COVID — 15 August 2021 - Part I

Part I — The Virus, its Variants and Vaccination.

Kris Vette is an independent analyst. In Part I, he looks at the virus, its variants and vaccinations. In Part II, (Herd Immunity or how will this all end?), he will use the latest peer reviewed research to try and predict how the pandemic will play out from here.

His earlier articles on COVID are found on Medium.

Photo by Anna Dziubinska on Unsplash

The world is witnessing the rapid spread of a new variant of SARS-CoV2 or SARS-2. This is the virus that causes COVID. The latest variant is called ‘Delta’. There is also talk of an even more dangerous, newer variant, called ‘Lambda’. Significantly, these new variants have caused a resurgence of the pandemic and some believe that it is never going away. The concept of ‘Herd Immunity’ now seems to be lost. The media are also reporting ‘breakthrough infections’ in those already vaccinated and that the vaccines don’t work against the new variants. I explore these points and to see what this means for the pandemic.

In Part II, I will look into the crystal ball to see if Herd Immunity is possible and if not, look to how this will all end.

1. What is the Delta variant?

The Delta variant has emerged as the latest variant of the ancestral strain (the original strain) of the COVID disease causing, SARS CoV-2 (sometimes called SARS-2) virus. The reality is that new variants are continually evolving as the virus spreads and infects new hosts and their cells. All viruses mutate. That’s how viruses have worked for billions of years.

Each time a virus infects a new cell it multiplies itself thousands of times. Each time it copies its own genetic code (or blueprint) it makes a few minute errors. Most of the errors mean nothing. However, with each new infection comes a small likelihood that a change in the blueprint (viral RNA) might produce a ‘fitter’ version of itself.

Every few billion changes or so a ‘fitter’ variant emerges. A fitter virus will adapt better to its human host. It may be better at spreading. A variant only needs to be a tiny bit fitter than its previous versions to become more widespread in the viral population. Right now the fittest variant of SARS -2 is the Delta variant.

We will continue to see new variants emerge. Usually these will be better at transmission and infect more hosts. This is normal evolutionary pressure — the forces of reproduction favour better ‘fitness’ between competitors. Effectively we are seeing Darwinian evolution at high speed.

2. Is the Delta variant more deadly?

The Delta variant is probably no more ‘deadly’ than the other variants (it’s not clear it has a higher ‘Case Fatality Rate’). Most likely it just spreads to more people.

However, if it spreads to unvaccinated or vulnerable people (older or with pre-existing conditions) it will be just as dangerous as the previous variants. Delta seems to be better at transmission and so has now become the ‘fittest’ of the SARS-2 variants to date.

3. Why is it spreading so fast at the moment?

The spread of this virus is caused by three main factors;

• Transmission properties of the virus itself. In the SARS-2 virus this relates to the binding affinity (attraction) of the spike protein on the viral surface to dock with cells of the human host.
• Behaviour of the hosts (humans) of the virus. Close interpersonal behaviour and interact without masks gives the virus the conditions it needs to spread.
• Vaccination rates. A vaccinated person is about 70% less likely to shed enough active virus to infect another person (see Notes — this is Alpha variant data). However, it is still possible to spread virus after you are vaccinated. So vaccination protects against disease but not necessarily infection. But protecting us against COVID disease is what we need — so vaccinations are doing what they’re supposed to!

Currently, Delta is spreading, causing an increase in hospitalisation rates and deaths, mainly through the unvaccinated population.

Sadly, much of the world’s population does not have access to COVID vaccines and live in conditions that are crowded which prevent them maintaining personal distance.

Even in countries with vaccines, the original SARS-2 or any variant of SARS-2 will continue to spread through the unvaccinated and unmasked population.

Photo by Giacomo Carra on Unsplash

4. Can young, fit people get severe COVID disease?

Many people take the view that if they are young and healthy they won’t die, so they don’t get vaccinated. This is faulty in two ways;

First, young fit people still have a small risk of dying or developing long term problems from a COVID infection. For example, a small percentage of professional athletes have developed long term problems, like heart muscle inflammation, after having COVID. So being young and healthy does not always protect you. And it is also possible for children to become infected and die. While the number is very low there are still a few hundred children to date who have died from COVID.

Secondly, if an unvaccinated person ends up requiring a hospital bed or ventilator, they use up health system resources for other people who have cancers and other disease that they can’t prevent. COVID can be prevented with a vaccination. Those other diseases can’t be.

5. Is there a difference between infection and disease?

Infection means that the virus has entered your body. You may or may not have any symptoms.

Disease is when you get sick and have symptoms.

6. Do you always know when you are infected with COVID causing virus?

No. You can be infected with a virus and not even know it. Once it enters your body you are infected.

If your immune system fights the infection fast, with your own ‘Neutralising Antibodies’ after the virus has entered the body (usually through the nasal mucosa) but before the virus enters your cells, then you might not have any symptoms.

In some people the virus may even get around most of their Antibody defences and enter the cells. If this happens the immune system could still wipe out the infection (with T-Cells or a combination of T-Cells and Antibodies).

There are three main defences available to your body;

• Antibodies attack the virus after it’s in your body (nose, throat, respiratory tract) but before in enters your cells.
• T-Cells attack a virus once it has entered your cells.
• B-Cells remember the attack and store Antibodies for future protection.

In SARS-2 infections it is thought that perhaps 30 or 40% of infections may be asymptomatic (without symptoms). So, you could be infected with SARS-2 and develop natural immunity and not even realise.

The problem with asymptomatic infections is that it is an infection without disease (you have no symptoms of COVID as a disease). However, the SARS-2 virus can still be transmitted from you to someone else, even if you have no symptoms.

In the first 14 days (highest risk is in first 5 days) of an infection you could still pass the virus on to others. This is why COVID is such a powerful pandemic. It is mild or unnoticed in most people, severe in others and deadly in a few but it can spread in any of those cases. And while it may only be 20% of infected people that do most of the spreading — most of the spread happens in the first few days when you have no symptoms.

7. What’s a vaccination?

A vaccination is a practice that mimics a natural infection but doesn’t cause an infection. A vaccination contains either a particle of the virus, a piece of the viral code or an imitation of the virus that tricks the body’s immune system into thinking it is infected with the virus. Our body mounts a response and our immune system remembers that response. If we see or sample a similar virus again, our immune system will fight it.

Photo by CDC on Unsplash

8. Can you still get COVID after being vaccinated?

Yes, but your risk of dying or developing severe disease drops hugely. Even with the Delta variant, you are not likely to die if vaccinated. Most likely, if you are vaccinated and you get infected with SARS-2 you will either not develop COVID or just get a cold.

If you are not vaccinated and get COVID you will have roughly between a 0.1 and 70% chance of dying or getting severe disease (depending on your age and existing conditions). But If you are vaccinated you will have about 25 times less chance of getting severe disease or dying.

So being vaccinated drops your risk to very low levels. If you are vaccinated and older or immune compromised you can add more protection to your risk by remaining masked and maintaining interpersonal distancing.

There is a view that all people should further drop their risk even if vaccinated by following these practices. Being inside (in non-ventilated areas) also increases risk of spread.

9. What about ‘breakthrough infections’ in vaccinated people?

A vaccination won’t prevent someone getting infected but it will prevent severe disease and death in most people. The term used in the media is ‘breakthrough infections’. That just means when COVID disease occurs in vaccinated people. That can happen but your chance of a bad outcome is extremely low if vaccinated.

10. How long does immunity to SARS-2 after a vaccination last?

It is likely you will get very effective protection against disease (94% reduction in severe disease) for six months to a year (see Note 1). While immunity could wane you could still be mildly protected for longer than a year — the data is still being gathered.

Based on data about infection from other coronaviruses (like the original SARS virus from the 2003 SARS pandemic) more than a year of protection from disease was gained (post infection). It seems likely this longer-term protection was from T-Cell mediated immunity.

Extrapolating that data — if this were similar with SARS-2 then it is possible that after about six months (post vaccination), you may have an increased chance of picking up an infection (once the IgG Antibody protection has waned). But if this happened, it would likely be just mild disease. The reason for this is that after six months and probably for a lot longer, any vaccinated person should have good T-Cell immunity.

Having T-Cell immunity means that if you do pick up an infection it should be well handled by your body [T-Cells will not neutralise a virus when it enters your body — but T-cells will signal (wake up) the antibody response and also attack virus once it enters your cells].

In short, it would be reasonable to expect 12 months protection from a vaccine (through a combination of IgG Antibody immunity and then longer-lasting T-Cell immunity). However, researchers still need to see longer-term data.

11. So will I need a booster shot or another vaccination?

Probably. Most people will likely require at least one booster vaccination to cope with the gradual loss of protection (after say 8 months to a year) and to give better immunity to new variants as they come along.

12. Does the vaccination stop the virus spreading?

No, but it reduces transmission a lot. If you are vaccinated the latest data is showing about a 70% reduction of transmission risk to others in a household or to close contacts in the first few months after vaccination (see Notes).

13. Does the vaccine protect against the new Delta variant?

Yes. The vaccine will still protect most people against severe illness and death with all of the variants to date. You could get sick with the Delta variant after vaccination but the protection against severe disease is still above 80%. You are unlikely to die from Delta providing you are vaccinated.

14. What about the Lambda variant or future variants?

There will always be new variants, just like there are with colds and flus. But most likely they won’t be any more deadly than the previous variants — viruses don’t usually get more ‘deadly’ (as measured by Case Fatality Rate). Evolutionary pressure doesn’t work that way. A pandemic with a virus that kills off most of its hosts usually burns out. Viruses mutate to get fitter but usually that fitness is for transmission.

However, note that more transmission can lead to more deaths in an unvaccinated population.

15. Can children get COVID? Should they get vaccinated?

Kids can still get COVID and transmit it. Most often they won’t have any symptoms so they won’t realise it. But there is still a low but real risk of severe disease in children and a few hundred children have died since the beginning of the outbreak in 2019.

Each country is developing its own recommendations on the age for vaccinating children. Currently 12 years old seems to be the cut-off. The data is currently being looked at for children below the age of 12 years to work out correct dosages.

16. Do vaccines have risk? Aren’t they untested? Some doctors have signed a petition saying they don’t support vaccination — they must be right?

The doctors who have signed the petition haven’t taken the time to read the evidence. They also aren’t considering the risk reduction between being infected and being vaccinated. The risk of side effects from a vaccine is grossly outweighed by risk of chronic organ damage or death after infection. Additionally, the tenets of Public Healthcare and Population Health involve reducing risk to others as well, not just ourselves.

In terms of potential adverse effects, the COVID vaccination programme now has the largest vaccination evidence base in history with 1.3 billion people vaccinated to date. There is always a statistical chance of a side effect from vaccination but it is tiny in comparison to being damaged from an infection.

17. If I don’t get vaccinated then I’m only putting myself at risk?

Unless you live in a desert you are also transmitting the virus and COVID disease to people at lowered immunity who can’t generate protection from a vaccine (some people with cancer or transplant patients on immune-suppressant drugs). You are also a lot more likely to end up in hospital if you don’t get vaccinated. That ends up taking medical resources away from people who need them, like cancer patients.

18. What if I’m older or have a lowered immunity from drugs or an illness or if I’m a transplant patient?

There is currently discussion among Immunologists about the possibility of using a third vaccination shot for people who have lowered immunity because of drugs they are on or pre-existing illness they have. It seems there is an advantage in doing this and it will probably become standard practice.

Summary

Delta is the latest variant of the ancestral strain of the SARS CoV-2 virus. It is the current ‘fittest’ variant. It is dominating the COVID viral population at present as it is better at spreading. But all viruses mutate over time. So there will be more variants down the line.

Vaccinations have so far proven to be very effective at preventing severe disease, hospitalisation and death against Delta and all variants of the virus, in most vaccinated people. However you can still get (usually mild) COVID disease after vaccination.

Vaccinations don’t prevent transmission of the virus but they do cut down spread by about 70%.

The way to solve this pandemic is through vaccination.

Notes

1. Covid-19 Vaccine Immunity and the Impact of Variants (FPC Briefing, Prof Shane Crotty, 29 Jul 2021).
2. Vaccine effectiveness against SARS-CoV-2 transmission and infections among household and other close contacts of confirmed cases, the Netherlands, February to May 2021 (Eurosurveillance Vol 26, Issue 31, Aug 2021).
3. Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant. (NEJM 12 Aug 2021).
4. Estimating infectiousness throughout SARS-CoV-2 infection course. (Science 09 Jul 2021:Vol. 373, Issue 6551).
5. Elapsed time since BNT162b2 vaccine and risk of SARS-CoV-2 infection in a large cohort (preprint medrxiv, 05 Aug 2021).
6. Reduced Risk of Reinfection with SARS-CoV-2 After COVID-19 Vaccination — Kentucky, May–June 2021 (CDC Weekly / August 13, 2021 / 70(32);1081–1083).
7. Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine (Nature, 28 Jul 2021).
8. Antibody Response After a Third Dose of the mRNA-1273 SARS-CoV-2 Vaccine in Kidney Transplant Recipients With Minimal Serologic Response to 2 Doses (Research letter — Jul 23 2021, JAMA)
9. This Week in Virology. https://www.microbe.tv/twiv/