There are 7 coronaviruses that are known to infect humans. Some like the SARS-CoV 2 can be absolutely lethal, while many others manifest only as milder symptoms. There are questions that fester in a climate of conspiracy theories and supposed anthropo-tinkered viral genetics, which are thrown about as carefree and careless theories. Its important thus to take a deeper look at this human-viral interface and subsequent infection to find solutions to burning questions of a frantic contemporary.
(1) Does the origin of SARS-CoV 2 entail a conspiracy theory?
(2) What animal was responsible for the zoonosis (jump from animals to humans) of SARS-CoV 2?
(3) What role does the Polybasic Cleavage site entail in relation to enhanced infectivity by SARS-CoV 2?
(4) What is the evolutionary story/origins behind SARS-CoV 2?
(5) How fast is “fast” in terms of evolution of SARS-CoV 2?
Answer (1) First and foremost, there has been a rapid response by scientists to the conspiracy theories that are flying about, which show that although this virus is not an evolutionary fluke, it is not manmade. First, the Receptor Binding Domain (RBD) of the SARS-CoV 2 is optimized to bind to the Angiotensin Converting Enzyme 2 (ACE receptor 2) and has been shown by scientists not to entail an anthropogenic origin. The enhanced recognition, precision and affinity of receptor binding, is thought to be due a few mutations (5 to 6) in the receptor binding domain of the SARS-CoV 2, that were selected by nature (natural selection). Remember how Charles Darwin coined the words “Natural Selection” to explain the mechanisms by which nature can adapt and optimize, for the survival of the fittest. The RBD of SARS-CoV 2 has been suggested to bind to a spectrum of high homology ACE2 receptors, namely from humans, cats and ferrets. The sequence analyses of RBDs of SARS-CoV 2, show that the optimization of binding to the ACE2 receptors, was gained from natural mechanisms and not using genome editing tools (such as Crispr-Cas9) in human hands.
Answer (2) There is a polybasic binding site in the Spike Glycoprotein of the SARS-CoV 2 virus that functions as a substrate for cleavage by a human host Furin family protease (or proteases), which is crucial for the infectivity of pulmonary epithelial cells by SARS-CoV 2. “Poly” means “many amino acids” and “basic” means either of the amino acids, arginine or lysine, which have an inherent positive charge, under most conditions. This polybasic substrate for Furin proteases is absent in Pangolins and Bat Beta coronaviruses. However, this is not a cardinal/universal truth in terms of both animal families, since only a few beta-coronavirus strains have been sampled prior to now, from such reservoirs. This means that the polybasic substrate may be present in some forms of Coronaviruses, which may be infective to such animal reservoirs, which is not known in the present, due to under-sampling. So to present a model here, a mutated RBD containing SARS-CoV-2 strain may have made the jump from a suitable animal reservoir (Pangolin etc) to humans, and this could be one zoonotic event or many, depending on how long (and how often) the SARS-CoV 2 has been inside the human host, prior to integration of a polybasic substrate sight for cleavage by a Furin family protease, for heightened pathogenesis.
Answer (3) The polybasic binding sites of the SARS-CoV 2 strains possess many arginines, which is why there is strong cleavage by Furin proteases, especially by the ones found in human lungs. A proline that acts as a leader insertion too, is crucial for post translation modification of downstream residues at a specific locality (addition of O-linked glycans, which is a common post translational modification, which are mechanisms by which proteins change specific amino acids by incorporating covalent modifications, in this case a sugar molecule). Although a polybasic excision site is thought to be as enhancing the function of pathogenicity, it needs to be proven in animal models. The binding of the SARS-CoV 2 to pulmonary epithelial cell (Cell-to-Cell fusion) is enhanced by the presence of a protease susceptible site.
Answer (4) Evolution is marked by two related but distinct events in relation to SARS-CoV 2.
– The mutations (5-6 in total) on the RBD domain of the SARS-CoV 2 virus (substitutions)
– The acquisition of a polybasic substrate site for cleavage by a host Furin family protease (insertions)
In terms of overall sequence homology of genomes, a Rhinolophus affinis bat based coronavirus genome is ~96% identical to SARS-CoV-2, however the RBDs are variable between the human and the bat genomes, suggesting that the bat coronavirus is unlikely to infect humans. Malayan pangolins (Manis javanica) too possess high homology Coronavirus genomes to the SARS-CoV-2 genome and contain all six key mutations that are important for the evolution of the RBD domain to be a near-perfect fit to the ACE2 receptor. However, both – bats and pangolins – do not possess a polybasic binding site, which tells us that this too is unlikely as the source of lethal infectivity.
There are three cumulative theories of how the virus became deadly in relation to its transmission.
1. The substitution mutations (This is when one letter of the RNA alphabet is changed at a time) and insertions (This is when whole words are added to the RNA text) were acquired during human to human transmission, which means that the virus that jumped from animals to humans, was non-lethal (innocuous) initially and only changed to become an infective pathogen once inside a human. This is discouraged by the presence of similar RBD domains and residues within genomes of coronaviruses from both pangolins and humans.
2. The substitution mutations and insertions were acquired from an animal host (the original virus from an animal source that infected Patient Zero was already lethal)
3. The most likely theory suggests that the RBD residues were mutated already when the SARS-CoV-2 jumped from animals to humans. However, it is likely that the polybasic binding site was acquired during human to human transmission. The addition of the polybasic side would have been likely to have taken place as a genome insertion or multiple genome insertions as one or many linear codons, that are capable of translating an exact substrate for cleavage by Furin family proteases.
Answer (5) The mutagenesis of the corona virus is slower than that of the seasonal common flu. It is said that the mutation of the common flu (as in mutations acquired during a year) is more than double that of the SARS-CoV-2.
RNA viruses, such as dengue, are known for their error-prone RNA polymerase activity due to the absence of proofreading (Think of an enzyme that has bad spelling which keeps on adding wrong alphabet characters to the RNA script and there is no editing or proofreading service at hand to correct) which can be a game changer in terms of our inability to develop a timely, universal and long lasting vaccine for dengue transmission. However, while the dengue genome is ~10.7 kb, the Coronavirus genomes are of the size ~27-34 kb (the largest RNA genomes), the latter being three times bigger and having a proofreading mechanism in place, due to the presence of an ExoN (nsp14) enyzme, that can correct mistakes in the newly designed RNA strand by proofreading. This is what makes the vaccine developers excited, since the rate of mutagenesis of SARS-CoV-2 is conducive to vaccine development.
Que sera sera, I suppose will be our consolation as we watch the daily news on TV to see the coming horizon, in a war of attrition, a fatal virus that is eligible for vaccine development, battling an intelligent species called man. So lets take the battle to a different level now – bring on the firepower of a vaccine! – and we will save ourselves. Science Carpe Diem!
Note: These are basically the interpretations of biology of Coronaviruses by the author Dilantha Gunawardana for science communication purposes.
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