Coronavirus Science

By | September 22, 2020

Coronavirus Science

Thankyou and goodbye! 11/05/2021)

Have you had enough of coronavirus?  With the government’s announcement, yesterday of the reduction of restrictions to take effect from 17th May (see the coronavirus emergency is largely over and this post will no longer be updated.  This is all assuming of course that no new virus variant which evades the vaccines does not suddenly appear; but this seems unlikely.  If it does appear we may be back in business.

One last thought: next time you get concerned about media reports of the horrors of genetic engineering remember that you have recently had genetically engineered products injected into you as have most of the folk campaigning about frankenfoods, tampering with nature etc.  The products are called coronavirus vaccines. 

National Status

There is a government 60 page document called Covid-19 Response Spring 2021 setting out the roadmap out of the current lockdown for England which gives full details of the new virus variants, vaccines and therapeutics, a four step “roadmap” to future relaxation of restriction, test and trace, economic issues etc.  This explains how the restrictions included in this guidance will be lifted over time.  There are even more details in the document’s data annex  for real enthusiasts.  Much of what you see in the media originates from here but shorn of the “interpretations” added by the media commentator.  The roadmap section is particularly useful if you are trying to guess what you may be able to do and when during early summer.   From 29 March, the ‘stay at home’ rule ended and up to 6 people or 2 households can meet outside, additionally “shielding” ended on the 31 March.

Local Situation

Covid 19 Mass Testing in West Lancashire

Information for testing sites for West Lancashire (derived from is given below:

Permanent Testing site at Westgate, Skelmersdale

A testing site has opened in the overflow car park close to Sandy Lane Health Centre in Skelmersdale. The site will be open 8am–8pm seven days a week.  Although it is close to the health centre and behind the shops on Sandy Lane, the full address of the site is: Westgate Overflow Car Park, Westgate, Skelmersdale.

Permanent Testing site at Edge Hill University, Ormskirk

A testing site is open on the tennis courts at Edge Hill University seven days a week between 8am and 8pm. This site is open to local residents as well as students.  This is a walk in facility. If you arrive by car, you will be asked to park your vehicle and walk to the testing site ready for your appointed time. If you arrive on foot, you will be directed by testing facility staff upon arrival and asked to follow clearly marked routes which avoid accessing the main areas of campus itself.  Members of the public attending for a booked test have been asked not to use any facilities on site during their visit and to follow the planned routes to reach the testing site and then leave the campus once they have taken their test.

A permanent testing site is also available in Haydock.

Mobile testing units in West Lancashire from January 2021

As well as the two permanent testing sites mentioned above there will be mobile testing units in different parts of the borough on different days open between 10 am and 3 pm.  One of these will be based at West Lancashire College Skelmersdale Campus College Way, Skelmersdale, Lancashire, WN8 6DX.  Dates of opening can be found from

Others will be in the car park at All Saints Church Hall Car Park, Station Road, Hesketh Bank, PR4 6SQ  on 4, 11, 18 and 25 March and Burscough Fitness and Racquets Centre, Bobby Langton Way, Burscough, L40 0SD.  Again, dates of opening can be found from

Testing at these sites will be available to West Lancashire residents travelling by vehicle and on foot. You must book in advance in order to get a test, and you will only be able to book from the previous evening.  If you have symptoms of COVID-19 and wanting to apply for a test visit the dedicated COVID-19 testing site alternatively you can dial 119.


Coronavirus Information

The main symptoms of COVID-19 include:

  • a high temperature – this means you feel hot to touch on your chest or back (you do not need to measure your temperature)
  • a new, continuous cough – this means coughing a lot for more than an hour, or 3 or more coughing episodes in 24 hours (if you usually have a cough, it may be worse than usual)
  • a loss or change to your sense of smell or taste – this means you’ve noticed you cannot smell or taste anything, or things smell or taste different to normal

Most people with coronavirus have at least 1 of these symptoms.

If you have symptoms of COVID-19, however mild, then you must self-isolate for 10 days from when your symptoms started and arrange to have a test. This means that you must not go to work, school, university or public places – work from home if you can.

If you live with someone who has tested positive, someone in your support bubble has symptoms or tested positive, or you are told to isolate by NHS Test and Trace then you’ll also need to self-isolate for 10 days.

Further information on COVID-19 symptoms and what to do if you display symptoms are available here.

I think the test you are most likely to have at one of these centres is the PCR test but two types of test have been used in Liverpool, the so called Polymerase Chain Reaction (PCR) test which detects the virus RNA genetic material and the Lateral Flow Antigen test (LFA) which detects the presence of the Covid 19 antigen on the virus.  The LFA test is rapid, giving results in perhaps 15 minutes rather than having to process the samples in a laboratory (as for the PCR test).  It has been used as a rapid turn around test at walk in centres for asymptomatic residents who wish to know whether they don’t have Covid 19, or do but are pre-symptomatic so that they don’t know that they do.  More recently you have been able to order online a free LFA test to use at home; you can order a pack of 7 tests from  After you have taken the test you report the results online.  This facility can be particularly useful if you are about to visit someone who is particularly vunerable and you want to be sure that you do not carry any infection.

All of this has caveats with regard to false positive and false negative rates for each type of test but these are relatively low.  I think that if you are offered a home testing kit this will be of the PCR type and you will take the samples yourself which will then be collected and taken for laboratory analysis, with you getting the results in a day or so.

It is important to understand that both types of test detect the current presence of the virus and therefore tell you that you may infect others and/or develop more severe symptoms yourself shortly.  It does not tell you that you have had the virus in the past and have developed some immunity; for this you need a serology (blood) test which will look for the presence of antibodies you have developed following the earlier infection.


Covid 19 Vaccination

Vaccination Safety

If you are concerned about adverse reactions to the Astra Zeneca and Pfizer vaccines especially following publicity about blood clotting in a number of European countries you can access the advice from the UK Medical and Healthcare products Regulatory Agency here but a brief abstract is shown below:

  • Data published from UK’s independent medicines regulator confirms approved vaccines meet strict regulatory standards for safety
  • Vast majority of reported side effects are mild and short lasting, reflecting a normal immune response to vaccines – including a sore arm and fatigue
  • The benefits of the COVID-19 vaccines outweigh the risks

Routine safety monitoring and analysis of the approved COVID-19 vaccines by the UK’s medicines regulator, the Medicines and Healthcare products Regulatory Agency (MHRA), shows that the safety of these vaccines remains as high as expected from the clinical trial data that supported the approvals. The safety profile of the vaccines remains positive and the benefits continue to far outweigh any known side-effects.

Over 10 million doses of the Pfizer/BioNTech and the Oxford University/AstraZeneca vaccines have been given across the UK and the MHRA has gathered a large amount of safety data. Data published today shows 22,820 reports of suspected side effects, or an overall reporting rate of 3 in 1,000 doses of vaccine administered from 9 December 2020 to 24 January 2021. This reassuring data has shown that the vast majority of reported side effects are mild and all are in line with most types of vaccine, including the seasonal flu vaccine. These include sore arms and mild ‘flu-like’ symptoms, which reflect a normal immune response to vaccines and are short-lasting.

The European Medicines Agency and the World Health Organisation also confirm the  conclusions of the MHRA that these vaccines are safe.

Vaccination Effectiveness

We, of course, want high efficacy in preventing us from catching Covid 19 or at least developing serious illness as a result, but we also need to know how well a vaccine inhibits transmission of the virus from one person (who may be asymptomatic) to another.  If inhibition of transmission is high it means that the virus will not be able to spread (the magic R number is driven well below 1) and the pandemic shrinks quickly allowing more normal living to resume.  Recent results from Public Health England on vaccine efficacy shows that both the Pfizer and Oxford-AstraZeneca vaccines are highly effective in reducing COVID-19 infections among older people aged 70 years and over. Since January, protection against symptomatic COVID, 4 weeks after the first dose, ranged between 57 and 61% for one dose of Pfizer and between 60 and 73% for the Oxford-AstraZeneca vaccine.

The data, details of which  can  be accessed here,

  • compares the rate of vaccination in symptomatic people aged over 70 years of age who test positive for COVID-19, compared to those who test negative
  • compares the rate of hospitalisation in confirmed COVID-19 cases aged over 80 who were vaccinated more than 14 days before testing positive, compared to unvaccinated cases
  • compares the rate of deaths in confirmed COVID-19 cases aged over 80 who were vaccinated with Pfizer vaccine more than 14 days before testing positive, compared to unvaccinated cases

In the over 80s, data suggest that a single dose of either vaccine is more than 80% effective at preventing hospitalisation, around 3 to 4 weeks after the jab. There is also evidence for the Pfizer vaccine, which suggests it leads to an 83% reduction in deaths from COVID-19.  The data also shows symptomatic infections in over 70s decreasing from around 3 weeks after one dose of both vaccines.  The new analysis adds to growing evidence that the vaccines are working and are highly effective in protecting people against severe illness, hospitalisation and death.

National Vaccination Availability

How likely are you to be able to get vaccinated against the Covid 19 virus?

In total the government has now placed provisional orders for 367 million doses of coronavirus vaccines; these are shown below:

Vaccine type Vaccine No of doses Status
Adenovirus Oxford/AstraZeneca 100 million Approved and in deployment
Adenovirus Janssen 30 million Phase 3 trials
mRNA Pfizer/BioNTech 40 million Approved and in deployment
mRNA Moderna 17 million Approved
Protein Adjuvant GlaxoSmithKline/Sanofi Pasteur 60 million Phase 1/2 trials
Protein Adjuvant Novavax 60 million Phase 3 trials
Inactivated whole virus Valneva 60 million Phase 1/2 trials

some of these may not be available until well into 2021.  However 3 vaccines which have demonstrated high efficacy and safety in trials have been approved by the MHRA agency, these are available sooner, they are:

  • AstraZeneca/Oxford University COVID-19 vaccine (currently in use)
  • Pfizer/BioNTech COVID-19 vaccine (currently in use)
  • Moderna COVID-19 vaccine (approved, available from 7th April 2021)

The Pfizer vaccine received regulatory approval on 2nd December 2020 and the AstraZeneca vaccine on 30th December 2020.  Vaccination using to Pfizer vaccine began 7th December; if you were vaccinated early you therefore probably had the Pfizer BioNTech vaccine, the Oxford Zeneca vaccine came into use a little later.  The Moderna vaccine was approved on 8th January 2021 and has been available from 7th April 2021. The Janssen vaccine by Johnson & Johnson which uses a similar technology to the Oxford Astrazeneca one but needs only a single injection and the Novavax vaccines are expected to be approved shortly and so could be in use later in the summer.

If you have been vaccinated you may be concerned about when you will get a second dose as the government extended the time for the second dose from 3 weeks to 12 to enable more people to have their first dose and gain some protection.  It is important to realise that the vaccine manufacturers base their advice for vaccination timing based on their phase 3 trials and the subsequent approval by the MHRA, this begs the question of course of why a particular spacing between vaccinations was chosen for the trials.  This may be just because this was an interval used in other vaccines which has been shown to be OK, there just has not been enough time to evaluate the vaccines with different timings between doses.  You should not be concerned about changes to the vaccination timings, the general expert opinion now seems to be that 12 weeks is perfectly OK for dose timings and that there is even some reason to believe that it is better than the 3 weeks originally planned.  Interestingly there is some thought that having a second dose using a different vaccine may be useful as different vaccines target different sites on the virus so using two different ones may give the virus more difficulty in developing resistance.  There simply has not been enough time yet to evaluate these alternatives as the time cycle for vaccine development has been compressed from maybe 10 years to 1.  My guess is that if we need a booster vaccination in the autumn it may be by with a modified existing vaccine or even a mixture of two or more of the existing vaccines.

The priorities for vaccination will be based on earlier advice from the government’s Joint Committee on Vaccination and Immunisation  ( i.e.

  1. older adults’ resident in a care home and care home workers
  2. all those 80 years of age and over and health and social care workers
  3. all those 75 years of age and over
  4. all those 70 years of age and over
  5. all those 65 years of age and over
  6. high-risk adults under 65 years of age
  7. moderate-risk adults under 65 years of age
  8. all those 60 years of age and over
  9. all those 55 years of age and over
  10. all those 50 years of age and over
  11. rest of the population (priority to be determined)

Local Vaccination Availability

You can see what is going on in the NHS in West Lancashire at , their frequently asked questions section is particularly useful.  Most U3A members are of an age where vaccination in Jan or Feb 2021 are probable, some U3A members in the 80s had their Pfizer vaccinations in December and have subsequently had their follow up 3 weeks later.

How will you get it?  For the Ormskirk area probably the Hants Lane Health Centre.  You might like to see the information your GP will have from the British Medical Association at 

If you are put off having a vaccination by things you might learn from social media or the more lurid stories in some of the press you should read the definitive information from the Medicines and Healthcare Regulatory Agency  (The MHRA is the approval body for new medicines in the UK).  Information for recipient of the Pfizer vaccine is at and for the Oxford/AstraZeneca vaccine at

Coronavirus Genetic Variants

The coronavirus, or more specifically the SARS-CoV-2 virus undergoes variations in its genetic composition as it reproduces inside human cells.  These are called mutations and generate headlines in the media about “mutant viruses”.  The coronavirus is a RNA virus which the human cell’s reproduction mechanism (which the virus takes over to reproduce itself) has particular difficulty in reproducing faithfully the genetic code of the virus: mutant variations are therefore easily produced.  Often the new variant may have more than one change to its gene.  Many thousands of mutations have already arisen, but only a very small minority are likely to be important and to change the virus in an appreciable way.  There is a consortium of laboratories in the UK called COG-UK .  The consortium is a partnership of the UK’s four public health agencies, as well as the Wellcome Sanger Institute and 12 academic institutions which undertakes random genetic sequencing of positive covid-19 samples around the UK.  Since being set up in April 2020 the consortium has sequenced 140 000 virus genomes from people infected with covid-19.  It uses the data to track outbreaks, identify variant viruses, and publish a weekly report (  They have currently identified around 4000 mutations in the spike protein which is the important part of the virus which enables it to enter and infect our cells.

Sharon Peacock, director of COG-UK, says “Mutations are expected and are a natural part of evolution. Many thousands of mutations have already arisen, and the vast majority have no effect on the virus but can be useful as a barcode to monitor outbreaks.”

Combinations of mutations at different sites on the coronavirus lead to different variants which have received names such as South African variant (B1.1.351), Brazilian variant (P1), Kent (or English)  variant (B.1.1.7), Indian variant (B1.617) – and even a Liverpool variant, all with particular names and codes.  This can get very confusing but there are three particular genetic mutations in the virus spike protein called E484K, K417N and N501Y which are of particular concern as they affect the ease with which the virus can bind to the ACE2 receptor on the surface of human cells. Changes in this part of spike protein may, in theory, result in the virus becoming more infectious and spreading more easily between people.  These mutations in the spike protein combined with other mutations have given rise to the variants listed above and no doubt will give rise to other variants in the future.

The important questions to ask of these variants are:

  • will they spread more quickly i.e. are these more contagious or transmissible
  • are they more dangerous i.e. are they more likely to cause serious illness or death
  • will vaccines still work against them.


The whole reason for a virus’s existence is to reproduce, it has no reproduction mechanism of its own and needs to infect cells so that it can take over the cell’s reproduction mechanism to produce copies of itself; it therefore is under great evolutionary pressure to develop improved transmission from person to person.  Interestingly it is not under pressure to kill the person infected as you cannot transmit the virus so effectively if you are dead: as a result viruses as they evolve often become less deadly.  It is thought that the mutations to the spike proteins change the shape of the folded protein chain making it more open and better able to penetrate cell walls allowing the virus to enter the cell.  The new variants recently identified have improved transmission and therefore have become widely spread, becoming dominant strains.  The Kent variant for example is thought to be up to 70% more transmissible.  This is the reason for the extension to the “post Christmas lockdown” – the R rate of the virus has increased and needs stricter controls to prevent runaway growth in infections, swamping the health services etc. before the vaccination program has had time to take effect on the spread of the virus.


Are the new coronavirus variants more dangerous than the original strain?  Probably not, if there is an effect at all it is small and has not been picked up strongly in epidemiology studies, for example the Kent variant although being more transmissible appears to be no worse than the original strain at causing hospital admissions.  As you might expect however this topic is currently being watched closely for all variants.

Will the vaccines still work?

The new variants have mutations to the spike protein that the three leading vaccines are targeting. However, vaccines produce antibodies against other regions in the spike protein also, so it’s unlikely that a single change would make the vaccine very much less effective.  There have been reports of reduced efficacy of vaccines against the newer variants; balanced against this the four laboratories in the UK who are working on evaluating the new variants against the current vaccines say that they are not seeing any strong evidence that the vaccines will be less effective.  Additionally the producers of the Pfizer Biontech and Moderna and the Oxford-Astrazeneca vaccine have recently stated that they believe their vaccines are equally as effective against the new UK strain.  This is a rapidly developing field of course as epidemiological data can only be collected as a larger statistical population people are vaccinated and available for study.  This means that much of the data on the performance of vaccines against the newer virus variants come from laboratory studies only.

Over time, as more mutations occur, the vaccines may need to be altered. This happens with seasonal flu, which mutates every year, and the vaccine is adjusted accordingly. The SARS-CoV-2 virus doesn’t mutate as quickly as the flu virus, and the vaccines that have so far proved effective in trials are types that can easily be modified if necessary.  The vaccines based on mRNA (e.g. Pfizer Biontech) should be particularly good at doing this quickly.  Work on modifying vaccines against the important spike protein mutations is progressing e.g. Oxford-Astrazeneca have already announced that they have developed an updated version of their vaccine which targets the significant mutated spike proteins and expect to have the modified vaccine available for the autumn when you might expect a resurgence of coronavirus infections similarly to the more common flu.

Interestingly through genetic engineering and computational biology science is now able to “evolve the virus” in the laboratory faster than nature.  There are two approaches; chemically modifying just free spike proteins in the lab and seeing how antibodies interact with them, and computer modelling to see how minor changes to the spike protein affects the way it folds and its subsequent shape.  Using these techniques one can predict what changes to the spike proteins may be dangerous and potentially develop vaccines to them before they occur naturally through virus evolution.  This is developing science which may be expected to drive vaccine development in the future.

More Coronavirus Background Information

We are being exposed to a huge amount of COVID-19 information on a daily basis and not all of it is reliable. Here are some tips taken from the World Health Organisation for telling the difference and stopping the spread of misinformation –

We want to understand the world around us and stay up to date: one of the ways we do this is by seeking out and sharing “information”, much of it from news articles and opinion pieces, messages from vloggers, bloggers, podcasts and social media perhaps shared by friends and family on social media or messaging apps.

Information is something which is accurate to the best of our current knowledge. For instance, COVID-19 stands for coronavirus disease 2019 and is caused by the SARS-CoV-2 virus. One of the difficulties with any new pathogen, like this coronavirus, is that information changes over time as we learn more about the science.

Misinformation, on the other hand, is false information which was not created with the intention of hurting others.  Misinformation is often started by someone who genuinely wants to understand a topic and share information with others who feel the same.  Everyone believes they are sharing good information – but unfortunately, they are not, and depending on what is being shared, the misinformation can turn out to be harmful.  At the other end of the spectrum is disinformation.  Unlike misinformation, this is false information created with the intention of profiting from it or causing harm to a person, a group of people, an organization or even a country.  During this pandemic it can be used to erode our trust in each other and in government and public institutions.  There are seven steps you can take to navigate this wave of information and decide who and what to trust:

1. Assess the source

Who shared the information with you and where did they get it from?  Even if it is friends or family, you still need to vet their source: to check for social media accounts, look at how long profiles have been active, their number of followers and their most recent posts. For websites, check the “About Us” and “Contact Us” pages to look for background information and legitimate contact details.  When it comes to images or videos you can verify their authenticity.  For images, you can use reverse image search tools provided by Google and TinEye, for videos, you can use Amnesty International’s YouTube DatViewer, which extracts thumbnails that you can enter into reverse image search tools.  Other clues that a source may be unreliable or inaccurate include unprofessional visual design, poor spelling and grammar, or excessive use of capitals or exclamation marks.

2. Go beyond headlines

Headlines may be intentionally sensational or provocative to get high numbers of reads or clicks.  Read more than just the headline of an article – go further and look at the entire story.  Search more widely than social media for information – look at print sources such as newspapers and magazines, and digital sources such as podcasts and online news sites; best of all look at formal sites e.g. from the NHS, professional or academic bodies such as those listed in “More Coronavirus Background Information” below.  Diversifying your sources allows you to get a better picture of what is or is not trustworthy.

3. Identify the author

Search the author’s name online to see if they are real or credible.

4. Check the date

When you come across information, ask yourself these questions: Is this a recent story? Is it up to date and relevant to current events? Has a headline, image or statistic been used out of context?

5. Examine the supporting evidence

Credible stories back up their claims with facts – for example, quotes from experts or links to statistics or studies. Verify that experts are reliable and that links actually support the story.

6. Check your biases

We all have biases, and these factor into how we view what’s happening around us; you need to evaluate your own biases and why you may have been drawn to a particular headline or story.  What is your interpretation of it?  Why did you react to it that way?  Does it challenge your assumptions or tell you what you want to hear?  What did you learn about yourself from your interpretation or reaction?

7. Turn to fact-checkers

When in doubt, consult trusted fact-checking organizations such as Poynter International Fact Checking Network

Up to date government coronavirus information is available at  There is also a science organisation which provides science briefings for the media, which is good if you want to miss out “the middle-man “.

Corona Virus Tracking

Government NHS COVID-19 Tracking App

When the official UK Government tracker app was first evaluated significant problems were identified.  The development and use of similar apps has faced problems in other countries.  As a result  a “hybrid” app with some of the characteristics of the existing Google/Apple contact tracing app and the UK Government app was developed and launched in 24th Sept 2020.  It is compatible with most Apple and Android based smart phones, unless the models are too old and is downloadable from the Apple App Store or Google Play: the name of the app is “NHS Covid-19”.  At last count over 14 million people had downloaded it.

The App will:

  • tell you what is the risk level for Covid 19 for the area you live in (you need to put in a part post code to tell the app where you are)
  • scan for nearby phone using Bluetooth so that it can identify if you have been near anyone who also has the app installed and later reports symptoms
  • allows you to scan for QR codes at any restaurant, pub or similar venue which has the NHS QR code on display, this registers you as having been present to aid tracking if you, or anyone else at the venue at the same time, later develop coronavirus symptoms.  I think that having a QR code on display will be compulsory for “hospitality venues” soon.  Being able to scan the code should mean that you do not have to give your details manually to the venue.  I have seen a QR code notice recently in some non hospitality venues (e.g. Hartley’s Nurseries!) so it is worth keeping a look out for them.
  • allow you can check coronavirus symptoms, report if you have them and book a test if you do.
  • allow you to read the latest NHS coronavirus advice
  • enter any test results you have received, this will help the tracing of other contacts you might have had and alert them.

You can find more detailed information from the official NHS web site at

COVID-19 Symptom Tracker (not the official NHS Covid-19 app)

  • Help slow the outbreak
  • Join millions of people helping to fight COVID-19
  • Help scientists identify high risk areas in the UK

The COVID Symptom Tracker was designed by doctors and scientists at King’s College London, Guys and St Thomas’ Hospitals working in partnership with ZOE Global Ltd – a health science company. The Tracker is an app that runs on an iPhone or an Android phone, and by using this app you would be contributing to advancing research on COVID-19 by the Kings College team. The app will be used to study the symptoms of the virus and track how it spreads. For more information go to the COVID-19 Symptom Tracker website.

Other authoritative sources of Coronavirus Information


The WHO – not the rock band!  Confused by all the media reports on Covid-19, want to keep up to date on what is going on worldwide?  The World Health Organisation provides daily high quality scientific information in an easily understood format at

“Advice to the Public” in the sidebar gives reliable information on e.g. masks, coronavirus myths etc.

CEBM - The Centre for Evidence-Based Medicine

The CEBM has a useful Oxford COVID-19 Evidence Service giving rapid reviews of primary care questions relating to the coronavirus pandemic. It is updated regularly.

Coronavirus: the science explained

Coronavirus: the science explained is an authoritative website maintained by UKRI (UK Research & Innovation) the government organisation which funds much of the research work in UK universities.  You have paid for it so you might as well see what it is doing with your money!  The site lays out the evidence and the facts about the virus, the disease, the epidemic, and its control and is regularly updated with the latest science information behind the coronavirus pandemic.  If you keep up to date with this you will be better informed than the average television commentator or newspaper journalist.