We all want to get back to some normality by defeating COVID-19. So we need to understand it, and what causes it. We also need to understand what we have in our armoury to defeat it, which will follow in a separate posting [link to follow].
To develop a suitable anti-COVID strategy, we only need to understand COVID-19 at a layman’s level So this post has been kept simple. Our understanding is developing all the time, so none of this posting is definitive. There is no medical advice.
This posting is based on my experience as a scientist studying biochemistry and genetics at university, and working in a biotech firm developing drugs. It is then what I have learnt specifically about COVID-19 from well-researched media articles and raw research papers, some of which I link to in this article.
I am also very grateful for the help received from a Professor at Oxford University who specialises in immunology, and a Professor at Birmingham University, who specialises in medical statistics and the RT-PCR tests used to detect the RNA in the virus that causes COVID-19.
HOW LONG WILL COVID-19 LAST IN THE UK?
COVID-19 is highly infectious. Countries that have already got infections down to near zero are now struggling with local outbreaks. These are often related to people arriving from abroad.
Near-zero is best, as that minimises deaths and gives best confidence for people to get back to normal. But as it is difficult to see how COVID-19 can be eliminated worldwide, there is always a risk of a comeback for the virus in any near-zero territory. Which is why it can only ever be "Near Zero".
The objective to eliminate must also be considered alongside other objectives. Total elimination would be extremely costly, not just financially but in the 'side-effects' of any elimination measures. So a balance that's #NearZero
We must therefore expect to be living with COVID-19 for the foreseeable future, with or without vaccines or other medications.
Vaccines and highly effective medicines are possible, but are not guaranteed. We'll likely to need to wait months into 2021 at least..
This includes the UK as much as anywhere. This is the basic message that Professor Chris Whitty, the government's Chief Medical Advisor (and England's Chief Medical Officer), has said recently/
Bear in mind that it is not just death that is the problem. The 98% or more who survive infection are susceptible
to serious ongoing medical problems, lasting a month or longer. One study suggests over 87% of survivors have significant symptoms after two months.
So this isn't a disease you want to catch. For the foreseeable future we each need to regard everyone else as someone who is potentially carrying the COVID-19 ‘poison’ that can kill us or make us seriously ill.
WHAT IS COVID-19 ?
COVID-19 is a disease as the official shorthand for CoronaVirus Disease 2019.
The first sign of serious illness came to light in humans in Wuhan, China in late 2019. It has spread globally from there by human-to-human transmission.
There is evidence that it existed in the Horseshoe Bat population in China or nearby. It likely moved to humans via a mammal called a pangolin, which is sold for human consumption in China, or somehow from a laboratory in Wuhan that has been studying a wide range of bat viruses. Though a very similar virus was found in bats in Yunnan province. So COVID-19's genesis is still a matter of conjecture. As the source is not relevant to how we defeat it, we’ll leave conjecture there.
WHAT CAUSES COVID-19?
The COVID-19 disease is caused by a virus, known as SARS2.
It is officially SARS-COV-2, which stands for “Severe Acute Respiratory Syndrome COronaVirus 2 “
The virus is a member of the Coronavirus family, not THE coronavirus as is often implied.
So just like the HIV virus causes the AIDS disease, SARS2 (SARS-COV-2) causes COVID-19.
It is the spoke proteins, and variants of them, that are key to how the virus functions and how the human immune system can 'neutralise' the viruses.
WHAT ARE THE OTHER CORONAVIRUSES?
The Coronavirus family includes four families of viruses, with seven types of viruses known to infect humans:
- The original SARS virus in China in 2002 This was more deadly and still contagious than SARS2, so was quickly eliminated.
- The MERS virus in the Middle East 2012, again quickly eliminated.
- Accounting for around 15-20% of common colds. Had a summer cold? May well have been a coronavirus
The problem with SARS2 was that China possibly did not set off the alarm about COVID-19 as early in 2019 as it could have done, although that too is conjecture.
There certainly was a significant number of people in the UK who developed symptoms similar to COVID-19 in the autumn of 2019. This included my cousin's husband, who died in February 2020. This may have been caused by another coronavirus. But there is an off-chance this developed into a more serious disease almost indistinguishable from its Chinese cousin.
But the distinction is not overly important to dealing with COVID-19, given there are more than a hundred variants of SARS2 itself.
COULD COVID-19 BE CAUSED BY 5G MOBILE PHONE NETWORKS?
There are a variety of theories about what else might cause the symptoms of COVID-19. The extent that SARS 2 has been isolated and studied makes us confident it is a virus.
Nonetheless there are conspiracy theories that can be countered by showing that COVID-19 spreads in territories where that theory wouldn’t make it possible.
- So they take the anti-viral techniques seriously, and
- So they do not damage important mobile phone masts
Estimates are that at least 50% and maybe 80% of those adults infected never have symptoms, but are nevertheless infectious. This is either because:
- They are pre-symptomatic, developing symptoms typically 5-14 days after infection
- Or remain "asymptomatic", without initial symptoms. But can develop more serious symptoms later
The primary initial symptoms relate to the airways of mouth. nose, throat and lungs:
- High temperature
- Persistent dry cough
- Loss of taste and smell
Whilst the disease is best known for its effects on the lungs, the disease is best regarded as a multi-organ disease. The virus can attack almost any type of cells in the body, with the exception of skin. If viruses get into the blood system, they can spread around the body to do damage Also COVID-19 can cause clots and micro-clots in the blood, that can themselves cause serious problems in organs. So a variety of other organs can be adversely affected by COVID-19, including:
- Organs such as heart, kidneys, liver and digestive system
- Even the brain
- And the clots can cause strokes, killing even young people
Some people acquire the SARS2 virus and do not show the classic airways symptoms. But they can have these other parts of their bodies affected.
A review of symptoms data from the King's College London study, published on 17 July, suggests many more symptoms, in six distinct groups
Death from COVID-19 can be from two main reasons:
- Difficulty breathing, requiring ever more tortuous oxygen delivery
- Multiple organ failure.
It is now estimated that 50% of those in hospital with COVID-19 also now have heart damage
So you don’t want to catch COVID-19 if you can avoid it, whatever your age or health. Risks vary by age and health, but are not near zero for anyone.
WHAT’S IT LIKE TO HAVE COVID-19?
So far my precautions have kept me clear of the disease, unless I had it mildly back in March. Touch wood. But typically I understand:
- Two to five days or so after infection (up to 2 weeks) a person will develop one or more of the initial symptoms listed above.
- Often symptoms get worse and the patient needs to stay in bed, much like in response to flu
- People can seemingly recover in a few days, although will remain weak for some weeks, as you would after any serious viral infection
- People can then become ill again, in a second phase. Initially it was thought to be caused by a “cytokine storm” as happens with other viruses, where the immune system over-reacts and starts to fight the body itself, especially by damaging the lungs
- This is often the reason that people can become seriously ill and need hospital treatment.
- For those that have weakened lungs, they will require pressured air or oxygen. Initially this can be using simple CPAP devices (air pumps), but more serious cases require the mechanical “ventilators” that take over the whole breathing process
- For those that have other parts of their body affected, other treatments will be used. Most people in hospital will be given anti-coagulants for the blood, to avoid the micro-clotting.
- Everyone who recovers will have post-viral malaise, and in some cases one or more serious ongoing medical issues
The two phases are basically what happened with PM Johnson. He seemed to recover, but his temperature didn’t subside, and he became ill enough to require hospital treatment. He did not need a ventilator, but had other unspecified forms of treatment. Matt Hancock, the Health Minister, also had COVID-19 but did not experience that second phase.
Dominic Cummings spoke about needing to test his eyesight, given that weak muscles in the eyes is a typical post-viral symptom.
To say it again, you don’t want to risk catching COVID-19 if you can avoid it. Whatever your age or good health.
BUT ISN’T THIS JUST A FLU?
Influenza (Flu) has kills between 2 and 28 thousand people in the UK in recent years, despite a programme of vaccines. This is because as a society we take no particular anti-viral precautions, and accept such a death toll as the price of freedom. The hygiene we learn as kids and adopted in home and commercial kitchens is primarily to avoid bacterial infection, with any anti-viral effect incidental.
Viruses are far smaller than bacteria. Bacteria are cells, and can be ‘killed’ in ways that do not affect viruses. Viruses aren’t really ‘alive’ and can be neutered by techniques that don’t necessarily kill bacteria. Indeed many anti-bacterial treatments do not deal with this coronavirus. More on this later.
Deaths from flu typically occur from complications such as pneumonia in the lungs when the immune system has been weakened.
COVID-19 tends to cause damage to the lungs by the production of sticky mucus that effectively drowns the patient, which can be seen on CT scans. But as COVID-19 can affect other organs, it shoyld be regarded as a far more serious disease than flu.
WHAT IS THE SARS2 VIRUS?
- An outer fatty sphere
- Protein ‘spikes’
- Containing viral RNA
It is the 'spoke proteins' that bind onto human cells, and are the key to the immune response.
Breaking down the fatty sphere is the key to neutering it through hand washing and other treatments.
HOW DOES SARS2 ATTACK THE BODY?
SARS2 attacks individual cells.
Human cells have an outer coat that has to do three things:
- Form a container for a nucleus and various other micro-structures that allow the cell to operate
- Stop foreign bodies from entering
- But allow sugars, oxygen, carbon dioxide and other matters to pass in or out as appropriate
We’ve all heard of DNA, which is kept in the nucleus of all cells. This is used to produce RNA, which goes out into the cell and is what is actually used to synthesise the proteins that the cell needs to produce. Here’s an explanation if you are interested, but is not necessary to understand how to defeat the virus.
When a SARS2 virus attacks a human cell:
- The protein spikes take advantage of the entry weakness by latching on to the “ACE2” receptors on cells.
- That allows the viral RNA to get into the cell
- The cell’s natural RNA mechanism is hijacked to create more viruses.
- In time the quantity of viruses cause the cell to burst and the new viruses go off to attack other cells,
HOW IS COVID-19 TRANSMITTED?
The SARS 2 virus that causes COVID-19 needs to be transmitted from one human to another. This is principally through the nose or mouth, but can be through the eyes. The two principal transmission mechanisms are:
- Through the air. The infected person unwittingly ‘spits’ out viruses into the air which are then breathed in by the person who becomes infected:
- In water droplets, that quickly drop to the floor (or table surface)
- In microdroplets of water, known as ‘aerosols', which can persist in the air for some hours
- Via a surface. The infected person breathes, coughs or spits onto a surface, or touches their nose or mouth and then touches a surface. The next person touches the surface, gets viruses onto their fingers, and then touches their own mouth, nose or eyes
Surfaces can include worktops, door handles, envelopes, food packaging, pet fur, and cricket balls. And many more. Fortunately the viruses are neutered reasonably quickly on surfaces outside the body, in a few hours or days on most surfaces. Research is continuing, but this study suggests 24 hours on cardboard, but up to 3 days on hard surfaces like plastics, for example. So food packaging should be free of the risk of active viruses by the time it reaches the shops.
But surfaces can be a problem where short timescales are involved. For example:
- For food packaging where shop staff have stacked shelves shortly before a customer picks up an item, or where another customer has picked it up and put it back down.
- Door knobs in shared premises which can get touched several times in a few minutes
- The mail or deliveries if the delivery person is infected
- Cricket balls that get passed around a team within seconds, especially risky when having been spat upon
There are other potential transmission mechanisms that are rarely discussed, but presumably can occur:
- Open wounds, allowing viruses to get into the blood stream and off around the body. In a COVID-19 world, it can be preferable to ensure open wounds are covered, rather than leave them open to the air, as is usual common practice
- Swimming in water, where water is spat out by one swimmer and swallowed by another
- It has just been confirmed for the first time that a baby had acquired COVID-19 inside mum's womb
- Now a cat in England has been confirmed to have COVID-19 there is the possibility of transmission via cats and other domestic animals, though as yet no such evidence.
In many cases the “dose” of viruses is very low, and most people can fight infection off easily. But a high dose, or a low dose for someone with a weak or over-active immune system, can result in COVID-19 illness.
How to counter these risks is covered in a separate post [link to follow].
WHY IS COVID-19 SO INFECTIOUS?
Unlike many other viral infections, someone who is infected with the SARS2 virus can be infectious before they show symptoms. Either:
- “Pre-symptomatic” in the period that the “viral load” in the body is increasing before symptoms
- “Asymptomatic” where the body’s natural defences keep the viral load down sufficiently to avoid symptoms, but the person can still be infectious for some time
People are typically most infectious 2 days before and 3 days after showing mild symptoms. Though those with severe symptoms may be infectious for up to 60 days (2 months).
The higher the initial dose someone receives, the more likely the body gets over-run by the virus and displays symptoms. A low dose can leave someone who has acquired SARS2 to be asymptomatic, but crucially still infectious.
That’s why outdoors and social distancing is effective, where the viral dose given to someone else is low or non-existent. Go indoors and sit with people a lot, talking, laughing, coughing and sneezing, inevitably the people around an infectious person will get a higher dose. I will not be sitting inside a pub, restaurant or office until infections are down to near zero. It's outside or nothing for me at the moment.
SEASONALITY
But it is believed the virus is more stable at lower temperatures, and with less UV light with lower sunlight, so can last longer in the air and on surfaces Furthermore seasons do affect how people behave, and therefore how easily the virus can spread.
So there is a seasonal effect:
- In warmer weather people are more outdoors, or indoors with windows open to produce a draught to take viruses away.
- In colder weather, people will tend to be stuck indoors with often poor ventilation. Therefore more prone to infection
- Though aircon systems that re-circulate air can be laden with viruses in all seasons. Which can make offices, hotels, cruise ships and theatres dangerous places all year. Aircon systems are being upgraded to reduce the risk.
Update 19/8/20: A new academic study,
awaiting peer review, suggests a strong correlation between temperature
and infection rates. Lower temperatures increase infection rates. Though the work does not distinguish temperature
differences from differences in human behaviour.
For the UK, the change from winter in February to summer today will have helped reduce transmissions. But as infections had plateaued in June, easings of restrictions in July are resulting in signs of infections increasing.
For the UK, the change from winter in February to summer today will have helped reduce transmissions. But as infections had plateaued in June, easings of restrictions in July are resulting in signs of infections increasing.
Scientists are concerned about the forthcoming winter in the UK, as we head indoors. But the transition into autumn will have a much earlier effect on transmission. The second wave is a very real risk right now.
The human immune system is complex. Whilst it is interesting to understand the whys and wherefores, only a basic understanding is required to develop a COVID-19 strategy. So the uncertainties described here do not stop us moving forward.
Firstly the body creates antibodies (immunoglobulins) : These come in five classes, Alpha (IgA) Gamma (IgG), Delta (IgD), Epsilon (IgE) and Mu (IgM). Within each class are variants for specific 'antigens' such as viruses.
The two most relevant classes for SARS2 ( COVID-19) are :
- IgM that is produced first in a non-specific form, and seemingly fights off the virus.
- IgG which is produced in a form specific to the virus, possibly later as the infection is nearly over, and can rise to much higher levels. The timescales make it unclear whether IgG actually fights the virus, or could do so later to provide immunity
Here is a timeline diagram of the infection (blue line) and the typical antibody levels, as published a couple of months ago:
Our understanding is still developing, and the graph above may need considerable amendment, such as:
- To reflect a range of timescales. such as a range of how long IgM lasts
- To reflect that some studies are suggesting IgM and IgG appear together, with IgA. although that would be unusual
- To reflect additional relevant aspects, such as T-cells and cytokines
Indeed it has become apparent that SARS2 triggers the body's production of T-cells, some of which are known as "killer cells". Alongside potentially triggering unwanted "cytokine storms" as mentioned above, resulting in an excessive inflammatory reaction Ideally these would also be added to the graph
It is not yet clear which of these agents is really causing the dangerous second phase of infection, nor what might be providing any natural immunity. Any vaccine must avoid the former and create the latter.
But on the face of it there are four consequences, on which there is yet little if any conclusive evidence:
- If it is mainly IgM that helps to fight off the virus, then its short life means it will potentially have to be produced again if the person is re-infected. It has not yet been established whether the second reaction is stronger or weaker than the first, and whether any ‘natural immunity’ is gained from having the original infection
- Does IgG confer any 'natural immunity'? And if so, for how long?
- As the “cytokine storm” that attacks the body is after initial symptoms have finished, this corresponds with the increase in IgG antibody. How are these two things linked? Do higher initial levels of IgG give prior warning of serious illness later?
- How do T-cells fit into this overall picture for immunity and/or the body's over-reaction?
Whist these questions are interesting, and vital for those working on treatments, they do not affect the overall strategy. So we can move on with these unanswered.
TIMESCALES
The diagram above shows a timescale of about a month. The following diagram shows timescale in other respects:
In terms of the presence of the virus, a study by Birmingham University (towards which I made a small contribution) shows that viral RNA shows up in RT-PCR tests (the current primary method) over these timescales. Bear in mind RT-PCR tests look for RNA not active viruses. So neutered viruses coughed up from the lungs may explain finding RNA in throat swabs (lower respiratory tract) longer than a month, and longer than nose swabs (upper RT):
VIRAL VARIANTS
There are already over 140 variants of the SARS2 coronavirus RNA. Variations do not occur as rapidly as with some other viruses, but the list of variants continues to grow. Already by the beginning of March, with each line denoting a variant:
Whatever the origin of the variants, and whether there are also viruses that have COVID-19-like symptoms in the UK before Wuhan, the ever-increasing range of variants causes two major problems:
- "Got it" tests need to identify all current and future variants as a positive result and only give a negative result in the absence of any variant. Crucially this means avoiding 'false negatives' that indicate someone doesn't have COVID-19 when they have.
- Vaccines would need to fight most variants current and future, and preferably allof them
WHY IS COVID-19 AGE-DEPENDENT?
Research is still taking place as to why children don’t show the main lung symptoms and rarely need hospital treatment. Though in rare occasions can develop PIMS, (Paediatric Multisystem Inflammatory Syndrome) which includes damage in other organs such as the heart.
It is also not yet clear why older people are more likely to require hospital treatment than youngsters. Nor
why men as a group are worse affected than women.
Though younger adults are susceptible to COVID-19. It is more likely to affect their other organs, as described above, and not necessarily require hospital treatment, But their health can be blighted for long periods if not life. Youngsters should not be fearless about COVID-19, by being lulled into a false sense of security.
Conditions such as obesity and diabetes type 1 (and to a lesser extent type 2) also increases the chances of serious illness, though not clear why.
Conversely various drugs, including one that treats diabetes type 2, indicate some protection from severe COVID-19 symptoms.
Children often catch illnesses that don’t affect adults so much, probably because their immune systems are less well developed. One theory is that is actually an advantage for COVID-19, in not setting off cytokine storms. But why not the basic symptoms? Still unclear.
What is also unclear is whether children can carry the virus and pass it on to other children and adults. Given how serious COVID-19 is, it is best to err on the side of caution. Until there is definitive evidence to the contrary, we should assume asymptomatic children can catch COVID-19 and transmit it to adults. This is especially relevant to grandparents, who will generally be more at risk than parents.
IN CONCLUSION
The COVID-19 disease is caused by a virus known as SARS2.
The virus is highly infectious amongst all ages from the unborn to the elderly. It can cause major problems not only in the lungs, but in all other organs including the heart and brain. COVID-19 is not something to risk acquiring at any age.
We’ll need to live with the virus being around for a very long time. Hopefully a vaccine or medical breakthrough will provide protection. But with neither guaranteed, we need to adopt anti-viral techniques for the foreseeable future.
Key aspects of Coronavirus are brought alive in this video. Enjoy. If that's the right word!
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