Insights

SARS-CoV-2 Variants: What Are They and How Do They Affect COVID-19 Spread?

January 26, 2021

How It Started

January 6, 2021, marked the one-year anniversary of the release of the first genetic sequence of the SARS-CoV-2 virus that causes COVID-19, the bedrock of the various diagnostic tests, vaccines, and therapeutics we have today. Unprecedented collaboration and cooperation in sharing data and information have enabled a swift pandemic response on a global level. While we have learned so much about the virus’s biology, there is so much more we haven’t understood and continue to learn. One additional silver lining in this devastating pandemic is the true democratization of genetic sequencing—in effect, sequencing has become possible in every lab globally, not limited to advanced labs with exceptionally large budgets and heavy infrastructure. Genome sequences are shared in real time as they are generated, leading to crowdsourcing the sequence analyses to understand the virus’s evolution as it moved through the world population and crossed borders. Scientists have traced and tracked the virus’s evolution and mobility using genetic relatedness, the so-called molecular epidemiology. Changes in a virus due to genetic drift help establish relatedness very much in the same way as human individual relationship or genealogy is established by companies such as ancestry.com and 23andMe.

How It’s Going

All organisms evolve and accumulate mutations over time. Viruses evolve and are therefore not exempt from mutating. Some viruses mutate at higher rates and some at slower rates. Fortunately, SARS-CoV-2 is mutating less so than other RNA viruses such as Ebola. Many viral changes are neutral, without any measurable effects on the virus’s property concerning infection, transmission, or disease severity. However, some genetic changes may lie in places in the genome used as signatures for diagnostic assays, such as the much talked about PCR, or polymerase chain reaction, which is one type of test to detect SARS-CoV-2 in samples. Other mutations affect key proteins such as the spike protein. These changes may affect the virus’s properties, including increased contagiousness compared with the original virus or vaccine efficacy.

At least three variants are on the watch list that possess such mutations: the UK, South African (SA), and Brazilian. The UK and SA variants appear to be more contagious and about 50% to 70% more transmissible than the wild type (non-mutated virus). This is because the spike protein has a higher affinity for the human protein that it used for entry and infection. One of the UK variant mutations affects the commonly used detection assay that serves as a proxy for identifying the variant. The UK variant does not appear to affect vaccine efficacy. The SA variant has some unique mutations that appear to evade immunity, meaning there is concern current vaccines may not work against that variant. It is critical that genetic sequencing and sharing of information be expanded.

The newest variant, the Brazilian version, has been found in the country it was named after and has been imported via travel to Japan. There are also variants here in the United States (CAL.20C) that are being watched closely. These variants and their impact on diagnostics and therapeutics require greater study. As of this writing, the SA variant is not present here while the UK variant is present at a low proportion of the overall positive samples in the United States.

What’s Next?

There is no urgency to hit the panic button yet, but know that the medical community is adaptive to change and will tweak the medical countermeasures if new variants become a problem. Fortunately, tests and potentially medical countermeasures are easily adaptable and will continue to be modified to overcome the rapid evolution of the COVID-19 virus.

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COVID-19 Mutation
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COVID-19 Mutation

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