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M. Ravi PhD, MNASc;


The taxonomy

The fundamental categorization of life forms into different taxonomical units or levels lie in the differences and similarities among life forms. The taxonomic classification levels of life forms range from the “Kingdom” which is the highest order to the “Species” which is considered the classification rank that is at the lowest level. Typically, a particular species of life form is named in accordance to the binomial nomenclature system, where the names of the Genus and Species form the two parts of the name; for example, Homo sapiens. However, the binomial nomenclature is no applicable to viruses. Different populations of a species inhabiting different geographical habitats are often refered to as the subspecies. Such subspecies vary in certain morphological features, largely as an adaptation to the particular habitat that they inhabit.

Microbial strains

Apart from the species level, one other classification level that is commonly applied to microbes is the “strain”. Microbial strains belong to a particular species however; the strain differences include several genetic and physiological variations as can occur in various populations of microbes belonging to the same species. The level of “strain” in the taxonomical classification is significant from the pathological or medical point of view. This is due to the genetic differences that occur among different strains of microbes (examples: fungi, bacteria and viruses) and such differences having a significant impact of the virulence of the different strains. Thus, microbial strains represent genetic subsets within a species and the genetic differences leading to variations among the different subtypes.


Viruses are generally described as infectious agents which are sub-microscopic and require living cells for their replication. Viruses have their nucleic acids (genetic material) enclosed within a protein covering or coat. Viruses require a living cell for its replication and viruses have been identified which can infect almost all types of cells, ranging from bacterial cells to several types of eukaryotic cells present in multicellular organisms. Usually, a particular virus has a small range of the type of cells it can infect and a particular type of virus cannot infect all types of cells. However, there are certain viruses such as the rabies virus which has a wide range of possible host cells that can be infected. Also, viruses that can infect bacteria, which are known as bacteriophages are known to have a narrow range of host bacterial, usually limited to a particular strain of viruses as can infect a particular bacterial type. 

Presence of different strains in viruses and their implications for human healthcare

Almost all known viruses occur as different strains and the presence of such strains have a significant effect on the pathogenicity of the viruses. Also, epidemics and pandemics have been known to occur largely due to the occurrence of several or emergence of new viral strains. The occurrence of several strains of a particular virus leads to uncontrolled infections and a rapid spread of the infections. Also, such strain differences can lead to pandemics as can affect at the global level. The most common example of such strain differences causing serious human healthcare effects is the influenza virus.

Three major mechanisms have been identified to explain the presence of different strains in microbes, especially viruses. These are the mutations, antigenic drift and the antigenic shift mechanisms. Mutations are random events that occur in viruses as they replicate within host cells rapidly. Such mutations lead to genetic differences which if result in the protein changes, will lead to an emergence of a new genotype. Antigenic drift refers to the accumulation of new mutations which are gradual and those leading to minor genetic changes. However, unlike antigenic drift, the antigenic shift mechanism occurs in a more pronounced manner and these genetic variations occur as the viruses move through different hosts. For example, the movement or transmission of the influenza virus through different hosts such as humans, pigs and birds can induce antigenic shift. Such antigenic shift will lead to development of viral strains with varied antigenic profiles and hence, pose a challenge for therapy and for prevention (development of vaccines). Although the human immune system is complex and is capable of generating protective responses to a wide range of antigens, the high pathogenicity and presence of different strains of a particular type of virus can lead to high pathogenicity. 

SARS-CoV-2 and COVID-19

The most recent and currently ongoing pandemic with severe global implications is the COVID-19 pandemic as caused by a novel type of the Corona virus, named by the World Health organization as the SARS-CoV-2. The pandemic known to have originated in Wuhan, China in December 2019, has estimated to have 6,177,120 cases as on 31st May 2020. Till the given date, the pandemic has claimed 371,287 deaths while 2,746,094 cases have recovered. The pandemic has affected 213 countries and continues to be a serious healthcare threat apart from the socio-economic implications.

The corona virus is a group of common viruses which can cause mild infections of the upper respiratory tract.  This family of viruses include the Severe Acute Respiratory Syndrome (SARS) virus and the Middle East Respiratory Syndrome (MERS) virus. Four major groups of the corona viruses have been identified, which are in turn grouped as the alpha and the beta types. The alpha subtypes include the 229E and the NL63 subtypes while the beta subtypes include the OC43 and the HKU1 types. Apart from these four subtypes, three more subtypes of the corona virus family include the MERS-CoV, SARS-CoV and the SARS-CoV-2 subtypes. The SARS-CoV-2 virus is thus far the most pathogenic of all the types of corona virus. Also, two strains of the SARS-CoV-2 virus have been identified, the L type and the S type.

Implications of new strain development

The development of new strains of the coronavirus (as true for any virus types) is due to random changes that occur in the viral genome as they replicate within host cells. The high replication rates tend to increase the chances of such spontaneous and random changes in the viral genome, the phenomenon of random mutations. Such changes apart from the phenomenon of antigenic shift lead to the changes in the antigenic profiles of the viruses. Thus, development of candidate vaccines will be a challenge as viruses with several antigenic profiles might be present. This will be confounded by the possibility of new variant development as time progresses. Also, as with the flu, development of permanent immunity will be difficult with the presence of several strains of the pathogenic viruses.   


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