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Since its first detection in China in 2019, the new coronavirus, like all viruses, has undergone changes in the underlying code that determines its structure and behavior. Many of these genetic mutations have little impact on the ability of the virus to infect humans or spread in populations. But others, like those seen in recent variants found in the UK, Brazil and South Africa, may produce a more transmissible pathogen, as suggested by growing infections in these locations.
The more people the virus infects, the more likely it is to evolve, according to Theodora Hatziioannou, a Rockefeller University virologist who studies the new variants.
Since the start of the pandemic, scientists using SARS-CoV-2 samples taken from around the world have documented these genetic mutations. This allowed them to build a family tree tracing the evolution of the virus.
Here are some important milestones in the evolution of the virus that causes Covid-19 and how changes to its genetic code have led to new, potentially more infectious strains making their way around the world:
Decisive change
Early last year, scientists detected a mutation in Europe that makes the virus more transmissible than the original versions detected in China.
The mutation, called D614G, changes the shape of the spike proteins on the surface of the virus, making it more efficient at binding to and infecting cells.
Coronavirus family tree
Evolutionary changes progress from left to right. The circles represent genetically similar groupings.
Ancestral virus
Detected in December 2019
Ancestral virus
Detected in December 2019
Ancestral virus
Detected in December 2019
Ancestral
virus
Detected
Dec 2019
Variants with the D614G mutation quickly overtook earlier versions of the virus.
“By June, it had replaced the ancestral virus,” said Jeremy Luban, a University of Massachusetts medical school virologist who has studied the mutation. “Everywhere he went, it became the dominant strain.
Prevalence among global coronavirus samples
Summer sprawl
A new variant, known as 20E (EU1), was first detected in Spain last summer.
It has since spread widely throughout Europe.
Prevalence of 20E (EU1) among coronavirus samples in each country
20E (EU1) does not appear to have mutations that make it more transmissible than the early variants. On the contrary, it might just be in the right place at the right time – a popular European vacation destination in the height of summer. “It could be a summer trip, it could be because you got rid of all your restrictions or because it’s more communicable,” said Emma Hodcroft, an epidemiologist at the University of Bern in Switzerland, who conducted a study on the variant.
The new variants
The variants recently detected in the UK and South Africa exhibit several novel changes in their spike protein genes.
Variant
from the United Kingdom
Sep 2020
Variant of
South Africa
October 2020
Variant
from the United Kingdom
Sep 2020
Variant of
South Africa
October 2020
Variant
from the United Kingdom
Sep 2020
Variant of
South Africa
October 2020
Variant
from the United Kingdom
Sep 2020
Variant of
South Africa
October 2020
Scientists believe that a mutation shared by these variants could help the virus attach itself and enter cells. The recently detected variant from Brazil shares a key spike protein mutation with that from South Africa.
“What we see is exactly what we expect to see. The surface proteins of the virus are under tremendous pressure to change, ”said Sean Whelan, a virologist at Washington University in St. Louis. “All the virus really cares about is multiplying … If it can get into the cells of the [host] and avoid the immune system of that host, it will multiply. Whether this causes the disease is another question. ”
Some scientists worry that the South African variant may be more effective in avoiding antibodies produced in response to natural infection and vaccination.
Preliminary estimates suggest the UK variant is 50-70% more transmissible than earlier versions of the virus. And British scientists recently said the first data suggested it could be more deadly, too.
The variants found in the UK and South Africa have become the dominant types in the countries where they were first detected.
Prevalence of variants among coronavirus samples in each country
New UK variant (501Y. V1)
New variant from South Africa (501Y. V2)
New UK variant (501Y. V1)
New variant from South Africa (501Y. V2)
New UK variant (501Y. V1)
New variant from South Africa
(501Y. V2)
New UK variant (501Y. V1)
New variant from South Africa (501Y. V2)
The UK variant has spread widely abroad. By the end of January, it had been reported in 70 countries and territories. The South African variant has been reported in over 30.
Countries and territories where the UK variant has been reported
The UK variant had been detected in more than two dozen US states by the end of January.
US states where the UK variant has been detected
The Centers for Disease Control and Prevention predicted that it could become the dominant household strain by mid-March to the end of March unless steps are taken to slow it down. Variants first found in South Africa and Brazil have also been detected in the United States
The extent of their spread is difficult to assess. Apart from the UK and Denmark, few countries with active outbreaks have performed extensive genetic sequencing of the virus, Dr Hodcroft said.
“Right now almost the rest of the world is in a blind spot.”
Additional sources: Nextstrain (phylogenetic trees); Emma Hodcroft, University of Bern
Write to Daniela Hernandez at [email protected]
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