Monday, March 16, 2020

VIRUSES, VIRUSES everywhere, so Flatten the Curve!

SARS-CoV-2 or COVID19 or Wuhan Virus
In the fog of daily chaos and confusion, a tiny little package of carefully folded nucleic acids within a lipid layer escaped into the human world. “Where” it originated remains a mystery. But “There” it has caused havoc. Perhaps it was from the delicacy diet of bats or from the blood of snakes as reported, or neither. Some claim it might have originated from within some deeply fortified building from well beyond the Great Wall. 

But what of this tiny package?

It replicates very quickly almost to the tune of every 5 days. The next question that should arise in our minds is, what is the fidelity of the replication? Does it stay true to its basic nature and continue with its original base pair fidelity? (Base-pair) meaning the A-T and the G-C complex as in the DNA But the COVIS19 coronavirus is an RNA virus. RNA viruses are mostly single chains, unlike the DNA which is a spiral helix of two separate chains tied together with a sugar-phosphate. Other major difference being that Thymine is substituted by Uracil in the RNA. The argument previously mentioned is met with a certain “No.” No, it does not maintain 100% fidelity in its replication process over time. Ok so much for basic biology. 

The Nature of this Tiny Beast.

Perhaps we should visit the nature and being of this little guy. It is a NOVEL menace. When a full-genome sequencing and phylogenic analysis was done the coronavirus or COVID-19 turns out to be a betacoronavirus in the same subgenus as the severe acute respiratory syndrome (SARS) virus (as well as several bat coronaviruses – more on that later), but in a different clade (evolved from a common ancestor). The structure of the receptor-binding gene region is very similar to that of the SARS coronavirus, and the virus has been shown to use the same receptor, the angiotensin-converting enzyme 2 (ACE2), for human cell entry. On reviewing the phylogenetic tree of several (103) strains of this novelty virus two different versions were identified: Type L accounting for 70% of the strains and Type S (30%) that are well defined by two different SNPs (called ”snips” or Single Nucleotide Polymorphisms) that show nearly complete linkage across the viral strains sequenced to date. Type L predominated the early Wuhan epidemic experience. Moreover, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

When further insight was gained into this little critter it was noted that there was a clear molecular divergence between SARS-CoV-2 and other related coronaviruses. Although there was only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated.

Delving deeper into this tiny life’s thief one finds another incredible piece of information: Phylogenetic analysis of the complete viral genome (29,903 (nt) nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China. The order of genes (5′ to 3′) was as follows: Replicase ORF1ab, spike (S), envelope (E), membrane (M) and nucleocapsid(N). WHCV has 5′ and 3′ terminal sequences that are typical of betacoronaviruses, with 265 nt at the 5′ terminal end and 229 nt at the 3′ terminal end. (nt = nucleotide).

The question then arises if viruses enter via a keyhole, then they must have a key, right? Actually, this little bugger has one, it has a spike protein. The spike protein is the major surface protein that it uses to bind to a receptor — another protein that acts like a doorway into a human cell. After the spike protein binds to the human cell receptor, the viral membrane fuses with the human cell membrane, allowing the genome of the virus to enter human cells and begin infection.

What is even more interesting and as Lewis Carrol termed, “curiouser and curiouser,” is the finding that the receptor-binding domain (RBD) of its spike protein was compared with those of SARS-CoVs and bat SARS-like CoVs. The RBD sequences of WHCV were more closely related to those of SARS-CoVs (73.8–74.9% amino acid identity) and SARS-like CoVs, including strains Rs4874, Rs7327, and Rs4231 (75.9–76.9% amino acid identity), that are able to use the human ACE2 receptor for cell entry. In addition, the RBD of the spike protein from WHCV was only one amino acid longer than the RBD of the spike protein from SARS-CoV. So perhaps we can call it “one degree of separation?”


One question that perplexed and instantly glommed on by the scientific community was that the five strains of the “common cold” coronavirus shared the spike protein to enter the human cell. The Wuhan Coronavirus only shared 90% of the homology. The four cold coronaviruses — named 229E, NL63, OC43, and HKU1 — all utilize humans as their primary hosts. However, the SARS-CoV-2 (COVID19) shares about 90% of its genetic material with coronaviruses that infect bats. And that is where they drew the conclusion that this Wuhan virus was a zoonotic disease jumping from bats that serve as universal reservoirs and as vectors to humans via their interactions. Further data showed that the Wuhan virus is most closely related to bat coronaviruses and shows 100% amino acid similarity to the bat. 

From where then?

In the initial epidemic in China, A third of the cases had direct exposure to the Huanan Seafood market. Fish, shellfish, wildlife, snakes, birds and several different types of meat and carcasses were sold at this market. The initial theory of animal to human transmission started to take a back seat in December 2019 when it was determined that the new virus differed significantly, raising questions about its origin. And subsequent investigations indicate that the first patient – who started experiencing symptoms as early as December 1, 2019, had no reported link to the market, or the other patients. Two reports from China emerged that found similarity between the flying bats and the Wuhan Coronavirus infecting the humans. The first study found a 96% similarity of the genetic makeup while the other found 89% homology between the two. Yet the problem remains; these similarities are still not enough to identify the direct spillover virus causing the current outbreak in humans. Earlier in bioRxiv preprint on SARS-CoV-2 found HIV-like genetic sequences, but online commenters pointed out that “the findings were at most a coincidence” and that research has since been retracted. However, a strange fact exists; in contrast to other retractions that usually happen when false data, omissions or acts of fraudulent commissions are committed in creating the research, this preprint, however, was withdrawn by the authors within 48 hours and before any questions were raised. Another interesting factoid that needs to be considered in the context of asymmetrical information available to date, is the proximity of the Level-4 Biosafety laboratory in Wuhan and the multiple breaches reported in the past several years augurs the mind into a conspiratorial web of deceit and deflection, but then thus far that is what it is. It is left to our imagination to conjure up stuff until facts are made opaque. However, proof from Zhou suggests that there is no evidence that recombination has facilitated the emergence of Wuhan Coronavirus. This needs further elucidation.

“Patient Zero”

So, where do we rest the origins of this little beast? “Patient Zero” has never been identified. In epidemiology “patient zero” has a significance because one can then build the blossoming tree of the spread from that single source. But none has yet been found. It is like a large blossoming tree with no roots. There are conflicting reports of the virus entering the human species in November 17, 2019, as reported by the South China Morning Post. This was a 55-year-old woman in the Hubei Province and perhaps she might also have been then first potential patient identified with symptoms in December 8, 2019. But neither of these reports suggest that she is “patient zero.” The root of the blossoming tree is more like moss on a tree trunk.

Mechanisms of spread:

Mechanisms of spread are fairly simple and easy to comprehend:
Using real-time reverse transcriptase polymerase chain reaction (RT-PCR), investigators detected COVID-19 RNA in lung wash (14 of 15 samples; 93%), sputum (72 of 104; 72%), nasal swabs (5 of 8; 63%), lung biopsy (6 of 13; 46%), throat swabs (126 of 398; 32%), feces (44 of 153; 29%), and blood (3 of 307; 1%). The 72 urine specimens all tested negative.
Further, the indirect transmission seemed to arise from fomites:
“Hence, the rapid spread of SARS-CoV-2 [the COVID-19 virus] in our study could have resulted from spread via fomites (e.g., elevator buttons or restroom taps) or virus aerosolization in a confined public space (e.g., restrooms or elevators),”


So how exactly does this Wuhan Coronavirus manifest it’s presence in the human body? By now there are several pamphlets that compare and contrast this virulence to that of the common cold and the flu, but the symptomatic hallmarks of its invasion are as follows:

Fever in 99%
Fatigue in 70%
Dry cough in 59%
Anorexia in 40%
Myalgias in 35%
Dyspnea in 31%
Sputum production in 27%

The informed data from China and elsewhere suggest that:
Mild (no or mild pneumonia) was reported in 81 percent.
Severe disease (eg, with dyspnea, hypoxia, or >50 percent lung involvement on imaging within 24 to 48 hours) was reported in 14 percent.
Critical disease (eg, respiratory failure, shock, or multiorgan dysfunction) was reported in 5 percent. Requiring ventilatory support has an almost 91% fatal results.

The Case Fatality Rate was 2.3%; no deaths were reported among noncritical cases. However, depending on the aggressive mitigation strategies utilized by various governments and localities have been able to show a lower CFR at 0.9%.

WHAT to do?

There are 3 (Three) very simple and practical preventative measures:
Wash Hands with Soap & Water or >65% alcohol after touching surfaces and before preparing, serving and eating foods.
Avoid crowds and Avoid touching any part of the face, especially the nose, eyes, ears & mouth. Maintain good Respiratory Hygiene, eg. Sneeze or cough into elbow or Kleenex.
Disinfect all surfaces before and after human contact.

Remembering that this Wuhan Coronavirus like other viruses is and like other RNA viruses, “accumulate mutations at a rate one million times faster than human DNA [does]. It gives them the ability to survive through mutation against an immune response,” Estimating how easily a virus spreads, virologists calculate its "basic reproduction number," or R0 (pronounced R-nought). R0 predicts the number of people who can catch a given virus/bacterium/parasite from a single infected person. R0 for SARS-CoV-2 is estimated at about 2.2, meaning a single infected person will infect about 2.2 others, on average. By comparison, the flu has an R0 of 1.3. The other issue to be aware of in viral business, is that it may go into a state of quiescence for a period of 4-5 months in the summer and return in the late fall and winter as the cold and social proximity increases. 


No known treatment exists at this time. Certain medications have been tried in other SARs Coronavirus (unrelated to Wuhan Coronavirus) with some success. Chloroquine has been used in South Korea and even in China with limited success. The data dates back to 2008 when in-vitro experiments showed inhibition of the virus in the laboratory.
And also in vivo: . Even using ACE Inhibitors to thwart the gateway access via ACE-2 have met with failure. (ACE inhibitors are used extensively in treating Hypertension and Heart Disease).


Prevention through social interactions and via an active vaccine seems to be the foremost mechanism to mitigate this tiny but dangerous foe. Targeting the protein spike of the virus seems to be the current thrust. Blunting the spike should blunt the entrance into the human cells and thus prevent spread. At least for the near future, until the virus mutates to change the spike. Remember it needs a host (animals, mammals or humans) to survive. And given that there are more than 120 million species of viruses and trillion and trillions of the total numbers. They survive via their ability to replicate and mutate inside the host. Eventually, parts of the virus will find a place in our genome as an Intron and live in harmony, creating isolated events of genetic misdemeanors as genes jump close in proximity to its location.

If you were intrigued to read till the end, then I beseech you to opine and as Walt Whitman asked, “What will your verse be…?” please write your verse to this human endeavor. 
Thank you!

REFERENCES: Wu, F., Zhao, S., Yu, B. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020).
Zhou, P., Yang, X., Wang, X. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020)

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