New coronavrius strain ravages Europe

Via MedRxiv:

Abstract

A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and has since spread to multiple European countries. The variant was first observed in Spain in June and has been at frequencies above 40% since July. Outside of Spain, the frequency of this variant has increased from very low values prior to 15th July to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about other European countries because few recent sequences are available. Sequences in this cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this variant was exported from Spain to other European countries multiple times and that much of the diversity of this cluster in Spain is observed across Europe. It is currently unclear whether this variant is spreading because of a transmission advantage of the virus or whether high incidence in Spain followed by dissemination through tourists is sufficient to explain the rapid rise in multiple countries.

CAVEATS

  • This variant rose in frequency in multiple countries, but we have no direct evidence that it spreads faster. The rise in frequency could also be due to epidemiological factors.

  • There are currently no data to evaluate whether this variant affects the severity of the disease.

  • While dominant in some countries, 20A.EU1 has not taken over everywhere and diverse variants of SARS-CoV-2 continue to circulate across Europe.

INTRODUCTION

Following its emergence in Wuhan in late 2019 (WHO Emergency Committee, 2020; Zhu et al., 2020), SARSCoV-2 has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines. The spread of the virus across the world has been tracked with phylogenetic analysis of viral genome sequences (Worobey et al., 2020; Hadfield et al.,
2018; Pybus et al., 2020) which were and still are generated at a rate far greater than for any other pathogen.

More than 157,000 full genomes are available in GISAID as of October 2020 (Shu and McCauley, 2017).

In addition to tracking the viral spread, these genome sequences have been used to monitor mutations which might change the transmission, pathogenesis, or antigenic properties of the virus. One mutation in particular, D614G in the spike protein, has received much attention. This variant (Nextstrain clade 20A) seeded large outbreaks in Europe in early 2020 and subsequently dominated the outbreaks in the Americas, thereby largely replacing previously circulating lineages. This rapid rise has led to the suggestion that this variant is more transmissible (Korber et al., 2020; Volz et al., 2020).

While the virus spread globally in early 2020 before borders were closed and viral variants circulating were distributed across the world, intercontinental travel remained suppressed through the summer of 2020.

The paucity of intercontinental travel allowed continentspecific variants to emerge. Within Europe, however, travel resumed in the summer of 2020. Here we report on a novel SARS-CoV-2 variant 20A.EU1 (S:A222V) that emerged in early summer 2020, presumably in Spain, and subsequently spread to multiple locations in Europe.

Over the summer, it rose in frequency in parallel in multiple countries. As we report here, this variant, 20A.EU1, and a second variant 20A.EU2 with mutation S:S477N in the spike protein account for the majority of recent sequences in Europe. It is unclear at present whether the rapid spread of either variant is due to association with particular demographics, properties of the virus, or chance but the dynamics of both should be carefully monitored.

Here are the latest charts for Europe:

The mortality rate is much better so far as increased capacity and treatments have advanced while RNA testing exaggerates case numbers:

But it is bad enough, leading back to this, at the BBC:

Prime Minister Boris Johnson has announced a second national lockdown for England as the UK passed one million Covid-19 cases.

He said the steps were necessary to avoid the “medical and moral disaster” of the NHS being overwhelmed.

Non-essential shops and hospitality will have to close for four weeks on Thursday, he said.

But unlike the restrictions in spring, schools, colleges and universities will be allowed to stay open.

…He said hospitals even in the south-west of England, where cases are among the lowest, will run out of capacity in weeks.

This situation raises the prospect that few like to contemplate. What if COVID-19 is actually COVID-permanent? The problem with herd immunity strategies is that they spread the virus much more widely and accelerate mutation. If lucky, this can result in weaker strains. But, it might also develop into stronger.

As well, vaccines are rendered very much less effective when new strains develop with regularity and we may face the horrible outcome of annual coronavirus winter seasons.

I fear that the more likely outcome for the world is not some magical vaccine but increasingly effective treatment to lower casualties and ever faster testing kits to enable a semblance of normal life to return to the global economy.

David Llewellyn-Smith
Latest posts by David Llewellyn-Smith (see all)

Comments

    • As well, vaccines are rendered very much less effective when new strains develop with regularity and we may face the horrible outcome of annual coronavirus winter seasons.

      I predicted this months ago when it first began. It will change the way society operates … permanently. Welcome not to Earth, but to “Eaarth”, as Bill McKibben says. First we have a new climate no other homo species has ever experienced, and now, new germs.

      “Therefore, send not to know
      For whom the bell tolls,
      It tolls for thee.”

      • rob barrattMEMBER

        Same here. I got the virus in March. Meet the new flu. As for Australia, just how are we going to know that someone who steps off an international flight hasn’t faked a vaccine certificate? Do we fill hotels with people permanently?
        To misquote Admiral Yamamoto “I fear all we have done is push back the next wave”.

  1. Have disagreed with some of the HnH covid analysis this year, but I certainly agree with the last few paragraphs there.

    I think there is precedent of another coronavirus pandemic becoming permanent. The 1890 pandemic, which many think was cause by the OC43 Coronavirus (still around, causes common cold);
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/

    For those reasons I see Trump/Atlas are suggesting a more realistic path forward than Biden/Fauci.

    • Trump is saying it will go away, you just showed it won’t.

      What’s wrong with this picture?

      • I know you haven’t worked this out yet but politicians bend the truth. Trump is right, one day in the future it will go away. But if you had lived on this world for more than ten minutes you would understand that is just another misleading statement from a politician….. it’s like every time Trump speaks you hold him to a higher standards than everyone other politician.

      • Sorry wasn’t meant to be reference to that specific comment (which is a stupid comment by Trump).

        More generally learning to accept and live with it rather than hide.

  2. “I fear that the more likely outcome for the world is not some magical vaccine but increasingly effective treatment to lower casualties and ever faster testing kits to enable a semblance of normal life to return to the global economy.” – agree. Inthemeantime markets going down hard.

    • I agree too. I think it will be a case of increase hospital capacities, maybe masks become a permanent feature on planes, things like that… The world has to get use to it now rather than praying for some miracle vaccine. The world of the 2010’s is long gone now. And for the most part, I say, good riddance.

  3. Jumping jack flash

    It is remarkably similar to standard flu which is pretty bad if you catch it, compared to colds like rhinovirus and the other couple which aren’t nearly as bad.

    I fear a treatment for coronavirus will look remarkably similar to the largely ineffective treatment for flu which is just 60% effective in ideal conditions and relies on computer modelling to predict mutations, and often these fall far short of reality.

    Once one is found for corona it will be immediately lauded as the panacea, the drug companies will get stonking rich and life will return to normal. Except it actually wont, and cant.

  4. Nobody is talking about now but China will pay. And that price will be higher the longer western countries have to deal with this

    • Have you seen China’s bad debt in the banking sector? Will the world accept being paid with Bitcoins? 😛

      • Hopefully in bitcoins. Only a complete numpty would accept Yuan.

        BTW I figure that if bitcoin was a CIA/NSA project then this maybe explains why Chinese state owned power companies make such a big effort to mine the stuff. They are trying to square the ledger so that bitcoin isn’t only held in US hands.

  5. PaperRooDogMEMBER

    If covid here to stay (with higherr death rate than typical flu when not treated) and with no permanent effective vaccine it raises they question who will come out ahead economically, countries like Aus/NZ/China or these like US/India/Spain (assuming enough herd immunity)?

    Or maybe we all start eating healthier, pretty much the opposite of current recommendations, ie less processed food, no low fat foods, less carbs, no vegetable oils so that we dish have so many people metabolically unhealthy & more susceptible to virus

    • C Diminished Chord

      We now know that the single worst dietary thing we consume is all plant based – we have been lied to HARD.

      Margarine and other hyrogenated plant oils are the primary cause of heart disease outside of sugar. The number one killer (sugar). Plant based oils are also a killer in themselves.

      While we now also know that we can fully process animals fats without cholesterol issues so long as we do not include sugar in our diets – if we do then then our stomach flora blooms and we have a “toxic shock” which breaks down our ability to process the animal based cholesterol which leads to plaque build ups in our arteries.

      Who would have thought its not eating meat but cotton, rice, palm oils, hyrogenated fats, and sugars that are killing us and the environment.

      • Agree with the environmental comments based on research, any data to share around the health links?

      • Interesting comment. I didn’t know about the sugar, animal fat, cholesterol heart disease connection.

        Any articles you can reference? Thanks

    • My money is on US/India/Spain coming out on top of Covid and they may lead the economic recovery.New infections seem to be falling off in India.

  6. The 1918 pandemic is still with us. It’s a much milder thing than it was then. It first got stronger, then attenuated.

    Looking at the total cases around the world, it’s difficult to see it being beaten globally at this point. There’s a good chance we’ll all get one of its descendents. Possibly several times over our lives.

    That doesn’t mean we should catch it now to get it over with. The most plausible outcome at this point is that it joins the annual flu and has a biannually updated vaccine targeting the handful of worse strains.

    If we can hold out, when we get it, we might due to partial vaccination immunity, just get the sniffles. Eg you can get a flu strain today that you’ve never had or been vaccinated against, but due to prior vaccines/infections of related strains your body doesn’t have to start its defence strategy from scratch. You have partial immunity. You get sick, but not as bad.

    It’s not ideal, but it looks like we’re long past ideal being physically possible.

  7. C Diminished Chord

    People constantly compare Covid-19 to linfluenza, the flu and other respiratory diseases – its nothing like it. This idea needs to die very quickly – its just so misguided.

    Viruses – HIV, Hepatitis, Rabies, Ross River, Measles- etc – this is the way to think about it.

    What we have seen with Covid is a deep impact on high blood capillary areas – hence the problems in liver, lungs, brain, reproductive areas.

    The current paradigm surrounding Covid is that the long term COSTS of the health impacts – particularly on the YOUNG who show no signs of any problems could be so massive that it outweighs the huge financial impact the world is currently enduring.

    Its not just some respiratory disease – it is looking very much like many of the long term health impacts we get from most viruses – including influenza.

  8. It is out of control and there is no putting this genie back in the bottle. There is no going back to a pre COVID world now.
    I have no idea how this will all work out but a vaccine is an absolute must.

    • Arthur Schopenhauer

      Historically, pandemics have been followed by power grabs, territory disputes & war. Since the Romans ruled the Mediterranean.

  9. Because they are leaving schools open they will be long shutdowns…….the question we progress to is how does a country where it isn’t endemic , like us, interact with countries where it is endemic, like all those with these huge infections.

    There will be people ( I am looking at you Mr Morrison ) who will say that for economic reasons we need to let it become endemic here and will try every under-handed trick in the book to make it happen.

    • When there is an effective vaccine, anyone who comes to Australia must be vaccinated. Same with anyone leaving Australia for a holiday.

    • Arthur Schopenhauer

      Hervey Bay said, “No way!”, over the weekend. Pensioners’ Paradise swung 11.2% to Labor (2PP) in the sunshine ☀️ state election.

      Scovid can try it on, but he’ll lose the blue rinse set in the process.

      • 1
        That result will definately temper Scummo’s enthusiasm. He is no use to his masters if he blows the politics of this thing. We are lucky in this country to still have a solid electoral system that reflects actual voter intentions. Scummo can’t lie his way out of election results.

      • Yep. Democracy is a wonderful thing. SloMo can try all he wants to open the floodgates but the QLD election has proven that COVID-19 is the new enemy at the gate and any government that keeps it out will be rewarded at the ballot box. Party donors be damned 🙂

      • Funny isn’t it, the grey demographic voting for something other than protecting their franking credits and entitlements.

        Labour should put the slipper into the grey vote for abandoning them for the last two decades – you can have your life but it will cost ya!

  10. https://www.euromomo.eu/graphs-and-maps/
    No evidence of excess mortality anywhere except maybe Belgium – where deaths are still lower than their August heatwave.
    France and UK deaths are flat. Certainly no justification for lockdown there.
    If hospitals are overwhelmed but deaths are flat it would suggest they are hospitalising too many people and need to more tightly control triage.

    • Hospitalisations for respiratory illnesses always increase at this time of the year. Where is the data showing there is more people in hospital now than in a normal flu season?

      • Hospitalisation data is basically unavailable or at least not consistently recorded and shares. The excess death data as a proxy for hospitalisations is the best we have to go on.
        Belgium by the way is basically a failed state. It hasn’t had a Government for several years and is a major terrorist breeding ground. Its no surprise that they have not prepared for this. The country should be torn in half with the south going to France and the North to the Netherlands. The little German-speaking bit on the east to Germany.

        • kiwikarynMEMBER

          The problem is that past deaths are irrelevant, as the virus has mutated. I want to know how many people are really sick with the virus today, not whether they died back in March or April. This allows you to make a judgement as to the risk that is currently presenting, not based on historical statistics that are no longer relevant due to the virus becoming less lethal. So how about we track excess deaths on a per month basis, not yearly, so we can exclude that first wave, and get a better picture of what is happening now. Only place I have seen that charted is Sweden, and total deaths are currently running lower than the 5 year average, which would indicate that the virus isnt killing as many people now as the flu did in prior years.

  11. Agree that the vaccine is not the magic solution. It’s a shame the focus isn’t on strategies to ‘sterilise’ surfaces and environments, particularly with ultraviolet treatments.

  12. Calm your farm! Peter Doherty said earlier in the year that this novel coronavirus appeared to be a slowly mutating virus and immunity and a vaccine (if found) should be long lasting. The scientific consensus remains that SARS-CoV-2 is a slowly mutating virus. So we shouldn’t be facing the same situation as seasonal flu (influenza virus mutates much faster). I think we’ll get a vaccine eventually because there is so much research going into it. But it could be 5 years away.

  13. If you are right then time to get on with accepting it, flattening the curve and forgetting about elimination as there is no point if it is here for good.

  14. “Going forward the answer will be better and more effective treatments”

    Too bad if you live in a third world country or don’t have health insurance.

    Basically if you’re poor, you’re stuffed.

  15. Ugh … herd immunity … people should look up the term and when it was coined … then consider its application …

    Hint … its not what most think ….