Wednesday, 5 February 2020

What could I find out with a Wuhan COVID-19 coronavirus sequence?

When I heard on the news that the sequence of the new Wuhan COVID-19 coronavirus had been made public, the nerd in me was awoken. It triggered memories of when I used to work with plant viruses two decades ago. Would I still be able to find out more about the virus using some of the methods I would have used back then? Would I be able to understand how the up-to-date and vastly more experienced teams in animal and human virology might approach the problem? Could I explain it to others who don’t work with viruses?

If you are simply looking for general information on the current COVID-19 epidemic, have a look at my earlier post here http://www.miltoncontact-blog.com/2020/02/should-i-worry-about-wuhan-2019-ncov.html. This includes up to date charts and tables on the progress of the epidemic using data from the WHO situation reports.

For my adventure with the Covid-19 sequence, read on.

Finding the Wuhan COVID-19 sequence


One of the great early benefits of the internet was the setting up of DNA databases accessible to all scientists, via The European Molecular Biology Laboratory (EMBL), a molecular biology research institution supported by 27 member states - https://www.embl.org/. This database is currently held by the EBI, the European Bioinformatics Institute, whose centre is based in Hinxton, just outside of Cambridge.

My first step was to see if I could find and download the 2019 nCoV (COVID-19) sequence, using the European Nucleotide Sequence Browser that I found at https://www.ebi.ac.uk/ena/browser/home. In the last week of January, I found a sequence of "A novel coronavirus associated with a respiratory disease in Wuhan of Hubei province, China" provided by F. Wu and a further 18 co-workers. It had been submitted on 05-JAN-2020 by the Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China and entered into the database on 13-JAN-2020. Its entry number on the EBI database is MN908947.

Note that if you search now, you will pick up a different set of 7 later sequences under the accession number MN988668: The first two are from "RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak"; Emerg Microbes Infect :0(2019) by Chen Land others, submitted 23-JAN-2020, State Key Laboratory of Virology, Wuhan University, Bayi Road, Wuchang District, Wuhan, Hubei 430072, P.R. China. These cover the first two sequences.

There are 5 further sequences from US laboratories from isolates of the virus from US patients in Arizona, California and Illinois, also from around the end of January.

Update 24 February 2020: 24 different COVID-19 sequences were available, from the US, Japan, China and Italy

The virus sequence is given as 29,881 nucleotides

Are there differences between the eight COVID-19 sequences?


I downloaded all the sequences and combined them into a merged file using the software SeqVerter, part of a downloaded freeware called GenStudio Pro. I then uploaded the merged file to Clustal Omega, an EBI program that compares multiple sequences online. After a cup of tea and a scone (with jam), the result appeared on the screen.

They were all 100% identical – the three Chinese and the 5 five different US isolates.

Short section showing sequence identity over the eight available 2019 nCoV (COVID-19) sequences

From a disease point of view, this was ‘good’ news. It showed that from the beginning of the outbreak in China to the first cases in the US, the virus had not mutated into a different strain.

From an old virologist’s point of view, this was quite an unusual result. Why? Well, virus RNA is replicated with a far higher error rate than DNA. The rate is 1 in 10,000 nucleotides. The virus RNA is almost 30,000 nucleotides long. So every time the virus reproduces, I would expect two to three differences to be introduced. When you get millions of virus particles made during an infection, the sequences are actually a spread of mutations that average out around a consensus sequence. An RNA virus is thus not a species as such, but technically a quasispecies. This hold true for another coronavirus disease, MERS (Middle East Respiratory Syndrom), as explained in Mandary et a; (2019) “Impact of RNA Virus Evolution on Quasispecies Formation and Virulence” https://www.researchgate.net/publication/335938867_Impact_of_RNA_Virus_Evolution_on_Quasispecies_Formation_and_Virulence.

I would expect it to be true for the COVID-19.

Diseases like polio, for example, took advantage of these spread of mutations. After infecting a body and causing mild symptoms, a few viruses were able to break through the blood brain barrier and cause the more severe paralysis. This spread of mutations is also what might make it possible for a virus to jump species and infect a host it does not normally reproduce in.

When I did sequencing more than 20 years ago, we had to clone virus fragments and then sequence each clone. We would have seen the different sequence mutations and would have had to sequence a number of clones to get the average quasispecies sequence.

Modern virus sequencing gets around the individual cloning by using NGS, next generation sequencing https://bitesizebio.com/21193/a-beginners-guide-to-next-generation-sequencing-ngs-technology/. The viral RNA, with its whole population of different sequences is extracted, amplified and sequenced. The sequence obtained is the most average sequence, the quasi-species sequence (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708773/pdf/1471-2164-14-444.pdf).

Update 24 February 2020: A news report stated that there were now sufficient sequences of COVID-19 for researchers to determine how the disease might be migrating into different countries. 

I therefore had a go myself,  generating a first phylogenetic tree. Here are the results I obtained with Clustal with unedited sequences straight from the EBA. 

I do not claim that these results are definitive linkages of relationship or origin at this point. 




24 February 2019: Phylogenetic tree showing possible relationships using unedited COVID-19 sequences from the EBA.


Tentative questions from my data. Are there really two major families of the virus? Are the Japanese and the Italian strains closely related?

A more comprehensive chart created by researchers can be found at the global flu initiative GISAID at https://www.gisaid.org/.


What is the closest relative to the COVID-19?


The beauty of having a public sequence database is that you can take a new sequence, like COVID-19, and use it to see if you find similar sequences amongst the millions already there. I did this online at EBI, using the nucleotide similarity search, Fasta. It was limited to finding 50 related sequences.

I had the results displayed as a “Phylogenetic tree cladogram”, a branching pattern showing the degree of similarity between the different sequences.

My first phylogenetic tree using 2019 nCoV (Wuhan Seafood Market, COVID-19) against the EBI nucleotide database
The tree showed that the closest similarity of the COVID-19 (Wuhan Seafood Market) coronavirus was to Bat SARS-like viruses, and more distantly to other SARS viruses. Those simply called SARS are human isolates. There was a SARS epidemic, which also originated in China, back in 2002, which was finally brought under control in 2004. SARS stands for Severe Acute Respiratory Syndrome. It killed almost one in ten of people infected.

It is interesting how many patent sequences were also picked up. Presumably from companies and organisations that wanted to provide detection and possibly treatment products against SARS.

I wanted a different display to put the COVID-19 in a wider context. I therefore downloaded a number of species specific Coronavirus sequences that I found by searching the European Nucleotide Sequence Browser for coronavirus. I also removed all the patent sequences from the original set found. The new set of data was uploaded for analysis.

The new phylogenetic tree is shown below. I’ve left the accession numbers in to make to make it easier for future work. I also stretched the tree horizontally from the original, to make the branching clearer and coloured different groups for interpretation.

My second phylogenetic tree from using the results from the first search, minus the patent sequences, plus 15 other coronaviruses from different animals


The different human SARS (simply called SARS) sequences in dark red divide into two groups. One has similarities to Civet SARS (in orange), the other has links that reach to Bat SARS strains (orange). The Wuhan COVID-19, marked in bold red, is more closely related to the Bat SARS. The MERS, Middle Eastern Respiratory Syndrome (dark red), was first identified in Saudi Arabia in 2012. It seems to be more lethal than SARS, with about 36% of individuals diagnosed with the disease dying from it. However, it does not seem to spread easily and there have been around 2000 cases recorded in the period 2012 to 2017. My and the professional advice is – keep away from sick camels.

The remaining animal coronaviruses marked in black cover a range from pig to human to rat. The human coronavirus OC43 is one of a number of viruses that cause the common cold.

Using the COVID-19 sequence to find a vaccine


Companies and organisations around the world, including the US and Porton Down in the UK, are now racing to develop a vaccine. One company in the news recently hoping to get to human trials in the Summer.

Where would I begin?

A search for antigenic regions in SARS on Google, after the last SARS outbreak, will find a number of publications. Researchers use blood serum from people who are ill with, or have just recovered from SARS and see if their sera cross react with any of the virus’s proteins (are they antigenic). If they do, they probably contain useful antibodies.

A paper I particularly liked studied the SARS spike protein. The spike protein sits on the outside of the virus capsule. It interacts with the human cells during infection and plays a part in the absorption of the virus into the cell. The spike protein has two domains (stretches), S1 and S2. S1 is not very antigenic, but S2 is. Hong Zhang et al (2004) used a strain of the human SARS called BJ01 (accession no. AY278488). They created 12 different overlapping fragments of the S2 domain of the spike protein. They labelled them F1 to F13. They looked at which of these fragments were bound by antibodies in sera from 15 different SARS patients. (published as “Identification of an Antigenic Determinant on the S2 Domain of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Capable of Inducing Neutralizing Antibodies” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421668/). 

The fragments F3 and F9 in SARS turned out to be antigenic, i.e., the patients’ sera reacted with them. Proteins are made up of chains of amino-acids. F3 stretched from the amino acid Arginine at position 797 in the spike protein to amino acid Proline at position 844. F9 stretched from amino-acid Leucine at position 1045 to Aspartic acid at 1109.

Using a single letter code for each amino acid, the sequences of F3 and F9 are:

F3=RSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLP

F9=LHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCD

First I compared how similar the human SARS BJ01, a Bat SARS, a MERS and a human coronavirus spike proteins were to that of COVID-19 (labelled 2019 nCoV). I did this in pairs using the alignment program in GenStudioPro. The results are shown in the figure below. You can get a good first impression how well sequences match by looking for how much of the aligned protein sequences is coloured darkly, indicating a 100% match.

Pairs of alignments between COVID-19 (2019 nCoV) and human SARS BJ01, a Bat SAR, a MERS and human coronavirus OC43. The locations of the antigenic fragments F3 and F9 from human SARS BJ01 are marked in red bars. The dark colours in the aligned sequences show a 100% match.
Just from the colour patterns alone, you can see that the spike protein of COVID-19 is very similar to both the human and the bat SARS sequences. There is much less matching between 2019 nCoV and the MERS or human coronavirus OC43.

I then looked more closely at the similarities between the F3 and F9 antigenic fragments from human coronavirus OC43 and a variety of sequences. I always included the F3 or F9 fragment, the human coronavirus OC43 sequence from which it was derived, and the COVID-19 sequence.

Looking at similarities to the F3 antigen from human SARS BJ01 with COVID-19  (2019 nCoV) and Bat SARS, a MERS and human coronavirus OC43. Differences just in the COVID-19 (2019 nCoV) are highlighted in red. Differences in the other sequences are highlighted in orange.
Looking at similarities to the F9 antigen from human SARS BJ01 with COVID-19 (2019 nCoV) and Bat SARS, a MERS and human coronavirus OC43. Differences just in the COVID-10 (2019 nCoV) are highlighted in red. Differences in the other sequences are highlighted in orange.
COVID-19 shows three differences in amino acids from F3, marked in red and a further three differences from Bat SARS marked in orange. Compared to F9, COVID-19 shows 9 differences marked in red, as well as a further three differences from Bat SARS.

The question I might try to answer in experimental trials would be, if I changed the F3 and the F9 sequences to match those of COVID-19, would these changes give me antigens that could generate antibodies, and therefore help create potential vaccines against the current COVID-19 outbreak?

Other approaches


The answer to my question might actually be no. Remember earlier on we learnt that an RNA virus like COVID-19 is likely to be a quasispecies. It is not one definite sequence but a population of viruses with an average around the published sequence. The altered F3 and F9 based vaccines would only affect those viruses in the population with exactly these changes. Those with a different mutation might slip through.

Vaccines made with live attenuated viruses are often the most effective and can be made by using such a mixed population found in a quasispecies virus. The other strategy could well be to create an attenuated version of the COVID-19. By being weakened in some functions so it did not cause disease, it might still being able to induce the same antibodies against the native and more dangerous virus and so create an effective vaccine. The availability of the consensus viral sequence and existing information on related SARS viruses might make this work easier.

Conclusion


I hope this gives an insight on what can be done if you have available sequences for a new disease like COVID-19. But do remember, I am just an outsider, 20 years behind the times, who used to work with plant viruses, which are very different to animal and human viruses.
It is reassuring to know, as the disease continues its growth and spread, that vastly more experienced research teams in public labs and private companies are racing to generate an effective vaccine.
They are likely to do so at a pace that I would have found unbelievable when I was working in my field.

Monday, 3 February 2020

Should I Worry About Covid-19, the Wuhan 2019 nCoV Coronavirus?

Photo: CDC/C.S. Goldsmith - https://www.cdc.gov/sars/lab/images.html

Updated 30 March 2020 15:04
data from 29 March 2020 



Executive summary

Yes. you should be concerned and proactive.

COVID-19 is now likely to affect many people in Europe and the US. We have entered a stage of faster COVID-19 multiplication and spread. The disease could be with us for the next few months and possibly into next year.

You need to change your behaviour to take account of the disease and help reduce its impact. Look out for and follow your country's medical and behavioural advice.


This article covers:


  • What is the COVID-19 coronavirus? Symptoms and risks.
  • The spread of COVID-19 in Charts
  • Will I be infected?
  • How can I protect myself?
  • What nations and the international community can do
  • So, should I be concerned?


What is the COVID-19 coronavirus? Symptoms and risks.


COVID-19, is the disease caused by SARS CoV 2, formerly known as the Wuhan 2019 nCoV by the WHO (World Health Organisation). This is a new coronavirus that began in the Chinese city of Wuhan and originated in bats.

Symptoms can include fever, sore throat, dry cough, fatigue and breathing difficulties. A recent report suggests digestive problems can by symptomatic in nearly half of admitted patients. There are lots of different coronaviruses infecting humans and animals. Some of the colds you had in the past were probably caused by a human coronavirus.

This COVID-19 appears to be mild in most cases. However, those with pre-existing health problems and the elderly are more likely to be severely affected.  In severe cases it can cause a viral pneumonia and cause death. See below for more information.

COVID-19 is different from flu and the common cold in that it affects the lower respiratory tract rather than the upper. A recent publication suggest that digestive issues often arise before the other symptoms. See the comparison of symptoms below:


Table 1. Comparison of symptoms between COVID-19, Flu and the common cold. Collated from various medical sources. Includes recent article on gastric problems in the American Journal of Gastroenterology.

COVID-19 seems to be at least as infectious as flu, with an average rate of one person infecting between 2 to 4 people, with suggestions tending towards the higher figure. One person with Rubella infects 5 to 7 people and one with measles, 12 - 18 people.

If you are fit and healthy, the COVID-19 disease is much less likely to be severe. You are at much greater risk if you have a compromised immune system or are affected by other illnesses. As with many diseases, the over 60s are more vulnerable.

Current estimates are that the death rate from COVID-19 from global figures is just under 5%, or 1 in 20 on average. For comparison, Measles kills 1 in 500, a previous coronavirus – SARS - killed  almost 1 in 10. Seasonal  flu usually has a death rate one tenth that of COVID-19.

Detailed figures on mortality rates for COVID-19 are now available based on 44,672 cases from the Chinese Centre for Disease Control and Prevention (figure 2). Age is an important factor. How healthy you are also has a significant effect.

Figure 2. Mortality rate for COVID-19 based on on 44,672 cases from the Chinese Centre for Disease Control and Prevention. I have deliberately set the vertical axis to 100% to avoid  over-emphasising the figures.


Figure  3. The effect of  pre-existing conditions on deaths by COVID-19. I have deliberately set the vertical axis to 100% to avoid  over-emphasising the figures.


The spread of COVID-19 in Charts


By the 28 March:
I have limited my monitoring to countries with historic high cases of COVID-19 up to 23rd March and European countries with more than 1000 cases. Of the countries I am monitoring:
  • Seven countries have 1000 - 2000 cases:  Finland,  Greece, Japan, Luxembourg,  Poland, Romania, Russia.
  • Eleven countries  have more than 2000 - 10000 cases: Australia, Austria, Belgium, Czechia, Denmark, Ireland, The Netherlands, Norway, Portugal, South Korea, Sweden.
  • Nine countries have 10,000+ COVID-19 cases - China, France, Germany, Iran, Italy, Spain, Switzerland, The United Kingdom and the United States of America.

I use the data from the WHO Situation Reports, which reflect figures that lag about 12-24 hours behind the final figures on any date. They are at least consistent and allow trends to be observed over time. US figures have been obtained from the CDC and UK figures from PHE when not available from the WHO. (UK counts are for hospital cases only.)

On the morning of 29 March, 2020, more than 634,835  people have been infected, As many people only have very mild symptoms and might slip through unnoticed, and some countries only test hospital cases, there is speculation that the figure could be considerably higher.

Figure 4 below shows that after the levelling off of cases in China, cases in the rest of the world began, and still are, increasing (figures 4 and 5).   The number of deaths to date globally is 29,957 (figure 4 and 5). There is still a daily increase.

Figure 4. Global cases of COVID-19 and global deaths.

Figure 5.  Same data as figure 4 but as a logarithmic plot of global cases of COVID-19 and global deaths.


The  top scoring locations after China are South Korea, Italy, Iran, and a number of European countries, and the USA, accounting for most of all ROW cases (figures 6 and 7).  

Many European countries have now implemented measures to contain their increase by locking the whole country down. There is possibly a hint the number of new cases in Italy (92,472) has gone from an exponential increase to a linear one. Other countries such as  France (37,145), Germany (52,547), Spain (72,248) and the USA (122,653) (figures 6 and 7) still increasing rapidly, the USA particularly so. 



Figure 6. Eight countries have 10,000+ COVID-19 cases. They are China,  France, Germany, Iran, Italy, Spain, the UK and the United States of America.
Figure 7. The same data as figure but using a logarithmic plot. Countries with  10,000+ COVID-19 cases. China,  France, Germany, Iran, Italy, Spain, the UK and the United States of America. 


A number of countries are still in the early stages of their exponential growth as seen in figures 8 and 9. The number of new cases in South Korea appear to be proceeding at a slower rate (figures 8 & 9). 

Figure 8. Eleven countries  have more than 2000 - 10000 cases: Australia, Austria, Belgium, Czechia. Denmark, Ireland, The Netherlands, Norway, Portugal, South Korea, Sweden.

Figure 9. The same data as figure 7 but as a logarithmic plot. Australia, Austria, Belgium, Czechia, Denmark, Ireland, The Netherlands, Norway, Portugal, South Korea, Sweden..


Table 3. Showing data for countries where COVID-19 has been increasing for charts 6 to 9.


Public Health England map and charts of COVID-19 across the UK


Will I be infected?

Information was that you have to be within 2 meters of someone. The consensus is that the main route of infection to avoid is - touching surfaces contaminated by the virus and then touching your mouth or eyes. Even when you do, this does not mean that you will always become ill (see 'How can I protect myself' below) as you have to receive a certain dose of virus for successful infection.

  • The virus is possibly shed into the air by an infected person. 
  • It seems likely that virus can even be spread by people who are not displaying obvious symptoms like fever or a cough. 
  • Your risk of infection is dramatically reduced the further away you are from ill people. 
  • The onset of warmer weather may help to control the spread of the virus later in the year.

However, it is possible that a significant percentage of the population will be infected eventually.

What does the virus COVID-19 do?

The COVID-19 coronavirus infects the cells lining the airways of the body, the epithelial cells.  In severe cases it seems to progress to the lungs, causing pneumonia.

The virus has a complex protein capsule that contains the virus genes. The virus genes are on a single strand of RNA – not DNA. This strand is 29903 bases (units) long. Numerrous isolates of the virus have been sequenced and their sequences made publically available for all scientists - see https://www.ebi.ac.uk/ena/browser/text-search?query=Wuhan%202019%20nCoV.

On contact with one of your epithelial cells, the cell is triggered to take up the virus. Inside the cell, the virus hijacks your cell’s own functions to make copies of its single RNA strand. The genes encoded on the virus RNA are translated into a range of virus proteins by the cell. New virus particles are then assembled within the cell. They are then either exported by the cell or released when the cell dies. Neighbouring cells are then infected.   If the conditions are right, the virus begins to spread along your airways.

COVID-19 can be symptomless in some people for between 5 to 12 days. If they appear, the symptoms you may get range from fever, sore throat, dry cough, fatigue and breathing difficulties. A recent paper in the American Journal of Gastroenterology suggests that digestive problems may be an early indicator of COVID-19 in nearly 49% of cases, in advance of other symptoms.

They are in part due to the virus affecting/killing cells but also due to your body going into overdrive to try to fight the virus infection. How ill you are is a balance between virus multiplication and how fast and effectively your body defence works. There is more information below in the next section on how you can protect yourself.

How can I protect myself?

Your choices NOW affect how many cases the NHS has to deal with in 14 days.

There is no vaccine for COVD-19 yet – but with the full sequence of the virus available, work is in progress to provide a vaccine in the next months. Therefore isolation and quarantine remain the most effective means to prevent the spread of the disease. Things you can do are:

  • Keeping healthy by eating and sleeping well, exercising*
  • Avoiding locations and people with the illness
  • Hand-washing
  • Use hand sanitisers
  • Good personal hygiene generally
  • Note, the use of even the best masks is more likely to protect others from you when you are ill, rather than protecting you from others.

*Keeping healthy is a great prophylactic as it means that your immune system is in best condition. Our bodies are actually geared to be alert to any foreign invaders and illnesses and the incoming virus does not have it all its own way.



Your body - your best defender!

If a cell in your body is overcome by an infection and dies, this triggers other chemical signals which alert a variety of white blood cells. Some, called macrophages, come to absorb the invading foreign viruses and take the information back to T-cells. The T-cells in turn use this information to help create killer T-cells and antibodies. There are also memory cells that will remember the antibodies required to fight any future infections by the same strain of virus.

Some of my neutrophils from a cold,
photographed at over 1000x magnification
using anoptral contrast

In the meantime, a whole army of another type of white cell, neutrophils, invade the infected area and gobble up all the debris of damaged cells and the viruses they come across. When you have pus from a spot, or your runny nose produces the thick white stuff, or you cough up thick phlegm - that is mostly made up of these short lived neutrophils that have gorged themselves on what is infecting you.

Incoming coronaviruses also trigger the production of interferons within the cell and initiate other yet unknown responses. These seem to slow down virus action. In turn, viruses continually evolve to overcome the cell’s defences. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593566/).

In chemotherapy and radiotherapy, these immune systems are weakened, hence you become more susceptible to infections taking over. So take extra care.

What nations and the international community can do

Countries and the World Health Organisation have plans and structures in place to trigger action when diseases are spreading. The WHO had expressed its opinion that this was still a controllable pandemic and that a shift from containment to mitigation would be wrong and dangerous.

UK Response

PM Boris Johnson acknowledged that this was "the worst public health crisis for a generation".

  • The UK has shifted from a policy to containment to a policy of mitigation. 
  • Individuals with a fever or cough must self isolate for seven days. Families with one infected person need to self isolate for 14 days to ensure everyone is in the clear. 
  • Schools and non-critical businesses have been closed from the weekend of  21st March, exceptions are for critical care workers and essential functions to keep the country running. 
  • People over 70 and those with pre-existing health conditions have been told to self isolate for the foreseeable future. 
  • Travel locally and abroad is strongly discouraged
  • The NHS 111 system is already under strain and people with symptoms are no longer required to call NHS 111. They are instead directly to look for information on the NHS website and 111 online.

Latest Documents from the UK Government accessible here: 


The plan

The aim is to slow down the rate of infection so that the peak in hospital cases is lower and spread, so that the NHS can cope.

Even after the virus has been brought under some degree of control, the virus and some degree of control measures are with us for the foreseeable future - possibly more than one year.

The number of tests for infection will be increasing to determine which key workers and individuals can work in critical posts.

In the near future, testing to see who has been infected and recovered will be possible. This will most likely be by using mass produced antibody kits, similar to pregnancy tests. Knowing someone has recovered and is resistant to the virus will give reassurance that they can return to work without being at risk to themselves and others.

Ultimately, the country needs to gain a significant proportion of the population that is resistant to the virus. This "herd immunity" (see below) can be obtained both by recovery from being infected and from vaccination.

Vaccines are being developed and tests have begun both in animal and small scale human studies. It could take a year or more before a vaccine is generally available.

Herd Immunity and Vaccination

Herd immunity by recovery is a real effect as the government expects that a significant percentage of the population will be infected over the coming year.

Natural herd immunity occurs when a significant proportion of the population has been infected and survived. The survivors are resistant to the illness and, if their numbers are high enough, it becomes more and more difficult for the disease to find uninfected persons. The progress of an epidemic slows or can even peter out if herd immunity is high enough.

With the current  estimate of an average rate of one person infecting between 2 to 4 people for COVID-19, this could mean that 50% to 80% of the population would have to go through infection to achieve full herd immunity against COVID-19 (based on figures in https://en.wikipedia.org/wiki/Herd_immunity#Mechanism).

However, it could be that the UK is hoping that a lower figure of herd immunity may reduce the level of general infection in the population, if not achieving outright cessation of the epidemic.

In the meantime, vaccine development, testing and then mass production will be undertaken as fast as possible to provide our protection in future years.

Other countries' responses

As Europe is the new focus of the pandemic, the US and other countries are increasingly stopping people from European countries (including the UK and Ireland) entering.

Within Europe, France, Germany, The UK and Spain have joined Italy and also introduced more control measures, promoting self isolation, banning public gatherings and restricting movement within and between countries.

The general global practice with new diseases prior to COVID-19


Every year, new strains of influenza arise naturally by mutation as the virus adapts to us changing humans. Rather than letting a large proportion of the world’s population become ill (letting many people die) with the survivors therefore gaining resistance to the newest strain, we humans are proactive. Up and coming new strains of viruses are identified and vaccines produced so that by the time the disease arrives in your part of the world, you are protected in advance and do not get ill, or only have mild symptoms

With totally new viruses, like the COVID-19 coronavirus, there is no immediate vaccine defence. It is therefore vital that a country keeps tabs on new illnesses that arise. They need to have plans in place to deal with the isolation of infected people. They also need to provide care whilst patients go through the illness, to mitigate symptoms until they get well.

Until we have a vaccine, severe cases may be helped by giving them antibodies from people who have recovered from the disease. This method was used against diphtheria in the early 1900's in Alaska, though the antibody serum was actually derived from horses. I do not know if this is currently being pursued. Cloned antibodies might be an alternative solution.

In this interconnected world, nations also have a responsibility to alert the WHO early about upcoming diseases. This time round, full marks for the Chinese response, because we were made aware of the issue earlier than in the past. The world was able to start monitoring for carriers of the illness and put in place travel restrictions.

Whilst China has to bear the brunt of the current epidemic with tens of thousands likely to suffer, we want to limit the disease before it spreads through our populations. New local outbreaks such as those in Korea and most of western Europe are now challenging us.

The UK and WHO have the following information on responses to epidemics and the teams and mechanisms in place. They can be found in public documents such as:


So, should I be concerned?

Yes. COVID-19 is now likely to affect many people in Europe and the US. We have entered a stage of faster COVID-19 multiplication and spread. The disease could be with us for the next few months and possibly into the coming years.

You need to change your behaviour to take account of the disease and help reduce its impact. Your choices NOW affect how many cases the YOUR HEALTH SERVICE has to deal with in 14 days.

COVID-19 virus is currently a pandemic. Many countries, including most of Europe and the UK are seeing a surge in cases.

Apart from China, China, France, Germany, Iran, Italy, Spain, The United Kingdom and the United States of America. are the most seriously affected.

Look out for public advice from the authorities dealing with the outbreak. The following advice is practical not just in this instance but to minimise your risk of getting ill from any disease that is circulating:
  • Keep healthy by eating and sleeping well and exercising
  • Avoiding locations and people with the illness
  • Regular hand-washing
  • Use of hand sanitisers where there might be a risk in public
  • Note, the use of masks , such as surgical masks, is best for protecting others from you when you are ill rather than protecting you from others.
If you have returned from a region seriously affected by COVID-19, or met an individual who has subsequently succumbed to the illness, and begin to experience chest and cough symptoms, stay at home and look online at NHS 111 in the UK https://111.nhs.uk/covid-19. This ensures that you get the right response and treatment and do not accidentally spread the disease further, endangering people in public places, doctors surgeries or hospital reception.

I have also been looking at some of the more technical aspects of the virus genome sequence in the article "What could I find out with a Wuhan COVID-19 coronavirus sequence?" here http://www.miltoncontact-blog.com/2020/02/what-could-i-find-out-with-wuhan-2019.html 


Tuesday, 28 January 2020

Preventing spread and getting a good bounce with a mixed rye-wheat bread

Mixed rye-wheat sourdough load with a good bounce
This ever happened to you? I had a break in baking my sourdough loaves over Christmas. The next loaves I set up in the new year all seemed to have a more plastic dough. it spread more during the final rise. When slashed and in the oven, it hardly rose, coming out of the oven like a slightly thicker discus. I tried again. Same result.

I checked through my method line by line. There was one small difference. I'd kept the last rise in a large but closed container to stop the dough drying out too much over the usual three to four hour rise. Before Christmas, I'd covered the floured dough ball with a tea towel.

The third time, I kept the last rise under a tea towel. The dough rose and spread less. The outer surface had formed a slightly drier skin, which resisted the expansion, leading to a more domed loaf. I cut a cross with a sharp knife as previously, to an inch depth and almost to the base the dough was on.

This time, the large bounce occurred within the first 10 minutes  of baking and continued slightly till the end of the bake.

Covering the floured dough with a tea towel prevented the dough from drying out too much. The the less flexible thin skin formed on the surface maintained the loaf's shape and also, I suspect, put the gas bubbles formed in the dough under a slight pressure. After slashing and placing in the oven, the heat caused the rapid controlled expansion which was helped by the cuts exposing the interior, still very moist and flexible, dough

Thursday, 15 March 2018

A STEM Afternoon With Polarised Light and Microscope

Polar Bear Fur at 100x magnification between crossed polarisation filters
Thirty year 3 primary school students, arranged in a horseshoe jostled each other as they held out 3D cinema glasses, with the arms of the frame pointing at the white desktop screen behind me. They turned the frames, gasped as the polarising lenses suddenly blocked out the light from the screen and then exploded into different directions in the library to get closer to other screens themselves. Soon, some of the more inquisitive also tried out viewing at the live projection screen, the windows, lights and white paper, discovering that the blanking out could only happen at the desktop screens (as these have their own primary polarising filters). Some students collaborated and found that you could also get the darkening effect on lights if you used two sets of glasses/two sets of filters

They were reluctantly dragged back to be still again in a wide circle around the screen. Glasses held at extinction, I slowly lowered an A6 sized rectangle of clear acetate sheet in front of the screen. the hubbub rose again and then got excited when I stuck a piece of Sellotape to the sheet and revealed a range of polarisation colours. From then on the class teacher and I were the focus of a constant stream of students coming back for more and more Sellotape for their own abstract hidden artworks.

This remarkably simple demonstration, of creating colour effects that could only be seen using polarisation filters, filled a good part of 15 minutes. It brought home to me that what seems like a simple everyday technique for many amateur microscopists (and geologists) still had the capability to bring a sense of discovery and wonder to those who saw it for the first time.

You could also tell that the school/teachers had a very positive and supportive nature in working with their young students as the latter were unafraid and open to trying things out and asking questions when they did not understand. Their enthusiasm only had to be curbed when it got too exuberant. Not everyone understood my explanations of polarisation, but they seemed to have come away having learned a new insight or experience of unexpected things you can do with objects they normally take for granted.

The two sessions of 30 students each took over 90 minutes, including talk, demonstration and the practicals. They were topped and tailed by the preparation and packing time in the library. As I was setting up over half an hour, there was a steady flow of students - to the workstations, and to the books. But this was not a reverent or even dull silent area. It was a place to talk about what books a reader might want to go to next after returning the last one, a discussion of preferences.

I found myself pulled in on a conversation as I saw Peter Bunzl's Clockheart and Moonlocket. I'd been drawn into the series after spending my birthday at Leicester Space Centre last November, when there was a simultaneous exhibition of Steampunk. Cogheart struck my eye as a memento to take home and enjoy with my new rocket adorned mug. The paperback versions of the Magyk series was also on the table, with its lovely black and white illustrations.

After the rush of the sessions, the library emptied and I began to pack,  the cheery librarian returned, and now it was the turn of parents and children to come and visit in ones and twos. The microscope stayed on the table, slides and filters were brought out again as the curious came to peer and delight  in what they saw, adult and child alike. The head louse slide was a common denominator for us parents!

Head louse, composite stacked images of 2D panorama
I found myself chatting to a German parent about the books I enjoyed as a child - from Ottfried Preussler to Michael Ende and Cornelia Funke, and recommending animal and vet related books by James Herriot, Gerald Durrell and, on a more fantastical side, the Redwall series.

After Stephen Hawking's death yesterday I also recommended the children series he'd written with daughter Lucy, as I'd enjoyed reading 'George's Secret Key to the Universe' in one go last night in his memory. I found it a much easier and yet scientifically informative read than the highly lauded but seldom finished 'A Brief History of Time'. It had hard facts as a part of the fiction (something done so well by the adult exponent of the hard SciFi genre, Hal Clement, with 'A Mission of Gravity').

The son of the last parent to arrive had been in one of the earlier sessions. His voice carried over as he explained to his amazed mum why a 3D cinema glasses lens could darken a PC screen "It works because there is already a filter on the computer screen!" Subconsciously turning to look at me after he had said it, I gave him a thumbs up across the room.

I left at 5 pm, having extended the STEM activity for a couple of hours, from a hectic full class session to a more calmly paced one to two with a number of parents and children. Tired but positive.

Monday, 15 January 2018

Going from from Micro to Macrophotography with Melolin

Multiple layers Melolin dressing taken though the microscope
Recently, I've had a play with macro-photography. I'm comfortable photographing through the microscope, creating panoramas and stacks but wanted to try capturing subjects more in the centimeter size range and ended up reading around and just experimenting.

I was trying to capture almost a whole specimen on a microscope slide. Initially I tried using my camera with its usual lens but with a lot of extension tubes (66 mm).  The sample was also between tow polarisation filters for colour effects. This worked reasonably well, especially when I took a range of images at different focus and combined them. However, when you look more closely at the image (Full screen), you could see a softening of the image around the edges.

Melolin membrane using 50 mm lens with 66 mm extension tubes
This bugged me, so the next day I thought, why not simply use a low power microscope objective as the lens for the camera?  Cutting some card and and using blue-tac I finally bodged the arrangement  below. Note that the camera is also mounted on a Newer two way rail which I am quite impressed with!

Using a low power microscope objective on the camera
Taking another stack of photos at focus through the slide, I generated a much more satisfactory image as shown below.

Melolin membrane between crossed polars, with low power objective attached to camera.
Trying the same method on a different slide with several layers of melolin membrane on top of each other gave this beautiful coloured image, created by the interference of the polarised light passing through the different filters.

Multiple layers of melolin membranes between crossed polars, taken with low power objective on camera
Of course, the final question is, what is Melolin membrane? The membrane is used in Melolin dressings. Melolin is a trademark of Smith & Nephew http://www.smith-nephew.com/uk/products/wound_management/product-search/melolin/.

As you can see from the image of the single layer, the membrane has numerous very small pores. It is made of poly(ethylene terephthalate) and can be applied to lightly leaking sutures, abrasions or wounds without sticking to them. Dressings can be provided with absorbant pads over the filter, so that the exudate passes through the filter and is absorbed on the pad.

There is a simple beauty in a practical everyday object, that makes even more sense when you know how it works.

Monday, 13 November 2017

An HBN 'Out and About' to Webtec, St Ives


HBN does a series of interesting visits to local companies in Huntingdonshire (our 'Out and About'), so it was with some curiosity that I took a lift with Nick Smith of EAM Consulting to this month's visit, mulling over the company name. I knew it was likely to be manufacturing, but obviously, judging by the name, internet related.

I couldn't have been more wrong! As Managing Director Martin Cuthbert soon explained after welcoming the select group of visitors, Webtec's name came from pre-web days, Web was an abbreviated version of Webster. The tec was, and still is, technology, specifically monitoring equipment for hydraulic systems.

Oversimplified, hydraulics is the use of liquids in pipes. Because liquids are by and large very difficult to compress, if you push plunger in at one end of a pipe, the pressure and movement will be transferred to the other end. As Martin wryly commented, whenever he travels down the building site that is the A14, he cannot help but notice the hydraulics in use in diggers, lifters, drilling rigs and a myriad of other machinery. Hydraulics also allow you to transfer energy at very high pressures, which can be used to drive specialised turbines or exert great force.

Working with hydraulic systems means that things can occasionally leak or systems go wrong. Webtec helps in providing measuring equipment that can help detect either the optimum performance of a machine or the first signs that a service might be in order. The company uses state of the art computerised machinery to make components from blocks of aerospace grade aluminium and steel. We could see how a component gradually developed from a simple block of metal to a high precision milled unit.

We learnt a very useful tip when checking for leaks in hydraulic systems, don't try to find the leaks with your hand. The liquid can be ejected at such high pressure from a pin-prick hole, that it is injected under your skin. This has to be treated quickly as it can cause you further damage and poisoning.

Webtec's products are exported globally, mirroring the UK in that 50 percent of exports go to the EU. Which naturally raised the question of Brexit. As with many other companies international exporters, the key frustration was the current uncertainty. This was coupled with pragmatically putting contingencies in place, to allow border free trading, a rapid response and the good customer relationships that clients will still be expecting within the EU.

The other fascinating story was the transition from an autocratic family-head led firm to a modern business. Martin is one of the two brothers who took over the company from their father, who had bought it from the American firm he was originally working for. Together, the brothers instigated a program of change, with devolved and shared responsibilities amongst the workforce.

One of the biggest problems for engineering firms is getting youngsters to join the business. Webtec has proactively built up a relationship with the regional colleges. Staff are challenged by going out to get involved in STEM activities.  They often get insights from the way the students bring new and unexpected solutions to the challenges they are given. The company in turn offers apprenticeships which look to find the best and maintain the continuing growth and development of the business.

I particularly liked the fact that Webtecc viewed the unusual requests or problems in hydraulics as challenges - ones that opened up new and unforeseen opportunities. When asked how Webtec survived in a competitive world, where big players had hoovered up a lot of the smaller companies, Martin's response was: flexibility, a genuine interest in your customer's issues and helping them find the best solution.

A good HBN 'Out and About'.






Friday, 1 September 2017

The CETC Annual Garden Party

Cambridge MP Daniel Zeichner Keynote Speaker at CETC Garden Party
The torrential rain cleared and a rainbow heralded the CETC (Cambridge Enterprise and Technology Club) Annual Garden Party. Around fifty members and guests wound their way through Wolfson College to reach its Lee Hall. Armed with drinks we chatted in groups and admired the  Betty Wu Lee Garden through the opened veranda doors.

CETC Chair, Dr Andrea Lorenz, wearing a shimmering red chinese jacket patterned with golden dragons, gave a welcome speech. Peppered with witty comments and reminiscences, she spoke of the past year's successful meetings and the ambitious 2017/18 program. Above all, she thanked the attending visitors and guests and invited them to take part in a competition to suggest future speakers and topics. The winner would win a flight over London in a four-seater plane - or the equivalent for those of a more nervous disposition.

Cambridge MP Daniel Zeichner, was our invited keynote speaker and he reflected on the vibrancy of business, science and technology interacting and collaborating in Cambridge, due in no small part to networking and events such as the CETC talks.

The food and the venue were excellent and the place was still buzzing with conversation at its close.

Friday, 14 July 2017

Evelyn Glennie, Musician and Businesswoman hosts HBN's Out and About


HBN had a fascinating visit to see Dame Evelyn Glennie, renowned solo percussionist - and discovered that there was also a surprising amount of business acumen needed to be an independent artist in the modern world.

Having literally created the concept of a solo percussionist, Evelyn found herself increasingly in demand and rushing around the globe at the behest of agents and events. In one of the few breaks in a hectic schedule, the moment of enlightenment came on a simple post-it note on the wall at a meeting with her small dedicated team. It simply asked, "Who owns your business?" 

It was time to answer "Evelyn Glennie".

Stopping to think about where you wanted to be, what you wanted to achieve and how to get there was that key stage at which so many of us small businesses fail. Even artists have to deal with the practical realities of when to get paid, logistics of moving material and products around, and most of all, business development.

Used to having shattered preconceptions of what a percussionist does, Evelyn and her team began to change the rules in how an artist finds work and gets paid for it. Rather than relying simply on agents, Evelyn increasingly used social media to reach out both to the audience, the venues and promotors who organised events. Facebook and particularly Twitter overtook paper advertising - and also reached out to new audiences. 

Taking control of her own business also meant being open to new opportunities and collaborations - with dance groups, scientists and of course other musicians. There was also space to engage in more socially minded activities. And of course there are the masterclasses, speaking engagements etc.

A lovely vignette was the story of The Letter. It had been a busy tour and Evelyn returned tired and expecting  the usual mass of accumulated letters. Her desk, however, was empty, bar a tray with a solitary letter and a cup of tea. Oh my, what could this portend? Bad news perhaps? It was the letter from the Palace notifying Evelyn that she had been chosen to be Dame Commander of the Most Excellent Order of the British Empire (DBE) in the 2007 New Year Honours. And this year, she was appointed to the Order of the Companions of Honour (CH) in the 2017 New Year Honours.

When the tables were turned and we recounted our varied business interests, Evelyn was not only genuinely interested but saw connections and links either to her experience or possible useful connections.

It was a relaxed, personable meeting as conversation and questions bounced across the room, intermingled with laughter. Unpretentious, unselfconscious, Evelyn Glennie was a gracious host and we all left grateful for an informative, educational and entertaining couple of hours in conversation shared with other local small businesses.

And a special thanks for being game for our group photo with the newest, if apparently reluctant, human percussion instrument!
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