Tag / #coronavirus

by Doctor Sophia

Mutation of virus is as sure as we pay taxes.

Viruses are efficient creatures that borrow human cells to reproduce themselves without our consent.

From the perspective of the virus, its function and purpose are to replicate and infect the host as much as they can and fast as they can.

Image of Coronavirus from CDC/Dr. Fred Murphy

Mutations in the virus’s genome are normal and guaranteed as it is copied over and over. The GISAID database identified thousands of changes along the genome. Viruses are clever and naturally select mutations that can result in a strain to be more transmissible or impervious to proposed vaccines. University College of London Genetics Institute researcher Lucy van Dorp is a co-author of a study that identified more than 12,700 mutations in the SARS-CoV-2 virus.

The naming of these variants is done by WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers in the established nomenclature systems for naming and tracking SARS-CoV-2 genetic lineages by GISAID, Nexstrain and Pango. The letters of the Greek Alphabet, i.e., Alpha, Beta, Gamma, Delta is chosen to be more practical for discussion by non-scientific audiences.

The working definition of Variant of Concern (VOC)

VOC of SARS-CoV-2 are Alpha, Beta, Gamma and Delta variants which meets the definition of a Variant of Interest (VOI) and one or more of the following changes:

  1. Increase in transmissibility or detrimental change in COVID-19 epidemiology,
  2. Increase in virulence or change in clinical disease presentation,
  3. Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

The working definition of Variants of Interest (VOI)

VOI of SARS-CoV-2 variants have genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape and to cause significant community transmission or multiple COVID-19 clusters to suggest emerging risk to global public health. VOI includes Eta (B1.525), Iota (B1.526), Kappa (B.617.1), and Lambda (C37) from various countries. Recently the Lambda variant has met the definition of VOC. 

So far seven VOC have surfaced throughout the globe:

B.1.1.7, (Alpha) first detected in the U.K. is known to be 50% more transmissible and found in Florida, Michigan and Colorado. 

P.1, (Gamma), first detected in Brazil and Japan, and the U.S. has reported 323 cases of this variant.  

B.1.351, (Beta) first detected in South Africa, again 50% more transmissible and the U.S. has reported 224 cases of this variant. 

B.1.427, first detected in California, 20% more transmissible, and 

B.1.429, another variant first detected in California, 20% more transmissible. 

All these variants do not have clear information whether the various vaccines are capable of protectinginfection or have significant effect on neutralization by antibodies. 

The trend appears that the states which had successful vaccine delivery seem to have decrease in death rate by COVID. 

B.1.617 (Delta variant), originated from India.

C.37 (Lambda variant), originated from South America, particularly Peru.

The coronavirus is composed of five different components: envelope small membrane protein (E), membrane protein (N), spike glycoprotein (S), nucleoprotein (N) and genomic RNA. 

The virus’ genomic RNA is a complete set of genetic instructions that is written in 30,000 “letters” of code composed of A, T, G and C.

Within the genome are various parts: see the diagram below.

Below is the process of how the virus enters into the host cell, which in this case is humans.
Schematic of the SARS-CoV-2 S protein and the mechanisms how virus enters into human cells to replicate themselves using human engines.  
a. The schematic structure of the S protein. 
b. The S protein binds to the receptor ACE2. 
c. The binding and virus–cell fusion process mediated by the S protein. 
d. The life cycle of SARS-CoV-2 in host cells. By Y. Huang et al Acta Pharmacologica Sinica (2020) 41:1141–1149; https://doi.org/10.1038/s41401-020-0485-4

Pfizer and Moderna vaccines are made from mRNA in the different spike protein area, a new type of vaccine to protect against infectious diseases by triggering an immune response unlike many vaccines which is made from weakened or inactivated viruses. Vaccines trigger immune response, which produces antibodies, which protects us from getting infected if the real virus enters our bodies. Before releasing these vaccines, both companies conducted rigorous studies and the vaccine effectiveness is proven to be 95% from the original coronavirus before mutations when tested among 30,000 people ages older than 18. This means 5% or less still can have a chance to get COVID-19 infection. While the vaccine is not effective in 100%, it is still excellent in preventing infection and at least subsiding its significant symptoms and deaths. 

Will the virus escape vaccines?

If the virus changes by mutation substantially, particularly the spike proteins, then it might escape a vaccine. The race against the virus mutations is on. As the entire population gets vaccinated, we seek herd immunity; likely ~70% of population vaccinated. The goal is to slow transmission globally and slow the clock. If people do not get vaccinations, the COVID-19 pandemic prolongs. We do not have to see any more additional deaths beyond 609,000 people. When the virus mutates increasingly, more vaccinated people will be susceptible to infection because the vaccines were not made from the variants. Time is of the essence to race against virus mutations by vaccinating most people. This is the only way to win over the war against the coronavirus.


God was with the science and scientists who developed these effective and great vaccines in the US. Both mRNA vaccines are superior to any other vaccines known from other countries including China and Russia. We can celebrate superior vaccine science in America and be thankful to live in such a great country.

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Read Dr. Apple’s fictional novel based on real events at:

https://www.amazon.com/dp/B08P7486XX

  • Ms. Apple is a practicing pathologist…she brings a perspective to the effect of the pandemic that unfortunately is seldom seen, and millions would be enriched and informed by her unique vision…The story begins with a woman intern pathologist arriving on Hart Island to an unimaginable scene of mass burials. The web of relationships and events expands to an international scope. This is a medical but personal story, not a political one. I hope everyone can read and share this book, whose proceeds are going to charity. – Amazon book review
by Doctor Sophia

Let’s first live and then talk about injustice!

Blog #8: June 7, 2020

Year of the Rat, 2020! It is indeed an amazing and extraordinarily difficult year thus far. The traumatic effects of the COVID-19 pandemic with a death toll of 118,000 as of today (but who is counting anymore?), unemployment rate hitting 20% (a record high surpassing the great depression in 1932), and now the national riots.

Recent murders of George Floyd, Breonna Taylor, and Ahmaud Arbery in our country have laid bare the realities of institutional racism. America is built on the principle of all people are equal, and deserve to be treated fairly and respectfully. The commitment to equality, diversity and inclusion in order to positively impact human rights and to reduce disparities are shared by most of us. We must reject injustice, violence and racism and strive to heal the division. It is powerful to see the protestors in all US major cities, calling out for justice and chanting, “Black lives matter!” And I would join the voice, “Hear, hear!”

I saw the image of a pool party in Missouri’s Lake of the Ozarks over Memorial Day weekend and cringed in disgust with people not respecting social distancing and potency of the coronavirus.  Now, news has reported that some who attended the pool party have the coronavirus despite having temperature checked before getting admitted to the party.

Similar images of crowds are seen in all major cities in the US day after day, but now, the images are protesters marching, not the pleasure seekers, with or without facial masks, disrespecting social distancing. But are we not in the midst of a pandemic? Gathering without social distancing and not wearing facial masks are a real concern. It will have a negative impact on our fight against COVID-19. Resurgence due to mass gatherings of protestors are guaranteed to bring a second peak of COVID-19, and it will probably have even a worst peak with a death toll of another 118,000 people dead, all too soon.  All the good works we have done for the last two months by lockdowns caused a huge unemployment and economic depression, and these sacrifices will have no fruit in return.  This requires health care workers to sacrifice even more. We have not complained much thus far because of our commitment to take care of the sick.  

Both scenarios have people gathering without social distancing, but this time I see myself cringe for a different reason. I see the protestors take their chances and risking their own lives to come out to speak, for them it is a life and death situation. It’s either coronavirus or police brutality to lose one’s own life. And when I see the people coming together regardless of their own colors of skin, it is very powerful and moving. 

Then, I think about the what ifs. What if I was down on the street with my neck pushed down by a Caucasian policeman for almost 9 minutes when I am pleading for my dear life to breathe? What if I died instead of George Floyd? Will the nation become outraged for me? Martin Luther King Jr. said, “The ultimate tragedy is not the oppression and cruelty by the bad people but the silence over that by the good people.” The situation becomes another story. I would like the people to come out and say something to the world protesting, in spite of the pandemic. It makes the whole thing more personal. The voice of collective people saying, “This is not right, enough is enough” is comforting. 

But then there are the opportunists. The looting; why do these come together? It is absolutely wrong, no matter how one explains it.  

What about the negative impact on the protestors? Killing and injuring both sides; lives of police, firefighters, and the protestors. Both are unwelcomed downstream effects.  Is the anger the appropriate emotion to use at this time?

Emotions put aside, can we come together first in fighting a pandemic? Many people do not realize the actual effect of the virus, a silent and deadly killer of COVID-19, because they do not see the killer first hand. Some believe that the media and the government made it up. But I saw the impact on our morgue with piled-up bodies in a hospital.  The media cannot come and show what I have seen because they cannot come inside to reveal what’s really happening in the hospitals with COVID-19. 

The question really boils down to, “Is the first amendment more important than a pandemic now?”  My personal answer is both are equally important. But there should be a sequence. First, pandemic and then, the first amendment. Let’s first live and then talk about injustice!

Let’s not give the virus the upper hand to control the fate of our humanity. Let’s try to have the rest of 2020 without losing additional hundreds of thousands of lives by the virus.  

The injustice I see in this country is as familiar as a dear friend, and this does not occur only in racism, but also in gender discrimination. Crying out for justice among all races has a powerful effect, but when it comes to gender issues, more than half of the population suddenly becomes shy and quiet. As a female physician in this country, this deeply rooted gender discrimination is very evident. Yet, everyone hesitates to stand up and fight for they will soon belittle the women who spoke up for the equality in pay and opportunity, for instance. The unwelcome inequality and ignorant complacency seem to be with us, some consciously and some unconsciously. 

But whatever our differences are, can we first fight against a pandemic together? Anger leading to violence and looting is dangerous and deadly at this time. Even COVID-19 is showing injustice in racism, killing African Americans and Latinos disproportionately more than other races. There are understandably predominant populations of African Americans protesting. Spreading the virus during the protesting will have a negative impact on the African Americans who are already dying disproportionately.  Then, these people visit their elderly parents, unintentionally killing their own. 

God hates these things; violent people, haughtiness, lying, murdering, scheming, eagerness to do wrong, a false witness, stirring up discord, and proud people. (Proverbs 6:16-19)

Where is God in all these? I think God is crying now. God is saying, “What have you done? Listen! Your brother’s blood is crying out to me from the ground!” (Genesis 4)