SARS-CoV-2 Variants - Coronavirus COVID-19 **NO DISCUSSION**

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Detection of a large cluster and multiple introductions of the P.1 SARS-CoV-2 Variant of Concern in Massachusetts
April 2, 2021

“Results
All three global VoCs (B.1.1.7, B.1.351, and P.1) have now been detected in MA. However, unlike B.1.1.7 and B.1.351, P.1 has shown a rapid rise in frequency in the few weeks following its first detection on March 16th, 2021 (Figure 1). Phylogenetic analysis of these 54 P.1 genomes from MA, alongside four additional P.1 genomes from neighbouring states (two from Connecticut (CT) and one each from Maine (ME) and Rhode Island (RI)) and 895 other global P.1 sequences from GISAID, 6 1suggests at least six introductions of P.1 into MA and at least eight introductions of P.1 into the New England region, likely from both international and domestic sources (Figure 2).

A second, smaller cluster of P.1 genomes contains four genomes from MA and two from Nebraska, from samples collected close in time to the MA samples. The direction of the link between the two sets cannot be reliably determined. The remaining five MA P.1 genomes likely represent four or five additional independent introductions into the state, given their substantial genetic distances from each other and the other MA genomes (4-17 SNP differences). Two of these genomes cluster with several genomes from Italy, suggesting a probable P.1 importation from Europe.

The single P.1 genomes available from Maine and Rhode Island are genetically distinct from others currently detected in New England, suggesting that they are further independent introductions into the region. Notably, these P.1 genomes cluster with genomes from Florida and Washington, respectively, suggesting domestic spread of the P.1 variant between New England and other US states.“

 

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Why Americans should "be very worried" about the COVID variant tearing through Brazil - CBS News

“Scientists believe the P-1 variant is fueling the surge. Dr. Miguel Nicolelis, a Distinguished Professor of Neuroscience at Duke University's School of Medicine, told CBS New that the strain is two-and-a-half times more easily transmitted from person to person, and that's a concern for everyone, even outside Brazil's borders.

"If I were talking to someone in Oklahoma, I would tell him or her to be very worried about it," Nicolelis told Bojorquez. "Because if Brazil is out of control, the world will be out of control in a few weeks. Because variants that are brewing here every day, every week… they will escape."

 

[margarita25]

This is how new Covid-19 variants are changing the pandemic
Jan. 7, 2021

“Included within this tiny piece of genome, however, were the instructions that altered a key part of the virus – its spike protein. This important protein studs the outside of the coronavirus and is the part that attaches to the outside of cells, helping the rest of the virus to sneak inside where it can replicate.

This change to Covid-19's spike protein meant it could hijack an enzyme found in the human body called furin. This enzyme acts like a pair of molecular scissors, normally cutting open hormones and growth factors to activate them. But when furin snips part of the Covid-19 spike protein, which is normally folded in a series of loops on the outside of the virus, it opens like a hinge.

"This exposes a new sequence in the spike protein," says Yohei Yamauchi, a reader in viral cell biology at the University of Bristol, UK, who has been studying how this change may have led Covid-19 to become more infective in humans. "It is one of the changes that make this virus really different from previous coronaviruses that caused Sars and Mers."

This new mutation meant Covid-19 could suddenly latch onto an important molecule found scattered around the outside of human respiratory cells called Neuropilin 1. This molecule helps to transport material inside cells and deeper into tissues – the mutation was like handing Covid-19 the keys to a new door into our cells and meant the virus could replicate in greater numbers in the human airways.

Although this mutation was just one in Covid-19's short existence, it proved to be important. Some researchers believe it may be one of the key mutations that allowed the coronavirus to jump species and begin causing a rapidly spreading disease in humans. But almost as soon as it did this, it began picking up other mutations.“

*much more at link

 

[margarita25]

Brazilian coronavirus variants (P1 and P2) found in the Netherlands | RIVM
January 29, 2021

“P1
The P1 variant is found mainly in outbreaks in and around Manaus, the capital of the Brazilian state of Amazonas. It is not yet clear whether the course of illness is different for this variant. Among other mutations, the variant has three changes in the spike protein, the lines bristling out from the coronavirus, that are considered cause for concern. These three changes are almost identical to the changes in the South Africa variant. The mutations in this variant may potentially make it more contagious and reduce the effectiveness of pre-existing or vaccine-induced immunity. This is currently being investigated at the national and international levels.

P2
The P2 variant occurs throughout Brazil. One of the three concerning mutations mentioned in P1 also occurs in this variant. This mutation could potentially make the variant more contagious and lead to reduced immunity after previous infection with earlier variants or following vaccinations. Whether this is actually the case is currently also being investigated at the national and international levels. Like the P1 variant, it is not yet clear whether P2 leads to any changes in the course of illness.”

 

[margarita25]

WebMD
March 24, 2021

 

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Updated March 24, 2021:
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html
SARS-CoV-2 Variant Classifications and Definitions
Cases, Data, and Surveillance

 

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Expert says Brazil variant of COVID-19 likely already in Texas | khou.com
January 26, 2021


'They're all here' | Expert says Brazil variant of COVID-19 likely already in Texas and other parts of country
The CDC says it detected the first case of the Brazil strain in Minnesota in a U.S. patient that had recently returned from the Latin American country.

 

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[margarita25]

Notes:
*”The Founder Effect”

* D614G aka “Doug”
* N501Y aka “Nelly”
* E484K aka “Eek”

*COG UK= Fast sequencing & Data Sharing

 

[margarita25]

Model-based evaluation of transmissibility and reinfection for the P.1 variant of the SARS-CoV-2
https://www.medrxiv.org/content/10.1101/2021.03.03.21252706v1.full.pdf
March 5, 2021


“Summary box
What is already known about this topic?
A new variant of concern of SARS-CoV-2 (P.1). emerged in the city of Manaus in November 2020. Since then, a sharp increase in COVID-19 cases in Manaus led to the collapse of the health system in early 2021.

What is added by this report?
Transmissibility and reinfection of P.1 were estimated using an epidemiological model-based fitting and public health data. The transmissibility is 2.5 times greater than the wild variant and reinfection probability is 6.4% on average.

What are the implications for public health practice?
This new variant poses a global threat due to its very high transmissibility. The results highlight the need to urgently monitor and contain its spread.“

 

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Brazil's P1 coronavirus variant mutating, may become more dangerous -study

 

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The Brazil variant is spreading in Canada. What do we know about it? - Macleans.ca

 

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March 17

““Once these mutations are correlated with the existing public health scenario, only then we can say that these new variants are a matter of concern. As of now, we need to do much more to build these correlations, and that is why it is important to do more genome sequencing on samples from Maharashtra. More scientific evidence is needed to say with certainty that the surge in Maharashtra is attributable to new variants,” he said.

More than 1,200 virus samples from Maharashtra have so far been sent for genome sequencing, at the Pune-based National Institute of Virology, and the National Centre for Cell Science. So far, two mutants, named E484Q and L452R, are being further investigated. Initial studies have shown that E484Q mutant can possibly escape antibody neutralisation, while L452R can increase the rate of infection. The samples that initially showed these two mutants were from Akola and Amravati. More detailed studies are being carried out.

“We do not have definite signals of any particular new variant that is pushing the pandemic surge, but work is underway at the genomic surveillance consortium of ten national institutes (called INSACOG) to work on genome sequencing of virus samples,” NITI Aayog member Dr V K Paul said at a media briefing in New Delhi on Wednesday.“

NCDC seeks more samples to explain surge in Maharashtra

 

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“New Delhi: Top sources in the Union Health Ministry reportedly revealed that the novel COVID-19 double mutant variant has been found in at least ten states in India. The double mutations could be responsible for the massive spike in coronavirus cases in the country, the sources said.

According to a report in NDTV, government sources said the states where double mutant strains have been found include Delhi, Maharashtra, Gujarat, Madhya Pradesh and West Bengal.“

[...]

“What is a double mutant variant?
A double mutation is when two mutates strains of a virus come together to form a new third strain.

However, health experts have said that the double mutant variant may be less dangerous than expected as the most vulnerable patients are having only mild illnesses.“

New Double Mutant COVID Strain In At Least 10 States; UK Variant In 18-19 States

 

[margarita25]

Explained: B.1.617 variant and the surge
Genome sequencing data have presented evidence of the 'double mutant' in 61% of samples in Maharashtra. But whether this new variant is driving India's ongoing surge can be said only after more data is available.

“What is the B.1.617?
The B.1.617 variant of SARS-CoV-2 carries two mutations, E484Q and L452R. Both are separately found in many other coronavirus variants, but they have been reported together for the first time in India.

The two mutations are found in the virus’s spike protein. The spike protein helps the virus to bind itself to the human cell’s receptors and gain entry into a host cell.

The E484Q mutation is similar to E484K, a mutation found in the United Kingdom (lineage B.1.1.7) and South Africa (B.1.351) variants of the coronavirus.

The L452R mutation has been found in fast spreading variants in California (B.1.427 and B.1.429). It can increase the binding power of spike proteins with ACE2 receptors on human cells, making it more transmissible. L452R can also potentially enhance viral replication.

Together, E484Q and L452R are more infectious, and can evade antibodies.“

*more at link

 

[margarita25]

Maharashtra: double mutant found in 61% samples tested

“The National Institute of Virology (NIV), Pune, has shared data with laboratories in Maharashtra showing that of 361 Covid-19 samples taken in Maharashtra from January to March and genome sequenced, 61% or 220 had the double mutation E484Q and L452R, now classified as B.1.617 lineage.

On March 24, the Central government had announced the detection of a double mutant variant in “15-20% samples in Maharashtra” but did not link the variant with the second surge in the state.

At a meeting on April 10, NIV officials made a presentation to all district heads of government laboratories. The meeting was organised by the Directorate of Medical Education and Research under the Medical Education and Drugs Department of Maharashtra.

The genome sequencing results were shared in the presentation, but officials said the state government is yet to receive a written report on this. “It has been communicated to us only verbally,” said an official. Health Minister Rajesh Tope said the state government had asked the Centre for a detailed report on the genome sequencing of all the Maharashtra samples.“

 

[margarita25]

Covid variant first detected in India is found in the UK

“In total, 77 cases of the variant, known as B.1.617, have been recorded in the UK up to 14 April, according to the latest update from Public Health England (PHE), released on Thursday. Of these, 73 were recorded in England and 4 in Scotland.

It is the first time PHE has reported the variant in the UK.

It currently has the label “variant under investigation”. If worries about it are borne out, for example it appears to be more infectious or more resistant to the body’s immune response, then it may be designated a “variant of concern”.

The UK has a handful of “variants of concern”, including ones first detected in Kent, South Africa and Brazil.“

 

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Can the Covid Vaccine Protect Me Against Virus Variants?

 

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B.C. could hit 3,000 new COVID-19 cases a day if contact trends don’t go down: health officials

“Variants now make up an estimated 65 per cent of all new COVID cases in the province. This is a massive surge from just nine weeks ago when variants first took hold in the province.

The P.1 variant, first detected in Brazil, now makes up 49 per cent of the province’s variant cases. The B.1.1.7 variant, originally detected in the U.K., makes up 50 per cent of the variant cases.

The B.1.1.7 variant continues to be dominant in Fraser Health, making up nearly 75 per cent of all the variant cases in the province. The P.1 variant dominates spread in Vancouver Coastal Health, making up about 70 per cent of variant cases that health region.“

[...]

“The independent modelling found the growth of variants of concern (B.1.1.7 and P.1) have driven recent rise in cases and transmission must be reduced by at least 40% to control case growth.”

 

[margarita25]

Half of all new COVID-19 cases are variant strain | 9news.com
April 14, 2021

“COLORADO, USA — State leaders say anyone who gets COVID-19 in Colorado right now has a pretty good chance of contracting a mutated version of the virus.

“If you contract COVID-19 today, it’s is more likely that you are exposed and have contracted a variant strain,” said Governor Jared Polis during a press conference on Tuesday.

“About half the specimens we're testing weekly are the B.1.1.7 variant,” he said, referencing the strain first discovered in the U.K.

Testing for COVID is a different process from determining whether each case is a variant. The Colorado Department of Public Health and Environment (CDPHE) says the state lab is currently conducting genome sequencing on about 7% of positive COVID-19 tests to determine if they are variant cases.“

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COVID-19 P.1 variant detected in Colorado | Colorado COVID-19 Updates
April 6, 2021