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UK COVID genomics head says new variant likely to come to UK

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It is likely that the new coronavirus variant B.1.1.529, which is spreading in South Africa, will end up in Britain, the head of the COVID-19 Genomics UK Consortium said on Friday.

A ban on flights from southern Africa came into force in Britain on Friday, and numerous other countries also restricted travel from the region.

“(B.1.1.529 is) something that I would guess is likely to be transmitted into the UK at some point, but it buys that time,” COG-UK Chair Sharon Peacock told reporters.

“I think buying time is important and it’s worthwhile, because we can find out what we need to know about that particular variant.”

Speaking at a briefing with other experts, Peacock praised the quick work of South African scientists who shared what they knew about the variant after a surge in cases centred on Gauteng province.

That early warning could be crucial in preventing the variant taking over rapidly from the Delta variant as the world’s dominant one, even as South Africa bristles at the swift imposition of barriers to travel.

“This is a different circumstance than Delta, and there might be some hope for maybe some amount of containment,” said Jeffrey Barrett, Director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute.

“The difference really is that the surveillance was so good in South Africa and other nearby countries that they found this, understood that it was a problem, and told the world extremely fast.”

S-GENE CLUE

Peacock said it was important not to assume that the variant had arisen in South Africa just because it had been detected there.

“Variants will fly under the radar in countries where there’s no sequencing capability,” she said.

A distinctive trait known as an “S-gene target failure”, which distinguishes the new variant from Delta, means that PCR tests can give a clue to the presence of the new variant without full genomic sequencing.

However, Wendy Barclay, a virologist who leads the UK National Virology Consortium G2P-UK, cautioned that some other variants also had the trait.

Many parts of Europe have been struggling with high and rising COVID rates for weeks, but Barrett said these were unlikely to be driven by B.1.1.529, even in places with less sequencing.

“They are consistently finding a mix of Delta variant, basically,” he said.

(Reporting by Alistair Smout; Editing by Kevin Liffey)

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Omicron subvariant appears more contagious, but not more severe, Denmark says

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The BA.2 subvariant of the Omicron coronavirus variant, which is dominant in Denmark, appears more contagious than the more common BA.1 sub-lineage, Danish Health Minister Magnus Heunicke said on Wednesday in a national address.

“There is no evidence that the BA.2 variant causes more disease, but it must be more contagious,” Heunicke told a news conference.

The BA.1 lineage currently accounts for 98% of all cases globally but in Denmark has been pushed aside by BA.2, which became the dominant strain in the second week of January.

The UK Health Security Agency has designated BA.2 a variant under investigation, saying it could have a growth advantage.

Preliminary calculations suggest BA.2 could be 1.5 times more infectious than BA.1, Denmark’s top infectious disease authority, Statens Serum Institut (SSI), said in a note on Wednesday.

However, an initial analysis by the institute showed no difference in the risk of hospitalisation for BA.2 compared to BA.1.

“There is some indication that it is more contagious, especially for the unvaccinated, but that it can also infect people who have been vaccinated to a greater extent,” SSI’s technical director Tyra Grove Krause said at the briefing.

This could mean the peak of Denmark’s epidemic will extend a bit further into February than previously forecast, Krause said.

BA.2 cases have also been registered in Britain, Sweden and Norway, but to a much lesser extent than in Denmark.

Denmark on Wednesday announced plans to scrap the last of its COVID-19 restrictions by Feb 1, the latest country in Europe to do so despite record high daily infection numbers.

(Reporting by Nikolaj Skydsgaard and Stine Jacobsen;Editing by Alison Williams, Kirsten Donovan)

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Pfizer, Moderna shots safe during in vitro fertilization; healthy gut bacteria may help prevent long COVID

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The following is a summary of some recent studies on COVID-19. They include research that warrants further study to corroborate the findings and that has yet to be certified by peer review.

mRNA vaccines safe during in vitro fertilization

COVID-19 vaccines using mRNA technology do not affect fertility outcomes during in-vitro fertilization (IVF), researchers have found.

They compared rates of fertilization, pregnancy, and early miscarriage in IVF patients who had received two doses of the vaccines from Pfizer with BioNTech or ModernaO> with those in unvaccinated patients. The 222 vaccinated and 983 unvaccinated patients who underwent ovarian stimulation – medical treatment to stimulate development of eggs – had similar rates of eggs retrieved, fertilization, and embryos with normal numbers of chromosomes. The 214 vaccinated and 733 unvaccinated patients who underwent frozen-thawed embryo transfer – where their eggs were collected from the ovaries and fertilized by sperm in a laboratory, creating embryos that were frozen and later thawed and transferred to the womb – had similar rates of pregnancy and early pregnancy loss, according to a report published on Tuesday in Obstetrics & Gynecology.

“Our findings contribute to the growing body of evidence regarding the safety of COVID-19 vaccination in women who are trying to conceive,” the researchers concluded.

Healthy gut bacteria may protect during COVID

The bacteria living in your small intestine may contribute to the risk for long COVID after infection with SARS-CoV-2, new findings suggest.

Researchers analyzed the “gut microbiome” in 116 COVID-19 patients in Hong Kong in 2020, when regulations required that every infected person be hospitalized. More than 80% were mildly or moderately ill, but more than 75% had at least one persistent symptom. After six months, the most common symptoms were fatigue (reported by 31%), poor memory (28%), hair loss (22%), anxiety (21%) and sleep disturbances (21%), according to a report published on Tuesday in Gut. Analyses of stool samples obtained at hospital admission and over the succeeding months showed long COVID patients “had a less diverse and less abundant microbiome,” said Siew C. Ng of The Chinese University of Hong Kong. “Patients who didn’t develop long COVID had a gut microbiome similar to that of people without COVID-19.”

Lack of “friendly” immunity-boosting Bifidobacteria species was strongly associated with persistent respiratory symptoms, Ng noted. While the study cannot prove that healthy gut organisms prevent long COVID, the findings suggest “maintaining a healthy and balanced gut microbiota via diet, avoidance of antibiotics if possible, exercise and supplementing with depleted bacteria species including Bifidobacteria” might be helpful, she said.

New PCR test can identify variants

A new type of PCR test can quickly tell which variant of the coronavirus is causing infection, helping doctors choose the most effective antibody treatments, researchers said.

Most current PCR tests can check broadly for the presence of the virus but cannot identify specific variants. The new test uses special “probes” – fluorescently labeled molecules – called “sloppy molecular beacons” that glow in different colors when they attach themselves to DNA or RNA in the virus. When the sample from the patient is heated, the probes fall off their DNA or RNA targets and their color disappears. They fall off at different temperatures depending on the DNA or RNA sequence they were bound to. Because the variants each have some unique sequences, they can be identified based on the pattern of color changes at each temperature, explained Dr. David Alland of \?

.

“We have already performed a clinical study which showed that the assay was 100% sensitive and 100% specific for identifying variants of concern including Delta and Omicron,” Alland said. “We are asking the N.J. Dept of Health to clear our test” so that New Jersey labs can use it, he added. A typical hospital molecular laboratory would be able to perform it, his team reported on Friday on medRxiv ahead of peer review.

U.S. study finds slight myocarditis risk with mRNA vaccines

There is a small but increased risk for heart muscle inflammation, or myocarditis, following receipt of the mRNA COVID-19 vaccines from Pfizer/BioNTech and Moderna, researchers from the U.S. Centers for Disease Control and Prevention have found.

The 1,626 cases documented in the Vaccine Adverse Event Reporting System from December 2020 through August 2021 “exceeded the expected rates,” the researchers reported on Tuesday in JAMA. Overall, 73% of reported cases were in people under age 30, and 82% were males. The highest rates were found among adolescent and young adult males. For every million doses of Pfizer’s vaccine, there were roughly 71 cases of myocarditis in males ages 12 to 15 and 106 cases in males ages 16 or 17. In young men ages 18 to 24, the rate per million doses was roughly 52 with the Pfizer shots and 56 after Moderna shots. About 96% of patients with myocarditis were hospitalized. In 87%, symptoms were gone by the time they were discharged. Non-steroidal anti-inflammatory drugs were the most common treatment.

“This risk should be considered within the context of the significant benefits of COVID-19 vaccination in preventing COVID-19 infection and potential serious complications,” said a spokesperson for the authors, who noted that COVID-19 itself confers a 16-times higher risk for myocarditis. “The benefits of COVID-19 vaccination continue to outweigh any potential risks.”

Click for a Reuters graphic on vaccines in development.

 

(Reporting by Nancy Lapid; Editing by Bill Berkrot)

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A third of airline pilots still not flying as pandemic drags on -survey

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More than one-third of airline pilots are still not flying as the pandemic continues to take its toll on aviation globally, according to a new survey, though the situation has improved from a year earlier when the majority were grounded.

A poll of more than 1700 pilots by UK-based GOOSE Recruitment and industry publication FlightGlobal, released on Wednesday, found 62% globally were employed and currently flying, up from 43% a year earlier.

The proportion of unemployed pilots fell from 30% to 20%, while 6% were on furlough, compared with 17% previously as air traffic began to bounce back from 2020 lows.

But in the Asia-Pacific region, the worst-hit globally by a drop in international travel due to tough border restrictions, the proportion of those unemployed rose from 23% to 25%. The region also had the lowest number that were employed flying at 53%.

“We have … seen some expatriates return home from the region due to concerns over quarantine or being stuck for long periods away from friends and family,” the report on the survey said.

Hong Kong’s Cathay Pacific Airways, a large expatriate employer in Asia, has lost hundreds of pilots through the closure of its Cathay Dragon regional arm as well as almost all of its overseas bases during the pandemic.

Pilot attrition at Cathay has also been rising amid strict layover rules that leave crew members locked https://www.reuters.com/world/asia-pacific/locked-hotels-hong-kongs-covid-19-rules-take-mental-toll-cathay-pilots-2021-11-26 in hotels when they are not flying.

Of the pilots still flying globally, 61% told the survey they were concerned about their job security.

“It appears only Northern America is back to post-COVID passenger numbers,” said an unnamed captain flying in the Middle East and Africa. “The rest of the world, especially developing nations, are still struggling to get vaccines, and are still not travelling.”

 

(Reporting by Jamie Freed in Sydney; Editing by David Gregorio)

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