Thread by @ewanbirney

Another bright day in London but with a pretty grim outlook here short term - but better mid to long term for COVID.

Context: I am an expert in human genetics and computational biology; I know a variety of experts in the COVID world from testing, infectious epidemiology, virus evolution, clinical trials and ICU clinical work.

COIs: I am a longstanding consultant to Oxford Nanopore, which make a COVID test (LamPORE) and portable DNA/RNA sequencing machines and I am a participant on the Oxford/AZ vaccine trial.

Reminder: SARS_CoV_2 is an infectious human virus which causes a horrible disease, COVID, often leading to death in a subset of people - this subset is older, more likely to be male and more likely to be overweight.

If we let the virus go through any population with substantial people at risk not only many people would get this disease, either dieing or sometimes with debilitating long term disease (LongCOVID) but also modern healthcare systems could not provide care for these numbers

In early Dec two new lineages of the virus have been identified, one detected in UK (B.1.1.7) and one detected in South Africa (B1.351) with different biological properties. The UK one almost certainly transmits more; the SA one might well transmit more+might by an immune escape

[A note on language; I prefer the word "lineage" as we expect this part of the family tree of SARS_CoV_2 viruses to have these biological properties. Some people use the word "variant" but (a) we use the word variant for other things here as well, so things get confusing and >>

(b) the "variant" does not have the descendent property implied. However, Public Health England use the "variant" term, eg this as "Variant of Concern" VOC with a designation, VOC 202012/01. I prefer lineage with the Pangolin designator B.1.1.7 which expands easily in the future

Finally, some people use specific RNA site changes (confusing also called variants) as indicators to split the family tree, most notably the nextstrain terminology 501Y.V1 - meaning the 501 position changing. All these things are basically equivalent]

The impact of the B.1.1.7 Lineage in the UK has been profound; the previous mixture of restrictions (NPIs in the lingo) and Test-Trace-Isolate (TTI) were not able to hold the B.1.1.7 reproduction rate below 1.

Because of the complications with testing, reporting +behaviour over Christmas we don't actually have a firm idea if the current "Tier 4 with no schools" will hold R<1 with this new lineage. London, South East and East of England have had ~4-6 weeks of exponential growth Nov/Dec

Thankfully there is no evidence in a change in disease (so far) but the depth of transmission has pushed London's hospitals to breaking point now. (Note: East of England and South East had better stratification of older generation to my amateur eye- need a pro to untangle things)

One conundrum is whether there is a shift in age range in the biology of the virus (either transmission or disease) but it is hugely complicated by the fact that schools were "on" during November and Early December. More data and analysis needed.

It is tense in London, and there are alot of people who feel very let down by the rapid change in rules, some of which is more triggered by events (the discovery of new lineage and its properties), compounded by changing decisions (eg, on schools open or not)

It feels like a lot of people are at rock bottom or lower - from NHS staff through to teachers through to the broader public. We have to be generous to the people around us to get through this.

It's worth noting that it took something like 6-8 weeks for the new lineage to establish and grow to the point of being dominant. For countries that don't have the lineage, it is best not to have it (travel restrictions/testing), however given the seeding that is already here >>

<< my view is that most countries should operate on the basis of this lineage in present in their country and growing; certainly high genomic surveillance is going to be important in 2021 for the new lineage and also potential other lineages in the future.

(A note: European public health groups are sharing data at both the assembly level and also the raw data level via @enasequence which coordinates with GenBank in the US and DDBJ in Japan, as well as GISAID for assemblies;

this is one part of what @emblebi helps coordinate in COVID19 data at the covid19dataportal.org. Despite the very national conversations / responses to COVID in policy, the science is very international and we should aim to continue this)

The silver lining are vaccines. Simply put they can't come fast enough. Israel is the country that has got itself organised as quickly as possible and will be the country to watch for the impact of deeper vaccination on progression of the epidemic.

Here the UK has got a pretty good start (around 1 million people vaccinated) but it is a long long way to go - many things could easily go wrong. Everyone needs to help the at risk people in their families get vaccinated over this month.

It is great that the BioNTech/Pfzier vaccine has approved by the EMA in Europe, and I hope both Moderna and Oxford/AZ can be approved. Full population vaccination logistics are eye watering at the best of times; even more so when the vaccines have to be transported in cold chain

I think the urgency and efficiency shown in Germany, Denmark and UK on vaccination is a good model for other European countries. Basically we're not going to be out of this until everyone at risk, across the *entire planet*, has been vaccinated.

As long time followers know, I am an optimist, and optimism is a curse in pandemic planning. These new variants have really changed the landscape but the fundamentals of this pandemic have not changed.

My final plea; be nice to people- friends and family, neighbours, teachers, hospital staff, random people on twitter - we're going to have to get through a pretty horrible couple of months - but there is a better 2021 we can aim for.