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Omicron: How did the coronavirus variant evolve to be so dangerous?

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Omicron has become a global threat to public health thanks to a particularly dangerous set of mutations, but where did it come from?



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17 December 2021

A technician at the Nelson Mandela School of Medicine in Durban, South Africa

New York Times / Redux / eyevine

We don’t know for sure where or how the omicron variant of the coronavirus acquired such an extensive and dangerous set of mutations before beginning to spread like wildfire around the world, and we may never know. It most likely evolved in a single immunocompromised individual, possibly someone who is HIV positive living somewhere in southern Africa who wasn’t receiving effective treatment, but there is no direct evidence for this.

How did we discover the omicron variant?

Researchers in South Africa noticed a small increase in cases in Gauteng province and decided to genetically sequence more samples. They found a variant with a lot of worrying mutations and alerted the world on 25 November. Researchers elsewhere noticed this variant around the same time from sequences uploaded to public databases.

What’s different about it?

Omicron has around 50 mutations compared to the original virus discovered in Wuhan, China, with 30 in the outer spike protein alone. That matters because the spike protein is the target of our antibodies. The extensive changes in omicron’s spike protein greatly reduce the effectiveness of the antibodies people have from vaccination or from infection with other variants.

How did it acquire so many mutations?

There are two main hypotheses. The first is that it evolved in a person with a compromised immune system. Normally all viruses are killed when our immune response kicks in fully, but if a person’s immune system is weak some viruses can keep replicating in their body and evolve over several months to become much better at evading antibodies.

Is there any evidence this is what happened?

There is no direct evidence, but this process of the coronavirus accumulating mutations has been observed happening in an individual with HIV who wasn’t responding to covid-19 treatment. The researchers who discovered omicron have called for efforts to tackle HIV to be stepped up.

What’s the other main idea?

That the virus infected animals of some kind, acquired lots of mutations as it spread among them and then jumped back to people – a phenomenon known as reverse zoonosis.

What evidence is there for omicron evolving in animals?

Some of the mutations in the spike proteins are the same as those seen in SARS-Cov-2 viruses that have adapted to spreading in rodents, and specifically mice. But this could just be a coincidence.

Could this have happened in mice in a lab?

Most of the 7 billion people in the world have rodents living near their homes, if not inside them, so there have been countless opportunities for this to happen with mice or rats. Very few labs are doing experiments that involve infecting mice with SARS-Cov-2, and none of them are in southern Africa. In other words, the lab mice idea can’t be ruled out but seems highly unlikely.

Are there any other possibilities?

Omicron could have evolved gradually as it spread from person to person in one of the many parts of the world where little or no sequencing is done. But given how infectious it is, it’s hard to explain why none of its ancestors spread widely enough to reach countries that do more sequencing. Another possibility is that the drug molnupiravir, which works by inducing so many mutations it kills viruses, could have played a part, but there is no evidence to support this speculation.

Where did omicron arise?

The earliest confirmed omicron cases to date were in South Africa and Botswana in the first half of November. However, it is estimated that omicron first started spreading in people in early October. We don’t know where that happened. That said, the fact that the first omicron wave is in South Africa does suggest an origin somewhere in the region.

I read that omicron was detected elsewhere before South Africa reported it?

Several countries including the US and the Netherlands have now reported omicron cases from mid November, but these don’t predate the earliest southern African cases and are almost all associated with travel from the region. There was a report of omicron being found in Nigeria in October, but this was later said to be a mistake.

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Solar storms may cause up to 5500 heart-related deaths in a given year

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In an approximate 11-year cycle, the sun blasts out charged particles and magnetised plasma that can distort Earth’s magnetic field, which may disrupt our body clock and ultimately affect our heart



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17 June 2022

A solar storm

Jurik Peter/Shutterstock

Solar storms that disrupt Earth’s magnetic field may cause up to 5500 heart-related deaths in the US in a given year.

The sun goes through cycles of high and low activity that repeat approximately every 11 years. During periods of high activity, it blasts out charged particles and magnetised plasma that can distort Earth’s magnetic field.

These so-called solar storms can cause glitches in our power grids and bring down Earth-orbiting satellites. A handful of studies have also hinted that they increase the risk of …

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UK Covid infection rate rising, with more than a million cases in England | Coronavirus

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Coronavirus infections are rising in the UK, figures have revealed, with experts noting the increase is probably down to the more transmissible BA.4 and BA.5 Omicron variants.

The figures from the Office for National Statistics (ONS), based on swabs collected from randomly selected households, reveal that in the week ending 11 June an estimated one in 50 people in the community in England are thought to have had Covid – around 1.13 million people.

The figure is even higher, at one in 45, in both Wales and Northern Ireland, while it was highest in Scotland where, in the week ending 10 June, one in 30 people are thought to have been infected.

While the figures remain below the peak levels of infection seen earlier this year, when around one in 13 people in England had Covid, the findings are a rise on the previous week where one in 70 people in England were thought to be infected. Furthermore, the data reveals increases in all regions of England, except the north-east, and across all age groups.

Experts say that a key factor in the increase is probably the rise of the Covid variants of concern BA.4 and BA.5.

“Infections have increased across all four UK nations, driven by rising numbers of people infected with the BA.4 and BA.5 Omicron variants,” said Kara Steel, senior statistician for the Covid-19 Infection Survey.

While Steel said it remained too early to say if this was the start of another wave, others have warned it may already have begun, with increased mixing and travelling among other factors fuelling a rise in cases.

Among concerns scientists have raised are that BA.4, BA.5 and another variant on the rise, BA.2.12.1, replicate more efficiently in human lung cells than BA.2.

Prof Azra Ghani, an epidemiologist at Imperial College London, said the latest figures were not surprising, and might rise further.

“This increase in infection prevalence is likely due to the growth of the BA.4 and BA.5 Omicron subvariants, which as we have seen elsewhere in Europe, appear to be able to escape immunity generated from previous Omicron subvariants,” she said.

“It is therefore possible that we will continue to see some growth in infection prevalence in the coming weeks and consequently an increase in hospitalisations, although these subvariants do not currently appear to result in any significantly changed severity profile. This does however serve as a reminder that the Covid-19 pandemic is not over.”

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NHS to offer women in England drug that cuts recurrence of breast cancer | Breast cancer

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Thousands of women in England with breast cancer are to benefit from a new pill on the NHS which reduces the risk of the disease coming back.

The National Institute for Health and Care Excellence (Nice) has given the green light to abemaciclib, which cuts the chance of breast cancer returning after a patient has had surgery to remove a tumour.

Trials showed that patients who had the drug with hormone therapy had a more than 30% improved chance of their cancer not coming back after surgery, compared with hormone therapy alone.

“It’s fantastic thousands of women with this type of primary breast cancer will now have an additional treatment option available on the NHS to help further reduce the risk of the disease coming back,” said Delyth Morgan, the chief executive of charity Breast Cancer Now.

“The fear of breast cancer returning or spreading to other parts of their body and becoming incurable can cause considerable anxiety for so many women and their loved ones.

“New effective treatments such as abemaciclib, which can offer more women the chance to further reduce the risk of the disease recurring, are therefore extremely welcome and this is an important step change in the drug options available for this group of patients.”

The twice-a-day pill is suitable for women with hormone receptor-positive, HER2-negative, node-positive early breast cancer at high risk of recurrence who have had surgery. About 4,000 women will benefit initially, Nice said.

Helen Knight, the interim director of medicines evaluation at Nice, said the draft recommendation came less than a month after abemaciclib received its licence.

“The fact that we have been able to produce draft recommendations so quickly is testament to the success of our ambition to support patient access to clinically and cost effective treatments as early as possible,” said Knight. “Until now there have been no targeted treatments for people with this type of breast cancer.

“Abemaciclib with hormone therapy represents a significant improvement in how it is treated because being able to have a targeted treatment earlier after surgery will increase the chance of curing the disease and reduce the likelihood of developing incurable advanced disease.”

Abemaciclib works by targeting and inhibiting proteins in cancer cells which allow the cancer to divide and grow. It normally costs £2,950 for a packet of 56 150mg-tablets, but the manufacturer, Eli Lilly, has agreed an undisclosed discounted price for NHS England.

“Thanks in part to this latest deal struck by NHS England, NHS patients will be able to access another new targeted drug for a common and aggressive form of breast cancer,” said Prof Peter Johnson, the cancer director of NHS England.

“Abemaciclib, when used alongside a hormone therapy, offers a new, doubly targeted, treatment option, helping to increase the chances of beating the cancer for good, as well as meeting the NHS’s commitment to delivering improved cancer care under our long-term plan.”

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