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How South African scientists spotted the Omicron COVID-19 variant

On Friday Nov. 19, Raquel Viana, Head of Science at one of South Africa’s biggest private testing labs, sequenced the genes on eight coronavirus samples – and got the shock of her life.

The samples, tested in the Lancet laboratory, all bore a large number of mutations, especially on the spike protein that the virus uses to enter human cells.

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“I was quite shocked at what I was seeing. I questioned whether something had gone wrong in the process,” she told Reuters, a thought that quickly gave way to “a sinking feeling that the samples were going to have huge ramifications.”

She quickly picked up the phone to her colleague at the National Institute for Communicable Diseases (NICD) in Johannesburg, gene sequencer Daniel Amoako.

“I didn’t quite know how to break it to them,” she recalls. She told Amoako, “To me, it looks like a new lineage.”

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The discovery of the Omicron variant in southern Africa has caused global alarm, with countries limiting travel from the region and imposing other restrictions for fear it could spread quickly even in vaccinated populations.

Amoako and the team at the NICD spent the Nov. 20-21 weekend testing the eight samples which Viana sent them, all of which had the same mutations, he told Reuters on Tuesday.

It was so bizarre that Amoako, his colleague Josie Everatt and other colleagues also thought it must be a mistake. Then they remembered that over the week, they’d noticed a sharp rise in COVID-19 cases, of the sort that might indicate a new mutant.

In addition, Viana had been alerted to an oddity in the sample earlier this month by a colleague – an S-gene dropout, one of the mutations that now distinguishes the new Omicron variant of the coronavirus from the globally dominant Delta one.

The only common variant with that feature was Alpha, “and we hadn’t seen Alpha (in South Africa) since August,” Everatt recalls thinking as they tested the samples.

By Tuesday, Nov. 23, after testing another 32 from around Johannesburg and Pretoria, “it was clear,” Amoako said.

“It was scary.”

Burning questions

On the same Tuesday, the NICD team informed the department of health and other labs across South Africa doing sequencing, which later started coming up with similar results.

The same day, the NICD entered the data into the GISAID global science database, and found that Botswana and Hong Kong had also reported cases with the same gene sequence.

On Nov. 24, NICD officials and the department notified the World Health Organization.

By that stage, Viana said, more than two-thirds of positive tests in Gauteng, the South African province that includes Pretoria and Johannesburg, were showing the S-gene dropout – a sign that Omicron was already becoming dominant.

Thanks to Omicron, South Africa’s daily COVID-19 infection rate is expected to quadruple to more than 10,000 by the end of this week, one of the country’s leading infectious disease specialists, Salim Abdool Karim, said on Monday.

The important questions – how good is the new variant at evading immunity from vaccines or past illness, how severe are the symptoms, compared with previous versions, and how will this differ among age groups – remain to be answered.

Three scientists interviewed by Reuters who are working on those questions expect answers in about 3-4 weeks.

In the meantime, South African President Cyril Ramaphosa is considering introducing mandatory vaccination in some contexts, with the country still reeling from 3 million COVID-19 infections in total during the pandemic and over 89,000 deaths.

There is much anger in South Africa at the foreign travel bans – some of it directed at the scientists. Amoako receives some angry messages saying they should just “stop looking” for new variants.

Wolfgang Preiser, a virologist at Stellenbosch University working on COVID-19, who also has received hate mail, worries that other countries might take this whole saga as a lesson not to be so transparent.

“It might encourage other countries to hide things, or rather, just not to look,” he said.

“That’s the fear. Looking is quite an investment, so maybe they will conclude, ‘let’s not bother’.”

Read more:

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COVID-19 variant Omicron brings back travel curbs worldwide: All you need to know

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Russia has no access to damaged Togliatti-Odesa pipeline: Reports


Russian Industry and Trade minister Denis Manturov said on Thursday that Moscow has no access to the damaged part of the Togliatti-Odesa ammonia pipeline, and does not expect to be granted it, the Interfax news agency reported.

Russia has made the restart of the pipeline, which before the war carried ammonia from Russia to Ukraine for export, central to future renewal of a deal allowing Ukraine to export its grain safely from its Black Sea ports.

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Both Russia and Ukraine this week reported damage to a section of the pipeline that runs through the front line between Russian and Ukrainian forces in Ukraine’s Kharkiv region. The two sides have blamed each other.

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EU launches new effort to resolve longstanding migrant crisis


European Union interior ministers on Thursday made a fresh attempt to overcome one of the bloc’s most intractable political problems as they weighed new measures for sharing out responsibility for migrants entering Europe without authorization.

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Europe’s asylum system collapsed eight years ago after well over a million people entered – most of them fleeing conflict in Syria – and overwhelmed reception capacities in Greece and Italy, in the process sparking one of the EU’s biggest political crises.

The 27 EU nations have bickered ever since over which countries should take responsibility for people arriving without authorization, and whether other members should be obliged to help them cope.

Arriving for the meeting in Luxembourg, the EU’s top migration official, Home Affairs Commissioner Ylva Johansson said it was an “extremely important day” to resolve what has “been a marathon” issue for Europe.

“Of this marathon, we have maybe 100 meters left. So, we are so close to actually find an agreement today,” Johansson said. “I expect the member states to be able to do the final extra meters to reach the agreement.”

“If we are not united, we are all losers,” she said.

Under the existing rules, countries where migrants first arrive must interview and screen them and process the applications of those who might want to apply for asylum. But Greece, Italy and Malta maintain that the burden of managing the numbers of people coming in is too onerous.

Later attempts to impose quota systems on countries to share out the migrants were challenged in court and finally abandoned. EU countries now seem to agree that the assistance they provide must be mandatory but can take the form of financial and other help rather than migration sharing schemes.

The EU’s presidency, currently held by Sweden, has proposed a system under which countries who do not want to take migrants in could pay money instead. Figures of around 20,000 euros ($21,400) per migrant have circulated in the runup to the meeting. It remains unclear if the idea will be accepted.

Diplomats said ahead of the meeting that an agreement is only likely if big member countries France, Germany and Italy back the plan. A deal requires the support of a “qualified majority” – roughly two thirds of the 27 members but crucially also making up about two thirds of the EU population.

German Interior Minister Nancy Faeser said the compromise on the table “is very difficult for us.” She said that “I am fighting for us to have a Europe of open borders,” and warned that “should we fail today … that would be the wrong signal.”

French Interior Minister Gerald Darmanin told reporters that he had come with compromise proposals and that plenty of work remains to be done on what is a “very difficult” issue.

“What we want to do is completely change the situation on migration,” Darmanin said.

His Spanish counterpart, Fernando Grande-Marlaska – whose country has struggled to deal with an influx of people trying to enter from North Africa through Spanish islands in the Atlantic – warned that “if we don’t reach that agreement, I think that all of us will be losers.”

Even if a political agreement is reached Thursday, the member countries must still negotiate a full deal with the European Parliament, which has a different view of solidarity – one that requires countries to draw up detailed “annual migrant support plans” in case of emergency.

Lawmakers have warned that this is a last chance to solve the conundrum before EU-wide elections in a year, when migration is likely once again to be a hot-button issue.

Should the EU fail, the project might have to be abandoned or completely overhauled as it’s taken up by the next European Commission – the bloc’s executive branch – and the new members of parliament after next June’s polls.

“If we miss this chance to make it right, I don’t think we will have another,” Spanish Socialist lawmaker Juan Fernando López Aguilar, a leader on migration policy, said in April. “The kind of a message would be: ‘Hey, listen, it’s not going to happen. Not this time. Ever.’

The long-festering dispute has led to the collapse of Europe's asylum system. Unable to agree, the EU has tried to outsource its migrant challenge, making legally and morally questionable deals with countries like Turkey or Libya, which many people transit through on their way to Europe.

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Indian leader Modi expected to visit Egypt after official US trip: Source


Indian Prime Minister Narendra Modi is expected to travel to Cairo on his way back from an official visit to the US in June, the Times of India reported Thursday, citing official sources.

It will mark the Indian premier’s first visit to the Middle Eastern country. No official announcement has been made.

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Egypt’s President Abdel Fattah al-Sisi joined India’s President Droupadi Murmu and Prime Minister Narendra Modi during a parade celebrating the south-Asian nation’s Republic Day in January 2023.

Ahead of the parade, al-Sisi met with Modi and held talks, including on deepening military cooperation, and invited the Indian premier to Egypt.

The January visit elevated ties between the two countries, especially in counter-terrorism, energy and economy. Egypt and India share historic diplomatic relations.

As for trade, it bilaterally expanded in 2021-22, amounting to $7.26 billion, registering a 75 percent increase compared to 2020-21, according to data provided by the Embassy of India in Cairo.

India’s exports to Egypt during this period amounted to $3.74 billion, registering a 65 percent increase over the same period in 2020-21, the same report said.

Egypt’s exports to India reportedly reached $3.52 billion, registering an 86 percent increase over the previous year.

US President Joe Biden will host Modi at the White House for an official visit from June 21 to 24. They will reportedly address a joint meeting of the House of Representatives and Senate, one of the highest honors Washington affords to foreign dignitaries.

The speech would be Modi’s second to a joint meeting of the US legislature and comes as Biden seeks to deepen ties with the world’s largest democracy as part of his bid to win what he has framed as a contest between free and autocratic societies, especially China.

With Reuters

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