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How South African scientists spotted the Omicron COVID variant

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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.

“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.”

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.”

Passengers queue to get a PCR test against the coronavirus disease (COVID-19) before traveling on international flights, at O.R. Tambo International Airport in Johannesburg, South Africa, November 26, 2021. Photo: Reuters

Passengers queue to get a PCR test against the coronavirus disease (COVID-19) before traveling on international flights, at O.R. Tambo International Airport in Johannesburg, South Africa, November 26, 2021. Photo: Reuters

Burining 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 Organisation.

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’.”

Source: https://tuoitrenews.vn/news/international/20211201/how-south-african-scientists-spotted-the-omicron-covid-variant/64473.html

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Police respond to ‘hostage situation’ at Texas synagogue

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Police were negotiating with a man believed to have taken people hostage at a synagogue in Colleyville, Texas, during a religious service on Saturday that was being broadcast online.

The Colleyville Police Department said FBI negotiators remained in contact with the hostage taker late Saturday afternoon, after a male hostage was released uninjured more than six hours after the crisis began.

Other hostages were still being held.

The police said it had evacuated residents from the area around Congregation Beth Israel as it deployed SWAT teams after responding to an emergency call at 10:41 a.m. No injuries have been reported and it remained unclear what weapons, if any, the man had.

There were initially four hostages, including the rabbi, according to a person familiar with the situation who was not authorized to speak publicly.

A law enforcement vehicle blocks the street where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

A law enforcement vehicle blocks the street where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

The man could be heard having a one-sided conversation in what appeared to be a phone call during a Facebook livestream of the Shabbat service of the Reform Jewish synagogue in Colleyville, which is about 16 miles (26 km) northeast of Fort Worth. The livestream cut off around 3 p.m. EST (2000 GMT).

Before the livestream was ended, the man could be heard ranting and talking about religion and his sister, the Fort Worth Star-Telegram reported. The man could be heard repeatedly saying he didn’t want to see anyone hurt and that he believed he was going to die, the newspaper said.

President Joe Biden has been briefed on the “developing hostage situation,” his press secretary said. Israeli Prime Minister Naftali Bennett said on Twitter that he was monitoring the situation and was praying for the safety of the hostages.

An armored law enforcement vehicle is seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

An armored law enforcement vehicle is seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

Texas Governor Greg Abbott said officials from the state’s Department of Public Safety were also on the scene working to get “the best and safest outcome.”

Barry Klompus, a member of the congregation since it opened in 1999, said he tuned into the livestream.

“It was horrible listening and watching, and it’s that much more horrible not knowing,” Klompus said in a telephone interview.

Though he was not able to clearly understand what the man wanted, Klompus believed the man wanted to talk to his sister.

Law enforcement vehicles are seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

Law enforcement vehicles are seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

A U.S. official briefed on the matter told ABC News the hostage-taker claims to be the brother of Pakistani neuroscientist Aafia Siddiqui, who is serving an 86-year U.S. prison sentence on her 2010 conviction for shooting at soldiers and FBI agents, and demanding she be freed.

But authorities have not yet confirmed his identity, the official told ABC News.

Siddiqui is being held at a federal prison in the Fort Worth area.

The president of the Union for Reform Judaism, Rabbi Rick Jacobs, said on Twitter the union was “very grateful to law enforcement who are working to free the hostages.” The Anti-Defamation League, a Jewish advocacy group, said it was aware of the standoff, and the Council on American-Islamic Relations (CAIR), a U.S. Muslim advocacy group, condemned the man’s actions.

Law enforcement vehicles are seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

Law enforcement vehicles are seen in the area where a man has reportedly taken people hostage at a synagogue during services that were being streamed live, in Colleyville, Texas, U.S. January 15, 2022. Photo: Reuters

“This latest antisemitic attack on Jewish Americans worshipping at a synagogue is an act of pure evil,” CAIR said in a statement.

Klompus said he did not know of any significant previous threats to the congregation.

“We don’t have a security officer on staff but we have what I would say is a very good relationship with the local police,” he said.

Source: https://tuoitrenews.vn/news/international/20220116/police-respond-to-hostage-situation-at-texas-synagogue/65255.html

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Concerns mount for Tonga after tsunami triggered by underwater volcano

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Pacific nations and humanitarian groups struggled to establish communications with Tonga on Sunday after a tsunami triggered by a massive volcanic eruption cut telephone and internet connections, raising concerns for the tiny island nation.

An underwater volcano off Tonga erupted on Saturday, triggering tsunami warnings and evacuation orders on the shores of Tonga as well as several South Pacific islands, where footage on social media showed waves crashing into coastal homes.

Internet and phone lines went down at about 6.40 p.m. local time on Saturday, leaving the 105,000 residents on the islands virtually uncontactable.

“The images of the volcanic eruption in close proximity to Tonga are hugely concerning,” Jacinda Ardern, the Prime Minister of New Zealand, located about 1,481 miles from Tonga, said in a statement on Instagram.

“Communication as a result of the eruption has been difficult, but our defence force team and Ministry of Foreign Affairs are working as we speak to establish what’s needed and how we can help,” she said.

The New Zealand foreign ministry said there were no reports of injuries or deaths as yet but communications were limited.

Ardern will address the media at 3 p.m New Zealand time (0200 GMT) to give an update on the situation.

A Planet SkySat image shows the underwater volcano Hunga Tonga-Hunga Ha'apai two hours before its eruption in Hunga Tonga-Hunga Ha'apai, Tonga, January 15, 2022. Photo: Planet Labs PBC/via Reuters

A Planet SkySat image shows the underwater volcano Hunga Tonga-Hunga Ha’apai two hours before its eruption in Hunga Tonga-Hunga Ha’apai, Tonga, January 15, 2022. Photo: Planet Labs PBC/via Reuters

The International Federation of Red Cross and Red Crescent Societies (IFRC) Pacific Office in Suva, Fiji said it was monitoring the situation and had no updates on damages or casualties.

Tongan churches in New Zealand organised prayers for their families back home.

“We pray God will help our country at this sad moment. We hope everybody is safe…,” Maikeli Atiola, the Secretary of the Wesleyan Church of Tonga in Auckland said, Radio New Zealand reported.

The Hunga-Tonga-Hunga-Ha’apai volcano has erupted regularly over the past few decades but Saturday’s eruption was so loud that residents parts of faraway Fiji and New Zealand said they heard it.

Satellite images captured the volcanic eruption on Saturday as the explosion sent plumes of smoke into the air and about 12 miles above the sea level.

The sky over Tonga was darkened by the ash.

The eruptions triggered tsunami warnings across the Pacific, with the United States and Japan urging people on their Pacific coastlines to stay away from the shores.

Australia issued a marine tsunami warning for the New South Wales coastlines, Lord Howe Island and Norfolk Island, and said local beaches along the state’s coast have been closed. A tsunami advisory was also issued in New Zealand.

Source: https://tuoitrenews.vn/news/international/20220116/concerns-mount-for-tonga-after-tsunami-triggered-by-underwater-volcano/65254.html

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Thieves loot freight trains in Los Angeles with impunity

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Dozens of freight cars are broken into every day on Los Angeles’s railways by thieves who take advantage of the trains’ stops to loot packages bought online, leaving thousands of gutted boxes and products that will never reach their destinations.

According to the tags found Friday by an AFP team on a track near the city center — which was easily accessible from nearby streets — many major US mail order and courier companies such as Amazon, Target, UPS and FedEx are being hit by the thefts, which have exploded in recent months.

The thieves wait until the long freight trains are immobilized on the tracks, and then climb onto the freight containers, whose locks they easily break with the help of bolt cutters.

They then help themselves to parcels, ditching any products that are difficult to move or re-sell, or are too cheap, such as COVID-19 test kits, furniture or medications.

Rail operator Union Pacific has seen a 160 percent rise in the thefts in Los Angeles county since December 2020.

“In October 2021 alone, the increase was 356 percent compared to October 2020,” UP said in a letter to the local authorities, seen by AFP.

The explosion in looting has been accompanied by an upsurge in “assaults and armed robberies of UP employees performing their duties moving trains,” the letter said.

The phenomenon spiked recently with the peak of activity linked to Christmas shopping.

An open box of unused Covid-19 tests is left behind on a section of Union Pacific train tracks littered with thousands of opened boxes and packages stolen from cargo shipping containers, targeted by thieves as the trains stop in downtown Los Angeles. Photo: AFP
An open box of unused Covid-19 tests is left behind on a section of Union Pacific train tracks littered with thousands of opened boxes and packages stolen from cargo shipping containers, targeted by thieves as the trains stop in downtown Los Angeles. Photo: AFP

According to figures reported by UP, more than 90 containers were vandalized every day on average in Los Angeles County in the last quarter of 2021.

To combat the trend, Union Pacific says it has strengthened surveillance measures — including drones and other detection systems — and recruited more security staff for its tracks and convoys.

Police and security agents have arrested more than 100 people in the last three months of 2021 for “trespassing and vandalizing” Union Pacific trains.

“While criminals are being caught and arrested, charges are reduced to a misdemeanor or petty offense, and the person is back on the streets in less than 24 hours after paying a nominal fine,” said a spokesman for the rail operator.

“In fact, criminals boast to our officers that there is no consequence,” he said.

Union Pacific wrote to the Los Angeles County attorney’s office at the end of December asking them to reconsider a leniency policy introduced at the end of 2020 for such offenses.

The operator estimates that damages from such thefts in 2021 amounted to some $5 million, adding that the amount in claims and losses “does not include respective losses to our impacted customers” or the impact on Union Pacific’s operations and the entire Los Angeles County supply chain.

Source: https://tuoitrenews.vn/news/international/20220115/thieves-loot-freight-trains-in-los-angeles-with-impunity/65252.html

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