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 


2 comments:

  1. This is the most comprehensive article I have read about the current coronavirus epidemic. Thanks Chris - I just wish the media would be as thorough!!

    ReplyDelete
  2. Thanks Holly. Charts updated since you looked at the post. They are updated and the text reviewed at the end of each day (or very early morning!

    ReplyDelete

Google