The Discovery of Lineage B.1.1.7, or Alpha, the First Major Variant of SARS-CoV-2

National Institute of Allergy and Infectious Diseases, an agency of the National Institutes of Health - via Wikimedia Commons.

Note: this piece was written in December 2020, well before the Delta, Omicron and other future lineages. Please note that the statistics mentioned in this piece will be inaccurate as a result of dated information. For example, there are a lot more than two million COVID deaths now; please keep this in mind as you read. Thank you.

For the last year, we have seen a virus forever alter our way of life. Typical work settings have evolved from offices to living rooms. Typical five day school settings have become zoom calls. Typical travel anywhere for vacations or jobs has become non-existent, and nearly 2 million people who have brothers, sisters, parents, children: kindred who experienced love and hate, anger and excitement, fear and confidence, discomfort and pleasure, hunger and thirst, dreams and goals, who died from a deadly virus that inexorably militates itself against us. In our struggle, we have pursued a vaccine that we believe will mitigate the oppression – the death, economic turmoil and mental health collapse resulting from this virus could be dramatically reduced with a single – or a double – shot. 

Unfortunately, when it comes to creating vaccines, evolution does not help us. With rapidly reproducing viruses, mutations can be common; some of these mutations could also strengthen the virus against us. A similar thing has happened with the coronavirus. A new strain, or a variant under investigation (VUI)-202012/01, has caused a massive outbreak in the United Kingdom; as a result, Prime Minister Boris Johnson announced a strict lockdown on London and its surrounding areas, and many countries also restricted travel to and from England. Let us learn about VUI-202012/01.

A “Novel” Novel Coronavirus

In October, health officials in the United Kingdom detected a unique coronavirus strain from a test sample conducted in September. Some coronavirus variants have been discovered many times since the beginning of the pandemic, but the new one is concerning for a few reasons:

• While most SARS-CoV-2 variants have few mutations, B.1.1.7 has 23. Health officials had yet to see such a significant number of mutations, many of which seriously affected the activity of the virus. 

• The virus was responsible for a third wave in the pandemic in the United Kingdom. Boris Johnson initiated an executive order initiating a stay-at-home order in late October, intending that it expire on December 2nd – which did not happen. The first two coronavirus waves lasted for around a month – assuming mitigation measures are taken seriously. However, the new COVID-19 variant quickly dominated infections in southeast England, where most cases in the country have occurred. Not long after the variant was discovered, 50% of the positive COVID tests conducted in southeast England that were sequenced by England’s public health departments came out positive for the B.1.1.7 variant. The new variant resulted in a COVID wave more serious than those before it in the United Kingdom.

• There is some evidence that this new variant of COVID is much more transmissible than the original strain, which is already significantly more transmissible and deadlier than the flu. Indeed, these are merely preliminary reports – more research must be done to conclude whether this new strain’s increased spread is due merely to irresponsibility or to viral dynamics. The World Health Organization noted the apparent transmissibility of B.1.1.7 on its website:

• “Preliminary reports by the United Kingdom are that this variant is more transmissible than previous circulating viruses, with an estimated increase of between 40% and 70% in transmissibility (adding 0.4 to the basic reproduction number R0, bringing it to a range of 1.5 to 1.7).”

Although, as of December 22nd, 2020, only 1108 cases have been identified, it is evident that the new wave results from the new variant.

On December 23rd, 2020, the United Kingdom discovered yet another COVID strain containing more mutations in a test conducted on a COVID victim who traveled from South Africa. Very little information is known on the variant so far, but I would recommend that you all pay closer attention for some time, for more information will reveal itself over the coming weeks.

The Mechanics of Viral Mutation

Before we explain how this new variant may or may not ruin everything, let’s first understand how viruses mutate:

Viruses are not alive based on the biological standards of life – viruses cannot themselves reproduce; they need a host to replicate.

Coronaviruses infect cells using an entry vehicle known as a “spike protein.” The protein connects with a receptor on the host cell and injects its genes into the cell. The cell, therefore, will contain and replicate the genes – which exist in an RNA structure – thereby building more viruses. In the cell, the virus replicates as fast as many bacteria.

With so much reproduction and an extremely low – though not zero – error rate, some mutation is inevitable. Mutations often are the result of a mistake by RNA polymerase, which replicates the genes in RNA viruses like SARS-CoV-2. RNA polymerase errs, on average, once every 300,000 bases – letters of RNA or DNA; for RNA, adenine, guanine, cytosine, and uracil; for DNA, adenine, guanine, cytosine, and thymine. Although RNA polymerase has an astronomically low error rate, mistakes occur often because of the sheer magnitude of replication. Nevertheless, there are methods proteins use to mitigate these errors, but those, too, are not perfect. Therefore, some mutations may occur without any mitigation by proteins. With B.1.1.7, 23 mutations went unfixed.

Ramifications

While this new virus is incredibly troublesome for global health, it is no reason to panic – especially with regards to vaccine efficacy. The vaccine does work with this new strain of coronavirus.

Conversely, the new variant is very detrimental to our recovery. With a new virus that is even more infectious than ones before it, countries that do not implement strict mitigation standards will be hit the worst, much worse than before.* The people of the United Kingdom will struggle with a virus that may overwhelm hospitals and kill many. The United Kingdom made the right choice in shutting down to curb the spread. The road will tread long, even with a vaccine, but the lockdowns and mitigation precautions may work to delay the spread until vaccines are widely available.

For now, we can only speculate on how this variant will affect us. There is still no indication that our recovery overall from COVID will be affected by this new virus, but there is much indication that the number of people infected and dead from the virus will increase relative to what was expected. There is some evidence suggesting that this variant is 40-70% more transmissible than the original COVID-19, which means that this new virus may require 40-70% stricter mitigation standards than the previous – for the same level of spread.

Effects on the United States

The United States is incredibly vulnerable when it comes to dealing with the coronavirus.

As of yet, the United States, having 4.2% of the world’s population, also has 23.5% of all infections and 18.9% of all deaths from COVID-19.

331 million people live in the United States; 448 million people live in the European Union and the United Kingdom. The total case count for the United States is 18,649,350, as of Christmas Eve, and the total case count for the European Union and the United Kingdom is 16,247,249. The United States has a case rate of 5,638.3 cases per 100-thousand people, while the European Union and the United Kingdom have a combined case rate of 3,626.6 cases per 100 thousand people. Simply enough, the United States has been significantly less restrictive with lockdowns and other measures, resulting in higher case and death rates.

The Americas saw delayed COVID-19 outbreaks because of their land disconnect with the rest of the world, which was where the coronavirus originated. As a result, while Europe toiled with the virus in February, the United States had much more time. For two months after the pandemic began, the United States had very few cases; and most of the recorded infections originated from Americans who went on the Diamond Princess cruise, traveled to Europe or Asia, or had close contact with infected family members. 

Although it had more time to prevent COVID-19’s spread, the United States struggled later in the pandemic after late lockdowns and mask ordinances. Early reopening and mass gatherings also kept US case counts up, even as European cases continued to fall.

66.7 million people live in the United Kingdom, and 331 million in the United States, and while the United Kingdom was reporting around 500 cases a day in July, the United States was reporting 50,000 to 70,000 – the United States, at the time, was reporting 20 cases for every case in the United Kingdom, a staggering difference.

Therefore, the United States will be particularly vulnerable to the spread of the new variants. The United States, with a healthcare system that is far more exclusive – due to expenses and access – than European countries, has already seen the virus completely derail its system. In many states, like California, ICU availability is 0%, and hospitals are sending patients with more mild severe cases – who would otherwise be in the hospital – home. Ithe United Kingdom, however, they face similar case rates to the United States, they have a greater testing capacity, more beds and better ICU access; they have, so far, had much less trouble responding to the virus than the United States. Transmission may increase with this variant, perhaps leading to overwhelmed hospitals and actual death panels.

The US must take this virus seriously before we hit 1,000,000 COVID deaths,** a terrible milestone. The US is currently at 329,055 deaths, half that of American deaths from the Spanish Flu Pandemic, which killed 50-100 million around the world. If we continue to laugh off this virus, we will soon and easily reach 650,000 deaths, making our irresponsibility the worst pandemic in American history.

Wrapping it up

Although this entry is ominous, it is a testament that science may sometimes carry foreboding or depressing truths – that, for example, the pandemic is set to continue, at least until the vaccine becomes widely available. As always, take care and stay curious, everyone.

* In the original text of this piece, I wrote “and will be essentially erased off the map” regarding countries that do not respond to the new variant with strict mitigation protocols. This is a blunt overreaction, as I see in hindsight. I have adjusted the sentence in accordance with the variant’s actual effects on countries with limited mitigation protocols; countries with poor protocols, like the United States, were affected much worse by the variant than countries like Canada, which had much more stringent implements.

** The United States has already hit 1,000,000 COVID-19 deaths; as indicated before the entry, the data in this piece is outdated (written in December 2020). Therefore, it does not accurately represent the current stage of the pandemic.

If you have any questions, comments, or corrections, please comment on this post or email learningbywilliam@gmail.com with your concerns. Thank you.

References

01. (2022, May 01). Retrieved from https://en.wikipedia.org/wiki/VUI_–_202012/01

Al Jazeera. (2020, December 24). UK detects second COVID mutation, linked to South Africa. Retrieved from https://www.aljazeera.com/news/2020/12/23/uk-to-widen-covid-lockdowns-as-new-strain-from-south-africa-found

Challenge 4: How do mutations cause viral evolution? (n.d.). Retrieved from https://medicine.yale.edu/coved/modules/virus/evolution/

Cuffari, B. (2021, February 24). What are Spike Proteins? Retrieved from https://www.news-medical.net/health/What-are-Spike-Proteins.aspx

RNA Viruses. (n.d.). Retrieved from https://www.sciencedirect.com/topics/neuroscience/rna-viruses

Team, F. T. (2020, December 23). UK health officials announce 2nd new COVID-19 strain. Retrieved from https://www.fox2detroit.com/news/uk-health-officials-announce-2nd-new-covid-19-strain

Viruses and Evolution. (n.d.). Retrieved from https://www.historyofvaccines.org/content/articles/viruses-and-evolution