World

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.

Read the latest updates in our dedicated coronavirus section.

“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.”

For all the latest headlines follow our Google News channel online or via the app.

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’.”

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

New COVID-19 variant triggers global alarm as WHO urges caution

World

Pakistan military raids suspected former Taliban stronghold, kills three militants

Pakistani troops raided a suspected militant hideout in a former Pakistani Taliban stronghold near the border with Afghanistan, triggering a shootout that killed three militants, the military said Tuesday.
A militant commander was among those killed in the shootout late on Monday in Khyber, a district of Khyber Pakhtunkhwa province, according to a military statement.
For all the latest headlines follow our Google News channel online or via the app.
The military did not provide any additional details, saying only the targeted militants had attacked Pakistani troops in the past.
The Pakistani Taliban, also known as Tehrik-e-Taliban Pakistan or TTP , are a separate group but allied with the Afghan Taliban, who two years ago seized Afghanistan as US and NATO troops were in the final stages of their pullout from the country after 20 years of war.
The Taliban takeover of Afghanistan has emboldened the Pakistani Taliban, who have stepped up attacks against police and troops.
Read more:

Pakistan general election to be held in last week of January
Pakistan’s $40 bln housing investment potential highlighted at Cityscape Global Forum
Pakistan ex-PM Imran Khan’s jail remand extended by two weeks

World

West’s failure to back Ukraine’s tactics risks handing Putin major advantage: Analyst

The West needs to fully support Ukraine’s battle strategies against Russia in the current counter-offensive and the ones to come next, because to do otherwise would hand Russia the gift of valuable time to regroup its forces, said an analyst at the Washington-based think tank Institute of Study of War (ISW).

“Ukrainian forces have adapted. Ukraine’s military decision-making is sound. Now is not the time for Western doubt but for the West to embrace Ukraine’s way of war and commit to sustaining Ukraine’s initiative on the battlefield,” wrote Nataliya Bugayova, non-resident Russia Fellow at ISW.

She highlighted that Ukraine recognized the realities of Russian defenses much faster than Western policymakers, who were expecting a rapid Ukrainian breakthrough.

Bugayova stressed that the US should wholeheartedly embrace its collaboration with a capable ally who takes the lead – Ukraine. In many instances, the US has been accustomed to working with partners who depend on it for leadership, whether it's the proxy forces it has trained or allies relying on its security assistance. Yet, in the case of Ukraine, the US finds itself in a partnership where Ukraine is leading on the frontlines. They possess an in-depth understanding of their operational environment, their adversaries, as well as their own strengths and weaknesses. Ukrainians have consistently demonstrated their grasp of the complexities of this conflict and their ability to adapt. Perhaps most crucially, Ukraine's unwavering determination to continue the fight remains undiminished.

For all the latest headlines follow our Google News channel online or via the app.

“Now is not the time for Western doubt. The West must reinforce its military and diplomatic commitments and lean in to help sustain Ukraine’s battlefield momentum. Ukraine is still facing an existential challenge from Russia, which requires Western aid to militarily defeat. Leaning in means embracing Ukraine’s campaign design. It means ensuring that the Western training of Ukrainian troops is done in conditions in which Ukraine fights at its best,” she wrote.

She added: “The West should also help shape strategic communications to set proper expectations around Ukraine’s progress. Ukraine can win this war militarily, but it will take more than one counteroffensive operation. It will take as many campaigns as it takes for Ukraine to liberate its territory and its people.”

“The West should be prepared to support them all because the fundamentals shaping this conflict have not changed: Ukraine can win this war, Russia can only be defeated on the battlefield, and what is at stake includes Ukraine’s existence and vital US interests.”

Bugayova wrote that the current objective of the Kremlin is obstruct and hinder Western and Ukrainian decision-making processes, as this stands as one of the few avenues through which Russian President Vladimir Putin can further his goals. Delays in Western decision-making, especially when it leads to sluggish deliveries of military aid, can offer Russia a respite from pressure. Granting Russia such respite, whether at the operational level or the strategic level, has proven to be disastrous.

She further elaborated that with additional time on their side, Russia has the opportunity to regroup and launch further attacks. However, Russia's Achilles' heel remains its incapacity to swiftly adapt when confronted with relentless pressure or a series of setbacks. Under sustained, unyielding pressure, the Russian forces are likely to begin to weaken. This is the desired outcome of Ukraine's present counteroffensive strategy, and it can only be realized if the West embraces Ukraine's approach to warfare for both the current phase and the future.

“Russia’s Achilles heel remains its inability to rapidly pivot when faced with relentless pressure or consecutive setbacks. Faced with constant pressure over time with no relief, the Russians will likely start to crack. This is the effect Ukraine’s current counteroffensive strategy is seeking to achieve, and it can only be realized if the West embraces Ukraine’s way of war for this phase of the counteroffensive and beyond,” she wrote.

Ukraine’s successes on the battlefronts

“Ukraine maintains the battlefield initiative and its forces are advancing in Zaporizhia Oblast and near Bakhmut. Ukraine continues to liberate its territory and people and is slowly but steadily breaking through an incredibly formidable Russian prepared defense — and the Russian forces are unable to stop the advance, which is now moving in two directions,” Bugayova wrote.

She added that Ukraine's military strategy has achieved notable victories against Russian forces. With backing from Western allies, Ukrainian troops have consistently thwarted Russian goals in various regions, including Kyiv, Kharkiv, Kharkiv Oblast, Kherson, and increasingly, in the southern part of the country. She stressed that Ukraine's efforts have prevented Russian forces from gaining complete control of the skies, while also challenging their naval dominance. This persistent resistance is gradually rendering the Russian military's presence in Crimea less sustainable, a development that was once considered improbable by many observers.

“Ukraine’s decision to keep pressure on Russian forces throughout the entire frontline instead of focusing all of Ukraine’s combat power on one line of attack in the direction of Melitopol, which some Western advisors preferred, was a good adaptation. Ukraine’s decision to hold and conduct counterattacks in Bakhmut allowed it to pin down a substantial portion of the combat power of Russia’s relatively elite airborne (VDV) forces and deny the creation of a strategic Russian reserve. The recent Ukrainian advances in Zaporizhia Oblast are likely forcing the Russians to laterally redeploy their units away from around Bakhmut, where Ukrainian forces are advancing too,” the Russia Fellow wrote.

Black Sea tactics

Bugayova highlighted Ukraine’s “asymmetrical tactics” in the Black Sea which she said are preventing the Black Sea Fleet from operating freely, “forcing Russia to reposition naval assets, and increasingly challenging Russian forces in Crimea — all operational developments of strategic significance.”

This is in light of Ukraine’s missile attack on the headquarters of Russia's Black Sea navy in the Crimean port of occupied Sevastopol on Saturday. The Special Operations Forces of the Armed Forces of Ukraine said on Monday that the strike killed 34 Russian officers, including the commander of the Russian Black Sea Fleet.

The Ukrainian Navy said on Tuesday that the Russians will face challenges in controlling their troops deployed in the Black Sea area after the Ukrainian strike on the headquarters of the Russian Black Sea Fleet killed their commander.

Ukrainian attacks on Black Sea Fleet leave it diminished but still capable: UK intel

Ukraine successfully holding territory while Russians struggle on offensive: UK intel

Russia faces troops control challenges after Black Sea Fleet commander death: Ukraine

World

China says it has not been notified about North Korea’s border reopening

China has not been notified through diplomatic channels about any re-opening of North Korea’s borders, a spokesperson at the Chinese foreign ministry said on Tuesday.

For all the latest headlines follow our Google News channel online or via the app.
On Monday, China’s national broadcaster CCTV reported that North Korea had allowed foreigners to enter, and that visitors would be subject to a two-day quarantine upon arrival.
North Korea has largely closed its international borders since early 2020 due to COVID-19.

North Korea’s Kim tells Xi in letter he hopes to promote cooperation with China

North Korea’s Kim receives drones as gift on Russian trip