Views this afternoon in the early spring in London; crocuses are coming out, some early daffodils, and coronavirus is falling, but we're not out of this pandemic yet, and even "out" is a complex endpoint.
Context: I am an expert in human genetics and computational biology; I know experts in infectious epidemiology, viral genomics, immunology, testing and clinical trials. COI: I am long established consultant to Oxford Nanopore and I am on the Ox/Az vaccine trial as a participant.
I will comment mainly from the perspective of UK and broadly Europe which are the places I know and understand the best.
Reminder: SARS-CoV-2 is a highly infectious viruses which causes a nasty disease, COVID, that is lethal or debilitating for a subset of people (older, more likely male and more like obese).
If we allowed the virus to freely spread through populations many people would die from the virus and healthcare systems would be overwhelmed, meaning many more unnecessary deaths and long term disease would happen.
Brilliantly vaccines work, as trialed over 2020 and now shown in practice in Israel; we can expect to see similar efficacy from the UK soon. This is far faster than expected, and with a diversity of vaccine options.
Vaccines do two things; they substantially reduce the chance of severe disease given infection, and they reduce the chance of infection and most likely reinfection. Although these sound very similar they are quite different >>
Reducing severe disease is largely about stopping the overreaction of the immune system which clearly spirals out of control in many people. Reducing infection and transmission is about priming and honing the immune response to infection
The mammalian immune system (humans included) is a complex thing, and just by "educating" our immune system with vaccines we can achieve both reduction of disease and reduction of infection. The first is the most important. The second is extremely useful.
This distinction is sharper still when it comes to new lineages of the virus. The dampening of the overreaction is likely more T-cell mediated, and thus less keyed into precise versions of the virus; the infection one has to be more on the money in the virus type.
(though, as always, the immune system moves in mysterious ways so it is quite a tangled web of responses and feedback loops; whatever the precise mechanism, vaccines are useful in education)
Sorting out the precise efficacy of the vaccines (different types too) for the different aspects will be complex with real world data, but it seems likely that it is 90% or better protection from severe disease, and hopefully (fingers crossed) with broad variant applicability
New, more infectious (certainly B.1.1.7; "British or Kent Variant") and potentially escaping previous immunity (likely B.1.351; "South African Variant", potentially P.1 "Brazil Variant") complicate the landscape hugely.
B.1.1.7 has forced far stricter lockdowns in UK, Ireland and Portugual; it is rising across Europe and the US - it is likely that quite restrictive NPIs (lockdown rules) will be needed to keep R < 1 for B.1.1.7. Thankfully the vaccines look pretty much as efficacious for B.1.1.7
For countries which are not majority B.1.1.7 (yet) - eg, Denmark, Germany, France - they have to monitor and craft their NPIs knowing the rising rates of B.1.1.7 - arguably more complex space to navigate.
More concerning is the South African variant which both in vitro and some small scale trial studies at least escapes immune response triggered by vaccines. Because of the large numbers needed to test this we don't know about severe disease.
Given the prevalence of old ("historic") lineages and B.1.1.7 this concern should not stop the rapid roll out of vaccines - vaccines are just a positive in the system, but it shows the complications we are going to have the next 6, 12, 24 months
Any reasonable scenario planning must expect new vaccine escape variants emerging at different points over this year; as well as ideally containing these new variants, in each case we will need to know whether severe disease is present on a vaccinated background +infection rates
This requires a step up in viral surveillance, ideally globally, and coordination of the data and information. Despite the sometimes shrill national conversations, broadly this works well given resources present in each country to actually do it. This is one the challenges Q1/Q2
Looking ahead, Israel and soon UK will be navigating how to lower NPIs given a large proportion of their populations are vaccinated, in particular in the at risk categories. As Israel shows, this is not a walk in the park.
It is not because every pocket of unvaccinated at risk people is a group of people who can easily turn up in hospital and it is hard to reach every corner; furthermore the suppression of severe disease takes a while to kick in (3-4 weeks it seems fully).
This means there is definitely a longish period when one needs R < 1 of the variant (which is hard for B.1.1.7) though every week the impact of more vaccination on infection rates (pushing R down) will help. Judging when one has headroom to do which NPI loosening... is complex
(this is a more heat than light discussion in my view about timing of the 2nd dose. A 12 week gap is optimal it looks like for onward protection of Ox/AZ, also good for vaccination rates. The Pfzier 3 week gap is unlikely to optimal; the "approved" 6 week relaxation is fine
The UK took the 2nd dose of Pfzier out to 12 weeks, where one should ideally get a trial / data on - the UK will have some data about any waning of 2nd dose. But all these options are reasonable in my non-expert, informed by experts view; Pfzier 3, 6 or 12; Ox/AZ 12)
(What is far more important than dosing strategy is rates: rates of supply, rates of vaccination. Due to complex procurement issues the EU supply rates for vaccines is tight for March, but will no doubt be solved; one needs to have vaccine application rates at or above supply)
Given good supply (fingers crossed, should happen) Europe should be well vaccinated by the summer; the UK at the start of the summer. This is great. But neither the UK nor Europe is somehow disconnected from the world.
Due to advocacy before the pandemic and fast moving work during it, the @covaxxvaccine and @gavi projects are a forum to help organise and distribute SARS-CoV-2 vaccine worldwide.
This is both a moral imperative - there are lives and livelihoods to be saved - but as important is that the population unit to be concerned about is the world - all humans.
It will be complex and much of the world is not so old for example - so the risk profiles are different - but there are plenty of people who will really benefit from the vaccine which will also push transmission and new variants down.
Where is the endgame of this all? I do think the most likely one is SARS-CoV-2 becoming the 5th endemic human coronavirus, and quite possibly by far the nastiest of the set; we may well be having regular SARS-CoV-2 vaccinations every year (or couple of years)
(An interesting aside here is one of the current Coronaviruses might well have been responsible for the "Russian Flu" of 1889, with some striking similarities to this pandemic, so as a species we've potentially been through this before)
Accepting an endemic endgame is *not* the same as advocating for a "let it rip" as soon as possible (indeed, quite the opposite!). It is more understanding the realistic scenarios of where this will all end up.
Just like the spring bulbs coming through on my walks I am optimistic - vaccines are the major change in the game - but we will be likely living a more complex life for a while - but one with more friends, family, cheer and enjoyment I hope.
My final plea as ever - do not think this is a problem best solved by nations or factions by themselves. It is an all of humanity problem, and it needs all of humanity's innovation and thinking to get out of.
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