Coronavirus Science

By | September 22, 2020

Coronavirus Science

Do you think that all we talk about and hear about is Corona Virus?  Do you want to make sense of all you read in the press or hear in media?  Perhaps become a Corona Virus expert to argue with your friends or win the prize in the online Corona Virus quiz (do we have one yet?).  Then read on, and learn all about it from formal government or reputable scientific sources.

Latest Corona Virus Information (updated 14/01/2021)

Local Situation

From 05/01/2021 we were under national lockdown restrictions which are common to all of England and so apply to Lancashire and Liverpool Metropolitan Region; in summary these are:

Leaving home

You must not leave, or be outside of your home except where necessary. You may leave the home to:

  • shop for basic necessities, for you or a vulnerable person
  • go to work, or provide voluntary or charitable services, if you cannot reasonably do so from home
  • exercise with your household (or support bubble) or one other person, this should be limited to once per day, and you should not travel outside your local area.
  • meet your support bubble or childcare bubble where necessary, but only if you are legally permitted to form one
  • seek medical assistance or avoid injury, illness or risk of harm (including domestic abuse)
  • attend education or childcare – for those eligible

Colleges, primary and secondary schools will remain open only for vulnerable children and the children of critical workers. All other children will learn remotely until February half term. Early Years settings remain open.

Higher Education provision will remain online until mid February for all except future critical worker courses.

If you do leave home for a permitted reason, you should always stay local in the village, town, or part of the city where you live. You may leave your local area for a legally permitted reason, such as for work.

If you are clinically extremely vulnerable you should only go out for medical appointments, exercise or if it is essential. You should not attend work

Meeting others

You cannot leave your home to meet socially with anyone you do not live with or are not in a support bubble with (if you are legally permitted to form one).

You may exercise on your own, with one other person, or with your household or support bubble.

You should not meet other people you do not live with, or have formed a support bubble with, unless for a permitted reason.

Stay 2 metres apart from anyone not in your household.

Much more detail is available from the government’s coronavirus web site at  https://www.gov.uk/coronavirus 

Coronavirus UK Genetic Variant

The information below, in italics, is copied with permission from the authoritative British Medical Journal and explains matters much better than I could.

What do we know about this new SARS-CoV-2 variant?

It’s been snappily named VUI-202012/01 (the first “Variant Under Investigation” in December 2020) and is defined by a set of 17 changes or mutations. One of the most significant is an N501Y mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of spike protein may, in theory, result in the virus becoming more infectious and spreading more easily between people.

How was the variant detected?

It was picked up by the Covid-19 Genomics UK (COG-UK) consortium, which undertakes random genetic sequencing of positive covid-19 samples around the 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.

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 (https://www.cogconsortium.uk/data/).

How common is it?

As of 13 December, 1108 cases with this variant had been identified in the UK in nearly 60 different local authorities, although the true number will be much higher. These cases were predominantly in the south east of England, but there have been recent reports from further afield, including Wales and Scotland.

Nick Loman, professor of microbial genomics and bioinformation at the University of Birmingham, told a briefing by the Science Media Centre on 15 December that the variant was first spotted in late September and now accounts for 20% of viruses sequenced in Norfolk, 10% in Essex, and 3% in Suffolk. “There are no data to suggest it had been imported from abroad, so it is likely to have evolved in the UK,” he said.

Does this variant spread more quickly?

Matt Hancock told the House of Commons on 14 December that initial analysis showed that the new variant “may be associated” with the recent rise in cases in southeast England. However, this is not the same as saying that it is causing the rise.

Loman explained, “This variant is strongly associated with where we are seeing increasing rates of covid-19. It’s a correlation, but we can’t say it is causation. But there is striking growth in this variant, which is why we are worried, and it needs urgent follow-up and investigation.”

Is mutation to be expected?

SARS-CoV-2 is an RNA virus, and mutations arise naturally as the virus replicates. 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. COG-UK says that there are currently around 4000 mutations in the spike protein.

Sharon Peacock, director of COG-UK, told the Science Media Centre briefing, “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.”

Is the new variant more dangerous?

We don’t know yet. Mutations that make viruses more infectious don’t necessarily make them more dangerous. A number of variants have already been detected in the UK. For example, the D614G variant is believed to have increased the ability of the virus to be transmitted and is now the most common type circulating in the UK, although it doesn’t seem to result in more severe disease.

Public Health England’s laboratory at Porton Down is currently working to find any evidence that the new variant increases or decreases the severity of disease. Susan Hopkins, joint medical adviser for NHS Test and Trace and Public Health England, said, “There is currently no evidence that this strain causes more severe illness, although it is being detected in a wide geography, especially where there are increased cases being detected.”

Will the vaccine still work?

The new variant has mutations to the spike protein that the three leading vaccines are targeting. However, vaccines produce antibodies against many regions in the spike protein, so it’s unlikely that a single change would make the vaccine less effective.

Over time, as more mutations occur, the vaccine 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 tweaked if necessary.

Peacock said, “With this variant there is no evidence that it will evade the vaccination or a human immune response. But if there is an instance of vaccine failure or reinfection then that case should be treated as high priority for genetic sequencing.”

Scientific views vary on the question of if the high incidence of this new variant in England is due to it originating here or if it is simply due to the good genetic sequencing facilities available in the UK which track new genetic variants so well (many countries do it hardly at all).  Also further different variants seems to be spreading in South Africa and more recently Brazil which may be more resistant to the vaccines which have been produced so far, you can read some expert opinion on this at https://www.sciencemediacentre.org/expert-reaction-to-the-south-african-variant/ and https://www.sciencemediacentre.org/expert-comments-about-what-we-do-and-dont-know-about-the-brazilian-variant-of-sars-cov-2/

Covid 19 Mass Testing

Information for testing sites for West Lancashire (derived from westlancs.gov.uk) 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 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.  One of these will be based at West Lancashire College in Skelmersdale between 10am and 3pm on the following days:

  • Saturday 16 January
  • Sunday 17 January
  • Saturday 23 January
  • Sunday 24 January
  • Saturday 30 January
  • Sunday 31 January

The address is: West Lancashire College, Skelmersdale Campus, College Way, Skelmersdale, Lancashire, WN8 6DX

The other will be in the car park at All Saints Church Hall Car Park, Station Road, Hesketh Bank, PR4 6SQ, between 10am and 3pm on the following days:

  • Monday 18 January
  • Tuesday 19 January
  • Thursday 28 January
  • Friday 29 January

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 NHS.uk dedicated COVID-19 testing site alternatively you can dial 119.

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.  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

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 340 million doses of coronavirus vaccines; some of these may not be available until well into 2021.  However there are 3 candidates which claim high  efficacy and safety in trials, these should be available much sooner, they are:

  • AstraZeneca/Oxford University COVID-19 vaccine
  • Moderna COVID-19 vaccine
  • Pfizer/BioNTech COVID-19 vaccine

The Pfizer vaccine received regulatory approval on 2nd December and the AstraZeneca vaccine on 30th December; the Moderna vaccine will most likely not be available until April 2021 because of manufacturing issues even though it has recently been approved.  Vaccination using to Pfizer vaccine began 7th December but because it needs to be stored at a particularly low temperature (-70 deg C.) its use initially may be limited.  The priorities for vaccination will be based on earlier advice from the government’s Joint Committee on Vaccination and Immunisation  (https://www.gov.uk/government/publications/priority-groups-for-coronavirus-covid-19-vaccination-advice-from-the-jcvi-25-september-2020/jcvi-updated-interim-advice-on-priority-groups-for-covid-19-vaccination) 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)

You can see what is going on in the NHS in West Lancashire at https://www.westlancashireccg.nhs.uk/2021/01/community-covid-19-vaccination-programme-in-west-lancashire , their frequently asked questions section is particularly useful.  My guess is that U3A members are of an age where vaccination in Jan or Feb 2021 seems quite possible, I know of some U3A members in the 80s who have already (21st December) had their Pfizer vaccination.  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 be seeing from the British Medical Association at  https://www.bma.org.uk/advice-and-support/covid-19/gp-practices/covid-19-vaccination-programme

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 https://www.gov.uk/government/publications/regulatory-approval-of-pfizer-biontech-vaccine-for-covid-19/information-for-uk-recipients-on-pfizerbiontech-covid-19-vaccine and for the Oxford/AstraZeneca vaccine at https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/948335/Information_for_UK_recipients_COVID-19_Vaccine_AstraZeneca.pdf

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 https://coronavirus.data.gov.uk/.  There is also a science organisation which provides science briefings for the media, https://www.sciencemediacentre.org which is good if you want to miss out “the middle man “.

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 https://www.covid19.nhs.uk/

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

Take 1 minute to report your health daily, even if you’re well.

  • 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.

WHO

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

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

“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.

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