Virus

The word virus comes from the Latin for "viscous liquid" or "poison", and its discovery is attributed to two scientists:

This discovery helped identify and combat viruses that cause human diseases such as yellow fever, poliomyelitis (a viral infection that causes a nerve injury, and in turn, partial or total paralysis), or the flu.

A virus is a particle of genetic code, DNA or RNA, encapsulated in a protein vesicle. Viruses cannot replicate on their own so they need to infect cells and use the components of the host cell to make copies of themselves, and often the virus damages or kills the host cell in the process of multiplication.

Viruses have been found in every ecosystem on Earth and since viruses do not have the same biology as the bacterias, they cannot be fought with antibiotics; only vaccines or antiviral medications can eliminate or reduce the severity of viral diseases, including AIDS, Covid-19, measles, and smallpox.

They have two or three components (depends on the virus):

1. Nucleic acid, which can be RNA or DNA. This can be single-stranded or double-stranded and owns the genome.

2. The capsid, which is a protein shell and capsomeres (series of monomers). Usually have a small variety of proteins, since if there were more of them there would be less space for the nucleic acid of the virus. Within it's the genetic material.

There are three types of capsid:

• Helical capsid (filamentous): it is typically from plants and bacteriophages. All its capsomeres are identical and have a protein of 158 amino acids. The most common example is TMV (tobacco mosaic virus)

• Icosahedral capsid: it typically occurs in viruses, animals, and to a lesser extent plant viruses and phages. It has three different axes: binary, ternary and binary; and it has two different types of capsomers: pentamers and hexamers. In some of the viruses, barbs appear, which act as an anchor to the infected cell.

• Complex capsid (head-tail): it typically occurs in bacteriophages. In this type of capsid, the virus has two parts: the nucleocapsid and a tail (viruses that possess it are called urophages). The nucleocapsid can be icosahedral or the sum between a hexagonal prism and a hexagonal pyramid; the tail can be simple or complex and it ends in the basal plate (perforated hexagonal structure).

3. And an envelope (or coat) that surrounds the virus (is an exception since not all viruses have one). A component that it possesses, in an optional way, is the glycoprotein, which allows the virus to bind to the cell. From this part, either the protein or the messenger RNA (RNAm) is extracted for the production of vaccines.

The only function that viruses have is that of reproduction, and even so they cannot perform it individually, so they must infect other cells and use their components (matter, energy, and machinery) for their own benefit. For this reason, they are called obligate parasites.

To achieve their reproduction, viruses have developed two main processes:

1. Lytic cycles: once the virus has penetrated the cell, it proceeds to the immediate transcription of its genetic material. It is a fast infection and is visible in the immune system because they directly attack the cell.

2. Lysogenic cycles: unlike the other process, in this cycle, the virus is capable of inserting its genetic material into that of the infected cell. They are difficult to detect since they are camouflaged and use the life cycle of the cell for their own reproduction.

During the reproduction of viruses 6 phases occur:

1. Adsorption phase: the virion comes into contact with the cell to be infected to gain access to its interior, which is why the structure of the virus directly affects this phase. In addition, due to the proteins in its structure, it recognizes the membrane receptors of the host cell to proceed with infection.

2. Penetration phase: once the virion is attached to the cell, it can access the cell in different ways, depending on the structure of the virus. If it has a lipid membrane, it enters through mediated endocytosis, whereas if it does not have this membrane, it enters through direct endocytosis. The above are the most common mechanisms, although there are more and more varied, as the membrane fusion, for example.

3. Stripping phase: during or through the penetration of the virus into the cell, it is stripped. It is freed from the proteins of its deck, freeing its genetic material. Depending on the structure of the virion, its DNA or RNA can remain attached to the viral proteins.

4. Multiplication phase: viral proteins and their genetic material multiply. Each type of virus uses a different mechanism in this phase, depending on its group (these are according to the Baltimore classification).

5. Packing phase: organization of all the elements found in the cell to form the structure of the virus. Before this phase, the viral genetic material is already replicated and has the necessary amount of proteins to form new viruses.

6. Release phase: virions are expelled to the outside of the cell until they find a new cell to infect. This release can occur in two ways: forcibly, breaking the cell membrane (if it does not have a lipid envelope); or by budding, where the virus is covered with part of the cell membrane (if it has a lipid envelope).

Viruses can be classified according to the mix of the system created by David Baltimore and the one currently in use by ICTV (International Committee on Taxonomy of Viruses). These are based on the mRNA production mechanism, since each family of viruses makes it differently. The importance of mRNA is because viruses need it to form proteins and reproduce.

• The genome of viruses can be single-stranded (ss) (which can also be positive or negative) or double-stranded (ds), made of RNA or DNA, and they may or may not use reverse transcriptase. This classification divides viruses into seven groups:

1. DNA virus: replication of the genetic material of the virus generally occurs in the nucleus of the infected cell. They are generally accessed through endocytosis and become completely dependent on the synthesis of genetic material and RNA processing of the infected cell. It can be divided in two depending on the DNA chain it forms:

• Double-Stranded DNA virus (dsDNA): its DNA is made up of a double-strand and is replicated using DNA polymerase. In general, these types of viruses must enter the cell nucleus before they begin to replicate and are dependent on the cell cycle. This type of virus is capable of forcing the infected cell to carry out cell division, which can lead to the formation of cancer.

• Single-Stranded DNA virus (ssDNA): it has single-stranded DNA and is replicated through the use of DNA polymerase. Due to its chain, it is necessary that, before infection, its DNA passes from single to double chain in the infected cell.

2. RNA virus: their genetic information is encoded in RNA, so they use this acid as genetic material or their replication process needs RNA. In this type of virus, replication occurs in the cytoplasm and they can be classified into four groups according to their replication mechanism (mainly due to the polarity of the RNA), in addition to using their own replicas to create copies of their genome.

• Double-Stranded RNA virus (dsRNA): they possess double-stranded RNA. Viruses replicate in the cytoplasm and do not depend on the polymerases of the infected cell, since they possess these enzymes in the virion. They have the particular characteristic of being able to transcribe segments of double-stranded RNA under appropriate conditions within the capsid.

• Positive (+) single-stranded RNA virus ((+)ssRNA): they have single-stranded RNA in the positive sense. Viruses are identical to the viral RNAm so they can be replicated immediately by the infected cell. Replication occurs primarily in the cytoplasm and is not entirely dependent on the cell cycle. Because their RNA has the same polarity as that of mRNA, they can be used directly for protein synthesis using the translation machinery of the infected cell. One of the proteins encoded in this way is RNA replicase.

• Negative (-) single-stranded RNA virus ((-)ssRNA): it has single-stranded RNA in the negative sense and replicates without using intermediate DNA. It is complementary to mRNA and therefore must be converted to positive RNA with the help of an RNA polymerase before translation. They use an RNA polymerase to form positive-sense RNA and must carry RNA polymerase due to its dependence on RNA. The resulting protein is responsible for producing elements for the structure of the new viruses.

3. Reverse virus: they replicate using a reverse transcriptase so they replicate through a chain of genetic material different from the one they are composed of, and it has two types of genome:

• 1. Reverse transcribed single-stranded RNA virus (ssRNA-RT): a single-stranded virus that replicates by reverse transcription (by DNA from RNA). They make use of an RNA-dependent DNA polymerase to produce DNA, where it is generally integrated into the genetic material of the infected cell.

  2. Reverse transcribed double-stranded DNA virus (dsDNA-RT): double-stranded DNA viruses that use a DNA intermediate to replicate (if they have an RNA genome), or an RNA intermediate (if they have a DNA genome)

Different types of viruses can infect only a limited range of hosts and many are species-specific.

The mutations suffered by viruses are due to antigenic drift (the bases of the genetic material mutate to other bases). The vast majority occur silently (they do not change the encoded protein), some others cause evolutionary advantages (such as resistance to drugs or certain vaccines). This only happens when there is a significant variation in the virus genome (recombination, the process by which a strand of DNA is broken and then joined at the end of another DNA molecule; or rearrangement, genetic mixing and matching for the production of offspring with unique characteristics). Recombination is common to both RNA and DNA viruses.

• RNA viruses are often made up of quasispecies (variation of viruses due to genetic mutations), which is essential for natural selection.