into the cell. In others, the virion will force itself into the cell and degrade within it, releasing its contents.

The virus requires two basic operations to replicate itself: it must alter or replace the cell's native RNA (known as "mRNA" in this context) in order to produce more proteins, as well as enzymes if needed. Second, it must replicate its genome. These two operations can be performed very differently when comparing two different viruses, but the end-result is the same: the cell produces so many virions that the internal pressure causes it to burst open, and the new virions will spread out to infect other cells. This is known as the Lytic cycle, and is the ultimate result of viral infection. Another cycle known as the Lysogenic cycle will have these viral genes dormant for perhaps decades, spreading throughout the body as daughter cells, before they are triggered into shifting to the Lytic cycle.

If a cell's DNA was altered and it produced daughter cells before dying. These daughter cells will also be at risk of producing the virus, though it may take days or even years to trigger viral expression. These viral diseases can cause the production of faulty cells, and can result in tumours. If Germ Cells are affected by this DNA-changing, it can result in an individual's offspring inheriting the viral genome in their DNA.

How is the genome copied?

All DNA and RNA can be divided into "positive-sense" and "negative-sense", known in shorthand as "(+)" and "(-)". The complementary strands are not perfect mirrors, and their amino acid sequences will differ, meaning their functions are different. For example, only positive-sense RNA (in this case, mRNA) can be read by the cell's ribosomes and made to produce the necessary proteins. Using certain protein enzymes known as "polymerases", DNA and RNA can be made to replicate their counterparts, as well as one-another.

• DNA Polymerase transcribes negative-sense DNA from positive-sense DNA, and vice versa. It is present in all organisms, so a virus does not need to carry it into a cell for its life cycle.
• RNA Polymerase transcribes positive-sense RNA from negative-sense DNA. It is also present in all organisms.
• RNA Replicase transcribes negative-sense RNA from positive-sense RNA, and vice versa. It is not naturally occurring in organisms and the cell's own mRNA (a type of positive-sense RNA) must be replaced with viral mRNA to produce it.
• Reverse Transcriptase transcribes mRNA into negative-sense DNA.
• Retroviral Integrase is another enzyme, which is used to break down nucleotides on each of the 3' ends of dsDNA, allowing it form a covalent bond with nuclear DNA.

Types of virus

In the widely used Baltimore classification, there are in all seven "Groups" of virus, which share certain characteristics. These groups separate viruses based on whether their genome is DNA or RNA, if it is single or double-stranded ("ss" and "ds", respectively), and if they are "positive" or "negative-sense". There are in all two groups of DNA virus, and four groups of RNA virus.

1. dsDNA viruses will replicate by using DNA Polymerase to create both strands of DNA, while RNA Polymerase is used to create mRNA to obtain the capsid and other necessary viral proteins. dsDNA viruses include Herpes, Smallpox and HPV.
2. ssDNA viruses will replicate in two different ways, so for simplicity will be listed separately.
   1. (+)ssDNA viruses will first replicate by using DNA Polymerase to create (-)ssDNA, which will create mRNA through RNA Polymerase as well as more (+)ssDNA through using DNA Polymerase again.
   2. (-)ssDNA viruses will use RNA Polymerase to create mRNA, and DNA Polymerase to create its counterpart (+)ssDNA strand. This positive strand will then use DNA Polymerase to transcribe more negative strands.
3. dsRNA viruses require the RNA Replicase enzyme to replicate themselves and, as such, must enter the cell with it. This enzyme is used to transcribe the positive and negative-stands. The mRNA includes coding in its genome to produce more of this enzyme when creating the necessary viral proteins. An example of dsRNA is BTV, which causes Bluetongue disease in livestock.
4. (+)ssRNA viruses will immediately replace the host's mRNA to create the necessary proteins. It will then create its own RNA Replicase to transcribe its negative counterparts, which can be used to make the intended positives. This virus therefore does not need to enter a cell with the enzyme. Examples of these viruses include the Coronaviruses, the Cold-causing Rhinoviruses, and Norovirus.
5. (-)ssRNA viruses will bring with it RNA Replicase to create positive-sense strands including the mRNA. From positive strands RNA Replicase will create more negative-sense RNA. Examples of these viruses are Ebola, Measles and Influenza.
6. Retroviruses use (+)ssRNA as their genome, but unlike the Group IV viruses, this RNA will use Reverse Transcriptase to transcribe double-strandad DNA. Like with the Group I viruses, this will interact with the nucleus, with Retroviral Integrase breaking down the ends of the dsDNA so it can be bonded to its own DNA. The cell's mutated genome will now create new mRNA that produces the necessary viral proteins as well as more of the retroviral RNA. Its mutant daughter cells will also be capable of producing retroviral RNA. Examples of these retroviruses include HIV, which causes AIDS.
7. Pararetroviruses will use dsDNA as their genome, but unlike Group I viruses will make the cell produce RNA able to produce Reverse Transcriptase. This enzyme transcribes it into dsDNA while inside the capsid. Examples of pararetroviruses include Hepatitis B.

Notable viruses

Prime universe

Naturally occurring

• Abyss - A retrovirus isolated in the genome of certain deep sea fish species in the Kermadec Trench.
• "Ancient Virus" - A retrovirus discovered in a whale carcass in Alaska.
• Ebola virus - A (-)ssRNA virus endemic to the Ebola valley in the Democratic Republic of the Congo.
• Norovirus - A genus of (+)ssRNA, of which Norwalk virus is considered to be the only known species.
• Poliovirus - A species of (+)ssRNA, which causes the disease, Poliomyelitis (otherwise known as "Polio").
• Progenitor - A retrovirus which was isolated within the genome of Stairway of the Sun, a species of daisy naturally occurring only within a cavern in West Africa. This virus played a significant role in Umbrella Pharmaceuticals' creation. A number of early strains were created outside of the t-Virus Project, including "Type-A" and "Type-B".
• SARS coronavirus - A species of (+)ssRNA, which cause severe acute respiratory syndrome. It was among the RNA viruses involved in bio-weapons research.
• Veronica - A retrovirus present in the genome of at least one species of ant. This was studied by Dr. Alexia Ashford as part of what became the t-Veronica Project.

Engineered

• Immortality Virus - A Progenitor strain developed by Dr. Alex Wesker, though research was left unfinished by 2006.
• t-Virus - The name given to various retroviruses related to Progenitor which were engineered for bioweapons research by Umbrella Pharmaceuticals and its subsidiaries.
  • α strain - A strain which existed at the Arklay Laboratory in the 1980s.
  • β-I strain - A strain which existed at the Arklay Laboratory in the 1980s.
  • β-II strain - A strain which existed at the Arklay Laboratory in the 1980s.
  • ε strain - A strain which was engineered at the Arklay Laboratory over the 1990s, and became the basis of the 'finalised' t-Virus strains.
  • T-JCCC203 - A retrovirus engineered by Umbrella in the revolutionary field of virus therapy. It is known to have successfully destroyed the cancer cells of one patient, but caused zombification afterwards. Data for this was accumulated by Umbrella for the bioweapons projects.
  • Neo-t - A retrovirus developed by Dr. Mylene Beardsley.
  • t-Veronica- A retrovirus created from splicing Veronica into a Progenitor strain.
  • "t+G" - A t-Virus variant created by exposing it to G antibodies.
  • t-Abyss - A t-Virus variant created by TRICELL alongside the FBC, combining "The Abyss" virus and the t-Virus.
  • t-Phobos - A retrovirus engineered by Dr. Alex Wesker to create superhumans, though is known to cause runaway mutation when triggered by excess stress hormones.
  • Prototype Virus - A t-Virus strain engineered for the Wesker Project.
• Animality - A retrovirus engineered through splicing genetic material from Las Plagas into a t-Virus strain. Its chief effect is mutating humans into intelligent Zombies able to distinguish friend from foe. A-Virus was engineered as three strains: Type I, which was dormant and would not trigger mutation until body is exposed to Type II, and Type III, which allows human mutants to maintain control of their actions while not being attacked by Zombies.
• Golgotha - A retrovirus which discovered in the body of a human test subject, which causes extreme and continuous mutation in hosts if infection if out of control.
• Uroboros - A Progenitor strain engineered by Dr. Albert Wesker and TRICELL as a doomsday weapon which would kill all humans lacking certain genes.
• Crysalid - A genus of retroviruses engineered by The Family and Neo Umbrella with genetic material spliced from t-Veronica and G-Virus. A number of strains were developed to turn humans into identical B.O.W.s to replace the need for cloning, with one project aimed at creating a strain that could turn humans into duplicates of Ada Wong. The "Enhanced C-Virus" was also engineered by Neo Umbrella to cause more extreme mutations.

Other universes

• Cameron Virus - An unidentified retrovirus created by Dr. Cameron as she treated herself for infection. Those infected can copy their consciousness into other organisms.
• Clay virus - A protocanonical equivalent to Progenitor.
• Anti-virus - The only compound capable of purging the T-virus.
• "Marburg virus" - A hemorrhagic fever virus in the family Filovidae, related to the Ebola virus.
• MS-Virus - A "Matchless Soldier" virus, made by Umbrella Lab in Raccoon City.
• T-virus - The Anderson universe equivalent.
• T-virus - The WildStorm universe equivalent.
• T-virus - The Perry universe equivalent.
• G-Virus - The WildStorm universe equivalent.
• G-Virus - The King's Fountain universe equivalent.
• X-virus - A virus only present in DC-canon.
• Chimera Virus - A virus only present in BIOHAZARD to the Liberty.