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Omicron: How dangerous is the B.1.1.529 variant found in South Africa?

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A woman in Johannesburg, South Africa, receives a nasal swab from a health worker

EMMANUEL CROSET/AFP via Getty Images

A new variant of SARS-CoV-2, known first as B.1.1.529 and now named omicron, has an unusually high number of mutations and appears to have triggered a recent surge in cases in South Africa.

When was omicron first identified?

It was first detected on 23 November in South Africa using samples taken between 14 and 16 November. Joe Phaahla, South Africa’s health minister, said on 25 November that he believes the variant is behind an exponential daily rise in covid-19 cases across the country in recent days. The same day, the UK Health Security Agency (HSA) designated it a variant under investigation, triggering travel restrictions for people travelling to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. The World Health Organization had listed B.1.1.529 as a variant under monitoring, but its Technical Advisory Group on SARS-CoV-2 Virus Evolution decided on 26 November to class it as a variant of concern. The WHO has now named it omicron after the Greek letter.

What is happening in South Africa?

National daily cases have gone from 274 on 11 November to 1000 a fortnight later. While the rate of growth has been fast, absolute numbers are still relatively low compared with the UK, which saw 50,000 cases on 26 November. More than 80 per cent of South Africa’s cases are currently in the country’s Gauteng province. All of the 77 cases sequenced in the province between 12 and 20 November were identified as being caused by the variant. The estimated reproduction number, the average number of people that an individual is likely to infect, is almost 2 in Gauteng compared with nearly 1.5 nationally.

What do B.1.1.529’s mutations tell us?

The variant has a “very unusual constellation of mutations”, says Sharon Peacock at the University of Cambridge. There are more than 30 mutations in the spike protein, the part of the virus that interacts with human cells. Other mutations may help the virus bypass our immune systems, make it more transmissible and less susceptible to treatments, according to the HSA. But the body notes that “this has not been proven”.

What the mutations mean is currently theoretical and based on experience of past mutations of SARS-CoV-2 rather than lab tests. Wendy Barclay at Imperial College London says “we don’t really know” if it will reduce the effectiveness of vaccines. Nonetheless, she adds that, in theory, the number of changes across the antigenic sites on the variant’s spike means the effectiveness of antibodies produced by covid-19 vaccines would be compromised.

Mutations on a part of the virus known as the furin cleavage site are similar to those seen in the alpha and delta variants, which could help the variant spread more easily. Barclay says “it’s very biologically plausible” that B.1.1.529 has greater transmissibility than delta.

The mutations also mean that the new variant is likely to be more resistant to antibody treatments such as those developed by Regeneron, which have been shown to save lives. “That is really a cause for concern,” says Barclay. One small bright spot is that, to date, there are no signs that the variant causes more severe disease.

How far has it spread?

Genomic sequencing has found the variant in South Africa, Botswana and Hong Kong. There are also reported cases in Israel, apparently originating from a traveller from Malawi, and in Belgium, from someone who had travelled from Egypt. UK health secretary Sajid Javid said it is “highly likely” that the variant has spread to other countries. As of 27 November, two cases had been detected in the UK, where about a fifth of positive cases are sent for genomic sequencing. Even in countries with low levels of sequencing, it may be possible to get early warning signs, because the variant is linked to a mutation called S-gene dropout, which is picked up by PCR tests, says Jeffrey Barrett at the Wellcome Sanger Institute in Hinxton, UK.

How have other places responded?

The UK and EU have both imposed restrictions on people travelling from countries in southern Africa, with Javid saying the variant is of “huge international concern”. Prime minister Boris Johnson announced further travel restrictions on 27 November.

Is it a given that this will outcompete the delta variant?

We don’t know. “We don’t have definitive evidence at the moment that this is more transmissible, but there are hints there that it may be,” says Peacock, pointing to the growth in South Africa and the higher R number in Gauteng. Some earlier variants have failed to get a toehold in certain countries because of the competition from other variants: beta hasn’t become established in the UK, for example, while alpha spread from Europe but never reached high levels in South Africa. “If this variant is not as transmissible as delta that would be good news for sure,” says Barrett.

What can I do?

All the usual measures of social distancing, handwashing, mask-wearing, getting vaccinated and having a booster shot still apply. The emergence of such a potentially worrying variant is, however, a reminder of the risk of uneven vaccination rates globally – only 24 per cent of people are fully vaccinated in South Africa.

How much do we really know about this variant?

Most of our knowledge is from the Network for Genomic Surveillance in South Africa, and the South African government, both of which have been praised by researchers for acting fast to share information on the variant. But there is more that we don’t know than we do. Tulio de Oliveira at Stellenbosch University, South Africa, said yesterday that the full significance of the variant’s mutations “remain uncertain.” Peacock adds: It’s important to stress how much we don’t know this new variant.“

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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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