Viruses

Viruses are not microbes, they are not properly microbes, but just an infection agent that contain a nucleic acid responsible for the infection of the host. Viruses are able to multiply and live only within host cells. These are parasites that contain nucleic acid and are responsible for example, of infection in the nose. They are able to multiply and live only within living host cells. Of course, we already see the difference between them and bacteria because of the size, they are very small and ancient beings. Viruses can range in size between 20-300 nm long, so much lower than bacteria.

We know that viruses replicate only within host cells, the genetic code they express will be DNA or RNA. Regarding the use of energy in the virus, they do not need any energy of course, to grow and reproduce. They can reproduce in a relative cell, they can change, this is a very important point. They can change over time because they do not have a system to repair the damage, so they can change every time the virus replicates. Instead, we have got a system to detect the mutation and repair it, this proper control is not present in the virus. What we know about viruses is that they don't have any nucleus, any cytoplasm, any cell membrane, just nucleic acid.

One of the viral components is the nucleic acid, and the capsid: the nucleic acid is protected within the capsid, which is made by proteins and sometimes (just in some viruses) we can expect an outside structure of the capsid that has got some proteins. It is very important for the virus to recognize the specific receptor of the host cell. The spike proteins are present in the envelope, if the virus has got it, or they can just be stuck to the capsid. The capsid is made of proteins and the envelope is a double phospholipidic membrane, because it arrives from the host cells, acquired by the virus when it exists the host cells.

Regarding the genome, we said it could be DNA or RNA. Regarding the DNA, it could be single strand or double strand and based on the structure of the genome we can classify the virus. So it could be double strand or single strand, linear or circular etc. These are again all the different classifications, you do not have to remember it, it's just general information. Then the classification includes also the structure of the capsid because it could be a specific shape, helical or complex shape. Remember that the RNA could be positive and can be present in different numbers of segments, going from to up to 10-18 segments.

The way the virus can enter the host cell depends on the type of virus and on the presence or absence of the envelope. Usually, it is the entire capsid that enters the cell and the virus is going to be intruded into a vesicle. So the capsid (the entire virus and the genetic material it contains) is going to be endocytosed or not by the host cell, and it is going to be intruded in a vesicle. From the vesicle the virus is going to be destroyed and the genetic material is going to exit and reach the cytoplasm in the host cell and from there the process in the main tissue is going to start. In case of viruses that contain the envelope, because this comes from the membrane of another host cell, the virus enters fusing the envelope to the new host cell's membrane. At this point the capsid can enter into the cytoplasm of the host cell and the DNA is going to be uncoated. So, we have two different mechanisms of entering based on the presence of the envelope, but the final result is that the DNA is going to be uncoated, so that the process of the production of the phenotype typical of the virus can start. The virus uses the machinery of the host cell, such as the ribosomes to produce the phenotype important for the replication and the assembly of a new capsid.

How can we grow viruses? Remember that the only way to “catch” them is by using living cells. We can use eggs to grow viruses, and this is the way we did in the past, for diagnostic but also for research. Now the eggs are still used to grow them, also for the production of vaccines. Some vaccines against viruses are made by growing them in eggs, but sometimes the viruses outgrow the egg. Otherwise, we use a cell culture: primary, secondary or immortalized cell cultures. The immortalized cell cultures are the best system, because they grow constantly, it is one of their main characteristics. Instead, for primary and secondary cultures, we can grow cells for several days or months, but they will eventually die. They best way is to use immortalized cultures. How can we visualize the virus when they grow in cells? The final result of viruses growth is their take over on the host cell, because the viruses exit after replication and destroy the cell. So if you have a monolayer cell culture, every time the viruses take over cell and destroy them, you will start to see this area with no cells, an area of lysis, because the cells are not there anymore, they are dead. So this clear (or black) zone is an indication that maybe a specific part of the population was taken over by a virus.

This is the life cycle of a virus. The virus goes in the host cell using different methods, based on the presence of the envelope. It starts to replicate, producing different proteins important for the assembly, using enzymes in the cell for the DNA replication (apart from retroviruses, because they need a specific enzyme that is able to replicate RNA from DNA, and it is not normally present in the cells). All the other cells divide and then, once the mitogenetic activity has been replicated, the proteins that compose the host cells are going to be reproduced, that is the assembly of the new virus. Once the virus is assembled, it is able to escape from the cells. And during this process, some of the virus acquire the envelope that is part of the cell. This is all the process of penetration, uncoated virus, maturation, release, and so on. As we already mentioned, that in some cases the genome of the virus could be segmented. This is an example of a SARS-CoV-2 virus. The genome is a positive RNA. And this is the size of the genome of the virus: it is very, very small, it’s 30,000 kb. It is very small, because it contains only the essential genes that are important for the mutation of the virus and the assembly in the host.