To start this piece, here is a picture of a goldfinch in my garden: something nice and simply beautiful to soothe the spirit at this time. With that in mind, I’ll turn to my main subject. 2020 has turned this blog - unfortunately - into the Covid-19 diaries.
Last time I wrote, we had just come out of lockdown and into Tier 3 restrictions. Since that time, reports of viral infections detected by PCR tests have (... searches for an approximately correct cliche) ballooned (probably not the correct cliche, but still...).
As of Saturday, we have now been placed into level 4 restrictions. This means we are in lockdown again, although it is a regional lockdown limited to Kent and other areas of the south-east of England.
The reason for the increased restrictions is the emergence of a strain of SARS-CoV-2 that seems to have much greater transmissibility. This strain is characterised by multiple mutations, including some in the spike (S) protein, which is both the binding site for the virus's receptor on human cells (ACE2, plus possibly DPP4) and the target of vaccines. Spike mutations are of great concern because they could, in general terms, make the virus more efficient at invading human cells or reduce the efficacy of vaccines, or both. Confusingly, different organisations give this strain different names: the PHE designation is VOC-202012/01; GISAID and the COG consortium use B.1.1.7 (or B1.1.7). , B.1.1.7 actually represents a lineage comprised of thousands of individual viruses identified in separate infections characterised by a common set of mutations.
By way of some notes about the new strain:
Virological.org summary of the new UK strain characteristics
Ewan Birney's twitter summary of what we know up till two days ago (subsequently published in The Spectator)
Emma Hodcroft (@Firefox66) description of its characteristics and relation to South African strain
Tony Cox (@The_Soup_Dragon) Lighthouse lab director chart of the new strain as a proportion of viral samples analysed in his lab
Notes from the Nervetag meeting describing this
DPP4 as a receptor for SARS-CoV-2, its link to Neanderthal ancestry, and relation to diabetes
Evidence that long Covid has a substantial auto-immune component
UPDATE 2020-12-22 : Public Health England’s summary of initial investigations (see Fig. 2 in particular for its growing prevalence)
UPDATE 2020-12-22 Preprint: Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ΔH69/V70. Mutations that delete two amino acids in S (ΔH69/V70) “enhance[s] viral infectivity”. Mutations such as those found in B.1.1.7 “have the potential to enhance the ability of SARS-CoV-2 to generate vaccine escape variants that would have otherwise significantly reduced viral fitness.” Oh boy …
One of the big problems is that the transmissibility of this strain has only become apparent in the last couple of weeks, despite it being in circulation since September. The strain seems to have emerged in Kent around that time; it is now the dominant form in this part of the country. Other areas of the country, especially in the North, don't seem to have it so much. UPDATE 2020-12-22 Government advisors now say it is “everywhere”.
However, on hearing of the new Tier 4 restrictions on Saturday afternoon, large numbers of people fled London for the Christmas holidays. Scenes from St Pancras and other stations looked horrific as large numbers of people gathered in confined spaces. A columnist in the Times this morning described the last trains out of London as "plague trains" drawing a comparison with the ships from Crimea that arrived in Messina in 1347 bringing the Black Death.
You can see the differential effect of the tiers and lockdowns in this comparison of Leeds (Yorkshire) and Ashford (Kent). The second coronavirus wave, which we had all be expecting in the Autumn, started early in Leeds and peaked well before the second national lockdown. Nonetheless, that lockdown appears to have had real success in pushing infection numbers down. By comparison, Ashford, which came out of the summer with low infection numbers, went into the national lockdown with still comparatively low numbers of infections, but came out of it with higher numbers. Tier 3 saw infection numbers accelerate steeply, doubling about every 6 days. Similar viral infections throughout Kent, and subsequently in London and Essex, led to an analysis that revealed the new strain was taking off in these areas and that Tier 3 restrictions were wildly inadequate to contain it.
Data from https://coronavirus.data.gov.uk/details/cases.
So now, here in most of the south of England, we are in our third lockdown. We are not going to know if it is of any use for at least two or three weeks. If we are very lucky, keeping the kids away from each other during the school holidays will help reduce the rate of infections. Only time will tell.
Meanwhile, other countries have taken fright at the new British plague and have blocked flights from the UK, as well as cross-Channel traffic. Operation Stack is in force, so lorries can be parked on the M20 to wait for eventual release as a protocol is negotiated between the UK and French authorities to allow the resumption of cross-Channel trade.
On top of all this, we still do not know whether or not there will be any kind of trade deal finalised between the UK and the EU. Operation Stack will turn into Operation Brock, and Kent could grind to a halt in the New Year.
Oh well. I think the only thing to do is to hunker down. If you have the chance, take to your bed for January and February in the company of a case or two of brandy (assuming there are any in the country).
Even so, there are still beautiful things in this world that can help keep us all sane. In the absence of my usual trips to Oare and elsewhere to photograph birds, I have set up my portable hide in the garden together with some perches near a feeder. The simple pleasure of quiet concentration on the birds is good for the soul (see the goldfinch picture at the start of this post). And I can still get my daily walk or cycle ride. Yesterday lunchtime was beautifully sunny and not too cold, so I went for a couple of hours walk, and some shutter therapy. The picture below is from yesterday's walk - just a stand of trees in a field, under a winter's blue sky. But like the goldfinch, good for the soul.
A stand of trees in a Kentish field. Panorama of twelve portrait format images (2 x 6 image rows), Sony A7III with Olympus OM Zuiko 100mm f/2.8 lens on an adaptor.