The race has begun to track down the new COVID-19 variant – Community News
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The race has begun to track down the new COVID-19 variant

Passengers briefly disembark from the MSC Europa cruise ship after docking in South African waters as the novel coronavirus strain Omicron spreads, in Cape Town, South Africa, Nov. 30, 2021. REUTERS/Shelley Christians

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LONDON/BRUSSELS/SINGAPORE, Nov. 30 (Reuters) – Governments around the world are urgently searching 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 has spread.

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

Records show it circulated before it was officially identified in southern Africa last week and has since been discovered in more than a dozen countries. Read more. Work to determine whether it is more contagious, more lethal or dodge vaccines will take weeks.

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Britain and other major economies have banned flights to and from southern Africa just days after the variant was first discovered, raising global financial markets and concerns about the economic damage.

The speed of 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 collecting data and assessing it. potential danger before imposing a nationwide lockdown in December.

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

Shortly after the discovery of the first Omicron case on Friday, Israel announced it would purchase an additional 10 million PCR kits that can detect the variant in an effort to contain its spread. It closed the borders to foreigners from all countries on Saturday.

Scotland and Singapore are rushing to check tens of thousands of recent positive cases for signs of the variant they may have missed, and the United States is stepping up 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 step up their efforts to detect mutations, as some are still nearly two years behind the pandemic. read more

The bloc has now confirmed 42 cases in 10 countries.

“Certain Member States are significantly behind on 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 portability of the Delta variant (…) we may now experience further or additional pressure due to the appearance of the Omicron variant,” she wrote.

“The World Health Organization has classified Omicron as a ‘variant of concern’ because of the number of mutations it could aid in the spread or evasion of antibodies from previous infection or vaccination.

ALL ABOUT THE S-GENE

Most PCR tests cannot distinguish Omicron from the Delta variant, the dominant and most contagious version of the virus to date.

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

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

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

If local PCR testing fails to identify this mutation, randomly selected PCR swab samples must undergo genome sequencing, which can take up to a week.

The WHO has said widely available tests can detect individuals infected with any variant, including Omicron.

However, so far it has only recommended the TaqPath test produced by the US company Thermo Fisher (TMO.N) as a proxy.

It is not clear whether countries will purchase kits due to the uniqueness of the test. Singapore is considering buying more, though no decision has been made yet, Kenneth Mak, health ministry director of medical services, told Reuters. read more

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

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

Now its labs check 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 use the TaqPath test, Scott Becker, chief executive of the Association of Public Health Laboratories (APHL), a network of state and municipal public health labs, told Reuters.

FEATURES OF THE VARIANT

Of the 150,000 positive tests reviewed in Belgium a month ago, 47 had S gene dropout and a high viral load. Only one of them was Omicron, according to Marc Van Rast, one of the virologists who dissected the samples.

Scottish authorities have been looking through swabs until Nov. 1 to help discover nine cases of Omicron, all of which are linked to the same event. read more

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

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

It means the government can begin to estimate how common the new variant is, identify people who may need to be retested and which samples should be prioritized for further decoding in labs, Smith said.

“It’s the best method we have for identifying cases right now.”

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Report 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. Written by Josephine Mason; Editing by Nick Macfie

Our Standards: The Thomson Reuters Trust Principles.