Virology 100x: Round and round we go; where we stop, nobody knows

Viruses are so varied because each virus has evolved to specifically infect one particular host. There are so many different types of viruses that it’s difficult to describe them with a generality; what they have in common is merely as I wrote in an earlier post – that they’re obligate intracellular parasites comprising of nucleoprotein complexes with a protective protein coat (and possibly a lipid envelope). However, with classification, we are able to make generalisations within a particular subset of viruses – particularly with respect to how they infect and replicate, then bust out of our cells. If we are able to figure out how viruses replicate and infect our cells, we are then in a better position to prevent them from replicating in, or even better, from entering and infecting our cells in the first place.

Viruses are primarily classified according to their genetic material; that is to say, whether they have DNA or RNA. After splitting into these two groups, there are further subsets, such as whether the genetic material is single- or double-stranded; if the viral genome is whole or segmented – amongst others.

Baltimore classification

See text for explanation on Baltimore classification

This method of classification is called the Baltimore classification, after its developer David Baltimore. The genetic nature of a virus is important because it determines where and how the replication of the DNA or RNA takes place (either the nucleus or the cytoplasm), which in turn partially determines what steps the virus must take to get its genome there. Thus, it is possible for us to predict certain features of a virus’s replication cycle based purely on its genetic nature.

The stages in viral replication are so closely linked that it is difficult to separate them sometimes, and the number of stages range from seven to eight, or even nine, depending on who you are talking to. Nevertheless, they can be grouped into three main areas dealing with Entry into, Replication in, and Exit from host cells. Adsorption & Attachment, Entry, and Uncoating are stages in how the viruses enter cells; Transcription, Expression/Synthesis, and Replication are stages in viral replication; Assembly, Maturation, and Release are stages in how viruses exit cells.

As viruses don’t have any means of moving around, they depend on collisions with other things moving around in our bodies to push them along, causing random movement (also known as Brownian motion). Viruses are adsorbed onto the surface of the cells they are trying to infect, where they attach to the host cell by inserting their protein key into the host protein/sugar-chain lock, and thus gain entry into the cell.

The virus then enters the host cell via one of three methods. First, the translocation of the entire virus particle across the cell membrane; not much is known about this process, unfortunately. The second and third methods both involve endocytosis, which is the process by which our cells engulf particles such as nutrients (and in this case, viruses) from outside the cell. Endocytosis causes the formation of little pockets called vesicles, which go on to merge with larger pockets (containing fairly hostile environments) called lysosomes, which break down the particles that are brought into the cell for use throughout the cell. Triggered by the change in environment in lysosomes, viruses undergo uncoating, where the viral genome is exposed to the cellular environment. In the second method of entry, no further direct virus-host interactions are required, whereas in the third method, often employed by enveloped viruses, the viral lipid envelope and the cell membrane fuse to allow entry of the viral genome into the cell.

Upon entry, the virus then takes over the cell machinery and uses the cells’ enzymes to start transcribing and replicating its genome, and synthesizing the protein components of more viral particles. The precise order and manner of these stages is dependent on the nature of the viral genetic material¹.

Finally, the assembly of the newly-synthesized viral proteins and newly-replicated genetic material forms new viral particles, which is followed by protein cleavage where necessary for the maturation of the new viral progeny, and the release of the new viruses into the world again, usually by budding from the cell, or causing the cell to burst.

By deciphering how the various steps of any particular virus’s replication cycle happens, we are better able to prevent and/or treat a viral infection; for instance, the various drugs available in HIV therapy are based around the steps HIV takes to replicate itself. HIV is a class VI virus, meaning that it requires reverse transcriptase to replicate; one of the first HIV treatments was zidovudine (commonly known as AZT), which was aimed at inhibiting reverse transcriptase. Many other HIV drugs have continued to be developed in the same vein, and research has gone into finding drugs that can inhibit virus entry, maturation and exit as well.

 

 

 

1. Viruses are classed using the Baltimore Classification scheme according to how they replicate.

Class I and Class II have DNA for their genetic material. Class I viruses are able to express their genes upon entry as the genes are made of double-stranded DNA; replication of the genome and expression/synthesis of proteins are then carried on concurrently. Replication is almost exclusively nuclear in Class I viruses, with the exception of poxviruses, which are able to replicate their DNA in the cytoplasm. Class II viruses, with single-stranded DNA, typically have to undergo genome replication in the cell nucleus first before protein expression can be carried out.

Class III, IV and V have RNA for their genetic material. Class III viruses have segmented double-stranded RNA genomes, which are transcribed separately to produce mRNA and synthesize proteins in the cell cytoplasm. Class IV viruses’ (+)sense RNA are able to synthesize viral proteins immediately after infection in the cell cytoplasm, as they use their genomes like mRNAs; Class V viruses, on the other hand, have to make a (+)sense RNA from their (-)sense RNA genome first.

Class VI and VII viruses both use reverse transcription in their replication, although the point in the viral replication cycle at which reverse transcription is carried out is different for both classes. Class VI has diploid single-stranded (+)sense RNA, but this genetic material does not serve as mRNA immediately after infection. Instead, they use viral reverse transcriptase to create a DNA intermediate for replication and protein synthesis after infection. Class VII has double-stranded DNA, much like our own cells, which can be transcribed into mRNA, and the resulting mRNA read to make viral proteins. Reverse transcriptase comes in near the end of the replication cycle, to re-create the virus DNA from its mRNA.

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Virology 100x: Let’s start from the very beginning

Tobacco Mosaic Virus

The tobacco mosaic virus; the first virus discovered and studied.

Let me get one thing straight first – viruses are NOT the same thing as bacteria. They’re just not. Okay? Great.

What are viruses, then? Well, I could tell you that they’re nucleoprotein complexes that make use of cells to replicate; I could tell you that they are obligate intracellular parasites – that is to say, they’re obliged to be parasites inside our cells; I could even tell you that they do not undergo cell division. But I won’t.

Oh. I already did.

Never mind then.

The point is, viruses are all that and more. One of the most interesting things in the world, we still can’t decide if viruses are living organisms or not. They carry genetic material, and are able to replicate themselves (but only after they’ve infected a host cell). However, outside of cells, they become metabolically inert – they can’t make their own proteins or copy their own DNA (or in the cases of some cells, their own RNA). Yet they can ‘die’ – if they’re outside of their host cell for long enough, or are otherwise exposed to adverse conditions, they can no longer successfully infect cells. This straddling of the line between life and non-life is very likely to be a clue to how life originated; most viral genes are so unlike the genes of the rest of the planet that they may well have come from a common ancestor before cell-based life existed.

The core of any virus is its genetic material – either DNA or RNA; this may be wrapped up with viral proteins to form a nucleoprotein complex (from combining “nucle”ic acid + “protein”). Viral proteins are also incorporated into the protective coat surrounding the nucleoprotein complex to give rise to the basic viral particle (or the virion). Some viruses, particularly those that infect mammals, may also have an additional lipid envelope over its protective coat.

You may think that all viruses are harmful to us, but this is not true. Because of the proteins embedded in their protein coat (or lipid envelope), viruses are very specific about which species they will infect, much like how only one specific key can open one specific lock. In fact, there are viruses, known as bacteriophages, which are beneficial to us because they are able to infect, and thus cause the death of bacteria that are harmful to us. It has been suspected that some “healing waters” may have been effective due to the presence of viruses that infect pathogenic bacteria. Viruses also infect amoeba, fungi, plants, and of course, other animals. In fact, every species on Earth has a whole host of viruses that is specifically only able to infect that species.

lock and key

In this case, the pink object refers to a viral surface protein, while the orange object refers to a host cell surface protein/glycoprotein. Only when viral protein keys are able to fit into host protein/glycoprotein locks can the infection of a cell start to happen, so viruses are VERY specific about who they are able to infect.

The gold standard for determining a new virus is by cultivating and isolating the virus, and viewing it under an electron microscope. Unfortunately, this species specificity means that it is very difficult to cultivate human viruses in order to study them, because they won’t infect non-human cells. The best way to go about studying human viruses would of course be by infecting humans, but this is ethically problematic, to say the least. One partial solution would be to culture human cells in a dish, and throw some human viruses on top to infect the human cells. This helps with studying how viruses infect cells in the first place, and what effects they have on cells in isolation. However, viruses are very finicky, and it first takes a lot of trial and error, and later, precision and time, to properly grow them. This still doesn’t answer how viruses act in the whole body, though – especially in the presence of our immune system, which has been implicated in a large amount of the cellular damage it causes as it tries to rip the virus from our bodies. Scientists thus have to use genetically near-identical species such as monkeys, or modify mice and other model organisms such that they carry human proteins, and are then able to be infected by our human viruses.

Because viruses are basically protein coats around genetic material, they are therefore also ideal as a mechanism for transferring genes to our own genomes. These engineered viruses are known as viral vectors, and have been modified such that they no longer cause disease. Viral vectors have a wide range of applications, including gene therapy, cancer treatmentvaccine development, and even in basic neuroscience research. Virus-like particles, which are viruses emptied of their genetic material, are also being investigated for use in nanotechnology applications like drug delivery and diagnosis.