Live Q&A on the new #COVID19 virus variant with WHO, @covidgenomicUK, and @sangerinstitute experts / Dec. 23, 2020
—-
SARS-CoV-2: Strains, Mutations, Variants:
Are there different strains of the SARS-CoV-2 virus circulating?
June 10, 2020
What is a virus ‘strain’?
When scientists use the word strain, they are referring to a genetically distinct virus lineage, distinguishable by one or more mutations from another strain. Strains may or may not be biologically (functionally) distinguishable from one another and some virologists use the term strain only for the former. Two strains would be biologically different if they elicited different responses from the human immune system, or if they varied in their transmission characteristics.
What are viral mutations?
When a virus infects a cell and begins making copies of itself, it starts by replicating its genetic information, which for
the COVID-19 virus is encoded in an RNA molecule. More complex organisms have a variety of “proof-reading” mechanisms to ensure high-fidelity replication; however, these are less developed in RNA viruses where the process is particularly error-prone, leading to a relatively rapid accumulation of mutations over time. SARS-CoV-2 does carry some proof-reading enzymes and its mutation rate is lower than many other RNA viruses, such as influenza virus, norovirus and human immunodeficiency virus (HIV).
—-
June 15, 2020
COVID-19 Will Mutate — What That Means for a Vaccine
“More infectious
A new
study from the Scripps Research Institute in Florida suggests
the new coronavirus has mutated into a variant that’s more infectious.
The mutation — named “the D614G mutation” — occurred on the spike protein, the part of the virus that helps it bind and fuse to our cells.
The D614G mutation makes it easier for the virus to infect our cells.
The Scripps researchers aren’t the first to identify the
tiny mutation on the spike protein.
In
March, researchers from the
Los Alamos National Laboratory announced they
detected the D614G mutation, and that it was likely responsible for most infections reported in Europe and the United States.
In total, the researchers
identified 14 strains of SARS-CoV-2 and released their findings to help those working on vaccines and treatments.
That being said, the new dominant strain identified does seem to be more infectious in laboratory settings. Scientists are now trying to understand how the variation behaves in the body — which may be very different from lab settings.”
—
June 30, 2020
Mutated COVID-19 Viral Strain in U.S. and Europe 10 Times More Contagious than Original Strain | BioSpace
“The mutation
does not appear to make the virus any more deadly than it already is, but it does appear to make it significantly more contagious.
The original strain in China is dubbed D614, while the one found in the UK, Italy and North America by May is dubbed G614.“
—
July 16, 2020
Second Coronavirus Strain May Be More Infectious—but Some Scientists Are Skeptical
“The paper indicates that a single amino acid change from D (aspartic acid) to G (glycine) on the SARS-CoV-2 spike protein(which such viruses use to grab onto human cells)
is the key to how infectious the pathogen is. “The spike protein has a critically important role in the biology of the virus,” says Bette Korber, a computational biologist at the Los Alamos National Laboratory and lead author of the new paper.
Korber and her colleagues came to this conclusion after employing multiple approaches to examine the two strains. First, they performed a statistical analysis that showed how
the mutated virus—often referred to as the “G strain”—achieved dominance across multiple continents, outperforming the coexisting original version of SARS-CoV-2, or “D strain.” Then the researchers tested the amount of the virus in individuals with COVID-19 at the Sheffield Teaching Hospitals NHS Foundation Trust in England.
The results showed that the G strain produced more of the virus in the human body than the D strain. But the former did not lead to a higher hospitalization rate, meaning it apparently did not cause more severe illnesses. Lastly, the team members created “pseudotype” pathogens by embedding SARS-CoV-2 spike proteins, containing either D or G amino acids, into other disease-causing viruses...”
—
Aug. 3, 2020
The six strains of SARS-CoV-2
“Source:
Università di Bologna
Summary:
The virus causing the COVID-19 pandemic, SARS-CoV-2,
presents at least six strains. Despite its mutations, the virus shows little variability, and this is good news for the researchers working on a viable vaccine.“
—
Sept. 8, 2020
“In
April, Korber, Montefiori and others warned in a preprint posted to the bioRxiv server that
“D614G is increasing in frequency at an alarming rate”1. It had rapidly become the dominant SARS-CoV-2 lineage in Europe and had then taken hold in the United States, Canada and Australia. D614G represented a “more transmissible form of SARS-CoV-2”, the paper declared
, one that had emerged as a product of natural selection.“
—
Oct. 30, 2020
Coronavirus mutation may have made it more contagious
“Source:
University of Texas at Austin
Summary:
A study involving more than 5,000 COVID-19 patients in Houston finds that the virus that causes the disease is accumulating genetic mutations, one of which may have made it more contagious. This mirrors a study published in July that found that around the world, viral strains with the same genetic mutation quickly outcompeted other strains.
A study involving more than 5,000 COVID-19 patients in Houston finds that the virus that causes the disease is accumulating genetic mutations, one of which may have made it more contagious. According to the paper published in the peer-reviewed journal
mBIO,
that mutation, called D614G, is located in the spike protein that pries open our cells for viral entry. It's the largest peer-reviewed study of SARS-CoV-2 genome sequences in one metropolitan region of the U.S. to date.”
[...]
“A study published in July based on more than 28,000 genome sequences found that
variants carrying the D614G mutation became the globally dominant form of SARS-CoV-2 in about a month.”
[...]
“Natural selection would favor strains of the virus that transmit more easily. But not all scientists are convinced. Some have suggested another explanation, called "founder's effects." In that scenario, the D614G mutation might have been more common in the first viruses to arrive in Europe and North America, essentially giving them a head start on other strains.“
—
RAPID RISK ASSESSMENT
Detection of new SARS-CoV-2 variants related to mink
12 November 2020
https://www.ecdc.europa.eu/sites/default/files/documents/RRA-SARS-CoV-2-in-mink-12-nov-2020.pdf
“The mutation Y453F”
SARS-CoV-2 mink-associated variant strain – Denmark
6 November 2020
“Since June 2020, 214 human cases of COVID-19 have been identified in Denmark with SARS-CoV-2 variants associated with farmed minks,
including 12 cases with a unique variant, reported on 5 November. All 12 cases were identified in September 2020 in North Jutland, Denmark. The cases ranged in age from 7 to 79 years, and eight had a link to the mink farming industry and four cases were from the local community.
Initial observations suggest that the clinical presentation, severity and transmission among those infected are similar to that of other circulating SARS-CoV-2 viruses. However,
this variant, referred to as the
"cluster 5" variant, had a combination of mutations, or changes that have not been previously observed. The implications of the identified changes in this variant are not yet well understood. Preliminary findings indicate that this particular mink-associated variant identified in both minks and the 12 human cases has moderately decreased sensitivity to neutralizing antibodies. Further scientific and laboratory-based studies are required to verify preliminary findings reported and to understand any potential implications of this finding in terms of diagnostics, therapeutics and vaccines in development. In the meantime, actions are being taken by Danish authorities to limit the further spread of this variant of the virus among mink and human populations.“
WHO /
SARS-CoV-2 mink-associated variant strain – Denmark / Nov. 6, 2020
https://www.oie.int/fileadmin/Home/...E_on_Sars-CoV-2_in_Denmark_5_november2020.pdf
Nov. 5, 2020
—-
Nov. 13, 2020
Study: New Mutation Sped Up Spread of Coronavirus
“Compared to the original strain, people infected with the
new strain -- called 614G -- have
higher viral loads in their nose and throat, though they don’t seem to get any sicker. But they are
much more contagious to others.“
—
Dec. 15, 2020
New coronavirus strain spreading in UK has key mutations, scientists say
“
The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19
spreading more easily between people.”
[...]
“As of Dec. 13, 1,108 COVID-19 cases with the
new variant had been identified, predominantly in the south and east of England, Public Health England said in a statement.
But there is currently no evidence that the variant is more likely to cause severe COVID-19 infections, the scientists said, or that it would render vaccines less effective.“
—
Severe COVID variant detected in South Africa, health minister says
“
Known as the 501.V2 Variant, it was identified by South African researchers and details have been sent to the World Health Organization, Zwelini Mkhize said in a statement.“
[...]
“The research team, led by Tulio de Oliveira, has shared its findings with the scientific community and alerted authorities in Britain, who have “
studied their own samples and found that a similar mutation… was the variant that was driving their resurgence in London,” he said.”
—
@DrZweliMkhize
Dec 18
Karim:
This new 501.V2 variant has become dominant in South Africa. This new variant has 3 mutations. #SARSCOV2MediaBriefing
South Africa identifies new coronavirus strain causing surge in cases
““The evidence that has been collated, therefore, strongly suggests that the
current second wave we are experiencing is being driven by this new variant,” Mkhize added.”
—
New Variant of SARS-CoV-2 Frequently Asked Questions - NICD
Dec. 19, 2020
“Q What is the new SARS-CoV-2 variant?
A This
new variant of the virus was discovered through routine genomic surveillance of SARS-
CoV-2 performed by a network of laboratories around the country (Network for Genomic Surveillance South Africa, NGS-SA).
The new variant has been identified in almost 200 samples collected from
over 50 different health facilities in Eastern Cape, Western Cape and KwaZulu- Natal. The new variant is different from the others that were circulating in South Africa because it has multiple mutations (changes) in the spike protein – this is the very important part of the virus that binds to the receptor on the cells inside our body and that is also the main target for many of the antibodies produced during infection or after vaccination. Work is being done to understand what effect these mutations have on the behaviour of the virus and our body’s response to it - particularly whether it makes the virus spread more easily, whether it might lead to more severe COVID-19, and whether the virus can evade our immune response.
Q What is the
geographical distribution of this
mutation?
A The
variant was
first identified in Nelson Mandela Bay but has
rapidly spread through the rest
of the Eastern Cape and to the Western Cape and KwaZulu-Natal provinces. Testing in other provinces is being undertaken to understand the extent of geographical spread but
it is likely that this variant has spread to other provinces too.”
[...]
Q Is this the same or different to the London variant?
A
It is definitely not the same variant, but there are similarities as they
both share the same change in the spike protein at the 501 position. What it does tell us is that if we do not control the spread of the virus then it is likely to evolve in similar ways in different parts of the world.”
—
UK Variant:
“The variant that’s being discussed was first identified in September...” - Alex Azar |
source
—
In the WHO Press Briefing from Monday, Dec. 21, 2020, Dr. Maria Van Kerkhove comments about the
UK VUI / source:
- It has a number of mutations that was identified through genomic sequencing, which is carried out across the country.
- The Variant Under Investigation was reported to WHO on 14th December, following detail analysis that the UK had done in the southeast of England, looking at their epidemiologic surveillance data and their laboratory data, noting an increase in transmission at the end of Nov/Dec, while interventions were in place.
- They did some file genetic analysis and identified this variant, “they’re calling it the “B-117 lineage which includes this mutation at the N501Y site”.
- She also said the reproductive number went up by .4, increasing from 1.1 to 1.5.
- Also note it was originally referred to as “VUI-202012/01”:
* From above notes, “Dec. 15, 2020: New coronavirus strain spreading in UK has key mutations, scientists say “The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19 spreading more easily between people.”...“As of Dec. 13, 1,108 COVID-19 cases with the new variant had been identified, predominantly in the south and east of England, Public Health England said in a statement.“
Additionally, the reporter specifically asks if there is a connection between the two new variants from UK and South Africa:
21:00 | Dr. Maria Van Kerkhove:
“So, at the same time, there was another variant that was identified in South Africa, and
it has one of the same mutations, this 501Y mutation but a different variant. They have arisen at the same time but it is a separate variant.”
—
Per this video, “doctors are reporting more young people who are seriously ill”; also, per Matt Hancock, this new South Africa variant is highly concerning because it appears to have mutated further than the one discovered in the UK.
source
