Israeli Labs See Spike in COVID Samples Suspected to Be Omicron

'We’re seeing a real jump' in suspected cases of omicron, says the director of laboratories for one of Israel's HMOs. Omicron cases, which take up to 7 days to confirm, appear to be spreading domestically, scientists say

Ido Efrati
Ido Efrati
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COVID test at an Israeli lab
COVID test at an Israeli labCredit: Hadas Parush
Ido Efrati
Ido Efrati

The first worrying signs that omicron is spreading rapidly and becoming the dominant COVID variant in Israel have begun to emerge this week, with test labs reporting a big jump in the number of suspect samples.

Meuhedet Health Services reported that over the past three days between 30 and 40 percent of all the positive tests for the coronavirus are suspected of being the omicron variant. Just 10 days ago the figure was only 3 percent.

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Official figures say that out of the 174 cases of omicron confirmed until Monday, only 17 were found to have originated domestically rather than through people returning from overseas. Another 400 reported cases are still waiting to be sequenced genetically.

But it now seems that these numbers are just the tip of the iceberg and that soon many thousands more people will be confirmed as being infected with the omicron variant. Unconfirmed omicron cases appear to explain the sharp rise in the number of confirmed cases and for the rising rate of infection.

Dr. George Prajgrod, the head of Meuhedet’s medical laboratories, said the health maintenance organization is currently carrying out between 3,000 to 4,000 tests a day, all of them from people who have not recently traveled abroad, including the second and third tests for those who tested positive already.

“We saw the first signs in the tests back about a month-and-a-half ago among about 3 percent of the tests. Starting December 10, we saw a rise, with the percentage of suspicious tests already between 5 and 10 percent. But four or five days ago, we suddenly saw a significant jump, and today about 30 percent to 40 percent of the tests we conduct are suspected of omicron,” said Prajgrod.

Leumit Health Services has also reported a noticeable change over the past few days, though a smaller one. “We’re seeing a real jump in the amount of suspect [tests] since the beginning of the week. The rate ... has already reached 10 percent of positive samples, compared to a lot less last week,” said Dr. Yotam Shenhar, the HMO’s director of laboratories.

The suspected omicron cases come from the within Israel, too, not just from those returning from overseas or those who were in contact with returnees, he added.

COVID tests of people returning from abroad are sent to private labs for testing; the HMO labs deal only with suspected cases of people who have not traveled overseas, plus a small number of people doing a second mandatory test a few days after returning from abroad. Thus, the great majority of cases being tested are of people who were infected locally.

Cases are deemed to have a “high suspicion” of the omicron variant based on the results of the appropriate PCR test, which is capable of identifying the variant with a high degree of probability due to observable genetic differences unique to omicron.

“For a person who tests positive for delta, we see an increase in all the genes; in omicron, there is no increase in the S-gene, because of a mutation that exists only in the variant,” said Shenhar.

COVID testing lab in IsraelCredit: Hadas Parush

The PCR tests provide an indication of omicron infection, but a certain diagnosis can only be made after a complete genetic sequencing of the samples, which is carried out in designated labs. The process takes three or four days, not including the time for collecting and transporting the samples and their initial handling. In the end, between five to seven days pass from the time a person is tested positive for the virus with a suspicion of omicron until the final results of the sequencing are completed. Cases are officially reported as being of the omicron variant only after the sequencing process is completed.

“This is a PCR test, but from a laboratory viewpoint in the case of omicron, it’s pretty conclusive. Unlike the tests of the British variant, where there was a lot of ‘background noise’ and a margin of error of 5 to 10 percent due to mutations, here the test is clean. There is hardly any background noise, so the PCR test provides a good indication for omicron,” said Shenhar. “Today, we report immediately online to the Health Ministry the moment we detect a suspicious case for an epidemiological investigation and for quarantine, but if these numbers continue to rise, that soon won’t be effective.”

Another indication for purely domestic outbreaks is monitoring for the virus in sewage. According to a report by the government’s Information and Knowledge Center published on Tuesday, those findings indicate the presence of omicron in the cities of Harish, Ashdod, Netanya and Ayalon-Nesher.

“Data from countries where the omicron variant is today already widespread shows that the number of people infected doubles every two-and-a-half days,” the report said. “The variant displays a partial ability to evade protection from infection provided by recovery and the vaccine – significantly more than the delta variant. Based on its contagion rate, it also seems to be spreading faster than the delta – so from 10 new infections per day in the community, we could reach 10,000 new infections a day within a month and a half.”

The report warned that “the characteristics of omicron increase the risk of a significant rise in infections and hospitalizations, even if the rate of severe illness is lower, due to an erosion in the protection provided by the vaccine and the potential of multiple infections, projected to take place rapidly. In light of the above, the risk of a sudden and heavy overburdening of the hospital system in Israel within a month and a half to two months is not unnegligible.”

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