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The race is on to trace the new COVID-19 variant

By Alistair Smout, Francesco Guarascio and Chen Lin

LONDON/BRUSSELS/SINGAPORE (Reuters) – Governments around the world are urgently scouring databases for recent cases of COVID-19 infections, screening travelers and decoding the viral genomes of the new variant as they try to measure how far it has spread.

The pace of the work highlights the pressure on governments and public health authorities to decide quickly whether they need to take unpopular, economically damaging steps to curb Omicron’s spread.

Data shows it was circulating before it was officially identified in southern Africa last week and it has since been detected in more than a dozen countries. Work to establish if it is more infectious, deadly or evades vaccines will take weeks.

Britain and other major economies banned flights to and from southern Africa just days after the variant was first detected, roiling global financial markets and stirring worries about the economic damage.

The speed of the action is in stark contrast to the emergence of other variants – when the first samples of the Alpha variant were documented in Britain in September 2020, the government spent months gathering data and assessing its potential danger before imposing a nationwide lockdown in December.

It took the World Health Organization (WHO) months to designate it a variant of concern – its highest level.

Soon after detecting its first Omicron case on Friday, Israel announced it would buy 10 million more PCR kits that can detect the variant in an effort to contain its spread. It shut its borders to foreigners from all countries on Saturday.

Scotland and Singapore are scrambling to check tens of thousands of recent positive cases for signs of the variant they may have missed and the United States is enhancing its COVID-19 surveillance to distinguish domestic cases of the Omicron variant from the still-dominant Delta.

The European Union’s health commissioner has urged member states to boost efforts to detect mutations, as some still lag behind almost two years into the pandemic.

The bloc has now confirmed 42 cases in 10 countries.

“Certain Member States lag behind considerably in terms of this crucial dimension,” Stella Kyriakides said in a letter seen by Reuters to health ministers of the 27 EU countries.

“Already faced with a challenging winter due to the high transmissibility of the Delta variant (…) we may now experience further or additional pressures because of the appearance of the Omicron variant,” she wrote.

ALL ABOUT THE S-GENE

Most PCR tests cannot distinguish Omicron from the Delta variant, the dominant and most infectious version of the virus so far.

To distinguish Omicron from Delta, the PCR test must be able to identify a mutation in Omicron known as the S-gene drop-out or S-gene target failure (SGTF).

It is not a fail-safe because the Alpha variant, first identified in Britain, also has that mutation.

Given that Alpha is no longer widely circulating, the presence of the S-gene dropout suggests the sample is positive for Omicron and alerts the lab to send the sample for genome sequencing for confirmation.

If local PCR tests cannot identify this mutation, then randomly selected PCR swab samples must undergo genome sequencing, which can take up to a week.

The WHO has said that widely available tests are able to detect individuals infected with any variant, including Omicron.

However, it has so far only recommended the TaqPath test produced by U.S. firm Thermo Fisher as a proxy.

It’s not clear if countries will buy kits due to the unique characteristic of the test. Singapore is considering buying more, although no decision has yet been made, Kenneth Mak, the health ministry’s director of medical services, told Reuters.

Thermo Fisher has said it is prepared to increase production to meet demand from countries in Africa and elsewhere as they work to track the spread of the new variant.

Within a day of the variant being identified, Israel started checking for the S-Gene in all positive tests taken from travelers arriving at the main Ben Gurion airport, Israel’s head of public health at the Health Ministry, Sharon Alroy-Preis, told Parliament on Sunday.

Now, its labs monitor for that mutation in all tests nationwide and when a positive PCR test indicates SGTF, the sample is taken for further sequencing, the health ministry said.

Most U.S. labs will be using the TaqPath test, Scott Becker, chief executive of the Association of Public Health Laboratories (APHL), a network of state and municipal public health laboratories, told Reuters.

QUIRKS OF THE VARIANT

Out of the 150,000 positive tests going back a month assessed in Belgium, 47 had S-gene drop-out and a high viral load. Only one of them was Omicron, according to Marc Van Rast, one of the virologists who parsed the samples.

The Scottish authorities have gone through swabs back to Nov. 1 to help in discover nine cases of Omicron, all linked to the same event.

They have found that around Nov. 16, S-gene target failure had started appearing in the tests again, a week before South Africa and Botswana identified the new variant. That feature has helped to direct genomic sequencing, as it did when Alpha emerged.

“That is one of the quirks of this particular variant that we can use to our advantage,” Gregor Smith, Scotland’s chief medical officer, said on Monday.

It means the government can start estimating how prevalent the new variant may be, identify people who may need to get tested again and which samples need to be prioritized for further decoding in labs, Smith said.

“It’s the best method that we have to be able to identify cases at this point in time.”

(Reporting by Alistair Smout in London, Francesco Guarascio in Brussels, Chen Lin in Singapore, Julie Steenhuysen in Chicago and Maayan Lubell and Ari Rabinovitch in Jerusalem; Writing by Josephine Mason; Editing by Nick Macfie)

Trump says getting close to a deal with Democrats on U.S. coronavirus stimulus

WASHINGTON (Reuters) – U.S. President Donald Trump said Sunday that Republicans were “close” to getting a deal with Democrats on another legislative package to help alleviate economic damage done by the coronavirus pandemic.

At a White House briefing, the president suggested there could be a resolution by Monday.

(Reporting by Nandita Bose; Editing by Cynthia Osterman)

U.S. urged to go slow on easing coronavirus lockdown, even as jobless claims surge

By Doina Chiacu and Maria Caspani

WASHINGTON (Reuters) – The top U.S. infectious disease expert on Thursday warned against reopening the economy too soon after a downward revisions in the coronavirus pandemic’s projected death toll, while a third week of massive jobless claims underscored the economic damage caused by social distancing.

While several officials have hailed the apparent success of mitigation efforts in bringing death projections down to 60,000 from more than 100,000, Dr. Anthony Fauci said it was important that people continue to stay home to avoid a resurgence in the spread of the disease.

“We’ve got to continue to redouble our efforts at the mitigation of physical separation in order to keep those numbers down and hopefully even get them lower than what you’ve heard recently,” Fauci, director of the National Institute of Allergy and Infectious Diseases, said on CBS “This Morning.”

Stay-home orders that have closed non-essential workplaces in 42 states have drastically slowed the once-humming U.S. economy and thrown millions of people out of work.

With several state unemployment insurance offices deluged in recent weeks, 6.6 million workers applied for jobless benefits in the week ended April 4, the U.S. Labor Department said on Thursday. That followed 6.9 million jobless applications the week before, the most since the Great Recession of 2008.

In all, some 16.8 million American workers have applied for jobless benefits in the past three weeks.

Fauci, appearing on several morning television programs, affirmed that recent models showing fewer deaths than previously projected were evidence that social distancing and other efforts at keeping people apart were slowing the spread of the virus.

“So I believe we’re going to see a downturn in that, and it looks more like the 60,000 than the 100,000-200,000,” Fauci said on the NBC “Today” program.

A University of Washington model often cited by U.S. and state officials projects that COVID-19, the respiratory ailment caused by coronavirus, will claim 60,415 American lives by Aug. 4, with the peak coming on Easter Sunday this weekend, when it projects that 2,212 will die

By Thursday morning, more than 432,000 U.S. residents had tested positive for the virus, and around 14,800 had died, according to Johns Hopkins University.

New Jersey Governor Phil Murphy on Wednesday tightened the virus-fighting efforts of his state, which has the second highest number of deaths, by halting all non-essential construction and ordering food and drug stores to limit the number of customers and require them to wear face coverings.

New York state, epicenter of America’s coronavirus crisis, set another single-day record of COVID-19 deaths on Wednesday, as veteran doctors and nurses voiced astonishment at the speed with which patients were deteriorating and dying.

Patients “look fine, feel fine, then you turn around and they’re unresponsive,” said Diana Torres, a nurse at Mount Sinai Hospital in New York City, the center of the nation’s worst outbreak.

The number of known coronavirus infections in New York state alone approached 150,000 on Wednesday, even as authorities warned that the official death tally may understate the true number because it omits those who have perished at home.

In Maryland, Pleasant View nursing home has become the site of one of the state’s worst outbreaks, 40 miles outside the U.S. capital of Washington, D.C.

Retired firefighter Gary Holmberg was only supposed to be there for a little while, recovering from a fall at his assisted living center. But about a month after he arrived, Holmberg, 77, became one of more than a dozen of the nursing home’s residents to die of COVID-19.

“He had a lot, lot more life left, there’s no question,” his said his son Rob Holmberg.

Officials have warned Americans to expect alarming numbers of coronavirus deaths this week, consistent with projections.

“We are in the midst of a week of heartache,” Vice President Mike Pence said during a White House briefing on Wednesday, but added, “we are beginning to see glimmers of hope.”

At the same briefing, President Donald Trump said he would like to reopen the U.S. economy with a “big bang” but not before the death toll is on the down slope.

Trump did not offer a time frame, but his chief economic adviser, Larry Kudlow, said on Tuesday a resumption of commerce was possible in four to eight weeks.

(Reporting by Doina Chiacu, Maria Caspani, Gabriella Borter and Peter Szekely; Writing by Peter Szekely; Editing by Alistair Bell)

Coronavirus wreaks financial havoc as infections near 100,000

By Lawrence White and Dan Whitcomb

LONDON/LOS ANGELES (Reuters) – Business districts around the world began to empty and stock markets tumbled on Friday as the number of coronavirus infections neared 100,000 and the economic damage wrought by the outbreak intensified.

An increasing number of people faced a new reality as many were asked to stay home from work, schools were closed, large gatherings and events were cancelled, stores cleared of staples like toiletries and water, and face masks became a common sight.

In London, Europe’s financial capital, the Canary Wharf district was unusually quiet. S&P Global’s large office stood empty after the company sent its 1,200 staff home, while HSBC asked around 100 people to work from home after a worker tested positive for the illness.

In New York, JPMorgan divided its team between central locations and a secondary site in New Jersey while Goldman Sachs  sent some traders to nearby secondary offices in Greenwich, Connecticut and Jersey City.

The outbreak, which has killed more than 3,300 people globally, has radiated across the United States, surfacing in at least four new states plus San Francisco.

More than 2,000 people were stranded on the Grand Princess cruise ship after it was barred from returning to port in San Francisco because at least 35 people aboard developed flu-like symptoms. Test kits were delivered at sea to the vessel.

Moves by some major economies including the United States to cut interest rates and pledge billions of dollars to fight the epidemic have done little to allay fears about the spread of the virus and the economic fallout with supply chains crippled around the world, especially in China.

“There’s concern that while there has been a response from the Fed, given the nature of the problem, is this something the central bank can really help with?” said John Davies, G10 rates strategist at Standard Chartered Bank in London.

SINKING MARKETS

European stocks continued their slide after the Japanese market dropped to a six-month low, with 97% of shares on the Tokyo exchange’s main board in the red.

Airline and travel stocks have been among the worst affected as people cancelled non-essential travel. Norwegian Air Shuttle <NWC.OL>, the hardest-hit stock among European carriers, has fallen almost 70% since the start of February.

U.S. stock index futures dropped sharply over fears about the epidemic, which has prompted a sharp cut to global economic growth forecasts for 2020. The benchmark S&P 500 looked set to close out the week more than 10% below its record-high close on Feb. 19.

“If this really ramps up, we could see a lot more kitchen-sinking updates from the travel industry and airlines,” said Chris Beauchamp, chief market analyst at IG. “What’s impressive about the current move is it probably understates the degree of disruption we could be facing across the U.S. and Europe.”

Yields on long-dated U.S. Treasury bonds fell to record lows, while gold was on course for its biggest weekly gain since 2011 as investors fled to assets seen as safe havens.

In Europe, British 10-year gilt yields also dropped to a record low, while German Bund yields fell to within striking distance of record lows.

Yields fall as prices rise.

CABIN CREW MEMBER INFECTED

More than 98,000 people have been infected in over 85 countries, according to a Reuters tally. Mainland China, where the outbreak began, has seen more than 3,000 deaths, while the death toll in Italy stood at 148.

At current rates, the number of confirmed cases of the virus will surpass 100,000 on Friday.

About 3.4% of confirmed cases of the new coronavirus – known as COVID-19 – have died, far above seasonal flu’s fatality rate of under 1%, the World Health Organization said this week.

Singapore reported 13 new infections on Friday, its biggest daily jump, including a cabin crew member from Singapore Airlines.

In the United States, the world’s economic powerhouse, at least 57 new cases of coronavirus were confirmed as the virus struck for the first time in Colorado, Maryland, Tennessee and Texas, as well as San Francisco in California. Some 230 people have been infected in total and 12 have died.

Google, Facebook, Amazon, and Microsoft advised employees in the Seattle area to work from home, after some caught the virus. The companies’ work-from-home recommendation will affect more than 100,000 people in the area.

The U.S. Senate on Thursday passed an $8.3 billion bill to combat the outbreak, joining a slew of countries including China and South Korea in bolstering their war chests.

(Additonal reporting by Steve Gorman and Cath Turner in Los Angeles, Hideyuki Sano in Tokyo, Pamela Barbaglia, Karin Strohecker, Thyagaraju Adinarayan, Ritvik Carvalho and Tommy Wilkes in London, Sruthi Shankar in Bengaluru; Writing by Pravin Char; Editing by Mark Heinrich and Nick Macfie)