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Inside South African Virology Labs: Hunting for the Next Variant – BNN

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(Bloomberg) — As the port city of Durban eases into South Africa’s annual summer holiday season, scientists at a virology laboratory at the Africa Health Research Institute are working around the clock.

The discovery of the omicron Covid-19 variant by South African and Botswanan scientists last month has lent urgency to efforts to isolate the virus and test its ability to evade vaccines the world is pinning its hopes on to end a two-year pandemic. 

The goal is to figure out “what happened? How does it happen? What can we do to decrease it,” said Alex Sigal, 51, who runs the lab that was the first to isolate the beta variant, the Covid-19 strain that’s been most successful in getting past inoculations. We “then figure out a way to quickly adjust our responses,” he said.

South African labs have been critical to combating the coronavirus. They’ve identified two of the five so-called variants of concern and trained scientists from across the continent on how to gene sequence to spot and track variants. 

Sigal’s lab was the first to test omicron against blood plasma from people who’d received two doses of the shot produced by Pfizer Inc. and BioNTech SE. It also updated a paper that hypothesizes that variants may develop in immuno-suppressed people who’re unable to easily shake off the virus, allowing it to mutate.

To many outside medical science circles, the role South Africa-based scientists have played in fighting the pandemic has come as a surprise. But with an HIV epidemic, the world’s biggest, nearing its fourth decade and hundreds of thousands of people infected with tuberculosis, South Africa has been a magnet for the scientists from around the world who track the pathogens that kill us.

The country has set up a network of seven genomic surveillance labs with one at the National Institute for Communicable Diseases and six at academic institutions.

Sigal is Israeli-Canadian and a few floors below his lab in an eight-floor glass and face brick building is Krisp, a gene-sequencing laboratory whose Brazilian head, Tulio de Oliveira, announced omicron’s discovery to the world. 

“There’s a lot of technical capacity in South Africa to do genomic sequencing of pathogens because we’ve built up that expertise over many years for HIV and TB, ” said Richard Lessells, a Scottish infectious diseases specialist at Krisp. “Very early on in the pandemic, we recognized that genomic sequencing and genomic surveillance was going to be very important.”

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With the onset of omicron that has meant sleepless nights for many of the scientists. 

“I’ve been working to get the Pfizer vaccine efficacy study ready,” said Sigal, who becomes animated when he watches a time-lapse video of the omicron variant attacking cells. “I worked through the night.” 

Sigal’s lab has made another important contribution to the country’s ability to monitor changes in the pandemic. When Covid hit, getting supplies across borders became tricky. 

The scientists quickly realized they couldn’t get cells in which to culture the virus, so they made their own line from human lung cells that had first been engineered by Sigal while completing his doctorate. This cell line, known as H1299-ACE2, is now being used widely in South Africa in various Covid-19 tests, including omicron.

Omicron hit South Africa first and so far there’s much to be concerned about. The variant appears to be much more transmissible than earlier variants with daily cases hitting a record this week. Still, hospitalizations and deaths, so far, are substantially lower than in previous waves.

While foreign scientists have flooded into South Africa to tackle the diseases that weigh on a country that straddles the first and third worlds, local talent is robust and developing rapidly.

Sandile Cele, a 33-year-old from a small village near Durban, is part of Sigal’s team of seven scientists who culture cells, spin out plasma and wash test plates. In all, the Africa Health Research Institute, founded in 2016, has 550 students, staff and scientists.

TB, HIV

It was quite challenging to suddenly switch from TB and HIV to coronaviruses, said Cele, who like most of the team is a graduate of the University of KwaZulu-Natal, about two miles from where he works.

“But now with the emergence of new variants there is pressure,” Cele said. “For omicron especially we’re expected to give answers. Everyone has been looking in our direction.”

While Sigal and his team are now focused on omicron, their aim is to help end the pandemic by getting ahead of a virus that rapidly mutates — a task that won’t be easy.

We need to start by “understanding how these variants evolve and in doing more surveillance,” he said.

©2021 Bloomberg L.P.

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Nova Scotia reports 68 people in hospital because of COVID-19 – CBC.ca

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Nova Scotia has reported that 68 people are in hospital because of COVID-19, including 10 in intensive care.

A news release from the province Sunday said the patients are receiving specialized care in a COVID-19 designated unit.

The average age of the patients admitted for COVID-19 is 65, the release states. The majority of the patients, 65, were admitted during the Omicron wave. 

There are also two other groups currently in hospital related to the virus, according to the release.

  • 60 people who were identified as positive upon arrival but were admitted for another medical reason, or were admitted for COVID-19 but no longer require specialized care
  • 112 people who contracted COVID-19 after being admitted to hospital.

The abbreviated release did not provide the number of COVID-19 admissions and discharges. 

Nova Scotia Health labs completed 3,711 tests on Saturday and 696 new cases have been reported.

There are 447 cases in the central health zone, 108 in the eastern zone, 105 in the western zone and 36 in the northern zone.

Less than than 10 per cent of Nova Scotians are unvaccinated, according to provincial statistics.

As of Friday’s update, unvaccinated Nova Scotians were about four times more likely to be hospitalized due to COVID-19 than someone with two doses of vaccine. That is based on average hospitalizations since the province started releasing the daily hospitalizations by vaccine status on Jan. 4.

Summary offence tickets

Halifax Regional Police issued 11 summary offence tickets Sunday for violations of health regulations.

Police responded to reports of a party at a Bayers Road residence shortly before 1 a.m. Sunday.

Tickets were issued to 11 occupants for failing to comply with provisions of the Health Protection Act. 

The tickets carry a fine of $2,422.

Atlantic Canada case numbers

  • Newfoundland and Labrador reported one death and 384 new cases Sunday. There are 5,503 active cases and 12 hospitalizations. 
  • Prince Edward Island reported five hospitalizations Saturday. There were 309 new cases and 222 recoveries in Saturday’s report.
  • New Brunswick reported four more deaths and 115 hospitalizations Sunday. The province has 5,265 active cases.
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UK’s Johnson plans to scrap COVID-19 self-isolation law – The Telegraph

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The United Kingdom is drawing up plans under which people will not be legally bound to self-isolate after catching COVID-19, The Telegraph reported on Sunday.

Prime Minister Boris Johnson wants to permanently revoke emergency coronavirus laws as Britain’s COVID-19 cases continue to fall, the report said, adding official guidance would remain but would not result in fines or legal punishment if ignored.

The plans will be worked up over the coming weeks, with an announcement expected as early as the spring, the report said.

Last week, Health Secretary Sajid Javid said COVID-19 self-isolation in England will be cut to five days from seven if someone tests negative twice.

Johnson is also set to lift Plan B COVID-19 restrictions, introduced last month to slow the spread of the Omicron variant, according to an earlier Telegraph report.

 

(Reporting by Maria Ponnezhath in Bengaluru; Editing by Daniel Wallis)

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'Choose increased antibodies over brand': Moderna appointments still being cancelled in London, Ont. area – CTV News London

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Doctors and pharmacists continue to advocate for people to get the first available mRNA vaccine for their COVID-19 booster dose.

“We have had some feedback that appointments are being canceled because people are holding out for Pfizer,” says Dr. Joyce Lock, the medical officer of health for Southwestern Public Health (SWPH).

“I strongly strongly urge everyone, particularly those over the age of 50, to choose increased antibodies over brand,” she added.

Lock made those statements during her weekly briefing on Jan 12.

“Our immunity following our original two doses is decreasing over time,” says Lock. “Our bodies don’t care what brand they receive. They follow the science, not the manufacturer. Studies show that immunity shoots back up after the booster and it doesn’t matter which brand.”

This week, First Ave. Pharmacy in St. Thomas, Ont. took to Facebook saying it had openings due to people refusing Moderna as a booster dose.“We send out a mass email saying that there’s a shortage of Pfizer and we might have to offer them Moderna and some people would cancel their appointment online or they would call us and cancel their appointments,” says Minh Nguyen, pharmacist at First Ave. Pharmacy. “Both Moderna and Pfizer are mRNA vaccines and equally effective at preventing severe illness from COVID. So I would say get whatever mRNA vaccine you can.”

Sunday, the Metrolinx Go-VAXX bus returned to London, Ont. It was stationed in the parking lot at the new East Lions Community Centre on Brydges St.

They had some appointments booked, but we were even taking walk-ins with Pfizer being administered.

“I’ve had Pfizer for my first two shots and that’s what I preferred,” says Michael Sean MacVoy, a truck driver getting his booster. “At this point, I didn’t care.”

Diane Crozman was in the same scenario, getting Pfizer a third time. “It doesn’t really make a difference to me,” she said. “They said the Moderna is going to work the same, but Pfizer that’s good because I’ve already got the other two Pfizer.”

Justin Seaward showed up for a walk-in booster, minutes after his wife went home from her booked appointment.

“I’ve had Pfizer, Moderna, then Pfizer now,” says Seaward. “It didn’t really make a difference much to me. I just wanted to be Vaxxed so I can feel safer for my family.”The Middlesex-London Paramedic Service (MLPS) had administered 2,194 doses of vaccine over the past six days since starting pop-up clinics in Middlesex County.

The percentage of people upset that Moderna was being administered is very low.

“It has happened a few times at the front door, but very rare,” says Miranda Bothwell, acting superintendent for special operations with MLPS.

They will be back on the road, continuing their pop-up clinic tour Monday in Lucan, Ont. 

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