Covid-19 Pandemic: Part 4: Understanding the Disease-Causing Virus & Their Variants

Published in January 2022

Having grasped the clinical features and diagnostic tests and their interpretation of results of the tests, in this paper we have discussed the nature of the original virus (Sars Cov-2) and how it enters the cells and causes disease. Various components of the virus like spikes, membranes and other parts are explained. Then the variants of the virus and how they came into existence and the nomenclature is discussed. Details of delta and omicron variants are discussed in the simple language.

We discussed historical context of Covid-19 pandemic, followed by the signs, symptoms and how it affects our body and then various diagnostic tests. In this month’s edition we discuss disease causing viruses and their variants including most recent and threating Omicron Variant of the virus.

Virus Causing Covid-19 Pandemic

COVID-19 is caused by a virus called SARS-CoV-2. It is part of the coronavirus family, which include common viruses that cause a variety of diseases from head or chest colds to more severe (but rarer) diseases like severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). So, our Covid-19 virus is known as SARS-CoV-2.

The word corona means crown and refers to the appearance that coronaviruses get from the spike proteins sticking out of them. The spike protein is the part of the virus that attaches to a human cell to infect it, allowing it to replicate inside of the cell and spread to other cells. Some antibodies can protect you from SARS-CoV-2 by targeting these spike proteins. These spike proteins can change over time and thus also change the characteristics of the virus and effectiveness of the vaccine! This mutation happens when viruses continue to get new hosts and transmission cycle continues.

What Do We Mean by Variants of Virus?

The virus that causes COVID-19 is constantly changing, and new variants of the virus are expected to occur. This is called mutation. Sometimes new variants emerge and disappear. Other times, new variants persist. Numerous variants of the virus that causes COVID-19 are being tracked in the United States and globally during this pandemic. Since this is fast changing, information about variants also gets updated with the time.

What is Variant of Concern or Variant of Interest?

Variant: A variant is a viral genome (genetic code) that may contain one or more mutations. In some cases, a group of variants with similar genetic changes may be designated by public health organizations as a Variant of Concern (VOC) or a Variant of Interest (VOI) due to shared attributes and characteristics that may require public health action.

Variant of Monitoring (VOM)

Variants that are being monitored are called Variant of Monitoring and there are 10 such variants that are being monitored currently.

Variant of Interest (VOI)

A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity is called a variant of interest. Lambda and Mu variants fall in this category. Others from this category moved to Variants of concern when they became more serious.

Variant of Concern (VOC)

A variant for which there is evidence of an increase in transmissibility and evidence of more severe disease is designated as Variant of Concern. When they reach to relatively high level and matter at the public health level, World Health Organization declares them as variants of concern. Two variates are of concern by now in USA while five are globally recognized and they are alpha, beta, gamma, delta and omicron. The two that are important in USA are Delta Variant and Omicron Variant. We restrict our discussion to only these two.

Delta Variant (B.1.617.2)

First identified in India in late 2020, and by that time vaccines had arrived. It was designate as Variant of Concern by World Health Organization on 11^th May 2021. Delta swept rapidly through India and Great Britain before reaching the U.S., where it quickly surged. It was the predominant SARS CoV-2 variant, accounting for more than 99% of COVID-19 cases until end of November and leading to an overwhelming increase in hospitalizations in some states. See figures.

The Delta variant is more contagious: The Delta variant is highly contagious, more than 2x as contagious as previous variants.
Some data suggest the Delta variant might cause more severe illness than previous variants in unvaccinated people.
People infected with the Delta variant, including fully vaccinated people with symptomatic breakthrough infections, can transmit the virus to others.
Fully vaccinated people with Delta variant breakthrough infections can spread the virus to others. However, vaccinated people appear to spread the virus for a shorter time

Good thing is that vaccine is quite effective in preventing infection by delta variants as well as SARS-CoV-2 infection

OMICRON, the Latest and More Powerful Variant: (B.1.1.529)

On November 24, 2021, a new variant of SARS-CoV-2, B.1.1.529, was reported to the World Health Organization (WHO). This new variant was first detected in specimens collected on November 11, 2021 in Botswana and on November 14, 2021 in South Africa.

On November 26, 2021, WHO named the B.1.1.529 “Omicron” and classified it as a Variant of Concern (VOC). On November 30, 2021, the United States designated Omicron as a Variant of Concern, and on December 1, 2021 the first confirmed U.S. case of Omicron was identified and by Dec 19. As of Dec 15, 2021 it is reported from 90 countries (as of Dec 20) but many more may have it spreading and spreading fast. CDC reports on Dec 20, 2021 that 73% of total cases in US that CDC studied are now Omicron variant infection and thus has become major variant in USA and most likely across the globe. It has out crowded the delta variant.

It is believed to be 50 times more infectious and also believed to be mild compared to other variants in causing disease and also believed to be not prevented by vaccine. It is also more likely to reinfect those who had earlier Covid-19 disease in the past. More data are being collected and more information will come in the coming days. With the holidays and people’s travel and social events taking place, Omicron infection would spread much faster in the coming days. Being vaccinated, boosted, continue to wear masks, avoid crowding and maintain social distance, continue to was hands and safer coughing and sneezing continue to remain crucial points.

As of now, what we know for treatment, prevention and protection of Covid-19 disease, stands true at public health level and we need to focus and continue to do what we have been doing to prevent the disease. All the diagnostic tests we discussed last month detect and are valid for all the variants of the virus including Omicron.

Coming Up

In the coming month, we will discuss what we can do to prevent Covid-19 infection for ourselves and to prevent the spread in the community. In the future editions we will be discussing various vaccines, their benefits, availability and myths circulating around them.