The new Coronavirus variants, immunity and vaccine effectiveness at January 2021.

Photo by Prasesh Shiwakoti (Lomash) from Nepal

2020 saw the world battling the most destructive pandemic seen in a hundred years. The SARS CoV-2 coronavirus had jumped from bats to humans. Now, at least three new variants of the virus (from UK, South Africa and Brazil) have emerged with concern. Just when we had vaccine victory in our sights it seems our hopes have been dashed. Can we beat it or will this virus keep outsmarting us forever?

Viruses are protein tubes filled with genetic code. They need to inject themselves into cells of living plants or animals to survive and thrive. They have been around since dinosaurs roamed the earth and for a few million years before that.

It seems probable that viruses are necessary for the spread of genetic diversity in evolution and therefore life itself. But when we are infected by them, we become hosts to viruses. To survive against them we need our own protection. That comes from our immune systems. By sampling foreign material in our own bodies our immune system learns to distinguish between an invader and our own cells and tissues.

Our immune system does that through a complex set of mechanisms. Broadly there are two main parts;

1. Anti-bodies — human produced proteins that mainly attach to viruses and block them from entering our own cells

2. T-Cells — human produced cells that identify and kill viruses once the virus manages to enter human cells.

Vaccines stimulate the immune system by ‘faking’ an attack. In the case of SARS-2 vaccines they all recreate the spike part of the real virus. However it is just a fake spike that causes no illness. And once tricked into thinking we are being invaded by a pathogen, the body’s immune system builds a ready-made solution to defeat any future attack. Hopefully it remembers that response for months, years or even a lifetime.

But viruses are always mutating. They mutate to survive. By mutating their genetic code their physical form is always changing, ever so slightly. Most of the time the individual mutations do nothing meaningful (known as antigenic drift). However, if by chance a mutation produces a survival benefit for a virus, the new change will be amplified within that population of viruses. A large change can see a new strain emerge in what is called antigenic shift.

It is useful to think of this as ‘viral fitness’. One way a virus can be fitter is by having better transmittability. If they can attain this, that newer virus form will survive and spread at a faster rate than the older variants.

Usually, viruses become better at spreading but less deadly. A virus that is fitter by replicating and spreading faster is more dangerous to the host population than if it were a deadlier form of the virus. Improved transmissibility results in higher numbers of infections in the host population. Sadly, in the overall picture that means more people end up dying.

What does this mean for the world now?

It seems at least one of the variants, (the UK variant known as B.1.1.7) has become better at transmitting itself. It may be able to replicate itself faster in the upper airways and nose. That could then mean more viral shedding from the infected person. Data from Oxford University suggests the UK virus variant may be 35% better at spreading. This is the ‘R’ number or the ‘Reproductive Number’ and it measures infectivity of a virus. So if the original (wild-type) SARS-2 virus spread to three people for every one person infected then the new variants would spread to four people for every one infected. The difference between three or four people may not sound like much but mathematically it increases the case doubling time at an exponential rate. So even if the new variants have the same mortality rate, they will end up killing more people in total, as they will infect more people in the same time. The major threat from increased spread is that critical resources such as ICU bed use and staff demand increases.

However, societies are not defenceless against infectious disease. Viruses with higher transmittability are still susceptible to our control measures. Viral spread can be brought down by our own efforts. SARS-2 spreads at a much higher rate indoors and when we are in close contact with others. If we could ensure that each infected person then infects less than one other person then the pandemic would eventually limit itself. We can control the spread with the tried and true Public Health measures we all know.

Are the new variants more deadly or able to outsmart the immune system?

Typically, viruses become better at spreading but not usually more deadly. But early reports published recently in Nature; ‘Fast-spreading COVID variant can elude immune responses’ — 21 January 2021, suggest that at least one of the new variants (the South African variant 501Y.V2) may be better able to outsmart our immune defences.

However, this data only looked at neutralising assays (anti-body effectiveness at neutralising the virus) in a lab. The ‘live’ human immune system has multiple mechanisms at work (including T-Cells), not just antibodies.

It would be highly unlikely for a new variant virus to totally escape an developed immune response gained either by a vaccine or natural infection. The immune system has a complex of many antibody and T-Cell responses to call on. So, anyone who has been vaccinated or recovered from a natural infection should still have reasonable protection against the new variants. If vaccinated and then infected with a new variant you would expect to have mild or at least a reduced level of illness.

How long will protection last after an infection or after vaccination?

There is not yet enough data over the longer period to be certain about durability (longevity) of protection. Typically, infection in humans from other coronaviruses (the ones that cause common colds) gives immunity for at least a year. Will immunity to SARS-2 and its newer variants last this long after vaccination or infection? It’s too early to say.

A logical guess would suggest that immunity to the new SARS-2 virus and its variants would last at least 12 months. That means we may need a rolling global programme of annual immunisation. It would also require constant sampling and genomic analysis of evolving viral infections to feedback into vaccine manufacture.

Lessons for now

Pandemic threats should not be underestimated. Public Health is the specialty of medicine that addresses threats to humanity and whole societies. Prior to the 2019 COVID outbreak Public Health had not received the focus it was due. Governments need programmes that continuously monitor and prepare society for these malevolent threats to our economy and even our very existence.

At an individual level we need to keep avoiding close contact and gatherings, particularly indoors.

Above all, maximal protection will be gained for an individual by getting vaccinated. The vaccines have so far proven to be effective at reducing illness in up to 95% of those vaccinated. They are also likely to be effective (with cross-protection) in the three recent variants of SARS-2.