Skylarks with Rosie

I’ve just finished reading the recently published new book by Stephen Moss – ‘Skylarks with Rosie – a Somerset Spring’. It is a very readable and enjoyable book all about his experiences with wildlife during the first lockdown in his home patch in the Somerset Levels.

I have known Stephen (who is a film maker and an author), on and off for nearly 20 years, I first met him when he and Bill Oddie came to Wicken Fen to make a 30 minute documentary on Britain’s oldest nature reserve, which at the time I was the manager of. My most distinct memory of that encounter was demonstrating how to use a ‘pooter’ – a piece on entomological equipment used to capture small insects – you hover a rubber tube over the said insect and then inhale which sucks the creature into a tube where it can be identified before being released. On this occasion, for some inexplicable reason I pooted a number of Red Ants and as a result ended up with a lung full of stinging formic acid – school boy error but made for good TV!

Skylarks with Rosie (Rosie is Stephen’s dog), gives a lovely account of his daily walks and cycle rides around the area where he lives – his patch, in birding speak. He describes the return of migrant birds, gives accounts of their lifestyles, where they have returned from and so much more from an ecological perspective. Whilst this book is about wildlife, particularly birds, it is about so much more and therefore has a much wider appeal.

Whether you are really into wildlife like myself and Stephen or whether you just like the outdoors, this book takes you through so many of the emotions we felt for the 13 weeks last spring – staring on the 23rd March. I focused on moths whilst Stephen focused on birds, but interspersed with all of that was the politics … the mixed messaging … Stay Alert …. Cummings …. Black Lives Matter ….. #bekind …. Marcus Rashford …. etc, Moss covers all of these aspects in a fairly brutal but very fair and accurate way. It brings the memories, both good and bad, flooding back.

He weaves in the biodiversity crisis we face along with the impending climate disaster but there are lots of moments of hope – how so many more people connected with nature during lockdown, how many more young people are showing a concern for nature and environmental matters. I loved this book and perhaps if I hadn’t spent so much time drinking Negronis I might I have penned something similar based on my Devon moth experiences ….. and with hindsight I wish I had ….

Can really recommend this book …. it is not a book for nature nuts … it’s a book for you, if you care about your world, your patch and the future. Perhaps the best thing about reading it now, is that everything from a wildlife perspective that it describes is about to start happening now …. my favourite time of the year …. swallows, cuckoos, warblers, butterflies and sunshine. The main message of the book is … connect with nature, it will make you smile, be happier and be less stressed in these on-going troublesome times. Couldn’t agree more.

And another fabulous Carry Akroyd cover painting!

I guess the only thing that let’s the book down is that it is set in Somerset and not Gloucestershire.

Celebrating VE Day in a pandemic

On the 75^th anniversary of VE Day, I am reflective of the sacrifices that were made and I want to celebrate the end of hostilities and the commencement of the post-war era of peace in Europe.

I am thinking of my late parents (who had yet to meet) and what they were doing on VE Day. My father spent the war in Belfast, during the day he worked for the General Post Office, maintaining the telephone system and by night he was a fire watcher in case the ship yards were bombed. My mother worked on the family farm in Hartland, North Devon before moving to Exeter to train as a nurse.

Mum and Dad on their wedding day

I’m also thinking of my late wife Cesca’s parents. Her father is British and her mother is German. Her stepfather was also German and was severely injured in Stalingrad, was evacuated to Eastern Germany where he had to hide underground as the Red Army advanced on Berlin, he then escaped to West Germany where he trained as a Doctor and ended his career as a District Surgeon in Kenya. Our lives consist of complicated and tangled webs.

Gunter and Renate (Cesca’s stepdad and mum), my mum, me, Josh, Cesca and Michael (Cesca’s dad)

My mother, who died 7 years ago would have looked forward to this celebration of VE day, she would be looking forward to seeing the Queen, her children, grandchildren and great grandchildren; she would be waiting expectantly to see what the Queen was wearing. My father, who died 12 years ago would have be less keen on those aspects of the day but would nevertheless have humoured mum. Afterwards, I think he would have dug out his treasured copy of Churchill’s World War 2 volume on VE Day ‘Triumph and Tragedy’ where he would have read Winston’s words – clearly and unambiguously managing the population’s expectations..

Dad

His treasured Churchill books

“I wish I could tell you tonight that all our toils and troubles were over. …… But, on the contrary, I must warn you, as I did when I began this five years’ task  ….. that there is still a lot to do, and that you must be prepared for further efforts of mind and body ….. You must not weaken in any way in your alert and vigilant frame of mind.”

And so, to the celebrations, I have decided to bake a cake, and not any cake, Churchill’s favourite fruit cake! The National Trust, who now look after Chartwell, Churchill’s home, are of course also renowned for their cakes and have published the recipe which Mrs Landemare, Churchill’s wartime cook, used to bake for him.

Chartwell

It is not just cooking the cake that matters, presentation is also important, especially as it is a National Trust cake! This takes me back to a glorious and happy day a couple of years before my mum died. We took her to London where in the morning we visited Buckingham Palace and in the afternoon we took tea at the Savoy. Mum really enjoyed the day and whilst we were at Buckingham Palace she bought a Queen Victoria cake stand which I now have.

Queen Victoria’s Cake Stand

Me and mum in the gardens of Buckingham Palace

But of course, these VE Day celebrations have not gone to plan, a virus has cancelled our street parties and forbidden us to go to the pub. There is no shortage of irony in the fact that our 75^th anniversary of Victory in Europe  coincides with a global pandemic. The end of World War 2 redefined the remainder of the 20^th century and SARS-CoV-2 will redefine our lives for at least the next decade. We have yet to ‘wrestle the invisible mugger to the ground’, we are not approaching VCovid Day, if we are lucky we might be close to Tobruk. Churchill however can help us again, by clearly setting out where we find ourselves and again managing our expectations. In November 1942, after the Desert Campaign he, of course, said this.

“This is not the end, it is not even the beginning of the end, but it is perhaps the end of the beginning.”

Right, I’m off to share Churchill’s favourite fruit cake with Josh and Hollie!

Churchill’s favourite fruit cake on the Queen Victoria Cake Stand

 

A journey towards transparency?

We have known for a while now that the reported daily ‘hospital deaths’ figure was not a true representation of total deaths for the country. Now that the Office for National Statistics and their Scottish and Northern Irish equivalents are publishing the total death statistics, albeit with an 11 day lag, we are beginning to get a clearer picture of what is unfolding in the UK as a result of the Covid-19 outbreak. It is also very good that data was presented at yesterday’s daily briefing regarding Covid-19 deaths outside of hospitals (care homes, hospices, home and other). However, we are still not being told the whole story yet. I will try and explain why.

Following the daily briefing the Government publishes the charts presented along with a spreadsheet containing the data which makes up the charts. Yesterday two new charts were shown: ‘All weekly registered deaths from COVID-19 compared with deaths in hospital (UK)’ and ‘Provisional weekly registered deaths from COVID-19 in England and Wales by place of occurrence’. Unfortunately, the data making up these charts are not included in the accompanying spreadsheet so at this point I have had to estimate the numbers by reading them off the y axis – they are thus approximate figures.

The UK wide chart tells us that in the week ending 17^th April around 9,500 people died from Covid-19, of these 5,600 died in hospital and around 3,900 died in care homes, hospices, at home and at other locations.

However, we also know from the UK wide data that in the week ending 17^th April, the UK death rate was 12,500 above the seasonally adjusted average. Direct Covid-19 deaths accounted for 9,500 people which leaves a further 3,000 people apparently having died that week from indirect Covid-19 impacts, which is 24% of the total.

At this point in time these 3,000 deaths are not included in the daily briefing figures and additionally we don’t know what their causes of death are. Some may have died of Covid-19 but it is not recorded on their death certificate, it is also possible that these 3,000 people have died of other causes such as cancer, heart attacks, strokes, suicide etc. At this point we have no idea. This group of 3,000 people are over and above the seasonally adjusted average – so they are ‘excess’ deaths, they are indirect Covid-19 deaths, these people would not have died if we had not had a Covid-19 outbreak.

With regards to care home in Great Britain the ONS and Scottish data appears to suggest that of the excess deaths in care home during the week ending 17^th April, approximately 2,200 people died from Covid-19 and around 2,800 people died from other causes – 56% of the total.

 

Trying to make sense of all this data and collating it to give a UK picture is a fiendishly difficult task Indeed it would appear that the Government are struggling with this. The hospital deaths chart for the UK states that in the week ending 17^th April 5,600 people died in hospitals, whereas the England and Wales graphs states that for the same period 6,100 people died in hospital. Can we even believe the data we are being presented with?

And remember these figures relate to the situation 12 days ago. The implication of all of this is that it is more than likely that approaching 50,000 people have already died from the direct and indirect results of Covid-19 and not 21,678.

 

 

 

 

 

Strategies for coming out of lockdown?

I found a very interesting paper on the internet today. It is a modelling exercise which looks at how future behaviours in society (post lockdown) might impact on subsequent Covid-19 transmission rates. You can download the paper here. It is a collaboration between social scientists at Oxford and Zurich Universities and is titled ‘Social network-based distancing strategies to flatten the COVID-19 curve in a post-lockdown world‘.

The modelling looks at 5 scenarios: going back to how we all lived before the lockdown; how we lived before but cutting our social contacts by 50% and three scenarios where social contact was curtailed in subtly different ways. These latter three scenarios are termed strategies in the paper and I set these out (as per the paper) below. The language is a little tricky but hopefully you get the general idea. Figure 2 aims to give an  illustration of how these strategies differ and figure 3 presents the results of the modelling in terms of new viral outbreaks for each scenario.

Strategy 1: ‘Birds of a feather’ homophily strategy: Reduce geographic, organisational and socio-demographic difference to contact partners (A to B in Fig. 2)

To implement the first strategy, individuals need to pay attention to characteristics of their contact partners. Individuals tend to have contact with others which share common attributes, such as the neighbourhood they live in (geographical), the companies they work at (organisational), or that are of similar age (demographic)

Strategy 2: Strengthen community cohesion triadic strategy: Increased clustering among contact partners (B to C in Fig. 2)

For the second strategy, individuals must consider with whom their contact partners usually interact. A common feature of contact networks is ‘triadic closure’, referring to the fact that contact partners of an individual tend to be connected themselves

Strategy 3: Create ‘micro-communities’ strategy: Repeated contact to same others, rather than changing interaction partners (C to D in Fig. 2)

For the third strategy, individuals need to pay attention to their latest realised interactions and restrict their interactions these same people. This strategy reduces the number of contact partners rather than number of interactions, which is particularly important when contact is necessary for psychological well-being.

As can be seen the model demonstrates that our behaviour in the future in a post lockdown world will determine whether we embark on a second major outbreak or not.

Both of the ‘business as usual’ scenarios show that the outbreaks are quick and serious. The three ‘strategies’ give delayed and lower peaks. The model does’t include a ‘testing, isolation, contact tracing and quarantine’ approach but it does demonstrate that behavioural change at a population level can reduce the severity of a new outbreak by ‘flattening the curve’. During these lower level outbreaks a test and trace approach could be utilised to flatten these curves even more.

It doesn’t at this point really matter if you completely understand the subtlies of the three different strategies – not doubt other academics will propose similar / slightly different approaches. The modellers at the London School of Hygiene and Tropical Medicine have produced outbreak models which do include the ‘test and trace’ strategy. Let’s see what happens next!

The modelling does indicate that we are not going back to where we were in early March for the foreseeable future – going back to where we were, will require a vaccine or a new effective treatment.

However this work does provide hope – we might be able to meet some of our friends and families albeit in a much reduced way, in due course if we follow a new set of rules which dictate our behaviours and social interactions, once we have flattened the current curve and dampened down new outbreaks.

Covid-19 and Vitamin D

I’ve been doing a bit of digging into why BME people seem more susceptible to Covid-19 – apparently 68% of medical staff who have died so far are from a BME background.

… and they I found this on Twitter this morning, Dr. Mark D’Arcy  is an academic molecular biologist.

and then this Covid-19 / Vitamin D advice from the Scottish Government (link to full advice here)and this from Public Health England in 2016

 

so ….. this won’t do you any harm ….

Eggs, oily fish and cod liver oil are rich in Vitamin D.

And on a day like today get some rays …. spring and summer sunshine naturally raise the Vitamin D levels in our bodies.

We have also heard that asthma suffers are at an increased risk from Covid-19, a bit of googling produced this (one of many many papers on the topic)

Full reference here

We have also heard that obesity can cause Covid-19 complications for patients … and this on the NHS website (again one of many many papers on the topic)

Full reference here

Obviously Covid-19 can cause major lung damage and create breathing difficulties. What about smoking and Vitamin D? (one of many many papers on the topic)

and the paper’s conclusions are as follows

Full reference here

And … I received this reference from a fellow Twitter follower (thanks @tivjon).

Full reference here

I haven’t cherry picked papers to make this point, the academic literature is full of papers on these topics. Of course this isn’t my field and I don’t really know what to make of it or what the implications are either but I did think it interesting enough to share and if you choose to eat eggs, oily fish and spend more time in the sunshine it won’t do you any harm and you never know it might do you some good.

BUT it is complicated .. this study (and a number of others) suggests that inappropriate dosages of Vitamin D can make immunosuppressed patient more ill.

Full paper here

So … here is the Government guidance (remember we are currently ‘staying at home’ and often largely indoors so ….)

This is what the guidance suggests if you feel vulnerable- 10 ug per day

 

or

 

 

 

 

 

Trying and Testing Times – attempting to understand what we should be doing

I don’t know about you but I have lost the track and any sense of time …. I’ve just looked at my phone – today is Thursday – lockdown day 9 (counted it on my fingers). Nevertheless, over the last ‘couple’ of days the Daily Briefing, my Twitter feed and the numerous articles I have read have been full of the following words.

‘Test, test, test’, ‘Anti-gen’, Anti-body, ‘PCR machines’, ‘Chemical re-agents’ and ‘Ramping up’

All these words are set against a backdrop of targets, expectations, jargon, obfuscation and a distinct lack of clarity. For me, this is not a time for tribal politics, it is a period where I desperately want to understand the strategy. It is a moment where I want all the ‘experts’ to come together and say ‘yes’ – as a country we are doing what we should be doing.

For me, three issues are dominating the UK’s COVID19 narrative at the moment: the appalling death rate, the lack of PPE for front line staff and testing. This piece focuses on the latter.

If you remember back to the beginning of this pandemic outbreak a ‘few’ weeks ago we were following the so-called ‘mitigation’ strategy. This aimed to slow the spread of COVID19 but not necessarily stop it. It involved testing people who appeared to have contracted the virus to see if they were infected, quarantining them and then attempting to trace and test those who have been in contact with those who had COVID19. This is the test and trace strategy. This is the strategy deployed, it would appear in China and South Korea for example. It enabled China to restrict the spread of the to predominantly one district – Wuhan, in the case of South Korea the epidemic was contained and eradicated in just two out of their 18 regions.

In the UK the mitigation strategy was replaced rather quickly by the ‘suppression’ strategy following the publication of the Imperial College model which stated that unless we shielded the vulnerable, self-isolated, closed schools and universities (i.e. lockdown) at least 250,000 people would die. However, it is now becoming clear that there was another reason that we switched from mitigation to suppression – the UK’s lack of capacity to carry out the requisite number of tests. Johnson at one of the early briefings stated that we were going to ramp up testing from 10,000 a day to 25,000 and then up to 250,000. Days and days later we have barely got about 12,000 tests a day. Indeed, a couple of days ago Gove suggested that one of the problems with testing was a shortage of ‘chemical reagents’, a claim successful be-bunked by ITV’s Robert Peston.

So, the question is, why can Germany test 500,000 people a week and the UK is struggling to carry 100,000 over the same period? If you are interested in a detailed answer to this question, this article by Jack Dickens provides it. In essence in England we have closed regional testing centres over the past decade or so and centralised the process at one location, in mid February the decision was taken to re-open 12 regional centres. England was not prepared for a viral pandemic and as a result we have been caught short when it comes to the capability to carry out the necessary number of tests.

By contrast Germany appears better prepared, it had a plan in place to utilise testing facilities in the public, private and university sectors – thus it is able to test 5x as many people a day compared to England.

It is important to be clear about what the testing is aiming to achieve. What I had written already refers to a test to determine whether you are currently infected – the so-called anti-gen test. Such a test is carried out on a Polymerase Chain Reaction machine or PCR for short and requires specific chemical reagents to test for COVID19, obtained via a nasal swab sample. As I understand it, in England we are using PCR machines in the 12 / 13 Regional NHS testing centres and as a result there is a capacity issue.

Whilst I have never heard of a PCR before, by all accounts it is a standard piece of equipment used in research. Dr. Mark D’Arcy, a microbiologist and university lecturer wrote this on Twitter today ‘I dont understand the delay in testing. PCR is used to test. Every uni in the country, and thousands of biology labs have PCR machines, and ppl who know how to use them. I spent half my PhD running PCR’s. We have the facilities & ppl, we just dont have the organisation.’ The issue is one of a lack of preparedness and a future logistics challenge. I will return to anti-gen testing a little later.

That neatly brings us to the second test, the anti-body test, this is the one that was discussed at one of the daily briefings by the Deputy Chief Medical Officer, Dr Harries, the pin prick blood test, the one we were going to be able to order on Amazon. The anti-gen test will tell you whether you have already had COVID19 and have recovered. Despite what Robert Peston asserted during the Q&A at yesterday’s Daily Briefing this test cannot tell whether you are currently infected. There is a video I watched earlier where a Consultant Epidemologist puts Peston straight on this point and tells him to desist from making such a claim as it was misleading, wrong and dangerous! We have 1 million of these testing kits already (purchased from China) and they are currently being evaluated thus the oft repeated line that we need to be sure they work properly as an inaccurate test is worse than no test.

It seems to me that the anti-body test could bring three benefits (along with some important caveats)

1. If you knew you had recovered from the disease you could ‘safely’ return to work, useful if you are twiddling your thumbs in lockdown and majorly reassuring if you are a front-line medical employee (caveat to follow)
2. Getting a community wide perspective on the percentage of the population who have already had COVID19 would help improve the quality of the mathematical models. Have 10% or 60% of the population been infected and have subsequently recovered? It would also provide us with greater clarity on the percentage of asymptomatic COVID19 ‘patients’. Anti-body testing therefore gives the modellers their ‘p’ value and gives some indication of the degree of ‘herd immunity’. (Caveat to follow)
3. People who have successfully survived a bout of COVID19 (as identified from an anti-body test) have a degree of immunity to the virus. Blood from such people can then be centrifuged, which separates the plamsa from the red blood cells, the plasma can then be transfused in those who suffering from an infection – potential clinical plasma immunotherapy for COVID19. I read that such an approach was being trialled in New York last week and I suspect such an approach is being used in the UK. (Caveat to follow)

And so, to the caveats, there is considerable uncertainty in academic circles about degree of immunity afforded to people who have recovered from COVID19, I have read that there are currently 5 clades (strains?) of the virus and that further mutations are possible. It is currently unclear what the implications of this are. Additionally, it is unclear what the longevity of immunity to coronaviruses is, previous epidemics have found that immunity deteriorates over time. This being a novel coronavirus, the research required to answer these questions is currently being undertaken – work in progress. Finally a single anti-body test on its own will not be enough to determine whether an individual has a continuous high anti-body level and therefore would not identify the best donors for use in plasma immunotherapy treatments. It is because of these caveats and no doubt others, that this pandemic will not be over until an effective vaccine is produced, thus the 12-18 month timeline.

All of which brings us back to the ‘ramping up’ the testing message and the ‘test, test, test’ mantra. Getting the strategy right going forwards will be vital. With regards to the anti-gen test (have you got COVID19 now), this needs to be prioritised now at front-line NHS staff and other key workers (as the Government has stated). Widespread community anti-gen testing at this point will not achieve a great deal, the virus in many areas is now far too widespread to enable a successful ‘test and trace’ strategy.

The implementation of anti-body testing programme, especially if it can be self-administered in the home will provide a lot of useful data and perhaps assist a gradual return to work and potentially help those suffering from COVID19 receive plasma therapy.

We are told that in the next 2-3 weeks the number of new daily cases will plateau and if we stick to the ‘rules’ the number of new cases will then decline exponentially. At this point it is anticipated that the lockdown measures will start to be relaxed. Of course, that will not be the end of the matter, the scientists expect that there will then be another COVID19 viral outbreak later in the year. By then we have all got to hope that the necessary preparations are in place – viz a viz, sorting out the logistics so that widespread anti-gen testing can be carried out – this will surely require expanding the existing NHS capacity by utilising the PCR machines and personnel located in the country’s Universities and ensuring the procedures, personnel and facilities are in place so that we can conduct an effective ‘mitigation’ strategy second time around consisting of an aggressive ‘test and trace’ policy.

I would like to thank Francois Balloux, Professor of the Genetics Institute at UCL , and an expert on viral pandemics, for taking the time to help me to understand the testing issue, via his Twitter feed (@BallouxFrancois).

Finally, I am certain that Government policy consists of, an albeit much more complex version or variant of the above, it would just be useful for them and for us if they clearly articulated their current thinking.

 

 

 

In other News: Spring is here

During the winter, nature goes into lockdown. Trees have shed their leaves and stand to attention …. birds scrabble around desperately searching for their next meal ….. insects live as eggs, larvae or cocoons. Waiting … patiently waiting for longer and warmer days.

And now spring is here! Birds are singing their heads off in anticipation of imminent breeding and the raising of a new family, butterflies are pursuing the same goal but rather than singing they are flittering. Trees are beginning to come into bud, leaves are magically beginning to appear.

But this is not a normal spring, we are part of nature, whether we think so or not, yet we now find ourselves in lockdown when the rest of nature is not. I am reminded of a poem …. The Waste Lands by T.S. Eliot, written in a different century about a far bigger catastrophe – World War One. Two of the most famous lines spring to mind ‘April is the cruellest month’ and ‘I will show you fear in a handful of dust’. The next few weeks are going to be difficult and traumatic for us, but, and I don’t want to sound trite, as a nation, we will get through this and life will go on, as The Waste Lands shows us.

Of course, elsewhere life is going on and watching it unfold is my favourite hobby, because whilst I think I know what is going to happen nature doesn’t always read my script. For many years now, I have been looking at the oak and ash trees in my garden, prompted by the old country expression ‘oak before ash – we are in for a splash and ash before oak – we are in for a soak’, I want to see who wins the race to be the first species to come into leaf.

In reality oak pretty much always comes into leaf before ash. In the last fifty years oak has always leafed before ash. It has not always been this way – in the 18th century when it was less mild ash did often produce leaves before oak – thus the quote.

Climate change has changed all of this – usually oak comes into leaf in late March-May which is about two weeks earlier than 30 years ago. Ash usually comes into leaf during April and May, about 7-10 days earlier than 30 years ago.

However, first in 2017 and now again this year, it is pretty much a dead heat – the ash is early. I’ve got 5 different oak trees in the garden and one big ash (seriously affected now by ash dieback). The oaks appear genetically different so I think they have come from different parent trees as the come into leaf at strikingly different times. One is way ahead of the others – the same happens every year. This particular oak has ‘beaten’ the ash, but the ash is ahead of the other four. I can’t really explain this as it has been a very mild winter in a warming world so oak should have beaten the ash by quite a distance.

When this pandemic madness has passed, at least for now, and we begin to reconstruct our lives and rebuild the economy, we need to remember that the global climate and biodiversity crises have not gone away and still need to be urgently addressed. If we learn one thing from all of this, it is that we live in a very connected world, and actions taken in one place can impact detrimentally elsewhere. Who would have thought three months ago that fruit bats and pangolins (the presumed original source of COVID-19) would play such a key role in our lives but we also need to remember that in reality they are the victims and not the villains in this whole saga.