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Origin, Structure, and Phylogeny of SARS-CoV-2

Madison Pascual Munar has a Doctorate degree in Molecular Biotechnology.


Severe Acute Respiratory Syndrome Coronavirus 2 or SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the etiologic agent of Coronavirus Disease 2019 also known as COVID-19. The SARS-CoV-2 belongs to the Family Coronaviridae, which is phenotypically characterized by its distinct spike structures on its outer membrane which resembles a crown or a corona.

The disease caused by SARS-CoV-2 was initially called 2019-nCoV by the World Health Organization (WHO). The first cases of viral pneumonia caused by SARS-CoV-2 were reported on December 31, 2019, in Wuhan, China.

SARS-CoV-2 Structure and Function

The SARS-CoV-2 viral particle is about 100 nanometers in diameter. The viral structure is composed of 6 major parts which include the spike protein (S), membrane protein (M), hemagglutinin-esterase (HE), envelope protein (E), nucleocapsid (N), and lipid membrane.


Spike Protein (S)

surface protein which is used for attachment and entry to the host cell

Membrane Protein (M)

determines the shape of the virion or the mature viral particle

Hemagglutinin-Esterase (HE)

a glycoprotein which recognizes the host cell receptor


Envelope Protein (E)

interacts with the membrane protein to form the viral envelope

Nucleocapsid (N)

protein bound with the viral RNA

Lipid Membrane

phospholipid bilayer which houses the nucleocapsid


SARS-CoV-2 Host Cell Receptors

SARS-CoV-2 uses two human membrane receptors to enter the cells. The ACE2 and TMPRSS2 receptors are used to penetrate the cell cytoplasm. Once inside the cell, the virus disintegrates and releases the single-stranded RNA. It will use the host cell machinery like the ribosomes to manufacture and build more virus particles. It takes 10 minutes for the viral particle to enter the host cell. Within 10 hours of replication and producing viral proteins inside the cell, the viral components will assemble into mature infectious viral particle or a virion.


Angiotensin-Converting Enzyme (ACE2)

used as the receptor for the SARS-CoV-2 spike protein in the human host cell

Transmembrane Protease Serine 2 (TMPRSS2)

present in human cell membrane and participates in viral spike protein priming


The viral particle can stay for about 1 hour in the air. Viral particles suspended in the air may get into the nasal cavity, then the virus will migrate towards the lungs. So wearing your mask is highly important to prevent getting infected with the virus. The viral particles can stay on surfaces for about 1-10 hours. Washing hands with soap and water, and the use of sanitizers will help to prevent contracting the virus. Social distancing, keeping a safe distance of 6 feet or approximately 2 meters, is also an important strategy to curb further spread of the virus. Incubation period for SARS-CoV-2 is about 14 days upon infection.

SARS-CoV-2 Genome

The SARS-CoV-2 whole genome sequence was published in January 13, 2020 at the NCBI Database. The whole genome sequence of SARS-CoV-2 is about 29,903 nucleotide bases. The genome has 14 Open Reading Frames (ORFs) which encodes for 27 proteins. Scientists identified 380 polymorphic amino acids between SARS-CoV-2 and SARS-related viruses.

Structural proteins such as the membrane protein (M), envelope protein (E), nucleocapsid (N), and spike protein (S) are highly conserved in the coronaviruses. Accessory proteins such as helices (H), RNA-dependent RNA polymerase (RdRp), papain-like protease (PL), and 3-chymotrypsin-like protease (3CL), involved in viral gene expression are highly specific between the groups.


SARS-CoV-2 Evolutionary Relationship With Bat SARS-CoV

Genomic analyses using five different genomes of SARS-related viruses, SARS-CoV, and MERS suggested that SARS-CoV-2 is highly related to bat SARS-CoV. Some scientists also speculated that SARS-CoV-2 could probably be a recombinant strain from different coronaviruses.

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SARS-CoV-2 Nucleotide Sequence Homology with Other Coronaviruses

Coronaviruses Homology

Bat CoV


Pangolin CoV






Common Cold CoV



Taxonomy of A New Virus

The International Committee on Taxonomy of Viruses (ICTV) is responsible in naming newly described viruses, while the WHO is the authority in naming the associated disease caused by a particular viral strain.

Polymorphic regions between reported and newly discovered strains are analyzed by pairwise alignment in the PAirwise Sequence Comparison (PASC) software in order to establish a clear demarcation between species, genus, and sub-family levels.

Coronaviruses and other related viral strains are commonly named using their genome sequences. Some scientists argued that SARS-CoV-2 is not consistent with the disease name, Coronavirus Disease 2019, designated by the WHO. The viral name SARS-CoV-2 was assigned by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. A group of scientists from China later suggested a new terminology to be used to refer to the causative agent of COVID-19 as Human Coronavirus 2019 (HCoV-19).


Virus Controversial Names

The WHO has pointed out controversial names given to some viruses which invokes concerns from people directly associated with the disease. The Spanish Flu, Creutzfeldt-Jacob Disease, Middle East Respiratory Syndrome, and Japanese Encephalitis to name a few can draw some negative association to certain ethnicities or nation. These kind of names should be avoided according to the International Classification of Diseases (ICD) who is the authority in establishing the taxonomic classification of new viruses.


Best Practices in Naming New Viruses

To harmonize the virus taxonomy, expert virologists recommend the use of computational approach which uses a single criterion, the whole genome sequence of the virus. DivErsity pArtitioning by hieRarchical Clustering-based analyses (DEmARC) is an open-source online tool that caters for the analysis of viral genome sequences.



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