The race is underway to track the new COVID-19 variant

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

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LONDON / BRUSSELS / SINGAPORE, November 30 (Reuters) – Governments around the world search databases for recent cases of COVID-19 infections as soon as possible, screening travelers and decoding the viral genomes of the new variant while trying to measure how far it has spread.

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

Data show that it circulated before it was officially identified in southern Africa last week, and it has since been discovered in more than a dozen countries, read more. The work of determining whether it is more contagious, deadly or evading vaccines will take weeks.

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

The pace of action stands in stark contrast to the emergence of other variants – when the first samples of the Alpha variant were documented in the UK in September 2020, the government spent months collecting data and assessing its potential danger before introducing a nationwide lockdown in December .

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

Shortly after discovering its first Omicron case on Friday, Israel announced it would buy 10 million more PCR kits that could detect the variant in an attempt to limit its spread. It closed its borders to foreigners from all countries on Saturday.

Scotland and Singapore are struggling to control tens of thousands of recent positive cases for signs of the variant they may have missed, and the US is improving its COVID-19 monitoring to distinguish domestic cases of the Omicron variant from the still dominant Delta.

The European Union’s Health Commissioner has called on member states to step up their efforts to detect mutations, as some are still lagging behind almost two years into the pandemic. Read more

The bloc has now confirmed 42 cases in 10 countries.

“Some Member States are lagging far behind in this crucial dimension,” Stella Kyriakides said in a letter that Reuters has seen to the health ministers of the 27 EU countries.

“Already facing a challenging winter due to the high transmittance of the Delta variant (…), we may now experience additional or additional pressure due to the appearance of the Omicron variant,” she wrote.

The World Health Organization classified Omicron as a “variant of concern” because of the number of mutations that can help it disperse or avoid antibodies from previous infection or vaccination.

ALL ABOUT THE S-GENET

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

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

It is not a failsafe because the Alpha variant, first identified in the UK, also has that mutation.

As Alpha no longer circulates widely, the presence of S-gene depletion suggests that the sample is positive for Omicron and warns the laboratory to send the sample for genome sequencing for confirmation.

If local PCR tests cannot identify this mutation, randomly selected PCR graft samples must undergo genome sequencing, which may take up to one week.

The WHO has said that widely available tests are capable of detecting individuals infected with any variant, including Omicron.

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

It is not clear whether countries will buy sets due to the unique characteristics 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. Read more

Thermo Fisher has said it is ready 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 after the variant was identified, Israel began checking for the S gene in all positive tests taken from travelers arriving at Ben Gurion main airport, Israel’s head of public health at the Ministry of Health, Sharon Alroy-Preis, told parliament d. Sunday.

Now its laboratories are monitoring for this mutation in all tests across the country, and when a positive PCR test indicates SGTF, the sample is taken for further sequencing, the health ministry said.

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

QUESTION OF THE VARIANT

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

The Scottish authorities have reviewed swabs back to November 1 to help detect nine cases of Omicron, all of which are linked to the same event. Read more

They have found that around 16 November, S-gen target failure had begun to reappear in the tests, a week before South Africa and Botswana identified the new variant. That function has helped control genomic sequencing, as it did when Alpha appeared.

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

This means the government can begin to estimate how widespread the new variant may be, identify individuals who may need to be retested, and what samples need to be prioritized for further decoding in laboratories, Smith said.

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

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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 Jeruselam Writing by Josephine Mason; Edited by Nick Macfie

Our standards: Thomson Reuters Trust Principles.

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