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Covid, Phase II. Commonsense is the order of the day.

The new Covid variants and mutations: what we know about them

Tom Whipple

Friday January 15 2021, 12.01am, The Times



The Kent variant
During the lockdown in England in November, public health officials noted a strange anomaly. By the middle of the month in every region of the country the number of cases was falling or flat. Except, that is, in one part of Kent. Here, apparently unperturbed by the restrictions, it kept on rising. Were people ignoring the rules? Were they behaving differently? Scientists could find no explanation. In December they sent in the geneticists — and they spotted that one variant was proliferating. This variant had become a pandemic within a pandemic.
Key mutation N501Y
The spike protein is what the virus uses to enter cells, and it is on its tip that this single mutation seems to have given B.1.17, as the Kent variant is known, its edge. This cannot be the whole story. This single mutation will have happened many times as the virus reproduced, yet not taken off. It must be something about its interplay with other, less well-understood, mutations that enabled its sudden rise to supremacy.

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The South Africa variant
South Africa did quite well in its first wave, peaking briefly at 300 deaths a day. By November cases were down to a little over 1,500, with 720,000 recorded through the whole pandemic. Then they rocketed. By December there were 800,000 cases. Two weeks later there were 900,000. Nine days after that, there were 1,000,000. Today there are 300,000 more. It took a while to identify a reason why. South Africa has less genetic surveillance than the UK. When they did look, they found their dominant variant also had the telltale N501Y mutation — which it had developed independently.
Key mutations
As well as N501Y, this variant has another mutation on the part of the spike that binds to cells, called E484K. John Bell, regius professor of medicine at Oxford, said this worried him. “If you get an immune response that protects you, one of the ways it protects you is it gets in the way of that binding event. You rely on antibodies to bind to that domain to stop the virus entering your cells.” If it changes, that means immunity might not be so high. “If you mess around with that you’re in trouble,” he said.
The Brazilian variant
In Manaus in April gravediggers had to work at night. Funeral homes ran out of coffins. Bodies were buried in trenches. In spring, this city of 2.2 million people let coronavirus rip. While the world was locking down, here the virus was left unchecked. They suffered for it, but they had every reason to hope that the worst was over. Many scientists thought that they had in fact reached that long-fabled state: herd immunity.

But, now, the hospitals are full once again. There are reports, equally worryingly, of reinfections. Here, too, a new variant has emerged — and once again there is evidence it has evolved to transmit more efficiently.
Key mutations
Like the South African variant, the Brazilian version also has the N501Y and E484K mutations. Experiments are under way to see what effect this has on immunity. It is possible that the E484K mutation will be able to evade some of our defences.
But most scientists think that while it might render vaccines or immunity less effective, it will not make them useless. And now we have the vaccines, they can be tweaked quickly to keep up.
 
Covid-19: 'One medic saw eight people die in a single shift'
Published
11 hours ago


Claire Goodwin-Fee: "People are being pushed to the brink"
Coronavirus has changed many people's working lives for the worse. Many of us have been isolated from our colleagues; others have been made redundant by employers citing the costs of the pandemic.
In the NHS and in care homes, though, the pressures have perhaps been the most intolerable. Ten months of Covid-19 has left many healthcare professionals' mental health at breaking point, according to Claire Goodwin-Fee.
The Frontline19 organisation she runs with fellow therapist Ellen Waldren has received more inquiries in the past week than it did in the whole of December. The free service, which is funded by donations, is currently helping about 1,800 healthcare workers a week.
Here, in her own words, Claire explains the scale of the mental health problem she is witnessing.
'People are feeling sick about going into work'

I'm waiting for the headline that says: 'Doctor takes own life because of the pandemic'. It is going to happen. If not today, it'll be soon because they are on their knees - and they want people to know that.
There is a huge amount of anxiety. People are feeling sick about going into work and what they're going to see.
They're seeing multiple deaths on a shift - someone the other day saw eight or nine people pass away. Someone else got in contact with us and said 'I know by the time I go back on my shift tomorrow six of my patients won't be there. How do I manage that?'
Frontline staff are not given any time to process it, so it's repeated, trauma after trauma after trauma. And yet these people go home, have their dinner, try and relax as best they can, get up, get washed - all the time worrying about if they're going to infect the people they live with.
Some people will function on autopilot, until such times when they physically can't, but they are being pushed to the brink.
'He put his head on the desk and sobbed'

London-based Frontline19 was set up by Claire Goodwin-Fee and Ellen Waldren to offer free therapy to healthcare professionals
We had a doctor who has a young family but is keeping separate from them, who was traumatised by the fact that he had lost two of his colleagues to Covid. On one shift he lost five patients pretty quickly into the shift and as soon as those beds were free, they filled up with more coming in.
He then had to phone up the relatives of the people who had sadly passed away. He said he wasn't equipped to do that - he didn't know what to say. He put the phone down and put his head on the desk and sobbed and he said: 'I can't manage it any more.'
Paramedics are getting called out on shifts where they're going to houses and they're telling us that they look at the people and they know they're going to die because they're so sick.
One of those events can happen and you could probably manage it with the right support. But this is happening numerous times a shift. How is anyone supposed to cope with that?
'It's horrendous out there'

Care home staff have really struggled throughout the pandemic.
The dedication and compassion to the people they look after is amazing; it's inspiring. A lot of them moved into the homes because they didn't want to risk the contamination of bringing things into the home.
Some have said they've lost 70% of the people in these homes. They've washed and dressed their bodies and these are people they've had relationships with; they've fed, they've looked after, they've talked to, they've shared memories with.
Then they have to dress them for their final moments, pick up their coat and go home or go upstairs and try to relax - how can anybody cope with that?
It's horrendous out there. It's absolutely horrendous and the care homes were ignored for a long, long time and they desperately need support.
I remember - it broke my heart - we had an email through at the start of the pandemic where someone very tentatively said: 'I don't suppose this service applies to those in care homes?' And I said 'yes of course it does, why wouldn't it?' And they said 'because we're not a professional service'.
It's heartbreaking that these are people who are professionally trained, who are saving the lives of numerous people, are being treated so poorly.
'NHS staff don't want to be clapped'

You've got doctors living in garages or hotels and are keeping separate from their loved ones because they know that this new strain is much more contagious so they need to protect them, while being mums and dads, grandparents and all these different things.
Their colleagues are dying around them and then you have these people saying 'Covid isn't real' or 'you've got time to do TikTok'.
I would love for people to see actually what's really going on in these wards. It's horrific.
We had a conversation with a few people this week about Clap for Carers, and I know it's meant in the best possible way but people are furious about it [returning]. They don't want to be clapped. What they want is for people to stay home and, if they have to go out, wear a mask.
'The system is starting to break'

We've had people that have been part of terrorist situations and they've never had support. They've now gone into this pandemic and they've got something called complex PTSD, which is when someone has seen numerous traumatic situations. We're getting a lot more people with that.
We're getting people who have post-traumatic stress disorder and yet a lot of them are still working.
There are people off sick with complete breakdowns. We've spoken to people who have been sectioned because they are so traumatised by what they're seeing.
The system is starting to break already but it's going to get worse.
In October, sick days in the NHS due to mental health was 500,000 days. This is going to be a bigger problem in the long term. This needs to halt now.
'What's going to happen to these people?'

It's amazing that people are reaching out for help, and of course we want to keep doing that, but at times it feels overwhelming. The need is so great. I think it's been that way for a while but obviously the more we talk about what's happening and share how difficult things are - and some people are really having horrific situations that they're having to work through - that increases the amount of people who seek support.
The positive side is with the right funding we could scale this. The psychotherapists [to whom Frontline19 refers healthcare workers] are all qualified and insured so they know what they're doing.
My concern is if we don't become sustainable and receive funding, in the long term what's going to happen to these people, the very backbone of the UK?
I'm really hoping that we can secure funding from the government so we can continue to support the amazing people in the NHS.
I strongly believe that we owe it to each other to look after one another. This could be a great time of connection and support but the changes need to be now.
As told to Sonja Jessup; produced by Rebecca Cafe
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Claire Goodwin-Fee's advice to frontline staff:
  • Talk to people; reach out to us - we're a very easy service. Don't wait until you're on your knees. There's a culture within the NHS about not talking about how you're feeling. That has to change now and that has to be a long-term change.
  • Don't blame yourself. It's a very natural response for anyone who has been through a traumatic experience to experience trauma. There isn't anything you're doing wrong and it's a very natural response to an abnormal situation.
  • There are resources out there - yes, they are busy but don't let that put you off.
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A Department of Health and Social Care spokesperson said: "Supporting the mental health and wellbeing of health and social care staff is a top priority, and we understand the huge pressures they face, particularly during this unprecedented pandemic."
The spokesperson added that the department had invested £15m to support the wellbeing and mental health of staff and developed a national support service for those most vulnerable to severe trauma. A mental health hotline, practical support and specialist bereavement and psychological support services were already available to staff, and since October the National Institute for Health Research has funded a range of research projects dedicated to understanding the impact of the pandemic on the mental health of frontline NHS staff, the spokesperson said.
"We would urge anyone struggling to come forward and speak to a colleague, their occupational health team or to call the helpline so that they can get the help they need."
 
Brazil ‘Covid variant of concern’ spotted in 11 UK cases

updated
Graeme Paton, Rhys Blakely
Friday January 15 2021, 1.30pm, The Times



A “variant of concern” of the coronavirus that was first spotted in Brazil has been identified in 11 cases in the UK, scientists have told The Times.
The variant — which is likely to be given the name “P2” — has a mutation that may help it evade some antibodies and it is being closely monitored by a consortium of researchers.
It is a different strain to the so-called “Manaus variant”, which is also thought to have originated in Brazil.
The P2 strain was first described in Rio de Janeiro in late December, from samples collected in October. It is not yet known where it has been identified in the UK.
It has caused concern, in part, because it contains a mutation known as E484K, which is thought to alter the shape of the spike protein that the virus uses to latch onto and enter human cells.


Laboratory tests have suggested that this mutation may help the virus evade neutralising antibodies.

Jeffrey Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute, said: “This mutation is one where some experiments have shown reduced, though not completely eliminated, binding of some antibodies, which is why any new variant that contains this mutation is monitored.”

The so-called “South Africa strain” also has the E484K mutation.
Another variant first seen in travellers from Brazil to Japan, and subsequently confirmed in the Brazilian city of Manaus, has not been identified in the UK. This strain — known as P1 — is believed to be part of the same lineage as P2.



The government has banned travellers from South America and Portugal under new measures designed to prevent the P2 variant being imported into the UK. The rules also cover Panama in Central America and the former Portuguese colony of Cape Verde.

The decision followed comments from Sir Patrick Vallance, the government’s chief scientific adviser, that the P1 Brazil variant could be resistant to vaccines.

A similar travel ban has been imposed on people entering the UK from South Africa, where another variant of concern is thought to have originated, since Christmas Eve.

All travel from Portugal will be banned under new government measures designed to prevent a Brazilian coronavirus variant being imported into the UK.
Grant Shapps, the transport secretary, said that direct flights from the country would be blocked from 4am today to limit the UK’s exposure to the highly contagious new strain.
The move comes on top of a ban on travel from 15 other countries covering the whole of South America plus Panama in Central America and the former Portuguese colony of Cape Verde.

Mr Shapps said that Portugal was included in the restrictions because of its “strong travel links with Brazil”. It covers the popular Portuguese holiday islands of Madeira and the Azores.

The decision followed comments from Sir Patrick Vallance, the government’s chief scientific adviser, that the Brazil variant could be resistant to vaccines.
Anyone who has been in one of the 16 countries in the past ten days has been told they will not be allowed to enter the UK. The measure is supposed to prevent travellers from taking connecting flights to the UK via third-party countries such as Spain, France and the Netherlands. However, critics said that the government was largely powerless to stop people from using these routes because the system relied on “honesty” from individual travellers.

A similar travel ban has been imposed on people entering the UK from South Africa since Christmas Eve. However, one passenger admitted to travelling from Durban to Heathrow via Paris yesterday, adding that there were no checks at passport control.

The Immigration Services Union, which represents border staff, said this week that only one in ten passengers was checked when they entered the UK to ensure they complied with rules.

A search of flights through Skyscanner, the travel website, showed that passengers could fly from Sao Paulo or Rio de Janeiro in Brazil to the UK using several one-stop routes over the next three days. These included flying with Iberia or Air Europa via Madrid, KLM via Amsterdam, Air France via Paris or Air Canada via Montreal.

Labour accused the government of being “too slow to act” over the emergence of new strains of the virus from Brazil and South Africa. It said that ministers had been made aware of the risks posed by the Brazil variant at the start of this week and waited five days to impose the travel ban.

No flights are operating between South America and the UK. It follows bans imposed by countries including Brazil on flights in the opposite direction, in response to the mutant strain of the virus that was first seen in the southeast of England.

However, regular services from Portugal have operated over the past month, with figures showing that it is the eighth biggest source of international flights into the UK.

An analysis from Cirium, the flight data company, showed that 87 flights had arrived or were due to operate from Portugal to the UK between January 6 and 21. There have been 11 into Heathrow, Stansted and Manchester this week.
More than half of scheduled flights are from Lisbon, which is a popular connecting route from South America into Europe.

Nick Thomas-Symonds, the shadow home secretary, said: “It is a necessary step that arrivals from Brazil, neighbouring countries and Portugal will be banned. However, this is yet another example of government incompetence, lurching from one crisis and rushed announcement to another.”
The new measures cover travel into the UK from Argentina, Brazil, Bolivia, Chile, Cape Verde, Colombia, Ecuador, French Guiana, Guyana, Paraguay, Panama, Portugal, Peru, Suriname, Uruguay and Venezuela. Anyone who has been in the countries in the past ten days will “no longer be granted access to the UK”. Those already in the UK will be required to quarantine for a full ten days.

British and Irish citizens will be exempt from the travel ban, although they will have to follow other rules, including a requirement to quarantine for ten days on arrival into the UK. Additionally, hauliers travelling from Portugal will be exempt to allow the transport of essential goods.

From Monday all travellers will have to register a negative coronavirus test result before boarding UK-bound flights.

Scientists believe that the Brazilian variant is the cause of an explosive second wave of Covid-19 in the vast state of Amazonas, where emergency services are close to breaking point (Stephen Gibbs writes).

In the capital of Manaus freezerlorries have been parked outside hospitals as their morgues fill up and there are reports of a chronic shortage of oxygen, vital for coronavirus patients with severe symptoms.

“The oxygen has run out and the hospitals have become asphyxiation chambers,” Jesem Orellana from the Manaus-based Fiocruz medical research centre told the Folha de São Paulo newspaper. Health workers were having to ventilate patients manually.

The Brazilian air force has begun transferring patients to the northeastern state of Piaui, where more hospital beds are available.

The fear is that the mutation, believed to be more infectious, was allowed to spread unchecked for weeks and could even be affecting those thought to be immune after the first wave.

It was Japanese experts who alerted the world to the new strain of the disease after routine tests in Tokyo among arriving passengers. Four Brazilians tested positive with the mutated version of Covid-19 after landing at Haneda airport on January 2. They developed mild symptoms and are in quarantine. All had recently passed through Manaus or other parts of the state of Amazonas, an area with a land mass six times that of the UK.

It is the second time that Manaus has been a hotspot for the pandemic. In April last year the city of 2 million people was seen as a warning to the world of what could happen if coronavirus was left unchecked.
Drone images showed the digging of mass graves in a forest clearing outside the city. Seriously ill people were being turned away from hospitals, which were recording 100 deaths a day at the peak of the outbreak.

By the summer it appeared that Manaus was through the worst of the crisis. Some researchers suggested the city had achieved “herd immunity” after one test indicated that 76 per cent of the population had been infected. That theory has been disproved with the second wave.

Manaus, built in the heart of the Amazon, is seen as vulnerable to Covid-19 as it is a free-trade zone and manufacturing centre with frequent traffic from Europe and Asia. It also has high levels of income divide, meaning that workers live in crowded homes while also mixing with employers who are regular travellers. The city is a stronghold of President Bolsonaro, who has referred to Covid-19 as a “little flu”.
 
the big question none of them will answer is how is the covid mutations more infective, their particle size is the same, their morphology is apparently more sticky (hydrophobic). My only answer is that it is being passed on by th kids!! And this something the everso clever sages do not want to admit!!
 
RafasLeftFoot said:
the big question none of them will answer is how is the covid mutations more infective, their particle size is the same, their morphology is apparently more sticky (hydrophobic). My only answer is that it is being passed on by th kids!! And this something the everso clever sages do not want to admit!!
Click to expand...

As viruses replicate, they change, or mutate. Some mutations give these viral variants an edge, such as being better able to latch on to and infect human cells. That’s what scientists now know happened with the mutation that has emerged here.

Mutations can also make a viral pathogen stealthier (smarter!), or better at evading the body’s immune system. This is why the WHO and local scientists find it particularly worrisome about another mutation seen in the variants that emerged recently in South Africa and Brazil.

Key mutations in these variants affect the coronavirus’s spike protein, which studs the surfaces of coronavirus particles. It’s the spike protein that helps the virus enter cells and infect people.

The spike protein is made up of three identical parts known as protomers. In the original version of the coronavirus that originated in China, these protomers usually assumed a closed shape, which is relatively inefficient at binding to human cells.

But the local mutation known as D614G makes it more likely for the spike protein to have a more open shape.. This open conformation enhances the virus’s ability to bind to human cells, according to Jeremy Luban, the University of Massachusetts Medical School, and that makes it more highly infectious as many who encounter the virus may well have a very small virus load that in the old variant your immune system could detect and respond to and stop it from replicating, however as is being shown by the younger ages now being admitted to hospital around the country, this mutation takes hold so quickly that even healthy young people are seeing it take hold faster than their immune system can react.

Hence its ability to infect more people is why it's doing the damage it is.
 
yet the method of transmission has effectively remained the same, which really begs the question how did the rate of transmission change. Deadly night shade are more poisonous then fox gloves, but you have to eat them first.

Spursex, I am not sure you actually understood what I said. First lock down effectively. Slowed the rate down, only when the kids are kept off school do we see the rates reduce. I do not deny that one form of virus can be more effective in breaking through the cell wall. But I am really concerned that the actual truth of transmission is being politically suppressed
 
RafasLeftFoot said:
yet the method of transmission has effectively remained the same, which really begs the question how did the rate of transmission change. Deadly night shade are more poisonous then fox gloves, but you have to eat them first.

Spursex, I am not sure you actually understood what I said. First lock down effectively. Slowed the rate down, only when the kids are kept off school do we see the rates reduce. I do not deny that one form of virus can be more effective in breaking through the cell wall. But I am really concerned that the actual truth of transmission is being politically suppressed
Click to expand...

Sorry, you're making no sense.
 
The method of transmission has not changed, the way transmission is progressing has changed. The impact of effectiveness of contracting the virus has changed.

It means people were getting it from a third source and that is children..
 
RafasLeftFoot said:
The method of transmission has not changed, the way transmission is progressing has changed. The impact of effectiveness of contracting the virus has changed.

It means people were getting it from a third source and that is children..
Click to expand...

So that's nothing to do with 'politically suppressed' then.
 
Nick Real Deal said:
Over 37,000 in hospital, that's way more than the first phase peak. A new covid admission every 30 seconds. The pressure is immense.
Click to expand...

It is, but thankfully, the admission rate locally is beginning to fall, sadly the death rate is still climbing, the army medics are assisting locally now, but we still will need this lockdown for some months to come as the NHS staff will all need a period of recuperation.
 
I was out for a walk today with the wife. We’ve been really impressed the past few weeks with more and more people actually following guidelines.

Most businesses in my town are closed, it’s a small town of approx 10k but has a busy town square (pre covid) the past week weeks it’s like a ghost town and I live in hope that community transmission will reduce and pressures on hospitals will subside.

To my shock and fury today I saw what I can only describe as a complete f**k wit driving around with a large screen on a trailer discouraging mask wearing and promoting endless covid conspiracy theories.

The mind truly boggles.

I can only hope that he is locked up and the key thrown away.
 
SheringhamNo10 said:
I was out for a walk today with the wife. We’ve been really impressed the past few weeks with more and more people actually following guidelines.

Most businesses in my town are closed, it’s a small town of approx 10k but has a busy town square (pre covid) the past week weeks it’s like a ghost town and I live in hope that community transmission will reduce and pressures on hospitals will subside.

To my shock and fury today I saw what I can only describe as a complete f**k wit driving around with a large screen on a trailer discouraging mask wearing and promoting endless covid conspiracy theories.

The mind truly boggles.

I can only hope that he is locked up and the key thrown away.
Click to expand...

Sadly, there are so many fcukwits in this World.
 
Spursex said:
So that's nothing to do with 'politically suppressed' then.
Click to expand...


Boris said the schools are safe, meanwhile introducing mass testing in schools, politically suppressed or a dichotomy ... YOU CHOOSE! The argument that children where not passing it on is frankly ridiculous. In the future there will be real evidence of whether children and what age they could spread the virus,instead of anecdotal guessing and not a policy decision to keep schools open, which was a huge mistake. Kids in school was the major difference in transmission not mutations
 
RafasLeftFoot said:
Boris said the schools are safe, meanwhile introducing mass testing in schools, politically suppressed or a dichotomy ... YOU CHOOSE! The argument that children where not passing it on is frankly ridiculous. In the future there will be real evidence of whether children and what age they could spread the virus,instead of anecdotal guessing and not a policy decision to keep schools open, which was a huge mistake. Kids in school was the major difference in transmission not mutations
Click to expand...

Boris seemed to have the misguided notion that schools were safe for children because kids dont get ill from Covid. That might be generally true but not 100%. Also it's the spread via children that is unsafe, where are they going, who are they mixing with, how responsible are their parents etc.
 
Nick Real Deal said:
I didnt need scientists to tell me schools were safe or not. Or wearing masks was beneficial, or closing our border was needed early etc. We have the worst death rate from Covid in the world for a reason.
Click to expand...

All goes back to the deaths in Care homes, in the first lockdown NHS and local councils were sending old people taking up beds straight into carehomes - without testing! - and that was the initial surge of deaths that drove the first wave.

You may not need scientists to tell you about the safety of schools, but their is a committee that does just that and the pressure to keep schools opening and functioning has been immense, and most of the European countries, if not all have also been keeping their schools open.

The problem has always been keeping open for business v complete and utter lockdown - the government lockdown down has had almost every business sector screaming blue murder.

We also calculate our deaths differently to many other countries claiming lower death per 100,000

edit: These are the great and the good who advise on safety in schools and who recommend which schools/ages should remain open:

Children’s Task and Finish Working Group

The group provides consolidated scientific health advice to government. Subject advice focuses on the transmission of COVID-19 in children and within schools, ensuring research questions are fed into relevant studies and UKRI/ funders for new funding.

Professor Laura Bear London School of Economics Professor Chris Bonnell London School of Hygiene and Tropical Medicine Dr Ellen Brooks-Pollock University of Bristol Professor John Edmunds London School of Hygiene and Tropical Medicine Dr Rosalind Eggo London School of Hygiene and Tropical Medicine Dr Thomas Finnie Public Health England Ms Clementine Fu Her Majesty’s Government Professor Julia Gog University of Cambridge Professor Peter Horby University of Oxford Dr Thomas House University of Manchester Dr Lorna Howarth Her Majesty’s Government Dr Michael J Tildesley University of Warwick Professor G. J. Melendez University of Exeter Professor Matt Keeling University of Warwick Dr Petra Klepac London School of Hygiene and Tropical Medicine Professor Graham Medley London School of Hygiene and Tropical Medicine Dr Gavin Morgan University College London Professor Cath Noakes University of Leeds Professor Michael Parker University of Oxford Dr Lorenzo Pellis University of Manchester Mr Osama Rahman Chief Scientific Adviser, Department for Education Dr Jonathan Read Lancaster University Professor Steven Riley Imperial College London Professor Brooke Rogers Kings College London Dr Edwin Van Leeuwen Public Health England Professor Russell Viner University College London Professor John Watkins Cardiff University and Public Health Wales Professor Charlotte Watts Chief Scientific Adviser, Department for International Development Professor Lucy Yardley University of Bristol and University of Southampton

7 participants have not given permission to be named.
 
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