Written By: Isaiah Hazelwood, Science Writer & Editor
In late 2019, a novel coronavirus emerged in Wuhan, China and spread in the local population. Unlike other viruses in the coronavirus family, it had much higher infectivity and a significant risk of mortality for those with comorbidities. As it spread internationally, the World Health Organization declared it a Public Health emergency on January 30, 2020. When infections appeared in almost all nations, spread in major cities, and escaped attempts at containment, WHO declared it a pandemic on March 11, 2020. As the disease became a topic of emergency for many nations, the WHO gave it an official name: the virus was named SARS-CoV-2, for Severe Acute Respiratory Syndrome Coronavirus 2, and the illness it causes was named COVID-19, with CO standing for Coronavirus, VI standing for Virus, D standing for disease, and 19 indicating its year of appearance. Designed to avoid connecting the disease to any specific place of origin, the terms quickly entered common use as the pandemic became the defining event of 2020.
Like all viruses, SARS-CoV-2 is a coat of proteins and fats surrounding some genetic material, meaning by itself it is inert and unable to spread. Unfortunately, when it approaches a cell, its surface proteins – the spike protein in particular – allow it to enter the cell and take control of the cell’s complex systems, proteins, and organelles. The infected cell reads the virus’s genetic material to create more virus proteins, copy viral genetic material, and package them together into new viruses. However, this copying process is imperfect and occasionally makes errors in new viral genetic material – a mutation. While mutations are often poor for the virus, making it unable to enter cells, unable to escape infected cells, or causing no significant change, some mutations make the virus more infectious, cause more symptoms, or more lethal. With these changes, these mutants spread rapidly, infect more people, and worsen the pandemic.
Because infectivity-increasing mutations cause the virus to spread faster than neutral or infectivity-decreasing mutations, viruses with these mutations have a higher likelihood of reproducing and surviving, being passed to more people, and being more common in the population. As a result, different virus strains may independently gain the same beneficial mutation and both become significant variants of concern; this process of convergent evolution, where the same beneficial trait or mutation appears multiple times in entirely independent contexts, is the cause for many similar mutations between SARS-CoV-2 virus strains found in dramatically different parts of the world.
D614G: The Mutant in Plain Sight
The most common SARS-CoV-2 mutant is one you probably haven’t heard about because of how common it is. In January, after scientists rapidly sequenced the genome of the virus present in Wuhan, China, scientists in the United States and Europe sequenced the genome of the virus in their cities. While most parts of the virus’ genomes were largely identical between the two regions, the virus in Europe and the US had one consistent important change: the spike protein was different in one spot, a change described as D614G (the 614th amino acid in the protein was a Glycine, G, instead of an Aspartic Acid, D). This seemingly small change in the spike protein was hypothesized to make the D614G mutant better at entering cells and infecting them, and this was supported both by laboratory experiments and infection data as roughly 70% of the 500,000 SARS-CoV-2 genomes recorded by July 2020 were the D614G mutant. As the predominant form of the virus, this mutant has become the “normal” virus even though it was not the original which caused the first infections.
B.1.1.7: Detected in the United Kingdom
In December 2020, scientists in the United Kingdom detected a new variant of COVID-19 containing a multitude of mutations: there are 8 changes to the virus’s spike protein and 9 changes to other parts of the virus which have unclear effect. Based on current evidence, the variant is 1.3 to 1.7 times as infectious than the D614G virus and may be approximately 1.3 times as lethal as well. Several different names were given for the variant including VUI-202012/01 (the first Variant Under Investigation detected in December 2020), B.1.1.7 (its evolutionary lineage), 20I/501Y.V1 (referring to the variant’s important N501Y spike protein mutation); in the media, it is most often referred to as the “UK coronavirus variant”. While most common in the United Kingdom, the variant has been detected in the United States, Canada, Australia, Japan, Germany, France, Italy, and several other nations. While its infectivity increase appears small, it has significant effects as the virus spreads exponentially: while the number of total COVID-19 cases doubles approximately every 40 days under the D614G strain, one model predicts the presence of the B.1.1.7 variant could decrease the doubling time to 10 or 15 days. The CDC expects B.1.1.7 will become the most common variant in the United States by March due to its higher infectivity, and Ontario scientists warn it will become the predominant variant in Ontario by late February unless its spread is reduced.
B.1.351: Detected in South Africa
The same week as the United Kingdom detected the B.1.1.7 variant of SARS-CoV-2, scientists in South Africa detected an additional virus variant. While it shares several mutations with the B.1.1.7 strain – including an important infectivity-increasing N501Y mutation on the spike protein – it arose independently, lacks several mutations present in B.1.1.7, and contains additional mutations absent in B.1.1.7. The mutations are hypothesized to increase the variant’s infectivity compared to the D614G strain, but its severity and lethality appear unchanged. The strain, named B.1.351 or 20H/501Y.V2, is believed to be partially responsible for a second wave in South Africa in December. Since its original discovery, it has been detected in Canada, the United States, Australia, Israel, and almost two dozen other countries. Information on the variant is still developing, and the full effects of its increased infectivity and simultaneous spread with the B.1.1.7 variant have yet to be determined.
While B.1.1.7 and B.1.351 are the main SARS-CoV-2 variants under investigation by scientists, several other virus variants have appeared. The P.1 variant, also named the B.22.214.171.124 variant, was detected in January 2021 by researchers in Brazil. With 10 spike protein mutations – again including the N501Y spike protein mutation also present in the B.1.1.7 and B.1.351 variants – and 10 other mutations, it is suspected to be more infectious than the D614G strain, but little evidence exists surrounding possible changes to its infectivity and lethality. While only discovered recently, the P.1 variant has been detected in Germany, Peru, Japan, South Korea, and the United States.
In late 2020, California scientists testing for the B.1.1.7 virus variant discovered an additional surprise as approximately half of the virus samples from Los Angeles were of a novel virus variant. Named CAL.20C or B.1.429, the variant contains several spike mutations but not the N501Y mutation present in the rapidly spreading B.1.1.7, B.1.351, or P.1 variants. While laboratory tests on the virus’ infectivity are yet to complete, the recent spike in COVID-19 cases in California indicates it may be more transmissible and a partial cause of California’s increasing cases. Until more research is performed, the variant’s infectivity and lethality have yet to be determined.
While most SARS-CoV-2 variants are more transmissible or deadly and present a risk of infecting more people and prolonging the pandemic, the Cluster 5 virus variant detected by Danish scientists in November 2020 is a notable exception. Through extensive viral testing and sequencing, the variant’s appearance in humans was traced to a mink farm, where minks grown for their furs were infected with the virus and spreading it to each other and to humans working near them. The virus’s mutations caused significant changes to the spike protein, which meant immunity against the D614G strain might not provide immunity against the Cluster 5 variant. To protect humans and limit the variant’s spread, the Danish government quarantined and culled infected minks. With this swift action, the variant’s spread in humans was stopped; by 2021, it was declared extinct.
While each viral variant has slightly different properties than the D614G strain, they are all still SARS-CoV-2. As such, they spread in the same way through close contact with infected people and through inhaling virus particles. The standard set of rules apply for not getting infected: wash your hands with soap and water, avoid touching your face, avoid crowded places, socially distance two meters or more from others, wear a mask in public, and minimize contact with people you are not living with. Wearing better masks which have a closer fit and more layers can provide more protection at relatively little cost or difficulty. Quarantining if you get infected, come into close contact with someone with the virus, or travel outside the country is important in preventing the virus’s spread. While the variants are more infectious, taking additional precautions and adhering to safety guidelines can limit the virus’s spread and prevent the higher number of infections models predict.
Will Vaccines Still Work?
To provide immunity to COVID-19, vaccines generate antibodies against the SARS-CoV-2 spike protein, which allows your immune system to detect the virus based on its spike protein and destroy it before it infects you. However, many of the virus variants possess changes in this spike protein. As a result, the vaccines may have different effectiveness against these different spike proteins: the E484K spike protein mutation, present in both the B.1.351 and P.1, reduces the spike protein’s interaction with antigens, limiting the immunity the antigens provide. Fortunately, preliminary evidence suggests the Pfizer, Moderna, Novavax, and Johnson & Johnson vaccines retain moderate, though slightly reduced effectiveness against the most common variants. In addition, the Pfizer and Moderna vaccine mRNA design allows the vaccine target to be easily switched, allowing them to create vaccines which target variant spike proteins rather than the original. Even while variants may reduce vaccine strength, the vaccines will still be better than nothing – as the FDA was originally seeking 50% efficacy, the vaccines’ 90% efficacy means they can suffer significantly while providing good protection to all forms of COVID-19.