Classification of viruses, variants and strains

Before explaining the classification of viruses, it should be remembered that they are made up of a fragment of genetic material, which can be made up of DNA or RNA, and a protein envelope endowed with receptors on its outer face. Some viruses also have a lipid coat, which can be made up of remnants of the host cell membrane .

They are considered obligate cellular parasites , since they need to introduce their genetic material into a cell in order to transcribe and replicate it, since they lack the required organelles (ribosomes). According to the cell theory , which stipulates that the cell is the structural unit of all living beings, viruses would not be living beings. 

It is not possible to trace the evolutionary ancestors of today’s viruses, due to their rapid mutation rate. Furthermore, many viral genes are of cellular origin, being “hijacked” by the virus when infecting a cell, so their presence in the virus is not due to evolutionary reasons.

Therefore, they cannot be classified according to the same criteria used for the taxonomic classification of living beings , in which there is traceability based on common ancestors. In this article we will explain how the different types of viruses are classified.

What is a viral species?

Classification of viruses
Classification of viruses

Due to the great variability and rapid mutation rate of viruses, something as relatively simple as defining what a viral species is is not an easy task.

Before the 1980s there was no defined criteria for what was or was not a viral species. The current classification is that a viral species is composed of different strains that belong to the same lineage (they have an evolutionary relationship) and occupy a particular ecological niche. Despite this, the classification does not follow a strict rule in the different groups of viruses.

Difference between strain and variant of a virus species

As a virus replicates, it accumulates copy errors in its genetic sequence due to point mutations. These changes gradually accumulate until there are significant differences between the genetic sequence of different samples of the same virus. When these differences exceed a certain threshold, they are called variants .

Different variants of a virus affect the same host and cause the same disease. However, when these differences continue to accumulate, a new strain of the virus can appear , which can affect another host or cause a markedly different disease.

It is not correct to speak of strains and variants as if they were the same. In the case of SARS-CoV-2, the virus that causes Covid-19 disease, it is a strain of a previous virus that mutated to the point of affecting a new host, humans. SARS-CoV-1 is another strain of the virus that appeared in China in 2004. However, the term strain is misused to refer to the different variants of the SARS-CoV-2 virus that have appeared in recent months. These would be the British (B117), South African (501Y.V2) and Brazilian (P.1) variants, which affect the same host and cause the same disease, so it would not be correct to refer to them as strains.

Classification of viruses

According to the International Committee on Taxonomy of Viruses ( ICTV ), viruses can be classified taxonomically in a similar way to species of living beings.

In this classification, the largest groups would be the domains (a total of 4,  Riboviria ,  Duplodnaviria ,  Varidnaviria  and  Monodnaviria ) and the smallest group would be the species. The ICTV classification does not distinguish between subspecies, strains or isolates within the same species (which is why they should be indicated in larger numbers). As of 2019, the virus classification includes 9 kingdoms, 36 classes, 168 families, 1,421 genera, and 6,590 different species.

It is due to the high mutability of viruses that to refer to a specific variant we do so by indicating the species to which it belongs , the variety within the species, the host organism, the year in which the variety was identified and the place where the one that was identified.

For example, a possible way to describe a variant of the Ebola virus would be the following: “Ebola virus H.sapiens-tc / COD / 1995 / Kikwit-9510621”. In this example, the virus in question is indicated first, then the host species ( Homo sapiens ), the place where the sample was taken (Democratic Republic of the Congo, COD), the year in which the sample was taken (1995) , the virus variety (Kikwit) and a numerical code of the variant (9510621). This classification proposal also indicates the way in which the sample was taken (tc, to indicate that it comes from a tissue culture).

Another way to classify viruses: the Baltimore classification

Another form of classification of viruses, which does not attend to taxonomic criteria but to the characteristics of the viral genome, is the Baltimore classification (named after its proponent, the Nobel laureate in medicine David Baltimore). According to this classification, viruses are divided into seven large groups identified with Roman numerals.

Group I

Group I, double-stranded DNA virus, which is transcribed into RNA for protein synthesis. Herpesviruses, chickenpox, HPV virus or smallpox belong to this group.

Group II

Group II, positive-stranded single-stranded DNA virus, which can be directly transcribed into proteins (such as parvoviruses).

Group III

Group III, double-stranded RNA viruses, such as reoviruses. Double-stranded RNA is rare in living beings, since RNA is transcribed from DNA in a single-stranded form ready for protein synthesis. An example is Rotaviruses that cause gastrointestinal illnesses that are mostly mild or virtually no symptoms in humans, although one of them causes severe diarrhea in children under 5 years of age.

Group IV

Group IV, positive single-stranded RNA viruses, such as yellow fever, polio, hepatitis A and E, rubella, tobacco mosaic, or SARS-CoV-2. These viruses can initiate protein synthesis from their genetic material without any prior enzymatic transformation process.

Group V

Group V, negative single-stranded RNA virus, such as rhabdovirus (rabies), measles, influenzavirus (flu), or Ebola virus . These viruses must transform their genetic material to a complementary RNA strand similar to messenger RNA in humans, using the enzyme RNA polymerase.

Group VI

Group VI, reverse transcribed single-stranded RNA virus, such as HIV. These viruses reverse transcription of their genetic material to DNA and subsequently transcribe it to RNA. These viruses do not affect prokaryotes (bacteria), so it is believed that their appearance could be after the existence of eukaryotic organisms.

Group VII

Group VII, double-stranded DNA viruses that perform reverse transcription for the replication of their genome, producing intermediate RNA that then gives rise to new copies of the DNA that the virus genome contains. It is, so to speak, the most complex way by which a virus can replicate its genetic material, due to the number of steps required and enzymes required. The virus that causes Hepatitis B and the cauliflower mosaic belong to this group.

Satellite virus

There is a type of virus, called satellite viruses, that have the genes that encode their protein coat but lack the necessary enzymes to carry out their own replication. That is, they need to be associated with another virus (larger) and depend on that virus infecting a cell in order to replicate and assemble new copies.

Depending on the relationship of each satellite virus with its associated virus, they can maintain a relationship of symbiosis (if the satellite virus has an enzyme that the main virus requires) or commensalism (if the satellite virus does not benefit the associated virus but does not harm it either) . Based on the Baltimore classification, satellite viruses can belong to groups I, II, III or IV. 

Other classifications

There are other classifications of viruses that are less widely used or outdated. One is the classification based on the structure of the viruses , which would make it possible to establish groups associated by kinship, but which could only be applied to the upper groups of the classification and not at the species level.

Another is Holmes’s classification , which classified viruses into  phaginae  if they attacked bacteria,  phytophaginae  if they attacked plants, or  zoophaginae  if they attacked animals. It is an early classification but it is not useful today (although it may be complementary to others).

Another classification in disuse is the LHT , precursor of the current ICTV, which classified viruses into groups in relation to their type of genetic material, presence of envelope, number of different parts that make up the envelope, etc.

For all that has been explained above, we see that the classification of viruses is not as simple as that of living beings, that kinship relationships cannot be established based on a common ancestor and that the most practical way to classify them is based on some distinctive characteristic, such as the type of genetic material they possess.

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