The Biology and Microbiology of Coronaviruses

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Microbiology and Virology were two branches of Biology I was always very interested, and since the pandemic I have been dedicating more time to these discipline

With the raise of cases all over around the world due to new variants, mutations, and other reasons our interest and concerns for the coronaviruses have regrown, and for this reason I have wanted to look to a much deeper way at the microbiology of these viruses. I am not here to talk about all the matter of this pandemic because I am certainly not qualified for this and, honestly, in the middle of not knowing what to believe myself; either way I am not going to talk about remedies and therapies; there is plenty of information out there, the best specialists and scientists are greatly conversing and debating about from both sides, conventional and integrative doctors, those who believe in vaccine and those who not. I have been treating in previous blogs, and many of the natural adjuvants of support and prevention therapies look like to be still valid and the same.

I have watched among others the last of a serial of webinars on Covid-19 hosted by Dr. Michael Murray, one of the naturopaths I trust most in regard of this complicate and complex dilemma we all are living; it seems that he has revalidated the most of his believes and founds with few more updates on the whole situation and results from clinical trials. It can be found on YouTube for whom is interested.


Coronaviruses- as of Wikipedia description, one of my preferred and recurrent sources of information- are a group of RNA viruses responsible of diseases in mammals and birds. In humans and birds, they cause respiratory tract infections diseases that can range from mild to lethal. Mild illnesses in humans include the common cold also caused by other viruses like rhinoviruses, while more lethal varieties can cause SARSMERS, and COVID-19.  


Coronaviruses belong to the family of Coronaviridae and are enveloped viruses with a positive-sense single stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses is one of the largest among RNA viruses and has a 5’ methylated cap and a 3’polyadenylated tail. They have characteristic club-shaped spikes that project from their surface, which under electron microscope appears as an image of the solar corona, from which their name derives.

This class of viruses are large spherical particles with unique surface projections. Their size is highly variable with average diameters of 80 to 120 nm. Extreme sizes are known from 50 to 200 nm in diameter. The total molecular mass is on average 40,000 Dalton. They are enclosed in an envelope surrounded of various protein molecules. The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.

The envelope and membrane protein are the structural proteins that combined with the lipid bilayer to form the viral envelope. Spike proteins are needed for interaction with the host cells. The membrane protein is the main structural protein of the envelope that provides the general shape. This protein is crucial during the assembly, growing, envelope formation, and pathogenesis stages of the virus lifecycle.

The envelope’s proteins are highly variable in different species. They are integral proteins and have two domains, a transmembrane domain and an extramembrane C-terminal domain. They are almost fully α-helical, with a single α-helical transmembrane domain, and form pentameric ionic channels in the lipid bilayer. They are responsible for virion assembly, intracellular operating, and morphogenesis.

The spikes, the most typical feature of coronaviruses, are responsible for the corona- or halo-like surface. A coronavirus particle on average is made of 74 surface spikes. Each spike is about 20 nm long and is composed of a trimer of the spike. The spike, or S protein is in turn composed of two subunits, S1 and S2.

The spike proteins are a class of fusion proteins which mediate the receptor binding and membrane fusion between the virus and host cell. The S1 subunit forms the head of the spike and has the receptor-binding domain. The S2 subunit secures the spike in the viral envelope and on protease activation enables fusion.

The two subunits remain noncovalently linked as they are exposed on the viral surface until they attach to the host cell membrane. In a functionally active state, three S1 are attached to two S2 subunits. The subunit complex is split into individual subunits when the virus binds and fuses with the host cell under the action of proteases like the cathepsin family and transmembrane protease serine 2 of the host cell.

S1 proteins are the most critical components in terms of infection. They are also the most variable components as they are responsible for host cell specificity. They possess two major domains, the N-terminal domain, and the C-terminal domain, both of which serve as the receptor-binding domains. The N-terminal domain recognizes and bind sugars on the surface of the host cell.

A subset of coronaviruses, specifically the members of beta coronavirus subgroup A, also has a shorter spike-like surface protein called hemagglutinin esterase. These proteins appear as tiny surface projections of 5 to 7 nm long implanted between the spikes. They play a role also in the attachment and detachment from the host cell.

Inside the envelope, there is the nucleocapsid, which is formed from multiple copies of the nucleocapsid protein, which are bound to the positive-sense single-stranded RNA genome in a continuous beads-on- a-string type conformation. Nucleocapsid protein is a phosphoprotein divided into three conserved domains. Most of the protein is made up of domains 1 and 2, which are typically rich in arginine and lysine while domain 3 has a short carboxy terminal end and has a net negative charge due to excess of acidic over basic amino acid residues.

-The chemical composition is what can influence the behavior and function of a molecule, specificity, site of attachment and more, and this is probably one of the characteristics that researchers study to try to find answers and solutions-

Replication Cycle

Cell Entry

Infection begins when the viral spike protein attaches to its complementary host cell receptor. After attachment, a protease of the host cell cuts and activates the receptor-attached spike protein. Depending on the host cell protease available, cleavage and activation allows the virus to enter the host cell by endocytosis or direct fusion of the viral envelope with the host membrane.

-This is where most of the drugs are, eventually, supposed to act to block the entrance of the virus into the cells-

Genome Translation

As into the host cell, the virus particle is uncoated, and its genome enters the cell cytoplasm. The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail, which allows it to act like a messenger RNA, or m-RNA and be directly translated by the host cell’s ribosomes. The host ribosomes translate the initial overlapping open reading frame and a same frame of the virus genome into two large overlapping polyproteins.

The larger polyprotein is a result of a -1ribosomal frameshift caused by a slippery sequence (UUUAAAC) and a downstream RNA pseudoknot at the end of open reading frame.  The ribosomal frameshift allows for the continuous translation of the overlapping reading frames.

The polyproteins have their own proteases, which split the polyproteins at different specific sites. Product proteins include various replication proteins such as RNA-dependent RNA polymerase, (RdRp), RNA helicase, and exoribonuclease.


Several of the nonstructural proteins come together to form a multi-protein replicase-transcriptase complex. The main replicase-transcriptase protein is the RNA-dependent RNA polymerase which is directly involved in the replication and transcription of RNA from an RNA strand. The other nonstructural proteins in the complex assist in the replication and transcription process. The exoribonuclease nonstructural protein provides extra reliability to replication by delivering a proofreading function which the RNA-dependent RNA polymerase lacks.


One of the main functions of the complex is to replicate the viral genome. RdRp directly mediates the synthesis of negative-sense genomic RNA from the positive-sense genomic RNA. This is followed by the replication of positive-sense genomic RNA from the negative-sense genomic RNA.


The other important function of the complex is to transcribe the viral genome. The replication process is followed by the transcription of these negative-sense subgenomic RNA molecules to their corresponding positive-sense mRNAs. The subgenomic mRNAs form a “nested set” which have a common 5′-head and partially duplicate 3′-end.

-I probably missed to interpret the nature of the coronaviruses transcriptase from the begin because I thought that the RNA-transcriptase were a reverse-transcriptase so as in Retroviruses, and that therefore they were producing DNA from RNA templates, but it does not look to be. In the same time I have read some articles from PubMed that were talking about the possibility of “reverse transcribed” of SARS-CoV-2RNA to explain the why of many positive cases and reinfection. I am going to discuss in a next blog-


The replicase-transcriptase complex is also capable of genetic recombination when at least two viral genomes are present in the same infected cell. RNA recombination appears to be a major driving force in determining genetic variability within a coronavirus species, the capability of a coronavirus species to jump from one host to another and, infrequently, in determining the emergence of novel coronaviruses. The exact mechanism of recombination in coronaviruses is unclear, but likely involves template switching during genome replication.

Assembly and release

The replicated positive-sense genomic RNA becomes the genome of the progeny viruses. The mRNAs are gene transcripts of the last third of the virus genome after the initial overlapping reading frame. These mRNAs are translated by the host’s ribosomes into the structural proteins and many accessory proteins. RNA translation occurs inside the endoplasmic reticulum. The viral structural proteins S, E, and M move along the secretory pathway into the Golgi intermediate compartment. There, the M proteins direct most protein-protein interactions required for the assembly of viruses following its binding to the nucleocapsid. Progeny viruses are then released from the host cell by exocytosis through secretory vesicles. Once released the viruses can infect other host cells.


Infected carriers can shed viruses into the environment. The interaction of the coronavirus spike protein with its complementary cell receptors is central in determining the tissue tropism, infectivity, and species range of the released virus. Coronaviruses mainly target epithelial cells. They are transmitted from one host to another host, depending on the coronavirus species, by either an aerosolcontaminated objects, or fecal-oral route.

Human coronaviruses infect the epithelial cells of the respiratory tract, while animal coronaviruses generally infect the epithelial cells of the digestive tract. SARS coronavirus, for example, infects the human epithelial cells of the lungs via an aerosol route by binding to the angiotensin-converting enzyme 2, (ACE2) receptors. Transmissible gastroenteritis coronavirus, which is an alfa-coronavirus, infects pigs’ epithelial cells of the digestive tract via a fecal-oral route by binding to the alanine amino-peptidase receptor.


Wikipedia, Coronavirus

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To be continued

Thanks for Reading

Mariarosaria M.

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