Covid-19 Mutations and Variants

It is in the nature of viruses to mutate. Often these die out but sometimes a mutated version will become the predominant variant in a population. New strains become more common by being in the right place at the right time. (Flu viruses behave in the same way, which is why flu vaccines are tweaked each year.) Vaccines train the immune system to attack several parts of the virus, so even though the spike has mutated, the vaccines should still work. Should we get to the stage where vaccines need to be regularly updated, the ones we have are very easy to tweak.

• The virus that was first detected in Wuhan, China, is not the same one you will find in most corners of the world. It probably spread at low levels initially, only being noticed when a serious outbreak of cases occurred. 
• By this time it is thought that it was already spreading outside China, maybe as early as September 2019 in Italy, and later that autumn in France, Brazil and the US. This strain was different to the original Chinese strain and became the dominant strain as it spread world-wide.
• The D614G mutation emerged in Europe in Feb. 2020 and became the globally dominant form of the virus.
• Another, called A222V, spread across Europe and was linked to people's summer holidays in Spain.
• The Alpha variant first detected in London UK in September 2020. (A similar strain was circulating in Italy as early as August 2020, before the first known cases in England. )
  
• The Beta variant emerged in South Africa.
• The Gamma variant was found in Brazil in Nov. 2020. 
• The Delta variant was found emerged in  India in Oct. 2020.
• Variant 20C-US (identified in Jan. 2021) now accounts for almost 50% of new cases in the US.
• A Nigerian variant (P681H) has a number of gene changes.
• Variant Omicron emerged in Botswana (reported on 24 Nov. 2021). It has an unusually large number of mutations which make it more transmissible, and is now present in many countries. So far cases are mild and few require hospitalisation. Symptoms are more like a common cold.

Covid-19 variants (mutations) are labelled in several ways.

Media reports typically refer to the country where the new variant has first been identified. For example, the Brazilian, South African or UK variants. However, this does not necessarily reflect the country where the mutation first occurred, as it may have spread to other countries before being identified. Some countries (e.g. UK) are doing more testing to identify mutations than others. 

• A new variant may initially be referenced by noting the area of the genetic sequence where the mutation occurred. For example, the D614G mutation. 

Scientists are now building a family tree that indicates where mutations have occurred and how they are linked. This starts with year date that the mutation was found and a sequential letter. The first virus is labelled 19A. This split into 19B and 20A, and 20A has further mutated into 20B and 20C. Further numbers indicate specific mutations.

• 20B.1.1.248: A variant with 12 mutations (including N501Y and E484E) identified in Brazil.
• 20B.1.1.7.: A faster spreading variant spreading identified in the UK in late 2020 and early 2021. 
• 20C-US: A variant found in the US. 

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Vitamin D Levels and Ethnicity

Why is vitamin D so important?

• It helps regulate the amount of calcium and phosphate in the body. These nutrients are needed to keep bones, teeth and muscles healthy. A lack of vitamin D can lead to bone deformities such as rickets in children and bone pain caused by osteomalacia in adults.
• It is widely thought that vitamin D reduces the amount of 'stress hormone' cortisol within the body. Cortisol is linked to high blood pressure, in turn increasing the risk of cardiovacular disease.
• There is some evidence from small studies that vitamin D may give some protection against Covid-19.

 Sources of vitamin D

The main source of vitamin D for humans is sunlight, the level of which varies over the world. Around the equator, sunlight levels are high year round. As you travel north or south, the level of sunlight varies over the year, with lowest levels in the winter season. Natural sources of vitamin in the diet are oily fish, red meat, liver and egg yolks, though these contain limited quantities.

Ethnicity

People with dark skin are especially vulnerable to vitamin D deficiency due to their high melanin levels, which inhibit vitamin D production and protect against skin cancer. The level of vulnerability varies with the amount of melanin, so those with the darkest skin are the worst affected. As more people with dark skin ethnicity move to live or work in lower sunlight areas of the world, their vitamin D levels are not enough; a finding which is supported by some research in the US. Note this research was carried out some years ago, and uses the terms "black people" and "white people".

• One study found that 97% of "black" people and 70% of white people had vitamin D deficiency. 
• Another study found that "blacks" have half the vitamin D levels of white people.

Other social factors can also reduce exposure to sunlight. 

• Workers on permanent might shift will spend less time in sunlight.
• In some strict Muslim areas, women are kept indoors for much of the time. 
• Some cultures rate paler skins as being more beautiful; people may therefore restrict time spent in full sunlight, and/or cover most of the skin with clothing when outdoors.

Supplements

Therefore people (especially those with dark skins) in countries with big seasonal variations are advised to take supplements of the vitamin. A dose of 10 micrograms a day will be enough for most people. Taking too many supplements over a long period of time can cause too much calcium to build up in the body (hyercalcaemia) , which can weaken bones and damage kidneys and heart.

Sources: various

Herd Immunity

With the current Covid-19 pandemic, some people have been advocating allowing people to resume normal life, suggesting that at some point herd immunity will happen.

If enough people become immune to an infectious agent, the entire population (or a specific community) is protected  because infectious people rarely encounter a non-immune person, so the transmission dies out.

The level of individual immunity to get to herd immunity level for a virus depends on how infectious it is - measured by R, the average number of people that each infectious person infects.

• The classic example is measles, which has an R number of around 15 and a herd immunity threshold of 95%.
• For Covid-19 the R number is about 3.5 and the herd immunity threshold is thought to be around 60 to 70%.

Herd immunity has only ever been achieved by vaccination. This is because herd immunity can only be built if the immune response totally prevents individuals from picking up and transmitting the virus. That sometimes happens but often it doesn't. While a person's immune system may stop them from falling ill if they reacquire a virus, it doesn't prevent onward transmission. The same is true of vaccines.

'Letting the virus rip' would mean letting between two-thirds and three-quarters of the population catch the virus. There are a number of issues with this proposal.

• Collateral damage: even if the death rate is 1%, letting the virus run free will hospitalise and kill millions.
• We can't take it for granted that individual immunity will automatically create herd immunity, since we don't yet know what immunity a person gets from having survived Covid-19, and how long this lasts.
• While they survive a Covid-19 infection, some people are now experiencing the symptoms of 'long covid'. These symptoms can be severe, and affect more than one of the body systems.

So, herd immunity is not the answer.

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Can MMR Jabs Protect Against Covid-19

 A study by scientists from the University of Georgia claims that the MMR vaccine may protect some people against severe Covid-19 (a 29% lower chance), and may prevent some people from catching the coronavirus. Those with the highest antibody levels specific to mumps were 'immune' to Covid-19, but the same effect was not seen for measles and rubella antibodies. This is a possible explanation of why children only seem to get mild Covid-19 illness, if any at all.

Other scientists have also theorised that this could explain the lower Covid-19 death rate in continents with measle-free status, including Africa and Asia.

A team at Cambridge University found in April 2020 that part of the coronavirus structure is similar to mumps, measles and rubella.

All children in the UK are offered the vaccine and around 91% currently are immunised by their second birthday. The first jab is given from nine months old, and another before they are six years old. While antibodies fade over time, they can still offer some protection against viruses. Mumps antibodies decline by the age of 14, which is the same age as coronavirus prevalence increases sharply.

The MMR II vaccine (introduced in the early 1970's) is considered a safe vaccine with very few side effects. Study researcher Dr. Hurley suggests that adults over the age of 40 should be given the MMR jab if they have never had it.

Source: Various news media.

Welcome to 2021

 I don't usually write this sort of post but 2020 has been a difficult year. Wishing every reader and their family and friends a happy and healthy 2021.

Here are the bad bits.

• Boris Johnson was Prime Minister and Donald Trump was US President. Neither competent at dealing with the pandemic crisis.
• The UK finally leaves the EU - being in Europe is better than going it alone.
• The pandemic has changed so many lives. People have died earlier than they would otherwise have done, many more have been seriously long term, education has been disrupted, and businesses have struggled or gone under.

There have been positive things too.

• Neighbours shopped for others in lockdowns.
• In our area, almost everyone kept to the rules on mask wearing and social distancing, so we are well down on the infection table.
• The internet proved a godsend, with WhatsApp messaging, and Zoom, Facetime and other virtual meetings.

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