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The Super-Spreader Strain of Coronavirus

Published on Dec 26, 2020 and last reviewed on May 26, 2022   -  8 min read

Abstract

A variant of SARS-CoV-2, the virus that causes COVID-19, is spreading fast in parts of the UK. Read how this variant can affect you.

Contents
The Super-Spreader Strain of Coronavirus

The novel Coronavirus (SARS-CoV-2), the virus that has claimed millions of lives worldwide in just a year, is said to have undergone a lot of mutations since it first emerged. This made scientists conduct extensive epidemiological and virological analyses. These investigations and studies of the viral genome identified that the majority of cases were due to a strain of the deadly Coronavirus. This variant was named iVUI-202012/01 (the first "Variant Under Investigation" in December 2020) or “SARS-CoV-2 VOC 202012/01” (the first variant of concern from 2020, December). The variant belongs to Nextstrain clade 20B, GISAID clade GR, lineage B.1.1.7. This strain was identified to have multiple mutations in the spike protein and other genomic regions. We already know that viruses constantly mutate and change, leading to the emergence of variants. But initial data carried out in the UK suggests that this strain is possibly more transmissible than the variants that are already circulating. It is estimated to be up to 70 % more transmissible.

The European Center for Disease Control (ECDC) has estimated this variant to be more transmissible and to affect the younger population. 17 changes or mutations have been identified in this variant, and the N501Y mutation in the spike protein is the most significant as the virus uses it to bind to the human ACE2 receptor. Mutation in this spike protein may make the virus more infectious and spread more easily between people.

Though this strain is said to be more transmissible, there is still no evidence that suggests that it can result in increased infection severity. Some cases due to the variant have been reported in Denmark, Netherlands, and Belgium too. With COVID-19 vaccines getting approved and showing positive results, the news of this strain has resulted in panic and a lot of questions, such as - Will the vaccine work on this strain? Is there an increased health risk? Will the treatment, isolation, and quarantine protocols change? We have tried to answer most of the questions about the impact of this COVID-19 variant that has made the UK impose lockdowns and close its borders again.

Firstly, What Does Mutation Mean?

A change in a microorganism's genetic material is called a mutation. A virus, when it enters our body, makes millions of copies of itself and then infects others. Not all the copy it makes is identical. These small errors accumulate as the virus spreads and gets replicated again and again.

How Did SARS-CoV-2 Mutate?

All viruses mutate. The mutations in SARS-CoV-2 may be due to random errors occurring when the virus replicates in the body. This error can be due to antivirals or recombination (genetic shuffling). Signs of genetic shuffling have not been detected in this virus.

Most mutations that occur in a virus do not majorly impact the nature of the virus. Since the pandemic started, thousands of mutations were noted, but none altered the virus's ability to survive and reproduce. But sometimes, like in the case of SARS-CoV-2 iVUI-202012/01, a certain combination of mutations may work in favor of the virus, changing some of its original characteristics. Once if the mutation is favorable, viruses with that specific mutation increase in frequency.

As similar mutation patterns were seen in chronically COVID-19 infected patients with weak immune systems, scientists believe that chronic infection in a single patient might be the reason behind this mutation. Meaning the immune response was not strong enough to kill the virus, allowing it to evolve. This would explain the multiple mutations, but there is still no proof of this.

The other possibility is the virus getting mutated in an animal and then infecting humans with the mutated virus. This was the cause of the emergence of a variant in Denmark during transmission among mink that caused multiple spike protein mutations.

It is also possible that the variant emerged in a country with almost nil or very low viral sequencing. The chances of this are less as random mutations due to the circulation of the virus do not explain the high proportion of mutations in the spike protein. Mutations to circulate for so long and go undetected are is highly unlikely due to global travel patterns.

What Do We Know So Far About This Strain?

The strain was noted to have 17 mutations (changes), including eight mutations in the outer spike protein, when compared to the original SARS-CoV-2 virus discovered in Wuhan, China, a year back. This variant, called SARS-CoV-2 VUI 202012/01, is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) and mutations in other genomic regions. One of the mutations (N501Y) is located within the receptor-binding domain (a key part of the virus's spike (protein). As the spike protein plays a vital role in the virus entering our cells and multiplying, these changes in the spike protein may theoretically make the virus more infectious and might allow it to spread more easily between people. Primary results suggest that this variant is significantly more transmissible than previously circulating variants, with an increased reproductive number and increased transmissibility of up to 70 %.

The other notable changes in the variant include:

  1. 69/70 Deletion - Such double deletion has occurred various times, leading to a change in the shape of the spike protein.
  2. P681H - It is another mutation seen in the spike protein, which has also emerged spontaneously many times.
  3. ORF8 stop codon - This is not a spike protein mutation but a different gene, and the function of which is not known. A strain with this mutation emerged in Singapore and disappeared on its own.

The mutations seen in this strain are rather large in number when compared to other variants we have in circulation worldwide. The genetic profiles of this variant have also been sequenced in the UK, Denmark, Australia, and the Netherlands. The discovery of this strain in a few countries does not reflect this virus's true distribution.

Is This Variant Similar to the South African Variant?

The national authorities in South Africa, on 18th December 2020, announced a variant, 501Y.V2 (due to the N501Y mutation), that is rapidly spreading in South Africa. The SARS-CoV-2 VOC 202012/01 has the same N501Y mutation, but the initial analysis showed that the 501Y.V2 variant found in South Africa is a different virus variant. Apart from this similar mutation, the other 16 mutations are different. Routine sequencing in South Africa has found that this variant has replaced the other SARS-CoV-2 variants in the population. Preliminary data suggest this variant has increased transmissibility, but more investigation needs to be done. The variant was discovered in South Africa and Botswana and has since been found in at least 185 countries as of April 2022.

How Does This COVID Variant Spread?

This variant also spreads through respiratory droplets. So you can get infected if a person infected with the COVID variant sneezes, coughs, or sneezes without wearing a mask or maintaining a proper physical distance from you. Likewise, you can also get infected by touching surfaces that are contaminated with the variant and then touching your mouth, eyes, or nose. The only difference that scientists could find in this variant is the rate at which it spreads from one person to another. The mutation has resulted in an increase in the reproductive rate of the virus from 1.1 to 1.5. This means that an infected person can infect 1.5 more people.

Is the Coronavirus Strain More Dangerous?

Viruses constantly mutate, and the emergence of variants is expected and not usually a cause for concern.

Can Recovered COVID-19 Patients Get Infected With the N501Y Variant?

As of now, no evidence suggests that patients who recovered from COVID-19 in the past are at risk of reinfections with the variant. Scientists believe that recovered COVID-19 patients have antibodies that may protect against this N501Y variant. A small number of reinfection cases have been reported worldwide, indicating that long protective immunity exists. During the second episode of infection, the majority of reinfected patients were asymptomatic. Several viral and host factors were implicated in reinfection, including:

Infections following vaccination have also been reported on several occasions, but they have mostly been associated with mild or no symptoms.

How Will This Affect COVID-19 Testing?

One mutation in the variant affects one of the three genomic targets that is used in some PCR (polymerase chain reaction) tests, which means that the tests that target that specific area will show a false-negative result. This will affect the ability of some COVID-19 tests. But, PCR tests usually detect more than one genome target. So if one target is mutated, it will only partially affect the test, reducing the risk of false-negative results.

Will COVID-19 Vaccines Work Against the Strain of Coronavirus?

COVID-19 vaccines stimulate a broad antibody response to the entire spike protein on the virus, so some mutations in the spike protein should not affect the efficacy. But, it is possible that we may reach a point where we might have to update our COVID-19 vaccines, similar to the influenza shots, to tackle the strains at that time.

How to Track Such Variants of SARS-CoV-2?

WHO advises an increased routine systematic sequencing of SARS-CoV-2 to monitor emerging variants of the virus better. Also, in case of unusual transmission events, such as rapid transmission despite control measures or unexpected disease severity and presentation, genetic sequencing should be done to know if the cause is a variant. Mutations of SARS-CoV-2 are expected, but it is essential to continue to monitor how virus variants will affect public health.

What Can We Do to Protect Ourselves Against This Strain of Coronavirus?

With such little evidence to indicate the extent of this strain's spread, efforts should be made to prevent and control its spread as soon as possible. This includes:

Instructions for International Travelers:

Suspected contacts and people who have tested positive for SARS-CoV-2 should avoid traveling.

If you have any symptoms compatible with COVID-19, do not travel. You can travel if you tested negative for COVID-19.

Postpone travel if you are unwell.

If you are at risk of developing severe disease from COVID-19 (people over 60 years of age or those with comorbidities), consider postponing travel.

If you reside in areas where community-wide movement restrictions are in place, avoid all non-essential travels.

If you are experiencing symptoms, suggestive of acute respiratory illness during or after travel, seek medical attention.

Has SARS-CoV-2 Mutated Before?

SARS-CoV-2 has undergone roughly 4,000 mutations in the spike protein so far.

  1. D614G, an earlier variant, dominated as it spread very easily.

  2. Another strain, 20A.EU1 spreads in Europe in summer.

So it is difficult to say whether any particular mutation is important as soon as it emerges. Lots of testing is needed to understand the effects of such mutations.

Can Radiation Be Used to Treat the COVID Strain and Make It Non-Harmful?

There are various studies going on to see the effectiveness of radiation as a treatment for COVID-19. A study was also conducted to see how low-dose radiotherapy can be used to treat pneumonia due to the Coronavirus. All studies have shown encouraging results. Radiotherapy might be an option to prevent the spread of the strain in the future, but more research is needed.

Conclusion:

As newer variants of COVID-19 are arising, it is of utmost importance to get oneself vaccinated and to follow the standard protocols like social distancing and wearing masks at all times. These steps protect not only the individual who follows them but also the loved ones around them.

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Last reviewed at:
26 May 2022  -  8 min read

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