Two cases of new (invisible) Omicron BA.2 substrain identified in Greece

Two cases of the Omicron BA.2 substrain have been detected among passengers on flights arriving at Eleftherios Venizelos International Airport in Athens, Greek media reported.

Samples from suspected cases were sent to the Institute for Biological Research at the Academy of Athens for genomic testing. Reportedly , the results became known on Thursday evening.

Gikas Maiorkinis, assistant professor of epidemiology and member of the country’s committee of epidemiologists, said that in early December 2021, a sub-variant of Omicron, also called “stealth” appeared, because it is not easy to detect.

The subvariant has a mutation at position 67 making it undetectable by the classical method used for detection. Currently, scientists seem to be waiting for more data, but do not hide their concerns.

But now experts are dismissing the notion that the substrain is as subtle as it first seemed. Experts say the BA.2 strain does show up in PCR tests, just not necessarily in the same way as Omicron BA.1.

“BA.2 can be detected by PCR…Depending on the PCR test used, it may not look like BA.1 (another Omicron). But it will still give a positive result.” wrote v Twitter Cornelius Roemer, computational biologist at the Swiss University of Basel.

Last week magazine Fortune reported that a sub-variant of Omicron BA.2, nicknamed the “invisible Omicron”, appears to be outperforming other Omicron subspecies in some regions of the world, raising concerns that an even more contagious version of Omicron could trigger a larger spread of COVID-19. 19 waves around the world.

The World Health Organization (WHO) reports that Omicron, also known as B.1.1.529, has three main substrains: BA.1, BA.2 and BA.3. As of December 23, the WHO reported that more than 99% of the cases it had sequenced were BA.1. But now the rise of BA.2 in Denmark and elsewhere suggests that BA.2 could outperform BA.1.

On Thursday, Denmark reported that the BA.2 Omicron substrain accounts for almost half of the country’s cases and is rapidly replacing BA.1, the parent strain of Omicron.

Denmark reported that in the two weeks from late December to mid-January, BA.2 accounted for 20% of COVID-19 cases in Denmark, and now 45%. During the same period, the number of COVID-19 infections in Denmark reached an all-time high. Denmark is registering more than 30,000 new cases a day this week, ten times more than the peaks of previous waves.

I made some new charts, since BA.2 has now clearly passed BA.1 in Denmark.

Delta seems to be reduced to less than 1% since 13th of January.

I cut of the last 3 days, because I think those days will change when more data comes in. https://t.co/pCmyHIYEtK pic.twitter.com/5PHLLWCOQz

— Josette Schoenmakers (@JosetteSchoenma) January 20, 2022

The Danish government also said the strain is spreading rapidly in countries such as the UK, Norway and Sweden. Meanwhile, scientists from places like France and India are warning that the BA.2 variant is spreading rapidly and could outpace other strains of Omicron.

It is not yet clear if BA.2 is more dangerous than BA.1. The researchers say the “silent” version is genetically different and therefore may behave differently, and because it is even worse than the first version of Omicron in tests, it may become a more serious problem.

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