Post holiday, having digested some sites+preprints from last week, I'd like to give my perspective on COVID. Context: I am a genomics + biological data science expert; for most other topics I am one-step-away from experts; I have a conflict of interest on SARS-CoV-2 testing

My second context: I am going to focus on a perspective across Europe (including UK) because (a) that's what I know/understand the best and (b) part of my role @EMBL is to support in anyway needed EMBL member states

First off, the standard starting place. SARS-CoV-2 is a highly infectious virus which causes a severe, often lethal, disease in a subset of the population. That subset is older (>65) and has co-morbidities (obesity and diabetes most notably).

Frustratingly many of the people who are infected and are infectious themselves do not have symptoms or very very mild symptoms and simply do not realise that they are transmitting the virus.

If we allowed the virus to follow its natural course of transmission across Europe we can be almost certain of a large number of people dying quickly, and many others having a debilitating disease.

The fundamentals of this situation does not change until we have substantially better treatments of the disease (via drugs or clinical care) or substantially lower transmission of the virus (via a vaccine).

Fast progress has been made on both fronts. By using large, well designed randomised trials we know 2 drugs definitely reduce the burden of the disease. There are other hopeful treatments to trial

On vaccines there has been a surprisingly quick response on vaccine development with now multiple vaccines in the large scale Phase 3 testing where both safety and efficacy are being tested (I am one such person who has been randomised!)

However, the treatments do not change mortality/burden of disease enough to change the fundamentals (though with enough of them... they might in the future); vaccines will not be ready at scale before the winter.

We - the global we and the European we - have to have a plan to navigate the next 6 months without a change in treatments nor a vaccine. In Europe, this means we have to navigate autumn and winter.

On the positive side, the large scale lockdowns in the spring clearly worked - transmission stopped across nearly all European countries, and during the early summer there was low transmission either with relaxation of lockdowns or a gradual titration of risky behaviour (Sweden)

Testing capacity and logistics were high from the outset in some countries (eg, Germany) and went to higher levels across most European countries. This means that currently most European countries can sensibly talk about cases and population infection levels

There is a huge host of details of how countries are organised internally, how testing is done and paid for, how data is aggregated - the details are fearsomely different; the broad view is similar.

Now that the vast majority of European countries have at least some level of situational awareness of infection levels both regional and local response *to infections* (rather than hospitalisations or deaths) can occur.

Again, the details are fearsomely complex ; red vs green zones in France; local lockdowns in the UK; regional public health messages in Spain and Lander by Lander rules and schemes in Germany. It can also work at the more local level - clusters, specific sites, specific events.

The clusters and specific sites are important - currently this is the only way we are getting at asymptomatic carriers.

However, given all of this is slightly dispiriting to see the up tick in infection rates across many places in Europe. The fact we can see this at the level of infection is great; the fact that our current set of behaviours is not fully adequate to control infection is worrying

It is worrying because the autumn and winter will be challenging. We want schools and universities to restart and certainly for older pupils and of course young adults they can transmit the virus. The change in contact patterns here create more transmission routes for the virus.

Furthermore winter in Europe is often wet and cold; the wet will prevent easy living outside where virus transmission is greatly reduced. The virus also clearly is happier in colder situations (which is why meat packing and food processing plants are consistent infection risks)

I believe we need to take the ability to control infection rates to a new level, across Europe and the world. Can we do this? With effort and organisation yes, but noone should imagine this is going to be easy.

What can we do? The first is that there are a lot of good ideas/things that work in one location that need to be operationalised elsewhere - digital apps that work with local tracing of infections, better cleaning procedures, good training of care home/elderly care staff.

Most of this is pretty unglamorous stuff, and although seems obvious, one needs real effort to push things to the next level. One example is routine mask wearing in many locations - certainly all high transmission risk areas.

Next I believe we should push for more widespread use of Sewage monitoring. The virus sheds early in the infection cycle through the digestive tract and shows up in sewage. A number of countries do this now (I think: France, Netherlands), many more have roll outs poised (eg, UK)

(For sure, I don't know the full extent of Sewage monitoring across Europe and I would love to know - please DM me or email me if you know of projects as I'd like connect some of this up).

Finally we should aim to increase the depth of testing by at least 10 fold, perhaps even entire local or regional populations. Here there is a host of both established technologies in new formats and new technologies coming in.

(Here I should point out my conflict of interest. I am a long established consultant to Oxford Nanopore, which makes one of the new technologies, called LamPORE)

There are alot of options here, and one can be somewhat paralysed both by choice and by the need to not only verify they work (naturally!) but more importantly to understand how best to deploy/use them.

I would far prefer us to over-engineer and over test than under test, and I think it is likely we will have a variety of testing schemes with a variety of technologies - we should be focused mainly on getting 10-fold testing levels (if not more).

Testing by itself needs to be backed up with societal messaging and support - the people who test positive must be in a position where they can easily isolate and one minimises the downside to the infected individuals

If we did all this can we navigate the next 6 months without substantial numbers of people dying or without having to use the most drastic transmission reduction, ie, society wide stay at home? I am not sure. But these are the tools we got and we should use all of them.