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Post by Admin on Dec 20, 2020 5:31:29 GMT
UK reports new variant, termed VUI 202012/01 The United Kingdom reported a new variant, termed VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01). It was defined by multiple spike protein mutations (deletion 69-70, deletion 144-145, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). There are currently 24,746 viruses from the UK in GISAID EpiCoV with a collection date since 1. November. A small fraction of them, about 6% (all from clade GR) share several of these mutations. Based on evaluation of effect on virus structure and function, the most relevant might be N501Y (orange in Figure; host receptor and antibody binding, also reported at gisaid.org/spike) and the deletions (cyan in Figure) in positions contributing to potential spike surface variation (Y145del is where some antibodies like neutralizing 4A8 bind).  The other mutations (blue in Figure) are further down the structure and their effect is less clear. There is also an early NS8 Q27stop codon in these strains which could be relevant as ORF8 deletions have been seen before for this virus (including in Singapore, notably resulting in attenuation). As seen on many occasions before, mutations are naturally expected for viruses and are most often simply neutral regional markers useful for contact tracing. The mutations seen have rarely been affecting viral fitness and almost never affect clinical outcome but the detailed effects of these mutations remain to be determined fully. A new coronavirus variant has swept across London and the South East and is spreading faster than the original strain. The government's chief scientific adviser, Sir Patrick Vallance, warned that the new Covid variant was becoming the dominant strain following a rapid rise in cases in recent days. Stood next to him at Downing Street's Saturday press conference was England's chief medical officer, Professor Chris Whitty, who said the new variant can spread more rapidly. Its rapid transmission through the region has led to London, the South East and parts of Eastern England being plunged into new Tier 4 restrictions from Sunday morning. So what is the new mutant form of coronavirus? Where is the new variant prevalent? And are there different symptoms? What is the new coronavirus strain? The new strain is a mutation in the SARS-CoV-2 virus that has been at the heart of the UK's coronavirus outbreak. It has been named VUI-202012/01, the first variant being investigated by Public Health England (PHE) in December. There are currently about 4,000 mutations in the spike protein gene. Is the new Covid variant more deadly or dangerous? Although the new variant is spreading faster, and therefore harder to control, there is currently no suggestion that it is more deadly or causes more sever symptoms. There have also already been various mutations of Covid-19 that have enter communities with no real consequence. However, Prime Minister Boris Johnson said that early analysis showed the new strain could increase the reproductive rate by 0.4 or more and that it may be up to 70 per cent more transmissible than the old variant. Sir Patrick confirmed this, saying the variant had a "significant substantial increase in transmissibility". New strains are not always necessarily a bad thing and it could even be less virulent, but if it spreads quicker and has the same severity then more people will become ill in a shorter period of time. Will vaccines work against the new strain? Prof Whitty said that there is no current evidence to suggest the new strain causes a higher mortality rate or that it affects vaccines and treatments. However, he said that "urgent work" was under way to confirm this and warned that it was "more vital than ever" that people continued to take action to reduce the spread of the virus. Health Secretary Matt Hancock also said the latest clinical advice is that it is highly unlikely that this mutation would fail to respond to a vaccine as it produces antibodies against many regions in the spike protein. But PHE said this new variant includes a mutation in the spike protein and that this may result in the virus becoming more infectious and spreading more easily between people. |
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Post by Admin on Dec 20, 2020 19:30:39 GMT
Covid-19: New coronavirus variant is identified in UK BMJ 2020; 371 doi: doi.org/10.1136/bmj.m4857 (Published 16 December 2020) England’s health secretary, Matt Hancock, has told parliament that a new variant of covid-19 has been identified and may be driving infections in the south east, leading to headlines about “mutant covid.” Jacqui Wise answers some common questions What do we know about this new SARS-CoV-2 variant? It’s been snappily named VUI-202012/01 (the first “Variant Under Investigation” in December 2020) and is defined by a set of 17 changes or mutations. One of the most significant is an N501Y mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of spike protein may, in theory, result in the virus becoming more infectious and spreading more easily between people. How was the variant detected? It was picked up by the Covid-19 Genomics UK (COG-UK) consortium, which undertakes random genetic sequencing of positive covid-19 samples around the UK. The consortium is a partnership of the UK’s four public health agencies, as well as the Wellcome Sanger Institute and 12 academic institutions. Since being set up in April 2020 the consortium has sequenced 140 000 virus genomes from people infected with covid-19. It uses the data to track outbreaks, identify variant viruses, and publish a weekly report (https://www.cogconsortium.uk/data/). How common is it? As of 13 December, 1108 cases with this variant had been identified in the UK in nearly 60 different local authorities, although the true number will be much higher. These cases were predominantly in the south east of England, but there have been recent reports from further afield, including Wales and Scotland. Nick Loman, professor of microbial genomics and bioinformation at the University of Birmingham, told a briefing by the Science Media Centre on 15 December that the variant was first spotted in late September and now accounts for 20% of viruses sequenced in Norfolk, 10% in Essex, and 3% in Suffolk. “There are no data to suggest it had been imported from abroad, so it is likely to have evolved in the UK,” he said. Does this variant spread more quickly? Matt Hancock told the House of Commons on 14 December that initial analysis showed that the new variant “may be associated” with the recent rise in cases in southeast England. However, this is not the same as saying that it is causing the rise. Loman explained, “This variant is strongly associated with where we are seeing increasing rates of covid-19. It’s a correlation, but we can’t say it is causation. But there is striking growth in this variant, which is why we are worried, and it needs urgent follow-up and investigation.” Is mutation to be expected? SARS-CoV-2 is an RNA virus, and mutations arise naturally as the virus replicates. Many thousands of mutations have already arisen, but only a very small minority are likely to be important and to change the virus in an appreciable way. COG-UK says that there are currently around 4000 mutations in the spike protein. Sharon Peacock, director of COG-UK, told the Science Media Centre briefing, “Mutations are expected and are a natural part of evolution. Many thousands of mutations have already arisen, and the vast majority have no effect on the virus but can be useful as a barcode to monitor outbreaks.” Is the new variant more dangerous? We don’t know yet. Mutations that make viruses more infectious don’t necessarily make them more dangerous. A number of variants have already been detected in the UK. For example, the D614G variant is believed to have increased the ability of the virus to be transmitted and is now the most common type circulating in the UK, although it doesn’t seem to result in more severe disease. Public Health England’s laboratory at Porton Down is currently working to find any evidence that the new variant increases or decreases the severity of disease. Susan Hopkins, joint medical adviser for NHS Test and Trace and Public Health England, said, “There is currently no evidence that this strain causes more severe illness, although it is being detected in a wide geography, especially where there are increased cases being detected.” Will the vaccine still work? The new variant has mutations to the spike protein that the three leading vaccines are targeting. However, vaccines produce antibodies against many regions in the spike protein, so it’s unlikely that a single change would make the vaccine less effective. Over time, as more mutations occur, the vaccine may need to be altered. This happens with seasonal flu, which mutates every year, and the vaccine is adjusted accordingly. The SARS-CoV-2 virus doesn’t mutate as quickly as the flu virus, and the vaccines that have so far proved effective in trials are types that can easily be tweaked if necessary. Peacock said, “With this variant there is no evidence that it will evade the vaccination or a human immune response. But if there is an instance of vaccine failure or reinfection then that case should be treated as high priority for genetic sequencing.” This article is made freely available for use in accordance with BMJ's website terms and conditions for the duration of the covid-19 pandemic or until otherwise determined by BMJ. You may use, download and print the article for any lawful, non-commercial purpose (including text and data mining) provided that all copyright notices and trade marks are retained. |
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Post by Admin on Dec 21, 2020 4:43:33 GMT
EU ambassadors are to hold a crisis meeting in Brussels on Monday to discuss travel restrictions on the UK as multiple countries began closing their doors to travellers from Britain after the discovery of a fast-spreading strain of Covid-19.
As the World Health Organization called on European members to step up measures, Belgium, France, Germany, Ireland and the Netherlands on Sunday announced the suspension of air links – and in some cases rail and ferry routes – from Britain.
The bans were mostly scheduled to last about 48 hours as a precaution while the threat of the new strain was evaluated and a coordinated response worked out at a European level, national governments said.
An EU official told Agence France-Presse that representatives from the 27-member states would meet on Monday under the bloc’s integrated political crisis response mechanism designed to swiftly react to crises.
France said it was suspending all passenger and human-handled freight transport, whether by road, air, sea or rail, coming from the UK to France for 48 hours from midnight on Sunday.
Eurotunnel’s last shuttle left the UK for France at 9.34pm, while the Dover port authority said its ferry terminal was closed to “all accompanied traffic leaving the UK until further notice due to border restrictions in France”.
Germany, which is suspending flights from midnight on Sunday, has not yet detected the new strain but is taking reports from the UK “very seriously”, its health minister Jens Spahn said.
A German government source said the restriction could be adopted by the entire 27-member EU bloc and that countries were also discussing a joint response over sea, road and rail links with Britain.
The German chancellor Angela Merkel held a conference call with the French president, Emmanuel Macron, and the EU chiefs Ursula von der Leyen and Charles Michel about the matter.
The Spanish government said it had asked the European commission and council to come up with a “joint, coordinated response” to the situation, but that it would “act in defence of the interests and rights of Spanish citizens” if one was not forthcoming.
Belgium is also suspending flight and Eurostar arrivals from Britain from midnight. The prime minister, Alexander De Croo, said the ban would initially be in place for at least 24 hours.
Italy, which said it had detected the new strain of the coronavirus in a patient who had recently returned from Britain, blocked all flights departing from Britain and barred anyone who had transited through the country in the last 14 days from entering Italian territory.
The foreign minister, Luigi Di Maio, said the government had decided to act after the UK raised the alarm about the new strain.
“As a government we have the duty to protect Italians and for this reason, after having warned the British government, the health ministry will sign a provision for the suspension of flights with the UK,” he said. “Our priority is to protect Italy.”
Austria and Sweden also said they were preparing decisions to ban flights from the UK, but were still working out the details.
The Dutch ban, which came into effect from 6am local time on Sunday, will last until 1 January. Ireland will impose restrictions on flights and ferries from Britain from midnight, while Bulgaria is suspending flights from and to the UK from midnight until 31 January. Romania also said it had banned all flights to and from the UK for two weeks starting on Monday afternoon.
The WHO said it was in close contact with British officials, and that outside the UK nine cases of the new strain had been reported in Denmark, one in the Netherlands and one in Australia. “Across Europe, where transmission is intense and widespread, countries need to redouble their control and prevention approaches,” a spokeswoman for WHO Europe said.
Were it to continue into January, the travel disruption could exacerbate transport problems caused by Brexit as Britain leaves the EU’s single market, which guarantees movement within its borders.
Israel, too, imposed new measures on Sunday, barring entry to non-citizens arriving from the UK, Denmark and South Africa, citing fears about Covid variants. Israeli citizens arriving from those countries will have to enter isolation at state-run quarantine hotels for up to 14 days.
The hastily enacted decision led to confusing scenes at Israel’s international airport, where according to domestic media about 130 passengers on two flights from London were informed of the new quarantine requirements on arrival. Police were called to the scene after several people refused, Channel 12 news reported, and 12 decided to return to the UK.
Ellen Steel, a British–Israeli citizen on one of the flights, said she was ordered to board a crowded bus without being told where she was going. “At Luton, check-in was normal, but then they called boarding 1.5 hours early. At the gate, they turned everyone away [all non-Israelis] who had a British passport,” she told the Times of Israel.
“When we landed someone from the health ministry came on [the plane] and announced we’d all have to go to hotels. If we wanted to have a fight about it we could but only at the hotel and not before,” she said. Police escorted the buses, she added.
The UK government announced emergency restrictions after Public Health England said it had identified more than 1,100 cases of a new variant of coronavirus that may be speeding up the spread of the virus, particularly in south-east England.
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Post by Admin on Dec 21, 2020 19:35:39 GMT
Reports from Britain and South Africa of new coronavirus strains that seem to spread more easily are causing alarm, but virus experts say it’s unclear if that’s the case or whether they pose any concern for vaccines or cause more severe disease.
Viruses naturally evolve as they move through the population, some more than others. It’s one reason we need a fresh flu shot each year.
New variants, or strains, of the virus that causes COVID-19 have been seen almost since it was first detected in China nearly a year ago.
On Saturday, Prime Minister Boris Johnson announced new restrictions because of the new strain. Several European Union countries and Canada were banning or limiting some flights from the U.K. to try to limit any spread.
Here’s what is known about the situation.
Health experts in the U.K. and U.S. said the strain seems to infect more easily than others, but there is no evidence yet it is more deadly.
Patrick Vallance, the British government’s chief scientific adviser, said that the strain “moves fast and is becoming the dominant variant,” causing over 60% of infections in London by December.
The strain is also concerning because it has so many mutations — nearly two dozen — and some are on the spiky protein that the virus uses to attach to and infect cells. That spike is what current vaccines target.
“I’m worried about this, for sure,” but it’s too soon to know how important it ultimately will prove to be, said Dr. Ravi Gupta, who studies viruses at the University of Cambridge in England. He and other researchers posted a report of it on a website scientists use to quickly share developments, but the paper has not been formally reviewed or published in a journal.
HOW DO THESE NEW STRAINS OCCUR?
Viruses often acquire small changes of a letter or two in their genetic alphabet just through normal evolution. A slightly modified strain can become the most common one in a country or region just because that’s the strain that first took hold there or because “super spreader” events helped it become entrenched.
A bigger worry is when a virus mutates by changing the proteins on its surface to help it escape from drugs or the immune system.
“Emerging evidence” suggests that may be starting to happen with the new coronavirus, Trevor Bedford, a biologist and genetics expert at the Fred Hutchinson Cancer Research Center in Seattle, wrote on Twitter. “We’ve now seen the emergence and spread of several variants” that suggest this, and some show resistance to antibody treatments, he noted.
WHAT OTHER STRAINS HAVE EMERGED?
In April, researchers in Sweden found a virus with two genetic changes that seemed to make it roughly two times more infectious, Gupta said. About 6,000 cases worldwide have been reported, mostly in Denmark and England, he said.
Several variations of that strain now have turned up. Some were reported in people who got them from mink farms in Denmark. A new South African strain has the two changes seen before, plus some others.
The one in the U.K. has the two changes and more, including eight to the spike protein, Gupta said. It’s called a “variant under investigation” because its significance is not yet known.
The strain was identified in southeastern England in September and has been circulating in the area ever since, a World Health Organization official told the BBC on Sunday.
Probably not, former U.S. Food and Drug Commissioner Scott Gottlieb said Sunday on CBS’s “Face the Nation.”
“Unlikely,” Gupta agreed.
President-elect Joe Biden’s surgeon general nominee, Vivek Murthy, said Sunday on NBC’s “Meet the Press” that there’s “no reason to believe that the vaccines that have been developed will not be effective against this virus as well.”
Vaccines produce wide-ranging responses by the immune system beyond just those to the spike protein, several experts noted.
The possibility that new strains will be resistant to existing vaccines are low, but not “inexistent,” Dr. Moncef Slaoui, the chief science adviser for the U.S. government’s vaccine distribution effort, said Sunday on CNN’s “State of the Union.”
“Up to now, I don’t think there has been a single variant that would be resistant,” he said. “This particular variant in the U.K., I think, is very unlikely to have escaped the vaccine immunity.”
Bedford agreed.
“I’m not concerned” because a lot of changes in the genetic code would probably be needed to undermine a vaccine, not just one or two mutations, Bedford wrote on Twitter. But vaccines may need fine-tuned over time as changes accumulate, and changes should be more closely monitored, he wrote.
Murthy said the new strain doesn’t change the public health advice to wear masks, wash hands and maintain social distance.
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Post by Admin on Dec 21, 2020 23:37:51 GMT
A New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) meeting on the SARS-CoV-2 variant under investigation, VUI-202012/01, took place on the 18 December.
Prof Martin Hibberd, Professor of Emerging Infectious Disease, London School of Hygiene & Tropical Medicine (LSHTM), said:
“With so many SARS-CoV-2 infections in the world, it is not unexpected that new strains may occur and compete for selective advantage. And it seems that the intensive surveillance programme undertaken by the UKs ICOG sequencing consortium (as part of a larger worldwide effort), has now identified a distinctive cluster of viruses, that they have termed the ‘B.1.1.7 lineage’. This lineage seems to be the first to be identified that has acquired a number of mutations that differentiate it from other viruses that have been reported around the world. Worryingly, several of these mutations may have functional significance. While new mutations occur at a steady rate, they have not, until B.1.1.7, accumulated into a single strain, suggesting that this new variant has acquired them through selection for improved properties. As viruses are transmitted, those that allow for increased virological ‘success’ can be selected for, which changes the properties of the virus over time. This typically leads to more transmission and less virulence and for human infecting coronaviruses the end result of this evolutionary process might look like the other 4 commonly found coronaviruses that cause symptoms that we recognise as the common cold – however, these 4 common cold viruses are highly contagious. The new B.1.1.7 may be on the path towards this but is not there yet, and still appears to have all the human lethality that the original had but with an increased ability to transmit. Hopefully, it does not alter the immune response sufficiently to interfere with the vaccine protection. While the consequences of this new strain are still being worked out, it seems prudent to try to reduce its spread around the UK and the rest of the world.”
Prof Rowland Kao, Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, said:
“There appear to be at least two lines of evidence for showing that the strain is more transmissible. First, by comparing the number of observed copies of the variant strain (i.e. virus taken from infected people with the identical or near-identical type) to the number of copies of different strains circulating in the same area, you can estimate directly the rate at which the type is reproducing itself compared to others. However this is reliant on having a good number of samples that capture the new variant and other types in reasonably close proportion to each other.
“Second, you can estimate the reproduction number R, around where the variants are, and compare it to the R number elsewhere, however this is less precise because you don’t always know what is causing the new cases (is it the new variant or another type?). The fact that these two lines of evidence give similar increases in transmissibility makes the overall case more robust. That the increase in transmission is so high (the central estimate being perhaps 70% higher) is a cause for some considerable concern, as reflected in the increasing transmission even when under Tier 3 restrictions.
“Of additional concern is that many people who were aiming to travel for the Christmas break likely would have already done so; add-in the anecdotal reports of people rushing to travel before restrictions, and this raises the possibility that travel bans are already too late to have prevented widespread circulation of the new variant across the UK, spread that will only increase due to people returning to their non-holiday places of residence, after the break. While it remains possible that this variant is actually less likely to cause severe illness, we shall not know one way or another for some time. In the meantime, the implications for this (less effectiveness of lower level tiers, more vaccinations needed to achieve herd immunity, for example) imply that these restrictions may be in place for some time, possibly at least until vaccination is able to achieve good protection of the most vulnerable.”
Dr Julian Tang, Honorary Associate Professor/Clinical Virologist, University of Leicester, said:
“The spread of this new virus variant could be due to many factors. As we saw with the earlier D614G variant – just higher viral loads in clinical diagnostic swabs or in cell culture may not necessarily translate to a more transmissible virus at the population level.
“A higher genomic growth rate in the samples sequenced, may not necessarily mean higher transmissibility, e.g. if there was a rave of several thousand people where this variant was introduced and infected many people mostly in that rave, this may seem very high compared to a lower background of non-variant virus, e.g. in an otherwise prevailing national lockdown.
“The NERVTAG team appear to be being very careful about such comparisons – and possible ‘founder effects’ that might be misleading – which is good.
“At least two of the mutations in this new variant, N501Y (since at least Apr 2020 in Brazil) and 69-70del (since at least Jan/Feb 2020 in Thailand/Germany) were already circulating globally prior to combining into this new variant.
“This is quite normal for viruses – like influenza – where different viruses may infect the same person, leading to a hybrid virus emerging. This is just one of the ways that natural viral variation arises.
“We are not seeing any increased virulence (clinical severity) or any gross changes in the S (spike protein) that will reduce vaccine effectiveness – so far.
“New viruses will adapt to a new host over time – with decreasing mortality, and possibly increasing transmissibility.
“It makes no sense for the virus to kill its host – rather better for it to replicate to high levels in the host, causing few symptoms – so that the host can stay mobile and appear well (asymptomatic) – to allow it to mingle further with those who are still susceptible – and spread its genes further.
“We are now likely seeing some of this new host adaptation process in SARS-COV-2, but it remains to be seen whether mortality will be different with this variant than with the previous one.”
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