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How genomic sequencing can spot the next coronavirus variant

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How genomic sequencing can spot the next coronavirus variant

A brand new coronavirus variant that fuses components of Delta and Omicron was recognized final week, based on the World Well being Group and GISAID, the organisation that tracks the mutation of viruses. Its detection, say consultants, highlights the essential position performed by genomic surveillance.

It has been detected in a number of areas of France, and in Denmark, the Netherlands and Germany. The variant — which is but to be named by scientists however has been dubbed Deltacron in some media reviews — has been in circulation since January. The WHO mentioned it’s not but clear whether or not the variant is distinct from its predecessors by way of infectiousness or severity, although research are beneath approach.

Two years after the WHO declared Covid-19 a pandemic, international circumstances are starting to subside however it nonetheless kills 50,000 folks per week. Round 6mn folks have died within the pandemic, based on official knowledge from governments, though a current examine suggests the true variety of Covid-related deaths could also be thrice larger.

Public well being officers have urged in opposition to complacency as nations world wide drop restrictions that had been imposed to cease the unfold of the illness. “We nonetheless face the specter of new Covid variants that may very well be extra extreme, they may very well be extra transmissible or they might even escape the safety of present vaccines,” Sajid Javid, UK well being secretary, mentioned final week.

Epidemiologists agree that the emergence of viral variants shall be crucial issue driving the course of the pandemic. Swift identification of variants of concern will play a key half in stopping future public well being crises.

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How do scientists determine and monitor new variants?

The principle approach is thru “genomic sequencing” of samples taken from Covid PCR assessments. The genetic code of Sars-Cov-2 — its genome — is saved as a sequence of 4 biochemical “bases” strung out alongside a protracted molecule of RNA.

To learn the genome, scientists convert RNA to DNA, a intently associated molecule that shops the genetic materials in dwelling cells. The genetic sequence of the virus can then be learn by machines which can be additionally used to decode human, animal, bacterial and plant DNA.

On the Wellcome Sanger Institute, the UK’s largest sequencing centre, it sometimes takes about 5 days to switch samples from testing labs across the nation to the sequencing machines after which two days to learn out all 30,000 biochemical “letters” of the viral genetic code in every pattern.

“It’s a giant logistical operation,” mentioned Ewan Harrison, a specialist in microbial genomics on the institute.

An alternative choice to analysing viruses from contaminated people is collective genomics, utilizing samples of sewage and wastewater that retain traces of coronavirus excreted by folks. This expertise is turning into delicate sufficient to differentiate totally different viral variants relatively than simply the presence of Sars-Cov-2 within the space.

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“Wastewater monitoring has made some leaps ahead throughout the pandemic and it’s going to be a part of surveillance in future,” mentioned Harrison, “however it could possibly by no means inform us as a lot as sequencing of people together with affected person knowledge that may inform us concerning the biology of the variant.”

Information graphic explaining the process of genetic sequencing

Why is surveillance so essential?

Surveillance by genomic sequencing have to be maintained at an efficient stage worldwide to determine new threats as governments reduce Covid testing, mentioned Peter Bogner, GISAID’s chief government.

“If we had been to ramp down testing general, there’s a important threat that we’d miss a number of new variants,” Bogner mentioned. “The facility of a great sampling technique is that related adjustments may be captured successfully. However such surveillance efforts need to be finished globally.” 

Importantly, recombination — when two molecules of DNA trade items of their genetic materials with one another — is to be anticipated, WHO officers and others have mentioned, particularly given the excessive viral circulation ranges within the background. It is usually fairly widespread in influenza viruses.

How are totally different nations approaching testing and sequencing?

Wealthier nations such because the US and European nations sometimes sequence greater than poorer counterparts. A lot of this distinction is because of superior economies having extra educated personnel and higher entry to the {hardware} — machines and reagents — wanted to carry out genomic sequencing.

Specialists say Omicron uncovered the extent to which inequalities within the dealing with of the pandemic weren’t confined to provide of vaccines or assessments and prolonged to key instruments like sequencing.

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However sequencing in locations with fewer sources can nonetheless yield highly effective outcomes, akin to in South Africa.

Tulio de Oliveira, a bioinformatics professor at Stellenbosch College and one of many scientists behind the invention of the Beta and Omicron variants, mentioned nations with giant sources and low an infection charges, akin to Denmark and Australia, might sequence “nearly every thing” earlier than the arrival of Omicron. However that strategy is now not as viable when circumstances rise as a result of sequencing can’t sustain with the variety of circumstances.

De Oliveira mentioned his group has since March 2020 targeted on random and proportional sequencing every week. It means his researchers choose provinces randomly and deal with samples to be sequenced in step with case numbers.

How involved ought to we be concerning the new variant?

De Oliveira mentioned he was not significantly involved by the recombinant variant, which has components of Delta and Omicron, due to the small case numbers amid lowering general infections and rising vaccination charges.

“We’re alert however we aren’t involved,” he mentioned.

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Maria Van Kerkhove, the WHO’s Covid-19 technical lead, mentioned it was too quickly for folks to be nervous. “We have now not seen any change within the epidemiology . . . [or] in severity,” she mentioned, including that a lot of research are beneath approach.

What’s the chance of a extra pathogenic variant rising and the way seemingly are we to identify it?

Virologists are unanimous within the view that new variants will emerge. Nonetheless, nobody can predict the timing of their look or how virulent they’re prone to be.

“We warning that the milder signs within the human inhabitants, and in animal fashions, related to the Omicron variant in contrast with earlier variants, is probably going an opportunity occasion,” warned Nervtag, a bunch of well being consultants who advise the UK authorities on new and rising viruses. “The lack of virulence as viruses evolve is a typical false impression.”

GISAID’s Bogner mentioned the identification of the recombinant variant “underscores the indispensable want for efficient surveillance, as a ramping-down of testing general bears the numerous threat that we’d miss recombinant viruses because the virus evolves”. 

“However such surveillance efforts need to be finished globally and with a great sampling technique,” he added.

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Popeye, Tintin and more will enter the public domain in the new year

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Popeye, Tintin and more will enter the public domain in the new year

An enlarged cartoon of Tintin pictured on display at Paris’ Pompidou Cultural Center in 2006. The Belgian cub reporter is among the characters and works entering the public domain in 2025.

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Jan. 1 marks the dawn of a new era for Popeye and Tintin. It’s the day the nonagenarian cartoon characters officially enter the U.S. public domain along with a treasure trove of other iconic works.

The copyrights of thousands of films, songs and books expire in 2025, making them instantly available for people to use, share and adapt. The list includes classics like Virginia Woolf’s book A Room of One’s Own, the Fats Waller song “Ain’t Misbehavin’” and the Marx Brothers’ first feature film, The Cocoanuts.

The main thing they have in common is their age — under U.S. copyright law, their terms all expire after 95 years. All of the works entering the public domain next year are from 1929, except for sound recordings, which (because they are covered by a different law) come from 1924.

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“Copyright’s awesome … but the fact that rights eventually expire, that’s a good thing, too, because that’s the wellspring for creativity,” says Jennifer Jenkins, the director of Duke’s Center for the Study of the Public Domain, which spends months poring over records to compile the most famous examples.

Once in the public domain, these works become fodder for remakes, spinoffs and other adaptations.

That explains the recent wave of horror films starring Mickey Mouse and Winnie the Pooh, characters that entered the public domain in 2024 and 2023 respectively. The trend seems poised to continue: Jenkins says there are already three Popeye slasher flicks in the works.

“They’re capitalizing on the incongruity of this comic book character in a different genre and they get a lot of buzz,” she adds. “[But] when I sit back and look at the universe of remakes of public domain characters or works … the things that we still talk about that stand the test of time don’t tend to be these buzzworthy, kind of ew, grossed-out features.”

More enduring examples include West Side Story drawn from Shakespeare’s Romeo & Juliet, screen adaptations of Jane Austen’s Emma, Percival Everett’s 2024 book James (a retelling of Huckleberry Finn) and Wicked, the musical-turned-movie prequel to L. Frank Baum’s Wizard of Oz. 

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But these artifacts don’t only become fodder for big-name directors and authors — they’re available for anyone who wants to use them, from artists to high school orchestra directors.

Jenkins says she gets “adorable emails” from people who are drawing their own little Winnie the Pooh cartoons, and parents whose kids are talented musicians, eager to finally be able to perform certain compositions publicly and post them online.

In other words, the impact of public domain works extends far beyond the box office and Billboard charts.

“I’m excited about those things that not everybody’s going to notice — people really re-discovering some of these older works and engaging with them and appreciating them and making them their own,” she adds.

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Here’s a look at some of the works that are just days away from the public domain:

Characters

A Popeye balloon flies over the 33rd Macy's Thanksgiving Day Parade in Times Square.

A helium-filled Popeye balloon participates in the 33rd Macy’s Thanksgiving Day Parade in New York in 1959, three decades after his comic strip debut.

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Tintin the brave cub reporter — and his dog, Snowy — will enter the public domain in the U.S. well before they will in the European Union, where they are copyrighted until 2054. That’s because EU copyright terms extend 70 years past creators’ deaths, and Belgian cartoonist Hergé died in 1983.

Closer to home there’s E.C. Segar’s Popeye, who made his debut in a January 1929 Thimble Theatre cartoon strip. He sports his signature pipe, sailor outfit, anchor tattoo and sense of humor, responding when asked if he’s a sailor: “Ja think I’m a cowboy?”

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He could have a whole new set of adventures starting in 2025. But there’s a catch: Popeye didn’t start deriving his strength from spinach until 1932.

As Jenkins explains, many cartoon characters develop over time and have been in copyrighted works year after year, meaning certain aspects of them may come into the public domain in different years. So only the original 1929 versions of Popeye and Tintin are fair game, at least for now.

“Definitely the Popeye from 1929 and everything that he says, all of his characteristics, his personality, his sarcasm … that’s public domain,” she says. “The spinach, if you want to be on the safe side, you might want to wait.”

Films

A promotional card for Clara Bow's movie "The Wild Party."

The Wild Party, Clara Bow’s first talkie, was released in 1929, making it public domain in 2025.

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Similarly, the original Steamboat Willie version of Mickey Mouse arrived in the public domain with much fanfare in 2024. In 2025, a dozen more Mickey animations will follow suit — including The Karnival Kid, in which he speaks for the first time.

“His very first words are ‘Hot dogs! Hot dogs!’ — so I guess that’s kind of cute,” Jenkins says. “And then he didn’t wear the white gloves in 1928, but next year, in 2025, we get the version of Mickey Mouse with the signature white gloves in the public domain.”

Sound is a big theme across the films making their public domain debut next year, since 1929 marked the end of the silent film era and the dawn of the sound film age.

The list includes the first sound films from major directors like Alfred Hitchcock (Blackmail), John Ford (The Black Watch) and Cecil B. DeMille (Dynamite), as well as Clara Bow’s first talkie, The Wild Party, and The Broadway Melody, the first sound film to win an Academy Award for Best Picture.

Other notables include Walt Disney’s The Skeleton Dance (the first of the Silly Symphony shorts); King Vidor’s Hallelujah, the first major studio film with an all-Black cast; and Alan Crosland’s On With the Show, the first all-talking, all-color, feature-length film.

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Books

This combination of photos show authors Ernest Hemingway in 1950, left, William Faulkner in 1950, center, and John Steinbeck in 1962.

From left: Ernest Hemingway in 1950, William Faulkner in 1950, and John Steinbeck in 1962.

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Among the many literary works entering the public domain next year are two of the most acclaimed books about World War I: Ernest Hemingway’s A Farewell to Arms, and the first English translation of Erich Maria Remarque’s All Quiet on the Western Front — both authors served in the war themselves.

The list includes several detective mysteries: Red Harvest and The Maltese Falcon by Dashiell Hammett, Ellery Queen’s The Roman Hat Mystery, and Seven Dials Mystery by Agatha Christie.

There are also some literary debuts, including John Steinbeck’s first novel, Cup of Gold, and Richard Hughes’ first novel A High Wind in Jamaica.

Musical compositions

George Gershwin writes sheet music while sitting at a piano.

George Gershwin’s “An American in Paris” is among the musical compositions entering the public domain in 2025.

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The latest crop of compositions spans the era’s jazz standards, show tunes, pop music and more.

They include: Arthur Freed’s Singin’ in the Rain (which was featured in the film The Hollywood Revue of 1929, also entering public domain), George Gershwin’s An American in Paris, Maurice Ravel’s Bolero, Jack Yellen’s Happy Days Are Here Again (the campaign song for FDR’s 1932 presidential run), Cole Porter’s What Is This Thing Called Love? and Tiptoe Through the Tulips (the Joseph Burke version, not the 1968 Tiny Tim one).

“But if you felt like singing like Tiny Tim for some reason, and you could, you can record your own version of Tiptoe Through the Tulips next year because that song’s going to be public domain,” Jenkins says.

The Center for the Study of Public Domain specifies that musical compositions refer to “the music and lyrics that you might see on a piece of sheet music, not the recordings of those songs.” Those are covered by a separate copyright.

Sound recordings

Marian Anderson poses for a photo outside.

Marian Anderson became the first Black singer to perform at the Metropolitan Opera House in New York in 1955. One of her early recordings from 1924 will enter the public domain next year.

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Under the 2018 Music Modernization Act, sound recordings are protected by copyright for 100 years. It’s the particular recordings that eventually enter the public domain, not the song’s music or lyrics or later recordings from those artists.

These are some of the 1924 performances that will become available for legal reuse in January: Marian Anderson’s “Nobody Knows the Trouble I’ve Seen,” George Gershwin’s “Rhapsody in Blue,” Jelly Roll Morton’s “Shreveport Stomp,” “Deep Blue Sea Blues” by Clara Smith, and “Everybody Loves My Baby (But My Baby Don’t Love Nobody But Me)” recorded by Louis Armstrong and Clarence Williams’ Blue Five.

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Dozens feared dead as Azerbaijan Airlines plane crashes in Kazakhstan

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Dozens feared dead as Azerbaijan Airlines plane crashes in Kazakhstan

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An Azerbaijan Airlines plane carrying 62 passengers and five crew has crashed while making an emergency landing at a Kazakhstan airport, with 29 survivors, including two children, taken to hospital.

Videos on local media showed a large explosion after the aircraft crashed into an empty field. Images from the scene showed passengers climbing out of the tail of the fuselage aided by emergency workers.

Those aboard were from Azerbaijan, Russia, Kazakhstan and Kyrgyzstan, Russian state Ria news agency reported, citing Kazakhstan’s transport ministry.

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Local media outlets reported that nine of those taken to hospital were in serious condition and that search and rescue operations were under way.

The plane, an Embraer 190, was travelling to Grozny in the southern Russian republic of Chechnya from Azerbaijan’s capital Baku, but was diverted to Aktau after flying into heavy fog.

Early media reports suggested that the plane hit a flock of birds, which affected control of the aircraft.

“After a collision with birds, due to an emergency situation on board the aircraft, its commander decided to go to an alternate airfield and Aktau was chosen,” Ria reported, citing Russia’s aviation agency Rosaviatsia. Local media also shared unconfirmed reports of an explosion of an oxygen canister onboard, leading many passengers to lose consciousness.

Baku has sent an official delegation to Kazakhstan to investigate the incident, Azerbaijan’s APA news agency said. The country’s president, Ilham Aliyev, left an informal summit of the Commonwealth of Independent States in Russia to return to Baku. He expressed his condolences to the those affected by the crash.

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Kremlin spokesperson Dmitry Peskov said Russian President Vladimir Putin had also extended his condolences to Azerbaijan’s leader.

Chechnya’s leader Ramzan Kadyrov expressed his condolences to the relatives of the deceased on social media. “We pray to the Almighty for [the survivors’] recovery.”

Photos on social media showed relatives gathering in Grozny airport to wait for news of their loved ones.

One man at Grozny airport said he had just received a video in which he could see his nephew had survived the crash. “Of course I am very happy,” he told a Ria news reporter.

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NYC cab jumps curb, injures 7 on Christmas Day

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NYC cab jumps curb, injures 7 on Christmas Day

STORY: :: A New York taxi jumping the sidewalk

injures 7 people on Christmas Day

:: Police said the incident happened after

the cab driver suffered a medical episode

:: December 25, 2024

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:: New York

The incident took place in Midtown Manhattan near Macy’s flagship store in Herald Square near the corner of West 34th Street and Avenue of the Americas, or Sixth Avenue. The store, with its elaborately decorated display windows, is a magnet for tourists and native New Yorkers around the holidays.

In addition to the 58-year-old taxi driver, the injured included a 9-year-old boy, two women aged 49 and four other women aged 19, 37 and 41, police added.

One 49-year-old woman with a leg injury, the 9-year-old boy who suffered a cut and the 41-year-old woman who sustained an injury to her head were taken to hospital, police said.

The remaining three pedestrians declined medical attention, according to police, which added that all injuries were non-life-threatening.

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Media images of the cab showed a heavily damaged vehicle with broken parts and dents all over it.

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