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The UK Health Secretary, Sajid Javid, has confirmed that two cases of the Omicron variant have been detected in the UK.
Comments sent out Sunday 28th Nov:
Dr Julian Tang, Honorary Associate Professor/Clinical Virologist, University of Leicester, said:
“So we have been through all of this before with the alpha and delta variants – but the main difference is that the scientific evidence for the effectiveness of masks and social distancing has increased – and there is more conviction now amongst scientists that these measures do work to reduce the spread of the virus.
“But note that protection is not black and white – masking, social distancing, improved ventilation just reduce these risks – they do not remove them completely.
“So wearing any mask or face covering (cloth, surgical, etc.) is better than none; some degree of social distancing is better than none; some ventilation is better than none. A combination of these is also better than just one, e.g. if you can open the windows (even just a little) on a bus, and sit spaced out in every other seat, and wear a mask, this will protect you more than any of these measures individually.
“Clearly, if restaurants and bars are to remain open then wearing masks in these settings is not practical – when people are eating and drinking. But of course, there is then the risk of acquiring a new infection in such ‘unmasked’ settings and bringing it home to others.
“So far, the current COVID vaccines have worked well against the predominant delta variant to reduce severe disease and death – though are not so effective in preventing infection/reinfection.
“This has allowed hospitality to stay open – but we are still seeing 30,000-50,000 new COVID-19 cases per day – with 500-1000 daily hospital admissions and 100-200 daily deaths. Yet we are choosing to live with this level of infection/morbidity/mortality in the UK – including the reopening of international travel and large crowded sports and entertainment events.
“So the crucial question with the new omicron variant in this context is – will this new variant change this balance?
“We don’t have enough data to assess this now – so some caution and reimposition of some restrictions is not a bad idea – whilst we accumulate more data to make such an assessment.”
Dr Peter English, Retired Consultant in Communicable Disease Control, Former Editor of Vaccines in Practice, past Chair of the BMA Public Health Medicine Committee, said:
“I published blogs relating to this issue. One, from May 2021, was about new variants: “New variants will become routine”, here.1 And I described how viruses mutate and evolve in another post, “Won’t the delayed second dose encourage the evolution of vaccine escape mutants?” available here.2)
“First, let’s have a recap on how mutations arise.
“Most of the plants and animals we see – and bacteria, fungi, and many viruses – carry their genetic material in the form of the famous double helix. DNA comprises two strands of genetic material, twisted together. When cells divide this is copied. A few errors are made in the process of copying; but remarkably few: DNA duplication has good error correcting mechanisms. These errors cause changes in the DNA of copied (“daughter”) cells. Unless they occur in the germ cells, they do not affect subsequent generations.
“Some viruses carry their genetic material in the form of single-stranded RNA. This is much more prone to copying errors as the virus replicates. Coronaviruses, like SARS-CoV-2, the cause of Covid-19, is an RNA virus with has reasonably good error correction mechanisms, so it mutates relatively slowly. Note that this doesn’t mean “slowly” in our terms; viruses replicate very quickly and in astronomically large numbers; they are just slower than some viruses like human immunodeficiency virus (HIV) and influenza (flu) virus.
“(The flu virus has another mutation trick up its sleeve. As well as errors in replication, it has “segmented” RNA, and can swap sections or segments of RNA with other, different influenza viruses, leading to novel viruses. One of our biggest fears is a flu virus which has the pathogenicity (ability to cause serious disease or death) of the “highly pathogenic avian influenza” – a form of bird flu that kills most birds, and very occasionally infects humans; combined with an ability to infect and transmit easily between humans.)
“Many of the errors that arise as viruses replicate will harm the new variants, and these will quickly die out. A few, however, by chance, can provide benefits, making the virus better able to bind to human cells (and thereby cause infection); or to increase the amount of virus in respiratory droplets. When variants arise which are more infectious, they tend, over time, to replace existing strains. We saw this, for example, with the delta variant, which has largely replaced the strains circulating previously.
“The Omicron variant has a large number of mutations: 50 mutations overall, 10 on the receptor binding domain of the spike protein (compared to 2 on the RBD for the Delta variant). This high level of mutation suggests the variant likely emerged from a persistent infection in an immunocompromised person.
“The number of mutations, per se, does not mean that the new variant will cause any problems; although it may make it more likely to look different to the immune system. If the immune system fails to recognise it, there may be “immune escape”, with people who have recovered from a previous Covid-19 infection, or who have been vaccinated, failing to recognise the virus, and becoming ill, despite their prior immunity.
“And the new variant may be more infectious, meaning that people who are not immune to it are less likely to be able to avoid catching it. Even if vaccines work just as well, we would need to have more people vaccinated and immune, to achieve herd immunity to a more infectious strain. I have discussed this previously eg in “How many people have to be immunised to provide herd immunity?” blog version here.3
“So, what do we know about how the Omicron variant behaves?
“It seems to be rapidly increasing in Southern African countries, suggesting either that it is more infectious than previous strains, or that there is less immunity to it. (Barclay describes clearly how this could happen in this twitter thread.4)
“These Southern African countries are relatively poorly vaccinated, the world has done a shamefully poor job of ensuring that poorer countries are vaccinated, and most people in the populations in which it has spread are unvaccinated, so we do not know how the virus would behave in a more highly vaccinated population. It is quite possible that people who have had two or, better still, three doses of existing vaccines will be well protected against it. But it is also possible that we will have much less protection, from existing vaccines, against this new variant. We do not yet have enough information to know.
“Given all of the uncertainties, we should take a precautionary approach.
“The NHS is already in dire straits. Another surge of cases might tip services over the edge. We have heard reports of delays to ambulances, very long waits for people with urgent conditions to be seen, and maternity services (where you cannot put things off) are at dangerous levels. We cannot afford another surge in cases.
“It is not possible to stop viruses from spreading from country to country; but we can take action to slow down the spread.5 Given that it is likely that vaccination will provide some protection – if not as much as it does against previous variants – the more people we can get vaccinated (with two, preferably three doses of vaccine) before it arrives, the better.
“From midday on Friday 26 Nov 2021, South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia were added to the UK’s travel red list. Passengers arriving from 4am Sunday in England are being required to book and pay for a government-approved hotel quarantine facility for 10 days. My concern is that, if we are to have a travel ban, it should be introduced immediately, to stop a rush of people trying to get in before the gates close. It is not clear to me why these actions were not taken with immediate effect.
“There have also been reports of people being allowed to leave airports having travelled from those countries, on public transport, and without prior testing. This must stop.
“We also need to recognise that the virus is already seeded elsewhere; and people may try to get around travel bans by travelling via third countries. It is also likely that the variant has been circulating unobserved, as only a minority of people tested get the viral genome sequenced (although, now we know about it, there are some markers that allow this variant to be detected using routine PCR tests – if you look for it).
“So we need to quarantine people entering the country again, at least until we understand this new variant better.
“We have learned a lot about Covid-19, nearly all of which applies to the new variant. It is an airborne virus, so we should take steps to reduce airborne transmission – indeed, we should already have been doing so to control the delta variant. Gurdasani describes these clearly in a twitter thread.6 They include:
Antivirals
“The mutations in the omicron variant mean that it is possible (we don’t know for sure) that vaccines and monoclonal antibody treatments will not work as effectively.
“Standard antivirals, however – like (for example) Molnupiravir – are likely to work as well against the new variant as against previous variants.
“I have reservations about their value, however.7 It is almost certain they will have to be given very early if they are to be effective. This will mean giving them to people who are not very unwell, to prevent subsequent severe illness. Since most people with Covid-19 infection do not develop serious illness, this will mean giving antiviral drugs to many people who would never have gone on to develop serious illness. This means that the drugs will have to be:
“Doing all this will be difficult in practice, and I think their use will be confined to settings like care homes, and possibly chemoprophylaxis of contacts.
The booster programme
“Is it sensible to boost the booster programme. I think we will come to think of the schedule as a three-dose schedule, at intervals of 8-19 weeks between the first and second doses; three to six months between second and third doses; and possibly subsequent booster doses every year, or every few years.
“Each dose of vaccine boosts antibody levels; and, if antibodies can neutralise this new variant, but less effectively, higher antibody levels can be expected to be more effective. In addition, extra (“booster”) doses can enhance the tightness with which antibodies bind to the virus, and broaden immunity to provide better cross-protection against variants.
“We know hardly anything about omicron and vaccine efficacy so far. The virus has surged in Southern Africa – in a largely unvaccinated population. (The population is also different in other ways: higher rates of TB and HIV; lots of people employed in mining; different socioeconomic factors.) It is very hard to predict how it will behave in more highly vaccinated populations.
“Work is already underway looking at what we know about variants and the likelihood that antibodies will work against them.8 9 The genetic sequence of the Omicron variant will provide clues to this.
“These can be built upon by studies looking at how well antibodies developed by people who have had Covid-19 disease (natural immunity), or who have vaccine-induced immunity, neutralise the omicron variant in the laboratory.
“Ultimately, however, while these can give indications of what to expect, we need to observe how the variant spreads in different populations, especially in people with prior immunity and in populations with high levels of vaccine uptake. This will require good testing that can detect the new variant, and discriminate between it and other variants.
“If the new variant is as transmissible as has been suggested, much higher vaccine uptake rates will be required if we are to achieve herd immunity; and this means we cannot afford to leave parts of the population unvaccinated.
“That said, the Delta variant is already so infectious that, to reduce transmission, we need to get as much of the population fully vaccinated (with three doses) as soon as possible.
“We do not have any reason to expect the Omicron variant to cause serious illness than previous variants; but if it is more transmissible, we can expect more cases. This will mean more disruption, not just to the health service, but to schools and the education sector.
“We should already be vaccinating children in my opinion; the Omicron variant adds further urgency to this.
“The mRNA and vector platforms allow very rapid changes to be made to the precise antigens used. This means that it would be possible, relatively quickly (within a matter of months) to produce a vaccine with antigens tailored to a new variant.
“Manufacturers have been working on (including some trials) such vaccines.10 11 I do not know whether the changes in the Omicron variant are included in the vaccines that are already in development.”
References
Comments sent out Saturday 27th Nov:
Prof Paul Hunter, Professor in Medicine, The Norwich School of Medicine, University of East Anglia, said:
“In regard to the precautionary measure such as the border entry requirements, increased face coverings and quarantining of contacts. These are sensible precautions that will not stop the spread of the omicron variant but will slow its spread to give us time to learn more about the omicron variant and critically increase booster uptake. Given the indication from WHO today that omicron is associated with more reinfections it is likely that we will see more breakthrough infections in vaccinated people and so the requirement to quarantine even if double vaccinated makes sense. The big uncertainty at present is how much omicron can escape from vaccine control. If there is substantial escape then even control measures as strict as March 2020 would not be sufficient to bring the R value to below 1.0. The hope, however, is that even if vaccination or prior infection is insufficient to stop spread then they may still be sufficient to substantially reduce the risk of severe disease. Given some of the reports from South Africa that infection with omicron is generally mild this may not be a forlorn hope. The combined impact of the booster campaign and continuing high incidence of infection could likely go a long way to reduce the severity of infection due to omicron, but we will not know for a couple of more weeks yet.
“Reducing the gap between the second dose and the booster dose from 6 down to 5 months is unlikely to substantially reduce the protective effect of the booster dose and would certainly mean greater coverage of the population as we approach winter proper. My personal view is that reducing this gap to 5 months would be the right thing to do. It is certainly appropriate to get an urgent opinion from JCVI on this issue. As for vaccinating younger children, the balance of evidence on this is less clear and I think it unlikely that the new variant would substantially change the risk to children under 11 to the point that a rapid role out of the vaccine to this age group becomes necessary. The majority of children in the 5 to 11 age group have probably already had an infection and recovered, many relatively recently so the need for vaccination is not as urgent. It has been argued by many, and I agree, that such available vaccine would better be used in countries where they have still not managed to roll out the primary course. It is now in these countries where the biggest risk of emergence of even more worrying variance rests and as the WHO says “no one is safe until everyone is safe”.
“How much omicron would impact on the antiviral use depends largely on the antiviral. I suspect that most effective therapies such as dexamethasone would not be particularly affected by omicron as this drug targets the bodies response the virus not the virus. Drugs that inhibit viral replication, such as the recently licensed Molnupiravir, could drive mutation of the virus such that covid develops antiviral resistance (we do see this with antivirals with other viruses). However, it would be surprising that such anti-viral resistance would develop before use of these drugs. Consequently I doubt omicron would be more resistant to this class of antivirals. However those drugs that are based on monoclonal antibodies are likely to be less effective against a heavily mutated virus. I personally do not think that the omicron will dramatically affect our treatment strategies will the exception of the monoclonal antibodies because of their probable reduced effectiveness.”
Comment before press conference:
“The reports today of two infections with the omicron variant in the UK are not particularly surprising. Given what we know already from South Africa, it was almost inevitable that this variant had already made its way to our country.
“There is still a lot we do not know about omicron in particular whether it is intrinsically more transmissible or whether the variant can escape from immune control. Also we don’t know if infection with this variant is more or less severe than the other variants.
“Today’s comments from the WHO that the variant causes reinfections suggest that is does escape immunity. But the big issue is by how much. It is likely that we will see this further reducing the effectiveness of vaccines compared to Delta though not entirely blocking them. It is also important to remember that vaccine effectiveness against severe disease is usually more effective and longer lasting than effectiveness against infection. It may well be the case that this virus will cause less severe disease than prior variants but if it does that is likely to be due to existing immunity rather than something intrinsic to the virus. In any event it is far too early to make any judgements about the severity of illness and ultimate outcomes of an infection with omicron.
“If omicron does start spreading widely in the UK and that is almost inevitable in my view then will we see marked increases in hospitalisations and deaths? To a certain extent the fact that we have had high levels of infection these past few months and we are also rolling out the booster vaccine should provide a worthwhile degree of protection at least against severe disease, though whether this would be sufficient to reduce pressure on the health service is too early to say.
“However, even after a booster vaccine dose is given it takes 7 to 14 days for the full protection to develop. So waiting to see if omicron does indeed become common in the UK before booking your appointment for the booster could be too late to protect you from any serious illness this winter.
Dr Andrew Freedman, Reader in Infectious Diseases & Honorary Consultant Physician, Cardiff University School of Medicine, said:
“We already know that this Omicron variant spreads readily, even among those who have been double vaccinated. However, vaccination does not confer complete protection from infection with the Delta variant, so we need to determine whether Omicron is more or less infectious than Delta in both vaccinated and unvaccinated individuals.
“What is also unclear is how much protection the current vaccines confer against more severe infection with Omicron that might lead to hospitalisation and death. The large number of mutations in the spike protein suggests that this may be less than for other variants.
“We also do not yet know whether the illness caused by Omicron is any more, or perhaps less severe, than the other variants including Delta, which accounts for the majority of infections globally at present.
“The answers to these questions should become clearer over the next few weeks, and only then will it be possible to decide whether the new restrictions announced today will be sufficient or whether indeed they can be relaxed.”
Dr Nathalie MacDermott, NIHR Academic Clinical Lecturer, King’s College London, said:
“The detection of two individuals infected with the Omicron variant of COVID-19 is unsurprising given the news over the last 48 hours of the rapid spread of the variant in Southern Africa and the emergence of cases in some of our European neighbours. The action to ban flights from the most affected countries is never a decision that should be taken lightly, but for a brief period it can buy the time needed to better understand the threat posed by this new variant and ensure the implementation of more robust identification and targeted contact tracing for individuals arriving from those countries now placed on the red list.
“The decision by the government to re-implement the need for a PCR test from all individuals arriving in the UK from abroad on day 2 with self-isolation until a negative test is reported, while frustrating for those travelling, is essential in order to rapidly identify cases of infection with the Omicron variant and implement prompt isolation and targeted contact tracing to limit the spread of the variant in the UK. The decision to implement a requirement to wear face masks on public transport and in shops is welcomed, and while it is not yet a requirement to wear them in other environments the British public would be wise to consider wearing them in all circumstances when they are indoors with gatherings of anyone other than close family and friends.”
Prof Richard Tedder, member of the Clinical Virology Network, said:
“I think the briefing from the PM and colleagues this afternoon was balanced and appropriate. We do not know enough about Omicron to inform how much it is going to escape vaccine protection, both in terms of reduction of the risk of infection and the reduction of disease when infected.
“The recognition of this variant should serve to reinforce everyone about the essential need to be sensible to avoid unnecessary close contact and to take sensible precautions such as continuing to apply the wearing of face masks in public places including transport and shops. It is very clear personally to me in public transport terms just how few people continue to wear face covering.
“One un-addressed concern that remains is whether the arrival of this variant is going to remove any degree of natural immunity protection. My concern is that the level of antibody and the nature of the antibody generated by SARS COV 2 infection may not be able to confirm protection against re-infection. This is borne out by the marked rise in antibody level and the increase in affinity with which the antibody reacts with viral proteins, changes of both which are seen in the recovered person when they are subsequently immunised with vaccine. The implication is that natural antibody dependent immunity to infection could be greatly enhanced by a single dose of vaccine. “These observations should be borne in mind by JCVI particularly in respect of emerging viruses bearing multiple sequence changes which may nullify natural antibody protection.”
Dr Shaun Fitzgerald, Royal Academy of Engineering Visiting Professor, University of Cambridge, said:
“There is a lot of talk about further restrictions, which is understandable. However, there are actions which aren’t restrictions but which can help a lot. These include regular self-testing, getting vaccinated or boosted, washing hands, wearing face coverings even indoors in places which aren’t mandatory, and ventilation (crack open that window). If we do all these things then it will reduce the spread … and lessen the risk of more restrictions being imposed.
“We need to live with this virus so giving it as little chance as possible to spread is a sensible thing.
“The news of Omicron cases here in the UK means that it is even more important to do the practical things to try and keep transmission rates down. It’s cold and may well get colder, but we still need to ventilate our spaces – this does not mean freezing though. It is important to get some ventilation into our indoor spaces so that they don’t become playgrounds for this virus, but we have to ensure that we are still warm enough otherwise we’ll just have to deal with other health issues.
“If we can avoid the really poorly ventilated, stuffy rooms then this will be a massive step forward. Let’s crack open the high level windows especially when in the company of others to get some fresh air and importantly prevent the potential build-up of high concentrations of virus particles.
Finally, let’s remember the other things such as testing regularly, washing hands and wearing face coverings.”
Prof Peter Openshaw, Professor of Experimental Medicine, Imperial College London, said:
“It is extraordinary how fast the information is coming out. There is no need to get alarmed, but we do need to be prepared and to take rapid action. It is better to act fast but be prepared to change as new information comes in. Travel restrictions may slow the rate of growth and buy time to establish the important facts about severity, immune evasion, transmission and susceptibility to treatment and prevention.
“There are 50 mutations in Omicron, 30 of these on the S protein and half of those in the Receptor-Binding Domain (Genome is 30,000 bases encoding 10,000 amino acids). Case numbers tripled in 3 days in South Africa to 2,828, but this is perhaps partly because of intensive monitoring, although it is possible that the transmission rate is double that of Delta (R=2) and the doubling time is about 4.8 days. South Africa is going into summer and rates of Delta are very low, so hard to say if Omicron competes over Delta.
“The report that 600 people arrived in Shipol airport and that 60 of them tested positive is remarkable: this suggests a 10% infection rate, but why were no infections detected at departure from South Africa? Were the departure tests faked? Was there some problem with the testing at arrival?
“There are many crucial bits of information that we need to have: do lateral flow tests work? How severe is the disease it causes? There are media reports that there have been no hospitalisations. If confirmed, this would be very reassuring.
“With or without this new variant, Delta is already a crisis in many parts of Europe and still causing a lot of illness and death in the UK, especially in those not vaccinated or in those who do not respond to vaccines. As Dr Emma Hodcroft says “The variant is a spark that should not distract us from the fact that we are already in a burning house.”
Prof Lawrence Young, Virologist and Professor of Molecular Oncology, Warwick Medical School, University of Warwick, said:
“This comes as no surprise. Once a variant is identified, particularly one that is likely to be more infectious, it will have spread beyond the few original cases and countries. At this stage it is important to do everything to slow and limit the spread of Omicron. That means restricting travel from countries where this variant is prevalent and operating a robust test and trace regime to identify infected individuals and their contacts and then ensure that they are isolating. The identification of these two cases in the UK, which are linked to travel in South Africa, demonstrates that the test and trace system via the passenger location form is working.
“We do need to get this situation with Omicron into perspective. We currently have very high daily case numbers infected with delta variant – far higher than the case numbers infected with Omicron in South Africa. It is very likely that current vaccines will protect against severe disease with Omicron as they do for all the previously identified virus variants. But this does all highlight the need to remain vigilant – the pandemic is not over.
“Increasing the uptake of vaccines including booster jabs, encouraging more widespread use of face coverings and restricting large gatherings in poorly ventilated spaces are important approaches to protect the population, ensure that the NHS is not overwhelmed and that Christmas festivities are not disrupted.”
https://twitter.com/sajidjavid/status/1464594748795146240
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