Tag / #Covid

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

Thanksgiving. What’s on God’s mind?

November 20, 2020
In the Book of Amos, Chapter 4: 1-13, God speaks through his prophet Amos that He sent several hardships and tragedies to wake up the people of Israel. God is humorous calling the privileged women of Israel, “Listen to me, You Fat Cows living in Samaria.” God was referring to the women who are pampered, sleek and well fed who selfishly oppress the helpless in order to support their lavish lifestyles. The Lord God sent famine, lack of rain, striking farms and vineyards with blight and mildew, locusts devouring figs and olive trees, plagues, killing young men in war, the stench of death filling the air and still the people of Israel did not return their hearts to God who shaped the mountains, stirs up the winds and reveals His thoughts to mankind. He turns the light of dawn into darkness and treads on the height of the earth. The Lord God of Heaven’s Armies is His name!

Almost two days, we had a dense fog in the mornings in Southern California. I couldn’t see just 6 feet away. Just a month ago, we had severe fires close to our mountains with eerie orange sky with soot on the very street I cannot see due to fog. 

Photo by Sippakorn Yamkasikorn from Pexels

As the Thanksgiving Holidays approaches, I am thinking and looking back what a tumultuous year this 2020 has been, thus far.  God allowed the world to experience the pandemic with a novel coronavirus with the death count of 1.34 million as of today and 55.6 million infections. The US leads the way with the death count of 252K and 11.8 million infections. It is still unbelievable that US is the top country to be affected by this unfortunate COVID-19. We are used to leading the technology, medicine, economy, wealth and respect for human rights and democracy but not in the viral infection rate, and I am embarrassed about this.

This year, we had seen the invisible and formidable virus affecting nondiscriminatory way; now we see our immediate families, friends and coworkers getting infected by the virus. We had more fires than any other years in southwestern states. We had more hurricanes in eastern states than any other times and we even ran out of naming the hurricanes and used the final alphabet letter Z, zeta 2020. We had the world’s largest hornet called Asian Giant Hornet, better known as murder hornets in Washington state alarming to infest the country. This is reminding me of the Amos time when God sent sequential calamities. 

Independence Hall, PA, site of the ratification for independence

These incidences are on top of the usual natural calamities such as tornadoes and floods, not to mention our man-made tragedies of racial discrimination outbreaks and violent demonstrations and looting. And to top it off, the election year for presidency manifested how our country is divided and the first time ever in 244-years-old history where our very definition of democracy is questioned by the current president not conceding since the Declaration of Independence was ratified by the US Second Continental Congress on July 4, 1776.

Is God saying anything to us? Is He saying return to me as He said through Amos for the people of Israel? Are we still ignoring God because we did not get the message? Is God allowing all these calamities for us to turn our heads toward Him? It is impossible to know what is in God’s mind.  

With Thanksgiving holidays coming around the corner,  I can reflect and even the very question what is the meaning of all these? What a year 2020 has been thus far! Still, I have this life, the miracles of time that I breath in this very life is not my own to waste. Each day is precious. Tomorrow is not promised nor guaranteed. And I am thankful for just the fact I can breathe.

Who can possibly fathom what’s on God’s mind. I do not know the meaning of all the happenings in 2020. What I do know is I have life today and I will choose to listen to what God has to say to me today with thanksgiving heart.