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:
- Increase in transmissibility or detrimental change in COVID-19 epidemiology,
- Increase in virulence or change in clinical disease presentation,
- 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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Finally the mutation evolution, categorizations and imminent risks are explained.