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Thanksgiving travel this year could strain people’s wallets — and patience


Thanksgiving travel is bouncing back this year — and so are expectations for holiday travel chaos on the roads, rails and in the air.

With rising Covid-19 vaccination rates and the reopening of U.S. borders to vaccinated foreign travelers, the travel industry is bracing for the upcoming holiday rush.

In its holiday travel forecast, AAA said this week it expects more than 53.4 million people to travel between the period Nov. 24 to Nov. 28, up 13 percent from 2020 levels. 

The Transportation Security Administration said it is already screening between 1.9 and 2.2 million people daily, and a looming Nov. 22 deadline for the agency’s workers to be vaccinated has sparked concern about a possible worker shortage and longer security lines during the holiday. A spokeswoman for the TSA told NBC News that it is focused on getting employees vaccinated by the deadline.

Spiking gas prices aren’t deterring travelers this year, either. Around 48 million people will take to the roads this Thanksgiving holiday, according to AAA. At around $3.40, the average price at the pump this week is the highest since 2014, said Patrick De Haan, head of petroleum analysis at GasBuddy.

Car rental prices also remain high, after a shortage of crucial semiconductor chips led to a dramatic slowdown in the production of new vehicles during the pandemic, exacerbated by rental companies culling their fleets last year during the pandemic’s travel lull. Daily car rental prices currently average around $84, according to a spokeswoman from travel site Hopper.

This means that travelers should adjust how they make bookings for the holiday season, said Michael Taylor, travel practice lead at JD Power. While travelers typically book a hotel room before looking for a rental car and flight, they should reverse that order, he said, especially in popular holiday destinations like Orlando and Las Vegas where rental cars are costlier and in higher demand.

“This is going to be an expensive holiday for some folks,” Taylor said.

Camille Jones, a clinical social worker in Birmingham, Alabama, plans to fly to Orlando with her husband and two-month-old baby to spend the holidays with her in-laws. While the family considered driving to Orlando, renting a car would have cost them about $590. The two roundtrip plane tickets they ended up purchasing totaled $530.

To further cut costs, the family bought tickets to fly to Orlando from Atlanta rather than Birmingham, saving them around $240. Jones said the two-hour drive to Atlanta is worth it, especially since they frequently visit family there. She and her husband plan to arrive at the airport two hours before their flight, especially since they have a baby in tow.

“We’ve never traveled with a baby, so I know we’re going to slow it down a bit,” Jones said.

Travelers should consider purchasing travel insurance or using travel credit cards with built-in insurance, said Sara Rathner, travel and credit card expert at Nerdwallet. She added that travelers should also look into cashing in airline or hotel credits from canceled 2020 travel. 

Last month, Southwest Airlines canceled more than 2,000 flights, costing the company $75 million and impacting tens of thousands of passengers. The company has since announced it has trimmed its flight schedule to better reflect staffing levels. More recently, American Airlines canceled more than 2,000 flights over Halloween weekend, citing staff shortages and inclement weather. 

Dennis Tajer, a spokesman for the Allied Pilots Association, the union representing American Airlines pilots, said the airline’s record of slow recovery after flight changes could pose problems during the upcoming holiday rush, especially if there is bad weather. Further complicating the problem, holiday travel occurs toward the end of the month, when pilots and flight attendants are close to maxing out their contract hours.

David Seymour, American’s chief operating officer, said in a note to staff on Nov. 5 that 1,800 flight attendants returned to operations this month and the airline plans to add 800 more in December. Seymour also said employees will receive holiday pay on peak travel days in November and December, and he expects 4,000 new staff members to join this quarter.

Weary travelers should be prepared for shuttered stores and restaurants at the airport, Taylor said. Labor shortages and inflation continue to plague the hospitality industry, meaning any stores and kiosks that are open will have higher prices, fewer options and longer lines.

Delaware North Travel, a New York-based hospitality company that operates food and retail concessions at airports, closed down some of its locations during the pandemic and cut back on hours due to labor shortages. The hospitality company’s operating hours are based on the number of passengers boarding each day and when certain gates are used, which means customers sometimes face longer lines. 

To combat inflationary pressures, Delaware North Travel increased prices on some of its menu items and re-engineered some items, said Bob Wilson, Delaware North Travel’s president. For example, a meal with eight chicken wings now features boneless wings, and some fresh food options were turned into grab-and-gos. Some portion sizes have been reduced.

Despite the anticipated hurdles, many travelers are planning a packed schedule.

Sarah Goldstrom, who works in the film industry, plans to fly on Thanksgiving Day from Philadelphia to Greenville, South Carolina, with a layover in Atlanta to spend the evening with family. After filling up on turkey, she plans on flying to New York to attend a Harry Styles concert before returning home to Atlanta. 

“Thanksgiving’s kind of chaotic anyways,” she said.



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Pilot shortage puts strain on travel


MADISONVILLE, Ky. (WFIE) – Pilot shortages have been affecting airlines across the country.

Madisonville Community College’s Aviation Program Director Todd Smith spoke with 14 News and explained that the industry often fluctuates, which causes shortages.

“As newer models of airplanes fly farther, the world opens up,” he said. “It creates that natural shortage.”

He said it’s always a struggle to fill open positions because it requires anywhere from six to ten years to become a pilot for a major airline, and that can be a deterrent for many would-be aviators.

With a shortage already growing in 2019, Smith said the COVID-19 pandemic made circumstances worse.

“Airlines did a lot of downsizing through numerous different methods – a lot of furloughing and early retirements,” he said.

This created a large deficit, and it has started to affect passengers.

“It creates an instant like what we saw with Southwest Airlines a few weeks ago where thousands – I know hundreds, maybe even thousands of flights had to be canceled,” he said.

Still, Smith said the industry has ways of recovering.

Typically, he said they will partner with universities and flight schools to make learning more accessible and to create straighter paths to employment.

He said it’s just a matter of time before the situation improves.

Copyright 2021 WFIE. All rights reserved.



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Traveling health-care workers deal with strain of pandemic


They’ve spent the pandemic on the road treating COVID-19 patients across the country. They are tired, burned out and begging people to get their shots.

COLORADO, USA — For 18 months, Grover Street has been traveling the country treating COVID-19 patients.

“I’m in Oceanside, New York, right now,” he said.

Street, a nurse, works for Colorado-based Fastaff Travel Nursing. He has worked throughout the pandemic, treating the sickest patients. When he’s not traveling, he calls Colorado home.

When vaccines opened to the general population, he and other health-care workers expected the burden to ease.

“When I first got here [in New York] … I think what I was hearing was 70% of people here on the island have been vaccinated,” he said. “I was like, this will be a cool assignment. Two weeks after that, it exploded. We’ve got COVID patients throughout the hospital right now.”

Most of those patients are unvaccinated, Street said. They are trending younger and younger than the patients he saw last year.

“The sad truth of the matter is, with these unvaccinated patients, they’re younger,” he said. “I’ve had 25-30 somethings, 40-year-olds. … And they’re like, really sick with the delta strain.”

Street said he asks his unvaccinated patients to make him a promise.

“I ask them, ‘If you get out of this alive, will you take the vaccine?’ ”

He said most are quick to say yes, scared by how close they came to serious illness or death.

Hospitals everywhere are facing staffing shortages. Like so many other health-care workers, Street said he feels the burnout.

RELATED: UCHealth nurse describes life inside the COVID unit

“The level of stress with the patients … the hostility, the aggression of patients, families … health-care workers, people arguing all the time …” He listed off the frustrations. “People who don’t see what’s going on, if they really knew what’s going on, they would get vaccinated. They would get vaccinated.”

Dr. Comilla Sasson, an ER physician based in Colorado, has taken several traveling assignments across the country as well.

“I knew I could be at home, working my shifts at home, but I knew there was a calling. Right?” she said. “I wanted to go out and help people because I knew these places were struggling and needed docs who knew what they were doing.”

But each trip is a sacrifice – away from her day job, her family – including two little kids, and a risk she takes for her own health. She said she’s feeling the burnout, too.

“I’ve been told I’m not a real doctor,” she said. “I’ve had somebody tell me COVID’s not real, even though I showed him the COVID test that was positive for that patient. Hostile, aggressive. It’s been tough.”

RELATED: “Everybody is running on empty” Inside Intensive Care Units, battling yet another wave of the virus

“It doesn’t end,” she said. “It’s not like my days are over when I finish my ER shift. I go home, and now it’s figuring out if my kids are safe in school. Trying to figure out whether or not we should do sports this year. It feels like it’s never-ending, especially as a doctor and a mom. It’s hard. It’s been a really hard year.”

But the requests for help keep coming. Just this week, Sasson said recruiters asked her multiple times whether she could travel to Texas or Mississippi for another assignment. She’s starting to reconsider.

“It’s hard, right? A lot of these states, Texas is the one I’m thinking about more than most, it’s a place where I know the governor [is] trying to ban masks. He’s actively trying to ban vaccinations that are mandatory,” she said.

“And part of me says – gosh, it’s hard to say I’m going to leave my family, I’m going to put myself in literally the most infectious pandemic that we’ve ever had in our lifetime, and I’m going to leave my family for 12 weeks. Oh, but you know, there are [COVID precautions] that could be done right now that could save all of this heartache.”

This time, Sasson said she passed on the travel assignment and continues to treat patients closer to home.

The decision to say “no” wasn’t easy.

“That part of me that wants to say ‘yes,’ I’m going to help anybody that needs it,” she said. “And I’ve done that for the last year. But there’s also that part of me that’s like – gosh, there’s a lot of stuff that can be done without [thousands of] new health-care workers that are literally going to leave their communities to come to a different community to help out when there is simple public health things that can be done.”

Like Street, she said she works every day to try to persuade her patients to get vaccinated. If someone comes into her hospital with COVID, vaccinated or not, she’ll treat them.

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Detroit Tigers place Eric Haase (abdominal strain) on 10-day IL


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Detroit Tigers manager AJ Hinch didn’t have much of a choice.

He evaluated his roster ahead of a three-game series with the Toronto Blue Jays from Friday through Sunday at the Rogers Centre in Canada. Of course, he realized Grayson Greiner was the only healthy catcher.

“That position is not one that we can tip-toe around,” Hinch said Thursday. “That position is not for a 75-80% availability.”

Slugging catcher Eric Haase, scratched earlier this week with low back tightness, wasn’t sure if he would recover in time to play in Toronto. To fill the void, the Tigers traded with the Colorado Rockies to acquire 34-year-old catcher Dustin Garneau. Needing all their bench spots for the road trip, the Tigers placed Haase on the 10-day injured list Thursday — retroactive to Monday — with a right abdominal strain. He can be reinstated as early as Aug. 26.

“We have capable guys and can get (Haase) right over the next seven or eight days,” Hinch said. “Going into a series in Toronto, we want to have a full team. It was uncertain whether or not he was going to be able to play in the next couple of days. That’s just getting too long to wait. It’s kind of in his back and abdomen.”

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If Haase were a position player, he might not need the injured list.

But the catcher position complicates the situation.

“We could have waited, but we chose not to given the fact that we have three bench players,” Hinch said. “With Greiner and Garneau, we can be fully stocked.”

Haase, 28, is hitting .238 with 19 home runs, 49 RBIs, 18 walks and 87 strikeouts over 70 games. He should generate some consideration for American League Rookie of the Year, but he is behind the frontrunners at this point in the season.

“He did some early work last weekend and came up a little sore,” Hinch said. “He was prepping to play the outfield against (Cleveland) and tweaked his back. Nothing more than it’s August. These guys are beat up a little bit. Kind of a freak occurrence that created some soreness.”

The Tigers have Haase’s schedule mapped out, beginning with catching a bullpen Thursday at Comerica Park. Over the weekend, he will travel to Triple-A Toledo to take batting practice. By Tuesday or Wednesday, Hinch wants Haase to start a rehab assignment with the Mud Hens.

“And then all systems go,” Hinch said.

Back to the big leagues

As Haase went to the injured list, outfielder Daz Cameron came back from his injury. He landed on the injured list July 7 with a right toe sprain, sustained by accidentally kicking the outfield wall during warmups in Texas. The injury is expected to linger until he rests in the offseason.

The 24-year-old rookie has been asked to play through the pain, something Hinch said most of his players — especially everyday players Jonathan Schoop, Jeimer Candelario and Robbie Grossman — are already doing.

“It becomes more difficult for him to move around a little bit,” Hinch said. “You may see him hit the bag and have a little bit of a limp. … There’s going to be some days he’s sore, and there’s going to be some days he looks like he’s moving around great.”

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Cameron is hitting .207 with three home runs, nine RBIs, five walks and 19 strikeouts over 18 games for the Tigers in 2021. He also played 17 games in 2020, posting a .193 batting average, two walks and 19 strikeouts.

The organization needs a closer look to prepare for the future. Cameron has played 23 games in Toledo this season, delivering a .309 batting average, two home runs, 14 RBIs, seven walks and 19 strikeouts. He started in center field for Thursday’s series finale with the Los Angeles Angels.

“We want to get him some more playing time,” Hinch said. “He can really spark us. He’s been swinging the bat pretty well down in Triple-A, and this opened up for him.

“Once we know there may be a tick of limitation here or there, or a tick of soreness here or there, we’re going to have to deal with that until the end of the season. It became apparent to us we needed to find a path for him back to the big leagues.”

What about Willi Castro?

Although Cameron has returned, the Tigers still plan to use second baseman Willi Castro in the outfield. They seem to view his defensive versatility as a long-term project, rather than a short-term fix to the numerous outfielder injuries.

Castro has played 71 games at second base, 18 at shortstop, five at designated hitter and four in left field.

“He’s going to play outfield in Toronto,” Hinch said. “We’ll continue to mix and match him. He’ll play a little more second base than certainly the last five or six days when he’s been in the outfield, but we’re going to continue this versatility for Willi.”

MORE ABOUT WILLI: Why Willi Castro learning the outfield is important for Tigers

Rogers to 60-day IL ‘procedural’

Catcher Jake Rogers has been sidelined since July 19 with right arm soreness. When the Tigers acquired Garneau from the Rockies, they shifted Rogers to the 60-day injured list to make room for their newest catcher on the 40-man roster.

Rogers is now eligible to return from the injured list Sept. 17, aligning with his recovery process.

“Jake is slowly but steadily getting better,” Hinch said. “His throwing and hitting programs are about to start, and that’s going to take a good three weeks to get him into a game. That’s going to lead into early September, which gives us the last couple of weeks in September to possibly activate him. A lot has to happen between now and then, but the timelines were starting to collide with his availability versus the 60-day, so it was more procedural.”

Other notes 

• For the Toronto series, the Tigers will carry four players on the traveling taxi squad: catcher Juan Centeno, right-hander Will Vest, righty Alex Lange and outfielder Jacob Robson.

“We’re going to take a pretty extensive list because of the COVID issues in Canada and getting in and out of the country,” Hinch said. “We’ve all tested, and we’ve all tested negative. We can leave today after the game.”

• Outfielder Derek Hill (left ribcage contusion) is also traveling to Toronto. He is expected to be activated from the injured list Saturday.

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• Outfielder Akil Baddoo (concussion) will stay in Triple-A Toledo to continue his rehab assignment, rather than traveling to Toronto. Baddoo needs to get comfortable with his swing again, and because the Tigers face three left-handed pitchers, there isn’t a rush to activate him before playing the Blue Jays. He should rejoin the team Tuesday in St. Louis for a two-game series with the Cardinals.

• Left-hander Matthew Boyd (left arm discomfort) made his second rehab start for Toledo on Wednesday. He fired three scoreless innings, allowing just two hits. He struck out four and didn’t concede a walk, throwing 29 of 43 pitches for strikes.

“Great day for him,” Hinch said. “He said he felt a little more in rhythm and his stuff was good. I got everything I wanted, including a nice report this morning that he feels really good. He’ll pitch again Tuesday in Toledo and extend out even further. Once we get him to four (innings) and 60 (pitches), he becomes a little bit more of a factor here. All encouraging steps along the way, given his stuff has ticked up, his mechanics are in-sync and he’s making pitches.”

Evan Petzold is a sports reporter at the Detroit Free Press. Contact him at epetzold@freepress.com or follow him on Twitter @EvanPetzold. Read more on the Detroit Tigers and sign up for our Tigers newsletter





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The travel-related origin and spread of SARS-CoV-2 B.1.620 strain


The last few months have seen the emergence of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), even as other variants fade away. Some of these variants have biological or epidemiological characteristics of particular interest since they may promote the virus’s rapid spread or cause more severe illness.

A new preprint research paper posted to the medRxiv* server describes a new variant B.1.620, which appeared in Lithuania, and is now prevalent in several countries in Europe, as well as in central Africa.

Earlier, three viral lineages have been classified as variants of concern (VOCs), namely the UK variant (B.1.1.7), the South African (B.1.351), and the Brazil (P.1) variant. A VOC has higher transmissibility or virulence, which potentially evades immune neutralization.

Background of B.1.620 emergence

The B.1.177 lineage spread widely in Spain first, before its transmission to the rest of Europe. Such phenomena are driven by restrictions on human movements, lack of monitoring of the outbreak, and time. In Europe, genomic sequencing projects have picked up the rapid rise to dominance of the UK strain, displacing other widely circulating strains.

In Uganda, too, the lineage called A.23.1 rose to prominence against a setting of low genomic sequencing. Such viral lineages are often observed first, not in their country of origin but as a single case or as a chain of transmission, beginning with a traveler from the host country, in another country that does sequencing on a greater scale.

As more countries launch their own SARS-CoV-2 sequencing programs, introduced strains are easier to detect since they tend to be atypical of a host country’s endemic SARS-CoV-2 diversity, particularly so when introduced lineages have accumulated genetic diversity not observed previously, a phenomenon characterized by long branches in phylogenetic trees.

For instance, lineage B.1.380 was prevalent in Rwanda and Uganda for a time but was then found to give way suddenly to A.23.1. The latter was first sequenced in Uganda, which had started sequencing by then. This program then detected the first occurrences of B.1.1.7 and B.1.351.

Maximum likelihood tree of lineage B.1.620 in Europe. Relationships between B.1.620 genomes, coloured by country of origin (same as Figure 1) with a thicker coloured outline indicating country of origin for travel cases. At least seven genomes shown (samples collected in Belgium, Switzerland, France, and Equatorial Guinea) are from individuals who returned from Cameroon, one is from a traveler returning from Mali and one Lithuanian case returned from France. Genomes from CAR and Czechia (returning traveler from Mali) are descended from the original B.1.620 genotype, while the genome from Equatorial Guinea is already closely related to genomes found in UK and happens to be a travel case from Cameroon. Each genome is connected to available geographic location in Europe with smallest circles indicating municipality-level precision, intermediate size corresponding to county level information (centered on county capital) and largest circle sizes indicating country level information (centered on country capital).

Maximum likelihood tree of lineage B.1.620 in Europe. Relationships between B.1.620 genomes, colored by country of origin (same as Figure 1) with a thicker colored outline indicating the country of origin for travel cases. At least seven genomes shown (samples collected in Belgium, Switzerland, France, and Equatorial Guinea) are from individuals who returned from Cameroon, one is from a traveler returning from Mali and one Lithuanian case returned from France. Genomes from CAR and Czechia (returning traveler from Mali) are descended from the original B.1.620 genotype, while the genome from Equatorial Guinea is already closely related to genomes found in the UK and happens to be a travel case from Cameroon. Each genome is connected to the available geographic location in Europe with the smallest circles indicating municipality-level precision, intermediate size corresponding to county-level information (centered on county capital) and largest circle sizes indicating country level information (centered on country capital).

B.1.620 lineage in Europe

B.1.620 genomes have been found not only in Lithuania but in other places in Europe, though they do not appear to have been triggered by the same introduction event. In both Germany and France, new clades are being observed which have nearly identical genomes.

France showed a cluster of asymptomatic B.1.620 infections as part of a single chain of transmission, with another four cases outside this area. The index case is yet to be identified, but this shows community spread rather than importation.

Again, Spain and Belgium have shown the presence of B.1.620 genomes on routine surveillance sequencing.

In Lithuania, the E484K mutation in B.1.620 has been observed only in B.1.1.7 other than 13 cases of infection with B.1.351 and one with the B.1.1.318 lineage. None of these latter lineages were present in Utena county.

Many cases in Europe have had a history of travel from Cameroon, and sequencing in central African countries, namely, Central African Republic, Equatorial Guinea and the Democratic Republic of the Congo, has repeatedly thrown up B.1.620 genomes.

Study aims

In the current study, the researchers characterized the mutations of this genome. Many have already been observed in one or other of the VOCs, but not together. They also concluded that the lineage probably cropped up first in Cameroon and is likely to reach a high prevalence in Central Africa.

Lineage B.1.620 has multiple mutations

Many Cameroon genomes uploaded to the GISAID (Global Initiative for Sharing All Influenza Data) database show surprising diversity. A few share mutations with B.1.620, with the earliest to appear being, possibly, synonymous mutations at 15324 and the spike mutation T1027I. These are also present in B.1.619.

The spike E484K mutation is also found in a closely related lineage from Cameroon. All these samples were collected in January and February 2021.

The B.1.620 lineage has 23 mutations and deletions compared to the reference strain. It carries a large number of unique mutations and deletions, which are dissimilar to the closest related strain in Lithuania. Though these mutations are shared by several VOCs, this lineage does not appear to have arisen by the recombination of such strains.

The D614G mutation is now present in most circulating strains, including this one. This promotes viral infectivity, perhaps by enhancing the ‘up’ conformation of the spike receptor-binding domain (RBD).

Immune evasion by B.1.620

The B.1.620 lineage also has several mutations in the N-terminal domain (NTD) of the spike protein, among which some remain of unknown impact. Of the rest, all partially resist neutralization by convalescent serum and NTD-targeting monoclonal antibodies. This may point to the origin of these mutations as immune-evading viral adaptations.

The S477N and E484K mutations in the RBD are found in other VOCs, but the B.1.620 does not carry either the N501Y or K417 mutations. Both the former mutations facilitate broad evasion of antibody-mediated neutralization. They also promote high-affinity binding of the RBD to its receptor, the angiotensin-converting enzyme 2 (ACE2).

Both are on the same peripheral loop at the binding interface of these two proteins, and their presence in combination improves the energetic profile favorably relative to the reference genome.

High frequency of B.1.620 likely in Central Africa

When local sequencing programs are not robust, sequencing of infected travelers is the second surveillance option to pick up and monitor different lineages. In the current study, the researchers point out that seven B.1.620 genomes were from Cameroon-returned travelers, while six were from locally collected samples in the Central African Republic (CAR), near its Cameroon border. Thus, this lineage appears to be prevalent in this geographic region.

Adequate sequencing is being carried out in several countries neighboring Cameroon, namely, South Africa and Angola to the south, Kenya to the east, Togo, and Nigeria to the northwest. The lineage, therefore, appears to have originated within the area of central Africa bounded by the borders of these countries.

Travel histories from European cases indicate separate introductions, from Cameroon, and from Mali. In one case, at least, community spread appears to have been established, with the index patient developing the infection in Belgium well beyond the incubation period of the virus and long after his return from Cameroon. Another case had no history of travel at all.

The phylogeny of B.1.620

Phylogenetic study in Africa shows that the variant probably arose in Cameroon, and then spread to both the Central African Republic and Equatorial Guinea. It then spread to various countries in Europe through multiple introductions. It appears to have entered the USA and England, while it entered Lithuania at least twice.

Many travelers have departed from Cameroon for other African countries, indicating this lineage is likely to be widespread in Africa by now. Even with the low levels of sequencing in Equatorial Guinea and DRC, its detection supports this assumption.

What are the implications?

The discovery of a novel lineage bearing many mutations of concern and with indications that they are introduced from locations where sequencing is not routine, is concerning, and such occurrences may become an alarming norm. The emergence of B.1.1.7 was unprecedented and has had a devastating impact on the state of the pandemic, so it is concerning that similar information gaps in global genomic surveillance still persist to this day.”

Poor genomic surveillance programs are available in much of the world, while vaccines continue to be largely the preserve of developed countries. However, this disparity will plague the world for decades as the virus continues to breed new variants and creep back into previously vaccinated countries.

Control measures against the new lineages coming up are bound to be knee-jerk responses, falling short of preventing the evolution of such variants. The long phylogenetic trail of B.1.620 itself hints at gradual evolution over time, and perhaps even over vast distances, or due to selection pressures during the course of chronic infection in immunosuppressed people.

The order of mutations leading up to this lineage is also impossible to recover, making it difficult to tell if any mutations here directly promoted the occurrence of other mutations by increasing viral fitness. This is a crucial shortcoming since this lineage has multiple concerning mutations.

Our work highlights that global inequalities, as far as infectious disease monitoring is concerned, have tangible impacts around the world and that until the SARS-CoV-2 pandemic is brought to heel everywhere, nowhere is safe for long. Additionally, we highlight the importance of collecting and sharing associated metadata with genome sequences, in particular regarding individual travel histories, as well as collection dates and locations, all of which are important to perform detailed phylogenetic and phylogeographic analysis.”

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.



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Mass Covid testing blitz in three London areas amid fears new South African strain cases are tip of iceberg


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ass testing in three London areas began today as a leading scientist warned that cases of a new mutant Covid-19 strain could be “the tip of the iceberg”.

Although the blitz was sparked by only 11 isolated cases in the communities, Professor Andrew Hayward, a member of the Government’s Sage advisory group, said there were likely to be many times more.

“We can multiply that number by quite a high level,” he told Sky News. “So we would expect that we are seeing, if you like, the tip of the iceberg of community transmission.”  

“Do you really need to go for that shopping or have you got enough in?” she asked. “Could you work from home? Could you have that extra conversation with your employer?”

Mobile testing units have been deployed in public spaces, while door-knockers were set to give out home testing kits. Carol Hall, 50, was one of the first to get a test for the South African variant at a centre near her home in West Ealing when it opened at 9am.

Mrs Hall regularly travels into central London for her job as a researcher and scheduler at BBC Parliament. She noticed online that the Sainsbury’s where she shops weekly is on the border of the W13 and W7 postcodes being tested. Mrs Hall said: “If anywhere, that’s where I may have come into contact with the variant.  

“I didn’t get the test because I was frightened. It was the right thing to do as I travel into central London. I don’t know how worried we should be about this South African variant or even if it’s any worse than regular coronavirus.”  

Mrs Hall said the test “was quite easy”. Staff showed her how insert a swab into her throat and nose. She was then given a card with a barcode to register the test online so as to avoid queues of people filling in forms at the centre.

The “surge testing” aims to obtain swabs of 80,000 people in eight postcodes — Hanwell, in Ealing; Tottenham, in Haringey; Mitcham, in Merton; Woking, Surrey; Broxbourne, Hertfordshire; Maidstone, Kent; Walsall in the West Midlands; and Southport, Merseyside.  

The massive effort was mobilised by Public Health England after 11 cases of the variant were identified among victims who have no links to people who have gone abroad.  

The discovery rang alarm bells, suggesting that the mutation has jumped from being found only in travellers and their contacts to spreading below the radar in communities. A total of 105 cases of the new strain have appeared in the UK, most with clear links to travel. Professor Hayward,  of University College London, said the new variant was identified through genetic sequencing, and about five to 10 per cent of all cases are sequenced.

“You can immediately tell from that that we have a big underestimate of the number of cases within this country,” he said. Professor Sir Mark Walport, a Sage member and former chief scientific adviser, said it was unlikely that mass testing would root out every case of the new mutation. “Sadly it’s very unlikely they will be picked up because there are so many cases and Public Health England can’t sequence all of them.”

He said the “inevitability” of new variants springing up made it essential to drive numbers down now by obeying lockdown.  There was evidence that the Covid-19 vaccines worked “slightly less well” against the South African variant, and he believed the Brazil mutation might be even more of a danger.

Dr Mike Tildesley, a member of the Sage subgroup Scientific Pandemic Influenza Group on Modelling, told Talk Radio: “This is the natural life course of viruses, they do mutate.” He added: “It’s certainly not the zombie apocalypse, not something we should be massively panicky about, just that we should be aware about as things move forward to try to make sure that we keep these new variants under control if they are more transmissible.”

Profeessor Robin Shattock, who is leading Covid-19 vaccine research at Imperial College London, said scientists are working on vaccines which could counter new variants like the one that had emerged in South Africa.  

“At the moment, there is some evidence that some of the vaccines are slightly less effective against the new variant but that does not mean that they are not effective.”

He revealed that work is already under way on an improved version of the vaccine to tackle the mutation.  

Asked if Imperial College have one already, he told Today: “We have one already and we are starting to look at the immune response to that to see whether it makes it more effective against for example the South African strain but also to see whether it can modulate the immune response in somebody who has already had a vaccine to make it more effective as a booster to target these variants as they arrive.”



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Biden to bring back travel bans to stop new strain


Anti-lockdown protests turn violent in the Netherlands, 240 arrested

Clashes broke out in several Dutch cities over the introduction of new nationwide lockdown measures on Sunday, resulting in over 240 arrests, according to police and local media.

Police used water cannon, dogs and mounted officers to disperse a protest in central Amsterdam on Sunday afternoon, according to eye-witnesses. Nearly 200 people, some of them throwing stones and fireworks, were detained in the city.

A car on fire in front of the train station in Eindhoven Sunday, after a rally by several hundreds of people against a Covid-19 lockdown.ROB ENGELAAR / AFP – Getty Images

One of the demonstrations took place in Amsterdam’s Museum Square, which violated a ban on public gatherings. The violent protests were prompted by tougher social distancing measures, announced by the government. The new national measures include a nightly curfew for the first time since World War Two. 

Dutch military police said in a tweet that they were deployed to at least two additional cities in the south to support local law enforcement and contain the violence.

Israel bans international flights amid fears of new variants

Israel is set to stop all international travel from Monday evening as it seeks to prevent the spread of new coronavirus variants.

The flight ban will come into effect from midnight tonight and last until the end of the month, according to a statement released by Israeli Prime Minister Benjamin Netanyahu’s office.

“Other than rare exceptions, we are closing the sky hermetically to prevent the entry of the virus variants and also to ensure that we progress quickly with our vaccination campaign,” Netanyahu said in public remarks at the start of a cabinet meeting.

Exceptions for outgoing departures include emergency medical evacuations and attending a funeral overseas of a close relative.

The country’s borders have already largely been closed to foreigners during the pandemic, with only Israeli passport holders allowed entry.

 

Mexican President López Obrador tests positive for Covid-19

MEXICO CITY — Mexican President Andrés Manuel López Obrador said Sunday that he had tested positive for Covid-19. His symptoms were light and he was receiving medical treatment, he said.

“As always, I am optimistic,” said López Obrador, 67, who has resisted wearing a mask.

Mexico is in the grip of a second wave of the pandemic, and it has the fourth-highest death toll worldwide. The Health Ministry on Sunday reported 10,872 new confirmed coronavirus cases and 530 deaths, bringing its totals to 1,763,219 infections and 149,614 deaths.

Read the full article here.





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Chicago Travel Order, When Regions Can Lift Tier 3, New Strain Warning – NBC Chicago


Chicago’s top health official is set to deliver an update on the city’s travel order Tuesday as well as the latest data on coronavirus across the city.

Illinois’ top doctor said Monday that the new, more contagious strain of COVID-19 first identified in the United Kingdom is likely already present in the state and could become dominant in just months.

Meanwhile, Illinois Gov. J.B. Pritzker also announced Monday that regions that meet specific criteria can roll back from Tier 3 coronavirus restrictions beginning Friday.

Here are the latest updates on the coronavirus pandemic across the state of Illinois today, Jan. 12:

Chicago Officials to Update Travel Order, Detail Latest Data

Chicago’s top health official is set to deliver an update Tuesday on the city’s emergency travel order requiring a negative test or quarantine upon arrival in the city.

Chicago Department of Public Health Commissioner Dr. Allison Arwady is scheduled to deliver the update during a news conference at 1 p.m. from City Hall. The news conference can be watched live in the video player above.

The update will include the latest info on the travel order, as well as new data on the coronavirus pandemic across Chicago, and the latest details on vaccine distribution, officials say.

‘It Will be the Dominant Strain:’ Illinois’ Top Doctor Warns of New UK COVID-19 Strain

While the new, more contagious strain of COVID-19 that was first identified in the United Kingdom hasn’t been officially reported in Illinois, the state’s top doctor said Monday the strain is likely already present and could become dominant in just months.

At a news conference alongside Illinois Gov. J.B. Pritzker, Dr. Ngozi Ezike, the director of the state’s Department of Public Health, warned of more infectious spread as early as March, which is when she said the majority of COVID-19 cases could be from the new variant.

The British variant was first detected in September, World Health Organization officials previously announced. Since then, cases have skyrocketed across the U.K., resulting in Prime Minister Boris Johnson’s decision to impose a national lockdown.

Unlike when the virus first surfaced in the U.K., Ezike said, Illinois officials are aware the new strain “is brewing.”

“Therefore we have the opportunity to use that information and make better choices around the mitigation…around avoiding gatherings so that we can get as many people vaccinated…before this variant inevitably takes over,” she warned.

Ezike emphasized that the strain hasn’t been identified, because it’s probably circulating at such low numbers. In Indiana, health officials there confirmed the existence of the strain Monday.

Pritzker to Announce This Week When Illinois Will Move to Phase 1B for Vaccinations

Illinois Gov. J.B. Pritzker is expected to announce this week when Illinois will enter Phase 1B of its coronavirus vaccine rollout, though some areas may already be allowed to do so.

“I expect to make a formal announcement later this week on when Illinois
will move into Phase 1B on a statewide basis,” Pritzker said during his coronavirus update Monday. “Of course, anyone in Phase 1A who has chosen not to get vaccinated yet will always be able to opt in during any subsequent round – this is about leaving no vaccine sitting on the shelves as we move forward.”

So far, 587,900 total doses of the Pfizer and Moderna vaccines have been delivered to Illinois, 478,175 doses have been sent to public and private healthcare providers outside of Chicago and 109,725 doses have gone to providers in Chicago.

Illinois as a whole has administered approximately 334,939 vaccine doses as of Sunday night.

“We are making important progress in Phase 1A and I appreciate the hard work of healthcare providers across the state to move as quickly through this phase as possible,” Pritzker said. “In some communities, they’ve even been able to substantially complete Phase 1A. IDPH is allowing any local health department in that position to move into the early stages of Phase 1B because we want to make sure any available vaccine is administered quickly to the priority groups we’ve laid out.”

Read more here.

Pritzker Lays Out Criteria for Regions to Lift Tier 3 COVID-19 Mitigations

Illinois Gov. J.B. Pritzker announced Monday that healthcare regions that meet specific criteria can roll back from Tier 3 coronavirus restrictions beginning Friday, Jan. 15.

All 11 healthcare regions in the state have been under Tier 3 mitigation rules since late November, which include reductions in capacity at businesses and a variety of other restrictions.

Beginning Friday, the governor says that regions can begin to move forward to Tier 2 mitigations if they adhere to three different statistical criteria beginning later this week.

Pritzker says that three key metrics must be met in order for a region to move forward from Tier 3 mitigations:

-A seven-day positivity rate of 12% or lower for three consecutive days.

-An availability of 20% or greater of staffed ICU and general hospital beds for three consecutive days.

-A decline in the number of COVID-19 hospitalizations on seven days in a 10-day span.

Illinois Officials Report 4,776 New Coronavirus Cases, 53 Additional Deaths Monday

Illinois health officials have reported 4,776 new confirmed and probable COVID-19 cases in the state over the last 24 hours, along with 53 additional deaths attributed to the virus.

According to the latest data from the Illinois Department of Public Health, Monday’s new cases bring the state to 1,033,526 confirmed and probable cases of the virus since the pandemic began, along with 17,627 deaths.

Another 1,736 deaths have been classified as “probable” COVID-19 fatalities, according to IDPH officials.

Over the last 24 hours, 66,697 new test results have been returned to state laboratories, bringing the statewide testing total to 14,169,986.

According to a press release from IDPH, the preliminary seven-day statewide positivity rate on all tests performed dropped to 7.6%, while the positivity rate on unique individuals tested now stands at 8.9% during that time.

Hospitalizations increased slightly Monday, with 3,540 patients currently hospitalized due to COVID-19. Of those patients, 759 are currently in intensive care units, while 401 are on ventilators.

Lightfoot Explains Why Chicago’s Stay-at-Home Advisory Was Extended

Chicago Mayor Lori Lightfoot extended the city’s stay-at-home advisory to remain “aligned” with state guidance, she said Monday.

The city’s stay-at-home advisory was extended through Jan. 22 as the coronavirus pandemic continues, officials announced Sunday.

“We extended it to make sure that it was aligned with I think what the state was doing, but we are making significant progress,” Lightfoot said during an unrelated press event Monday. “We have been coming back down even through Thanksgiving and then Christmas and New Year’s so we are making steady progress overall so the advisory is really about making sure that we’re doing everything that we can to give people the best information.”

Lightfoot noted that while some questioned why the order’s extension came at the same time Chicago Public Schools began bringing some students back to classrooms, anyone attending school or leaving for essential purposes, including teaching, was exempt “from the very beginning.”

Chicago’s top doctor echoed that claim.

“We specifically say people who are going to work who are going to school or who are performing other essential activities should continue to do so,” Chicago Department of Public Health Commissioner Dr. Allison Arwady said, adding that the city continues to make “very good progress.”





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Doctors say COVID-19 variant, now in US, no more deadly than main strain


After first being identified in the United Kingdom in September, the mutated variant, which is roughly 55 percent to 70 percent more easily transmitted than other strains of COVID-19, led to an emergency lockdown in London over Christmas.

Colorado’s governor announced Tuesday that the first case of the variant in the United States had been found in a man in his 20s who had “no travel history” and is in isolation in Elbert County.

This month, Maria Van Kerkhove, the World Health Organization’s technical lead on COVID-19, told the BBC that the vaccines now being distributed likely would be effective against the variant virus, and several drugmakers said they believed their vaccines’ efficacy would remain unaffected.

Karan said the vaccines are likely to work on the variant but added, “I think it’s too early to say with certainty.”

“We suspect that the vaccine should still be highly effective against this, but we just don’t know for sure yet,” he said.

The variant caused 62 percent of COVID-19 infections in London in the first full week of December, up from 28 percent in early November, according to researcher Paul Hunter, a professor of medicine at the University of East Anglia’s Norwich School of Medicine.

After first being identified in the UK, the variant was soon found in more than a dozen other countries, including Australia, Canada, Germany, Italy, Japan, Lebanon, the Netherlands, Singapore and South Korea.

It was inevitable that the variant would reach the United States, Karan said. “It was just a matter of time for us to sequence it and detect it.”

Since the Colorado man reportedly had not been traveling, he likely was infected through community spread, suggesting that the variant has been in the United States for some time, doctors said.

“This is incredibly concerning because it probably only represents the tip of the iceberg,” said Dr. Cassandra M. Pierre, an assistant professor of medicine at Boston University School of Medicine and a physician at Boston Medical Center. “We believe that there probably are more variants within the United States.”

So far only “a small fraction” of coronavirus infections are subjected to genetic sequencing, Pierre said, so it’s unclear how many variants of the virus exist.

“There could be many more out there,” she said. “We don’t know.”

Karan said his concern is that a more easily spread virus will mean more people become sick enough to require hospitalization, leading to overwhelmed hospitals.

International travelers could bring more cases of this or other COVID-19 variants into the country, and domestic travel over state lines could spread variants around the country, Pierre said.

New travel restrictions could help slow that spread, she said, but it’s too late to do anything about the holiday trips that many Americans have made in recent days. And to make interstate restrictions more effective, there needs to be much more genetic sequencing of the virus to determine where variants are present, she said.

Karan said travel restrictions can be effective if put in place quickly, but the apparent community spread of the variant in Colorado suggest that it’s too late for such measures to work. And travel restrictions can have unintended consequences, leading to overcrowding on routes of travel that are abruptly shut down or that remain open when other routes are closed.

Asked whether Massachusetts was considering new travel restrictions in response to the Colorado case, a spokesman for Governor Charlie Baker pointed to the Commonwealth’s existing rules for visitors from out of state.

“Massachusetts has implemented strict travel restrictions that require travelers to the Commonwealth to quarantine or produce a negative COVID-19 test result unless they meet a limited number of exceptions,” the spokesman, Terry MacCormack, said in an e-mail. “The Administration has contacted the CDC and the federal government requesting more information about the new variant.”

The variant has not been associated with a higher risk of death, though its higher transmission rates will inevitably lead to greater numbers of people dying, Pierre said.

“The more people who are infected, the more hospitalizations we will have, and … more deaths will come with that,” she said. “It’s a question of numbers rather than the overall virulence of the strain.”

Material from Bloomberg News was used in this report.


Jeremy C. Fox can be reached at jeremy.fox@globe.com. Follow him on Twitter @jeremycfox.





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