COVID-19: WHY OMICRON BEHAVES DIFFERENTLY

STOP PRESS:  A paper just published by Glasgow University shows the evidence for Omicron infecting human cells by a different mechanism from Delta and earlier variants. 

In an earlier blogpost, we noted that the spike proteins of the COVID-19 virus (SARS-COV-2) bind to a receptor on human cells, which allows the virus to infect the host cell.  The receptor is called ACE2 "Angiotensin-converting enzyme 2" We also noted that other coronaviruses bind through a different mechanism.

The Omicron variant has a substantial number of changes to the spike protein, especially in the area known to bind to human cells.  

The work by Glasgow University shows that is enough to change how it binds to human cells:

SO WHAT IS HAPPENING?

The report says, in technical language:

"Entry of SARS-CoV-2, and related coronaviruses, can proceed via two routes 

• Cell surface fusion following proteolysis by TMPRSS2,or
• By the endosomal proteases Cathepsin B or L

The ability of SARS-CoV-2 to achieve cell surface fusion is dependent on its S1/S2 polybasic cleavage site; this is absent from most closely related sarbecoviruses, which are confined to endosomal fusion Given the reduced fusogenicity and replication kinetics of Omicron, we used HIV pseudotypes to evaluate entry route preference. We evaluated Wuhan D614G, Alpha, Delta and Omicron spike and as a control we included Pangolin CoV (Guangdong isolate) spike, which exhibits high affinity interactions with human ACE2 but lacks a polybasic cleavage site and, therefore, enters via the endosome only."

The key results show how Omicron closely matches Pangolin CoV, whereas Delta is entirely different:

WHAT DOES THAT MEAN?

Although the Delta and Omicron variants are clearly related, there are clear differences:

• The difference in the way they bind to human cells, as above.  
• Consequently Omicron causing different symptoms more like mild flu, but with the possibility of serious disease, much like flu
  
• Omicron escapes natural and vaccination immunity for Delta and previous variants
• Other differences set out in an earlier blogpost
• Differences in how we should respond to Omicron, including the UK Government's response.  Arguably the danger of hospitalisation is being eclipsed by the risk of closure of key organisations in society, even serious disruption to food supply.  As written over a week ago. 

The Government is now asking each public sector organisation to prepare contingency plans for staff absenteeism rates of up to 25%.  Private sector organisations need to plan likewise.  But what if that means you simply don't have the staff to provide a full service? What should be the priorities at that level of absence?  How can you keep the organisation open? 

It would have been better to prevent Omicron spreading at such high rate, as this blog has been advocating in several posts in the last couple of week.

The differences suggests Omicron should be regarded as a different disease.  The response from individuals, organisations and the Government being specific to Omicron.  Call the disease from Omicron  "COVID-21" ?  Maybe naming the virus "SARS-COV-3", rather than "-2".

Will the World Health Organisation do this?  When they do, you heard it here first !

 

COVID-19: SO YOU’VE HAD OMICRON, WHAT NOW? (Plus notes if you haven't had it)

Self-isolation almost over?

You’ve had a positive test for COVID-19.  But you haven’t been told whether it is Omicron. 

With COVID-19 cases in the UK now over 100,000 a day, in some areas over 95% Omicron, it's most likely an Omicron infection.  You’ve also read this blogpost, looked in detail, and have concluded that you've had infection from Omicron.  

What does it mean for you after self-isolation ends, having had Omicron?

• How freely can you live your life?
• Should you continue with basic precautions, such as using Lateral Flow Tests and wearing masks?

This depends on your wider circumstances. including:

• Have you had COVID-19 before, some time before Omicron reached your area?
• How many vaccinations have you had?  Most younger people won’t have had chance to have 2 vaccines and a booster.  Many children none.
  
• Are you deemed "clinically vulnerable"?
• Age and other factors that can affect the risks of serious disease

WHAT IF YOU HAVEN'T HAD OMICRON?

There's also a section at the end of this blogpost, relevant if you, your family and friends haven't had Omicron.  Yet.

WHAT DO WE NEED TO CONSIDER?

We need to consider these principles when assessing each person’s risks:

1. Omicron successfully bypasses almost all cases of 2 jabs, and can also partially ‘escape’ the booster, as confirmed by research work by Glasgow University:
   
   
   
   Which is why you caught it, if you are double- or triple-jabbed
   
2. Existing vaccines are very effective at stopping Delta and earlier variants, at least in preventing serious disease, as explained in this BMJ article
3. Having natural immunity from having had Omicron, it is extremely unlikely in principle to be re-infected by Omicron, though it is too early to know for sure.  Similarly unlikely to be reinfected by the same earlier variants.  But reinfection by a different earlier variant is possible.  (Best to regard Omicron and other variants as different diseases, albeit related)
   
4. It is unclear whether infection from Omicron reduces chance of infection from Delta and earlier variants
5. We should expect other variant(s) to appear that are different from both Delta and Omicron, and bypass immunity from vaccines or natural infection. Sooner rather than later, and you may be exposed to it before it becomes public

Let’s consider someone, fictional, who:

• Is older, could do with losing a few pounds, and deemed of ‘medium’ vulnerability by GP
• Triple jabbed, over 2 weeks ago
• Has had Omicron, but not disease from any other COVID-19 variant

RISK ASSESSMENT

That person:

• Is very unlikely to be reinfected by Omicron
• Has high immunity to Delta and earlier variants, and if catch it, symptoms are likely to be mild
• Is open to infection from any future new variant that can bypass vaccines and natural Omicron immunity.  

i.e.

• Very low risk of being re-infected with Omicron
• Very low risk of catching Delta or earlier variants
• Very low risk of catching a new variant before its existence is publicised, when behaviour can be adjusted
• At least until immunity fades
  

In each case with symptoms likely to be light, if COVID is caught.

Whilst risk can never be eliminated, this person has very low risk of catching any form of COVID-19 and for that to result in serious disease.

Life is all about risk, such as crossing a road or cycling down the road. The risk of COVID-19 to life and health is somewhat similar.  At a low enough level that the risk can almost be ignored, provided you take as much care as crossing the road or cycling..  

That means generally going about life as before the pandemic, attending any event, going to work, and.. living life ‘free’.  At least until the next nasty variant appears.

But there are people who ought to take more care:

• Those who are clinically vulnerable. It is up to them to assess their own risk/reward balance for specific situations, and what risk is worth taking.
• Those who have not been fully booster-vaxed, including children
  

WHAT ABOUT ONGOING PRECAUTIONS?

As there is a risk of catching COVID-19, and potentially passing disease on to other people, continuation of basic precautions is sensible.  This is mainly for protection of others, and should be regarded as a civic duty:

• Taking a Lateral Flow Test before prolonged contact with other people, if necessary daily
• As far as possible meet in outside or well-ventilated areas
• Wearing masks on public transport and other places where you could easily pass infection to others.  Pubs and restaurants where food and drink is consumed need to be a practical exception.
  
• Other basic precautions, such as washing hands
  

WHAT ABOUT CATCHING OMICRON DELIBERATELY?

If you, friends or family haven’t had Omicron, is it worth catching it deliberately?  Going to a 'COVID party', like 'chicken pox parties' perhaps.

In most cases, it looks like Omicron infection is milder than Delta.  But:

• It’s too early to tell how serious infection from Omicron is going to be, and how common especially in people who are inherently more vulnerable
• It’s too early to tell how bad LongCovid is going to be.  Probably more common than with earlier variants, due to the speed it can spread around the body to damage other susceptible organs

So no, it is unwise to atttempt to catch Omicron deliberately.  

But take a few more risks?  Frankly that’s how I caught it, when it was raining and I had the choice of sitting indoors in the pub or going home.  Knowing it was a risk to sit indoors, but feeling I was going to catch Omicron some time anyway, and knowing I had the protection of being triple vaxed against Delta.  Likewise taking risks is up to you.
 

IN CONCLUSION

If you've had Omicron:

• If you're triple vaxed, and not highly vulnerable, you may consider the risk of a further serious COVID-19 infection to be low enough to get back to living life 'normally'. Albeit taking basic precautions, pricipally to protect others
  
• But not fully vaxed, and/or vulnerable, continue to take care!

If you haven't had Omicron:

• Don't catch it deliberately
• But perhaps be willing to take a few more risks 

 

UPDATE 4 JANUARY 

New Year events provided the opportunity to test the 'live life normally' freedom proposition.  Here's what happened.

COVID-19: OR IS IT NOW COVID-21 ?

A week or so ago, this blog ran a post called "COVID-19: SURELY OMICRON'S DISEASE SHOULD BE CALLED COVID-21?" This reflected a host of differences between the diseases caused by the Delta and Omicron viruses.

Since then a similar notion has been appearing in the mainstream media. (Isn't it good to be ahead of them again!). For example the Guardian ran a story this week headlined "Omicron is ‘not the same disease’ as earlier Covid waves, says UK scientist".  That's Sir John Bell, regius professor of medicine at Oxford University and the UK Government’s life sciences adviser.

The last week has also allowed us to get a better understanding of Omicron disease, although there are still some major uncertainties.

Let's examine what we do know, and what we don't, and consider:

• Whether it would be helpful to regard Omicron as causing a different disease, let's say COVID-21, regardless of official World Health Organisation conventions and names
• Whether the Government is right to avoid further disease prevention controls (which is the positive side of 'restrictions')
  

FIRSTLY, A BASIC INTRODUCTION TO CORONAVIRUSES 

The virus that causes COVID-19 disease is officially called SARS-COV-2.  It is one of seven types of coronaviruses found in humans, with many more found in other animals such as bats: 

Coronaviruses are so-called because they have a central ‘body’ out of which poke ‘spike proteins’ that look like a crown, or ‘corona’.  

These spike proteins bind to a receptor on human cells, which allows the virus to infect the host cell.  In the case of SARS-COV-2 and some other coronaviruses, the receptor is called ACE2 "Angiotensin-converting enzyme 2".

‘Variants’ are slightly different from each other, especially in having different spike proteins.  Here are the changes in Omicron::
 

Simplistically for SARS-COV-2:

• The different spike proteins in the different variants have different binding capabilities.  The better they bind to the ACE2 receptors, the faster the disease will spread from person-to-person and within each individual (see update in this post, re Omicron using a different mechanism)
  
• Differences in the body of the virus determine how severe the disease will be.  Especially the RNA it contains

The four viruses that have mild symptoms like ‘common colds’, with only occasional serious symptoms, spread at different rates.  At the other end of the severity spectrum, SARS-COV-1 and MERS-COV viruses produce much more serious disease (SARS and MERS respectively).  Too often including death.  But fortunately these two viruses do not spread easily, and so were relatively easy to stop spreading much further outside of the local area in which they were first found.

The fear after SARS and MERS was that there could be another coronavirus that spreads more quickly and easily, whilst also causing moderate to severe symptoms.

SARS-COV-2 is that virus family, with moderately bad symptoms (between common colds and  SARS/MERS), with variants that have become increasingly good at infecting people:   

Omicron is the fastest-spreading variant so far.  But how serious is it?
 

LET'S FIRST CONSIDER LONG COVID

A significant proportion of people who have been infected byearlier variants of COVID-19, whether they have been hospitalised or not, have long term symptoms.  Longer than three months, and sometimes longer than a year.  These may be ongoing symptoms similar to originally experienced, or additional  symptoms.  Collectively called LongCovid.

We need to realise that it is not just cells in the respiratory tract that have ACE2 receptors.  These are present in many organs including heart, intestines, kidney, gallbladder and testis.   Yes you men, your testicles!

When SARS-COV-2 gets into the bloodstream, as can happen when infected cells burst:

• The virus is transported to other organs, where cells can become infected, damaging the organ
• The virus also causes microclots in the blood, which can themselves cause organ damage.  The brain is especially susceptible, with a common symptom being fatigue and cognitive impairment or ‘brain fog’

The higher the case rate, the higher the number of LongCovid cases:

• Affecting the lives of a large number of people, with worst cases not having the health to work
• Putting additional strain on GPs, who are already over-stretched
• Putting additional strain on NHS specialist services, taking expert medics away from dealing with other health conditions

In addition, a proportion of people will have long-term and sometimes severe lethargy.  This can be the body’s response to any severe illness.  Lethargy is a common complaint of people who have had COVID-19, even mildly.

But how common is LongCovid in people who have had Omicron?  As discussed below, Omicron has attributes that could make LongCovid more common. Too early to tell, but the risk is more LongCovid with Omicron - potentially worse symptoms in a higher proportion of people.

WHAT WE KNOW ABOUT OMICRON SO FAR

Speed of spread

All viruses can mutate as they replicate.  SARS-COV-2 mutates less than many other viruses.  But it still mutates, to produce different variants such as Omicron.  This has mutations on the spike protein which has three results:

• Even when the body’s immune system is primed through vaccination or prior infection, the system does not recognise Omicron as the same threat as earlier variants.  Omicron therefore substantially ‘escapes’ our immunity to other variants
  
• It looks like Omicron’s spike proteins bind more easily to host cells than the original virus and earlier variants
• As a result, people become infectious more quickly, in just a few hours

Studies on how fast Omicron can spread include this published by Imperial College London last week:

1. "In human nasal airway epithelial cells (HAE) Omicron showed a large early replication advantage, yielding viral load titres ~100-fold higher than for Delta by 24 hours post infection."  This graph has a log scale, so adding 2 means multiplying 100 times:

2. Omicron propagates differently to Delta, forming smaller plaques:

Omicron spreads very fast!

Severity of Symptoms 

If Omicron caused only mild symptoms similar to the four common cold coronaviruses, we could just let it spread, and everyone have maybe a couple of days unwell and off work.   Much like colds and flu 

If we could easily test for specific variants, there could be different rules for self-isolation with Omicron, and we could possibly be more relaxed about high case rates, subject to the uncertainties below.

Fortunately it does seem that symptoms are mild, at least for people who are well jabbed.  Hence the UK Government putting stress on people getting the booster. 

The common symptoms of Omicron are different to those for Delta and earlier variants.

• Delta and earlier variants:
• Continuous cough
  
• Loss of taste and smell
• High temperature
  
• Omicron:
• Like a common cold (like some other Coronaviruses)
• Sore throat, and importantly a hoarse/scratchy voice as the first symptom
  
• Runny nose
• Different
• Headache
• Fatigue

WHAT ARE THE MAJOR UNCERTAINTIES?

But there are still some major uncertainties, as Omicron is so new, even after pooling knowledge from around the world:

• Omicron infection has been mainly in younger generations.  We don’t yet know how severe infection will typically be in older generations and for others who are at higher risk.
• We don’t know what proportion of those infected will typically require hospital treatment, of those who will need intensive care, and how many will die.  We need to know by age group.  Whilst the proportion of serious cases may be below that for earlier variants, very high case rates could still mean large numbers requiring hospital care. 
• We also need to know the difference for people of different vaccination status.  Omicron is likely to be more serious for the unvaccinated.  Hopefully vaccines may make symptoms less severe, even if vaccinated people are still getting infected
  
• As hospitalisation lags infection by a week or two, it is still too early to tell whether the surge in cases in the last week or so will translate into high numbers requiring hospital treatment. Though early indications are not good. That's because if high numbers do result, it will be too late to do much about it.  High numbers infected and about to require hospital treatment will already be 'baked in’
• LongCovid:  We don’t know what proportion of people infected will have long term symptoms. More or less in number?  Different symptoms, perhaps?  But as Omicron spreads more quickly through the body, our intial assumption should be a higher proportion of those infected with Omicron may suffer from LongCovid, more seriously.
  

SO IS OMICRON CAUSING A DIFFERENT DISEASE? 

We know:

• There is a different set of initial symptoms, somewhat milder than for Delta and earlier variants
• Cases are spreading and growing far more quickly than earlier variants
• Omicron is ‘escaping’ immunity, both from vaccines or prior infection
• Therefore the best Government response to Omicron could be different from that for earlier variants
  

It is therefore sensible to regard the disease as different, with a different name.  With 2021 almost at an end, let’s call it COVID-21.  (See Update at foot of this post)

We effectively have two overlapping pandemics:

• COVID-21 caused by Omicron
• COVID-19 caused by Delta and other variants

Yet our tests cannot yet distinguish Omicron from other variants.  We have to fight it as if it were a single COVID disease

WHAT ARE THE IMPLICATIONS FOR THE UK GOVERNMENT’S RESPONSE? 

We asked earlier “Whether the UK Government is right to avoid further disease prevention controls (otherwise known as 'restrictions')”

In reality, we have to manage all COVID-19 infections in the same way at the community level, given:

• So many uncertainties on the severity of Omicron  disease, beyond relatively mild initial symptoms
• No easy way to identify which cases are Omicron

But where an individual is clearly infected with Omicron, it is more useful to think in terms of a different ‘COVID-21’ disease.  “COVID” could be the term covering both 19 and 21.

In the UK, the length of self-isolation has been reduced from '10 days' to '7 days'. Though the definition of day differs, so that it actually means nearly 4 days earlier., not 3 . Counting infection day (or positive test) as day zero, the original rules were that infected people should self-isolate for the next 10 days, and can stop self-isolating as day 11 starts at 0001 hours.  Subject to certain conditions, the new rules allow someone to stop self-isolation after a negative test on day 7, nearly four days earlier than before. (not 3).  The USA has gone a stage further, reducing that to 5 days. 

Five days would be good for Omicron, to avoid as much disruption as Omicron is causing, with organisations having to close or run on substantially reduced staff.  The NHS is currently suffering the combination of high case rates and being short staffed.  Furthermore the worry is the risk of major disruption to the food supply chain.

Perhaps 5 days may be comfortable for cases of Omicron, if we can be confident of  low consequences, such as low incidence of LongCovid.  But 5 days is difficult to accept for other variants, where the co0nsequences of infection we know to be serious in many cases.

Or could we say that Omicron is now so dominant, the chance of catching another variant is substantially reduced?  If that was the case, perhaps we could treat all infections as Omicron and potentially be more relaxed on restrictions. 

But we have major uncertainties of the severity of Omicron:

• Generally
• In older people, and others at higher risk
• For LongCovid

There are also unacceptable risks to society due to so many people being off work ill.  It is therefore madness to allow high case rates.  Hospitalisation levels are only one consequence.

Whilst nobody wants to see tougher restrictions, not to do so is taking enormous risks with NHS, food supply and much else.   Action is needed to reduce spread of the disease.  There’s no time to lose, given how quicjkly Omicron / COVID-21 is spreading.

As Imperial College says in conclusion of their report last eyar, where NPI means Non-Pharmaceutical Interventions such as lockdowns:

UPDATE 31/12/21:  Research by Glasgow University shows Omicron infects human cells by a different mechansim to ACE2.  All the more reason to regard Omicron as a different disease.  Let's call it COVID-21

COVID-19: ALREADY NEGATIVE

I've woken up this morning full of the joys of spring.  Well, full of the joys of Isolation at Twixtmas.

Having tested positive on Boxing Day, two days ago, could I already have overcome COVID?  A negative LFT provides the answer, using the same brand and box as was positive 2 days ago.  Though I cannot rely on one test alone. No guarantee I am yet virus-free.

Will try again tomorrow.  [Drum roll:  Negative again] In any case I cannot legally leave isolation until 7 days are up.

But looks like my jabs and booster has prepared my body for the COVID onslaught.  Flattening the curce, and/or getting the infection to turn down more quickly.

 

This graph suggests an LFT should be able to detect infection betweem 3 and 8 days after exposure to the virus.  Though this is just a guide.  Everybody and every infection is different  As discussed here, the most likely source of my infection was less than 36 hours before the positive LFT, consistent with the rapid growth of Omicron.

Now just three and a half days after infection, it looks like I may no longer be infectious.  But will continue to self-isolate just in case.  And of course to comply with the law.

COVID-19: HOW TO CATCH IT (AND HOW TO AVOID IT)

The pub empty last Wednesday

On Christmas Eve, I went to a pub for a drink and to meet friends.  It was raining.  The outdoor area we normally use is well-ventilated but the covered seating was full.  Another covered area was dry, but these tables were not being served by the table-ordering system.  

The choice was sit inside the pub proper, or go home. My pals had chosen the latter.  There was one empty table that was a couple of metres away from anybody else.  Should be OK.  I knew it was a risk.  But let's take it.

On Boxing Day morning, the LFT came up positive. Given how easily Omicron spreads, and how quickly it can replicate in the body, it is almost certain that I caught Conid-19 on Christmas Eve in that pub.

How?  After we'd been told about social distancing and the 2-metre rule, it turns out that this advice was erroneous.  With Omicron (and Delta) so prevalent, it is now so easy to catch COVID simply by being indoors with other people.  Especially if they are laughing and shouting, spreading virus-laden droplets and smaller 'aerosols' far into the air.

This article describes the battle to get COVID's primary means of transmission, through the air, recognised.  That 2 metres is simply not enough.  Any area needs to be well-ventilated, so any virus-laden droplets and aerosols are blown away.  My table in the pub was not well ventilated.  I paid the price..

COVID-19: OMICRON OR DELTA?

Earlier we looked at the consequences of getting a positive PCR test result.  The notification of the result was received without statement of the variant.  But it is important to know whether the infection is Omicron, or some other variant such as Delta.  That is because:

• Someone who has not had Omicron can be easily infected by it, as it can easily bypass vaccines (including a booster) and prior infection from another variant.  Although vaccines make infection from Omicron less serious, best to stay vigilant and cautious to prevent an Omicron infection
  
• Someone fully vaccinated who has had Omicron is very unlikely to be re-infected by Omicron or by one of the other variants, or at least not be seriously ill.  As near to 'Freedom' as is feasible - at least until another Variant of Concern' comes along.
  

So how do we find out which variant?

TESTING METHODS

The current PCR testing looks for specific fragments of the virus, which all variants exhibit.  So PCR tests cannot currently identify and distinguish specific variants.  New testing such as this makes testing more accurate, to more reliably spot new variants, but also cannot identify which variant is present. 

In a fast-moving field, there are at least three ways to specifically identify Omicron:

1. Whole genome sequencing (WGS), following a positive PCR test result. This process can take a few days, which is obviously not ideal
2. S gene target failure: The Omicron variant of the virus has a number of mutations which mean that the S gene does not show up in PCR results. This is referred to as 'S gene dropout' or 'S gene target failure' and it can be used as marker for this variant pending the WGS results.
3. New tests such as this one published last week, which can be rolled out to all test centres
   

In the meantime WGS and S gene target failure are only being carried out at some test centres in the UK.  The results are only used for a better understanding of community prevalence of Omicron and other variants.  Not notified to individuals

SO HOW CAN WE TELL IF WE'VE HAD OMICRON?

There is currently no sure-fire way to tell if you have had Omicron.  But we can get a strong inkling of likelihood by a combination of:

• Known incidence in the local area, when such statistics are available, and
  
• The type of symptoms experienced

Known Incidence

Oxfordshire, for example, has a Dashboard of COVID-19 statistics.  This doesn't yet indicate the levels of each variant.   But after several months at around the same rate with Delta, the number of cases is now rising steeply.  Almost certainly dominated by Omicron, with Delta still in the mix, perhaps in ratio 2:1 and increasing:

Symptoms

It is possible to be infected by any variant and have little or no symptoms.  But if symptoms are strong, the top three are different between Omicron and the others:

• Delta and earlier variants:
• Continuous cough
  
• Loss of taste and smell
• High temperature
  
• Omicron:
• Like a common cold (like some other Coronaviruses)
• Sore throat
• Runny nose
• Different
• Headache
• Fatigue
  

STOP PRESS Update 28/12/21:  It is now being reported that "The first sign and symptom of Omicron could present itself in your voice, meaning you need to keep an ear out for any changes.  This is because Omicron has been linked with a hoarse or scratchy voice, after causing havoc in your throat.  You could HEAR the very first warning sign of Omicron before you feel ill"

MY OWN ASSESSMENT

In terms of symptoms:

• Tickly sore throat, not requiring any treatment, rather than a continuous cough.  Plus a scratchy voice
  
• Mild fatigue for a couple of days.  Not like flu where it is difficult to get out of bed
• No change to taste and smell
• No high temperature

In terms of local prevalence, it looks more likely to be Omicron than Delta.  Adding in the symptoms, and it's looking like a 99%+ chance of Omicron.  

Indeed this new symptom of a scratchy voice started for me the day before the positive tests, on 25th before 26th tests.  That would allow me to exit isolation a day earlier, provided I can comply with the 7-day regulations.  Based on the NHS advice published 24 December:

Tweaked to suit the actual dates:

'This means that if, for example, your symptoms started at any time on the 25th of December (even if your first positive COVID-19 test was taken on the 26th), you may take daily LFD tests from the 31st December. If your LFD test results are negative on the 31st  and 1st, and you do not have a high temperature, you may end your isolation period after the negative test result on the 1st of January." Not the second of January had I not noticed that new symptom.

So under the 7 Days rules you can exit isolation just after 0000hrs on 1st of January, not the 4th as would have been the case with the 10 Days rules.  In this case the 25th would have been defined as Day 0, day 10 as 4th January, and isolation exit on 5th.  That means 4 days earlier.

Armed with this new symptom information, I tried to edit my Test & Trace account to bring the 10-day end date back a day.  But "You cannot change information about...your symptoms."  WTF! 

I'll have to carry a copy of thsi blogpost with me on 1st, in case I get stopped.  Assuming of course that I have two negative LFTs and no high temperature.

Then it's a matter of how 'free' I can feel going out that soon.  OK if I've had Omicron.  I reckon there's a 99%+ chance it's Omicron.  But it would be good to get a definitive test.

COVID-19: THE POSITIVE PCR TEST

Yesterday I reported that I had a positive Lateral Flow Test.  This was the first time using that brand, and I had none of the classic symptoms.  So I used an LFT test from a different brand that up to then had always given negative results.  Again positive. Virtually certain to have COVID-19 infection.

Today my PCR result came through by email, 24 hours after the test:

    "Test date: 26/12/2021    Your recent coronavirus (COVID-19) test came back positive."

So that's definite.  I have COVID-19.  Despite being double-jabbed and boosted.  Though hopefully vaccination will have better prepared my immunity, such that illness will be milder than had I not been vaccinated.  So far so good (touches wood!)

The SMS text was clearer, especially on self-isolation and other actions to take: 

WHAT ABOUT THE COVID-19 APP?

Both the text and email asked for the Covid-19 app to be updated with a code.  This is so likely contacts would be notified, and the user would get self-isolation advice.  

But does anyone use the app now?  I never used it, as I had major concerns about the contacts function of the app. The chance of false notifications too high, as: 

(a) No check-out function to identify clearly if two people were actually in the same place at the same time.  

(b)  Inherently able to show proximity despite a physical barriers between the phones, such as a wall

Certainly no venues have been asking for sign-in recently.  Especially the venue most likely to have been the source of my infection.

Per the email:  

Update 28/12/21:  I've reluctantly downloaded the app, in the hope for clarity on which day I can exit isolation.  Although freshly downloaded, it doesn't mention the new 7 day rule.  It's talking 10 days, and confusingly says "You need to self-isolate until 5 Jan 2022 at 2359" and "9 days to go".:

• Why doesn't it say "end self-isolation from 6 Jan at 0001"?
• Then "9 days to go" would make clear sense. With 9 days to go on 28/12, then 1 day to go would be on 5 January, with freedom on 6 January 

So does the 7-day rule for people who comply with the conditions mean 'freedom' on 3 January?  What if had 'symptoms' the day before testing?  Would that legally be 2 January?  I need to know!

(As a former Computer Audit Manager for a Big4, the clowns who are responsible for developing and maintaining the app (or those managing them) would not want to see my review!  Key components in the app have come from reliable sources, but their use in the app is poor.  Well below an acceptable standard.)

NO SMARTPHONE?

What about for people without a smartphone?  No advice.  Not good enough!

SYMPTOMS

So far, touch wood, symptoms have been virtually non-existent.  None of the classic COVID-19 symptoms that would have prompted a PCR test, had there been no positive LFT.

But there has been one odd symptom, that started on Christmas Day when I was probably just infected.  Maybe a coincidence, as there are other possible causes.  As those could be serious, I am going to have to consult a doctor if this does not disappear by say a week's time.

CONSEQUENCES OF MY INFECTION

So far so good.  Touch wood.   All being well, I will not become seriously ill, certainly not enough to need hospital admission.  But that doesn't mean this infection has been without consequences.  Especially if we look at community effects by scaling up the effects for the exceptionally high number of new infections in communities throughout the land.  

In the next week or so:

• If I have to consult a doctor, who might refer me to a specialist, then that is additional strain on the NHS.  Resources taken away from handling other health issues
• I was rostered to volunteer at a Food Bank.  With other volunteers off ill too this week, staffing this essential service is under strain.  I've been watching calls going out for volunteers regularly through the day to keep the service running.
• Employers in other organisations are also struggling with staffing, such as trains and the NHS.  Some closing, such as football matches called off due to covid-stricken teams

Imagine if supermarkets started to shut, due to lack of staff or lack of supply.  Not just loo rolls.  Nor petrol.  But actual food.  Wouldn't there be panic?  Why is the Government taking the risk?  Surely someone has raised this realistic possibility!  Maybe the risk is small.  But just like insurance, when the consequence is large, the wise take action.  No action today in England, it's been announced.

There's then longer term consequences:

• People losing their sense of taste and smell for an extended period
• Prolonged exhaustion, common after any major infection
• Other LongCovid symptoms, that can also keep people off work, and unable to function as normal.  Massive consequences to the individuals affected.  Also to society if many people are affected, as numbers will be proportional to case rates
  

There is no need for more data.  It is abundantly clear that the Government is taking unacceptable risks with our lives and communities.  The economy very much at risk in 2022.

The situation is screaming out "Action now."

CONTACT TRACING

I have also been asked to complete various details on a web site for contact tracing purposes.  Utterly useless.

COVID-19: SHIT'S JUST GOT REAL

Testing positive with LFTs

Yesterday I went down to the river, wishing Merry Christmas to many of the people I passed.  Most returned the wishes.  But one man said "Hopefully next year will be better than this year".  I added "or last year".  To which his response was "And hopefully we've got rid of that clown, Johnson."

That clown has allowed infection rates to rise to silly levels, making infection by Delta or Omicron almost inevitable if you leave your house, such as for essential food shopping.  The consequences of infection are broad and potentially severe.  Not just potential hospitalisation and death, but a whole host of personal and societal issues that could be as bad if not worse.  Madness.  And now I am caught up with it, having tested positive with two brands of  LFTs, as in the photo, and waiting for a PCR result.

SO YOU TOO HAVE TESTED POSITIVE

Shit's just got real, as it will for many of you too.  So what does it mean to test positive?:

• Self-isolation for at least 7 days, legally unable to leave the house or garden
• Potentially longer, 10 days or even longer
• Worrying myself about serious illness, ongoing lethargy and not wanting to lose my sense of taste and smell.  Also worrying about more serious LongCovid symptoms, and whether the virus has been passed to other people who end up having serious symptoms
  

According to the NHS  website, today 26 December 2021, the self-isolation rules for when tested positive are::

What isn't explicit in these words, and needs to be tweaked is:

• The 10-day count starts the day after a positive test or first symptoms:
• So are days 6 and 7 are on that same basis?  Many people will count the day of test/symptoms as day 1, and finish self-isolation a day too early (if day 1 is the day after)
• Indeed do you have to wait until day 8 before going out, 8 days after test/symptoms?  From 26 December as day 0, day 8 is 3 January.  After New Years Eve. 
  
• Whether to stop taking LFT tests until day6?  How about after that?
  

 THE CONSEQUENCES OF INFECTION

I'm on annual leave this week, but was supposed to be helping with my local Food Bank.  I'm now not available all next week, till the following Monday. If I was working for any other organisation, and had passed on the virus to colleagues before realising I was contagious, it is quite likely that organisation would have to close for lack of staff.  For example my local pub has closed for the last two weekends for lack of staff, with New Years Eve "in the balance", even if we are not into actual lockdown.  Supermarkets?  Other essential services?  Imagine!  

ACTION REQUIRED

The Government and media must stop focussing totally on hospitalisations, it seems.  High case rates are madness in any case, and the Government should take immediate steps to get rates down.  If that means a form of lockdown, then so be it. 

COVID-19: WHY HIGH CASE RATES ARE MADNESS

The Omicron variant is spreading like wildfire. Bypassing the immunity provided by two jabs, and finding the boosters are only around 75% effective.  Vaccines much better than nothing, but still not perfect.

Today comes the good news that Omicron is less prone to cause serious disease, requiring hospitalisation.  But this is somewhat of a red herring:

• Hospitalisation is not the only COVID-19 matter to be concerned about
  
• Omicron has been spreading mainly amongst younger age groups, so the real world data for the more vulnerable older age groups is not yet available
  
• A small proportion hospitalised out of a large number infected is still a worryingly large number that could overrun the NHS
  

 OTHER MATTERS TO BE CONCERNED ABOUT

1. The number of people becoming physically ill means train operators, football teams, the NHS and every other organisation is now short of staff.  What if food supply were to be affected?  Imagine the panic!
2. People are typically ill longer than from flu.  Five days at least, and its nasty.  Reducing self-isolation from 10 days to 7 days (subject to various constraints) will help.  But further growth in infections will still mean major disruption, with some organisations having to close completely
   
3. People can be left exhausted after any major illness. Covid-19 is no exception.  Meaning people take longer to get back to work.  Further low-staffing consequences
   
4. You don't need to have severe illness to suffer from LongCovid, often serious enough to prevent being able to live life as normal:

• Bad news for the individuals affected
• Extra pressure on GPs and specialist services, taking resources away from treating other health conditions

"Health is wealth" they say.   The only way to live with COVID-19 is to control infection levels, so these troubles do not occur.. That will do less damage to people's health, businesses, the NHS - and the economy.

The Government missed a trick not doing a 3-week FireBreak lockdown whilst the schools were on holiday.   High case rates are madness.  Christmas will have cost the nation a fortune.

COVID-19: GETTING HOLD OF YOUR LATERAL FLOW TESTS

Lateral Flow Tests (LFTs) are not perfect but they are better than nothing:

• The tests identify Omicron as well as Delta, as the test are looking for portions of the virus that are identical, not affected by the new Omicron mutations
• But suffer from the same issue for Omicron as for Delta, which is that the tests do not detect lower viral loads, as is the case in the early stages of infection
• As Omicron grows very quickly in the early stages of infection the advice is:
• Take a test just before meeting people, potentially on the doorstep
• If you've done another test earlier in the day, do a second one at least ,
  

So how do you get a kit?  In the UK, test kits are given out free by the NHS in boxes of 7, which is ordinarily for a week if you are having to take daily tests.

There are two ways you can order on-line:

• Order for delivery to any UK address, not necessarily home.  Delivery within 3 days, proven
  
• Get a "Collect Code" to collect from a pharmacist or other collection point

Given that pharmacists have typically been out of stock, and delivery might be unreliable, the system does let you order both.

Bear in mind the NHS advice:

"Do not use a rapid lateral flow test if you have COVID-19 symptoms. Get a PCR test as soon as possible and self-isolate, even if symptoms are mild."

COVID-19: EVERYTHING ABOUT OMICRON part 2

Key blogposts just published:

COVID-19: FOOD SUPPLY. THE REAL DANGER OF OMICRON
Not just hospitalisations

"It's a blinder of a blog post." Retired company director:
COVID-19: HOW GOOD ARE LATERAL FLOW TESTS WITH OMICRON? (Updated)
Telling it like it is.  What impact on Government policy?

COVID-19: TIPS FOR YOUR FAMILY GATHERING
A useful checklist

COVID-19: SO YOU OR SOMEONE IN YOUR HOUSEHOLD HAS TESTED POSITIVE
What you should do

COVID-19: SO YOU OR SOMEONE IN YOUR HOUSEHOLD HAS TESTED POSITIVE

So you live in England and have tested positive for COVID-19 using a Lateral Flow Test or PCR test.  Or someone in your household has.  What should you do, according to current guidance and regulations?

The guidance here is self-explanatory, including:

• Self-isolating for 10* days if you do (or could) have COVID-19
• Taking Lateral Flow tests for 7 days in certain circumstances where you have been a contact of someone who has tested positive

* [Update 22/12/21]  "

"People infected with Covid in England can stop self-isolating up to three days early if they test negative twice, it has been announced.

They will now be able to end quarantine after seven days instead of 10 by providing negative lateral flow results on day six and day seven."

This is how one hospital suggests staff who have symptoms of COVID-19 should act:

WHAT IF YOU TEST NEGATIVE?

Bear in mind that LFTs and PCR tests cannot detect low quantities of virus, and so a negative result is not a guarantee that you are not infected.  Take precautions in mixing with other people, both to protect yourself and to protect others.

COVID-19: TIPS FOR YOUR FAMILY GATHERING

Yesterday, Tuesday, PM Johnson gave the green light for people to hold family gatherings at Christmas.  But with the possibility of restrictions from 27 December.

As you decide whether to go ahead with your plans, and how best to arrange gatherings, here's a checklist presented by the IndependentSAGE group.  Called "Making a Plan for Household Mixing", it's good sense, usefully organised.

The advice includes "take a Lateral Flow Test immediately before mixing".  That can be on the doorstep, though you may also want to do a test before people travel.  But remember LFTs have a serious limitation, as described here.

Fingers crossed and enjoy.  Merry Christmas!

COVID-19: HOW GOOD ARE LATERAL FLOW TESTS WITH OMICRON? (Updated)

An LFT pack issued this week

We've planned for our Christmas family gatherings, and PM Johnson has given the go-ahead.  We’ll be relying on negative Lateral Flow Tests nearer the time to check whether we should get together.  How reliable are these LFTs?

Furthermore, the UK Government passed their ‘Plan B’ measures last week, two of which rely on negative Lateral Flow Tests:

• "Covid passes" to get into venues such as nightclubs and larger sports gatherings, being either vaccination status or negative LFTs (or proof of exemption)
• Anyone who's been in contact with a positive Covid case, and is fully vaccinated, now has to take lateral flow tests for seven days.

Again, how reliable are LFTs?  Are they good enough to support the Plan B measures?

As these questions have not been widely addressed, let's take a look.

 

FOR WHAT ARE THE LFTs DESIGNED?

The previous blogpost called “How Good Are Lateral Flow Tests?” mentioned limitations of LFTs. Specifically quoting the UK's MHRA as saying "lateral flow tests are only authorised to be used as a 'red light' test in order to find infectious people and ensure they self-isolate quickly, and not as a 'green light' for people who test negative to enjoy greater freedoms.”   

Yet that is exactly how we and the UK Government want to use them.

 

SO HOW EFFECTIVE ARE LFTs?

 All types of tests have two effectiveness measures:

1.  Sensitivity: How well they find positive cases. Conversely what proportion of tests will be ‘false negatives’.  For example, what if sensitivity is 80%?  That may sound high, but it would mean some 20% will be false negatives.  That's 1 in 5.
   
2.  Specificity: How often positive results are actually correct. Conversely not ‘false positives’

Sensitivity

As a positive test means the person self-isolates, we want a high sensitivity, and minimal false negatives.  Sensitivity falls below 100% for three reasons:

•  Lateral Flow Tests from different manufacturers vary in quality
• No LFTs pick up low levels of virus, as is the case in early or late stages of infection.  Especially early stages, as described below
  
• The test is only as good as how well people carry out the test, especially how well swabbing is done

The UK Health Security Agency (UKHSA) has just published their Technical Briefing 32 "SARS-CoV-2 variants of concern and variants under investigation in England".  In it they describe the initial testing of the various Lateral Flow Tests in use in the UK:

For the wet lab testing, "In summary, [all] the LFDs evaluated .....have detected the new Omicron variant".  Good news:

WHY ARE EXISTING LFDs WORKING?

This graphic from the FT shows the extent of mutations and their implications, without mentioning LFTs:

 

 

The FT goes on to say that fortunately  "Experts believe the UK tests are likely to continue to work because they detect a different protein from the much-mutated spike — and the variant’s potentially far higher viral load means they could even be more effective."

 

But...

WHAT ABOUT REAL-WORLD USAGE OF LFTs?

The UKHSA says:

The key issue is that LFTs are not as sensitive as PCR tests, and do not detect infections in their early stages.  People can be infected and become infectious before they take their next LFT:

In other words we cannot trust LFTs to detect infection with Omicron before we become infectious, and spread diseases amongst the people we meet.

This has been confirmed in the real world, such as at the Oxford Playhouse.  "Unfortunately, we are no longer able to go ahead with performances on Sunday 19 December (11am & 4pm), Tuesday 21 December (11am & 4pm) and Wednesday 22 December (11am & 4pm) of Robin Hood due to a positive Covid case within the company." The cast and crew have been taking both PCR and LFT tests every day.  Some negative LFTs have been accompanied by a positive PCR, which is more sensitive.

[Update 28/12/21 from the USA]  The CDC has just announced that their tests of LFTs with Omicron has preogressed from lab tests to real-world live cases.   "Early data suggests .... MAY have reduced sensitivity".  Not 'does have':

There is also some concern about brands of LFTs that only require a nose swab rather than also a throat swab.  Nose-only tests may not be as sensitive, and be prone to a higher level of false negatives.  Though it was one of the nose-only brands that showed positive for me on Boxing Day.

 

WHAT DOES THAT MEAN FOR US?

It is therefore vitally important:

(1) Not to regard a negative LFT result as not being infected, especially if have symptoms

(2) In any case to minimise close contact with others, especially indoors, to avoid catching the disease and avoid spreading it, even if everyone has recent negative LFTs

(3) To continue to adopt all other basic precautions, such as good ventilation, social distance and washing hands.  Especially when mixing with vulnerable people, such as older family members

WHAT DOES THAT MEAN FOR THE GOVERNMENT'S 'PLAN B'?

Last week MPs in Westminster debated and passed four proposals as elements of 'Plan B'.  The plan includes:

• The use of LFTs by the contacts of anyone confirmed infected with COVID-19
• The use of negative LFTs as an alternative to vaccination status as a condition of entry into many venues, such as nightclubs and sports stadia. 

Are LFTs good enough to be suitable for either purpose?

We know:

• Double jabs provide little protection against symptomaticinfection from Omicron, nor provide much protection against transmission.  Effectively now worthless for control of entry to venues
• Triple jabs with the booster only getting to around 75% protection
• As discussed above, LFTs do not identify Omicron (nor Delta) in the early stages of infection, and people can become infectious before their next LFT
  

So we shouldn't over-rely on LFTs, for any purpose, given false negatives are likely to be 1 in 5 or higher. Better than nothing, but there must be doubts about their use in Plan B.

Indeed is control of entry to venues as stipulated worthwhile?  Do we instead have to go back to closing venues and use lockdowns to try to reduce the speed Omicron is spreading?  Accompanied by suitable financial support from the Government.  Like it or frankly not!

The choice really should have been between:

• Double/triple jabbed AND negative LFT, or
• Close venues, despite the economic and societal consequences?

 

WHAT ABOUT AVAILABILITY OF LFTs?

LFTs can only work if they are readily available.  

The problem is that LFT kits are now in short supply.  Difficulties in distribution of such high numbers of them, even if they are in the country.

Deliveries to people's homes suspended nationally last week, and locally all three pharmacies were out of stock in recent days.  

What is someone supposed to do if cannot get necessary LFTs?  Legally, would they have to self-isolate?

Realistically we cannot rely on the availability of LFTs, on top of concerns about sensitivity.

 

WHERE DOES THAT LEAVE 'PLAN B' AND OUR FAMILY GATHERINGS?

LFTs are better than nothing, but do not really look good enough to be relied upon in the fight against Omicron.  Not adequate to self-test before visiting relatives at Christmas, nor suitable for Plan B measures 

That a significant number of Conservative MPs voted against the relatively mild 'Plan B' measures suggests they don’t believe the potential harms of Omicron.  They don’t see the risks of potential societal problems such as empty supermarket shelves. Yet good risk management is 'Hope for the best but prepare for the worst."

Is the risk of consequences such as empty shelves an over-reaction? Let’s hope that never happens.  The issue is that at every turn COVID-19 has proved to be at the worst end of expectations.  Risks of major adverse consequences, however low, surely cannot be ignored?

Indeed this is war.  It makes sense to reduce the spread of Omicron by whatever means we can.  Immediately. That means reducing the size and occurrence of groups of people indoors.  Not just Plan B, with ineffective LFTs, ineffective double vaccination, and boosters that are nowhere near perfect.  The Government needs to do more,. And quickly. Before society gets overrun by Omicron infection.

Of course this "Too little too late" Johnson Government has today (21st) taken no action.  Hang on for the ride, folks!