US biggest source by far of Israel’s COVID-19 cases, genome sequencing shows
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US biggest source by far of Israel’s COVID-19 cases, genome sequencing shows

Team of scientists, drawn from 9 institutions, also assesses 800 ‘super spreaders’ responsible for 80% of those infected

Illusrative: An Israir flight attendant wearing full protective gear walks next to passengers during an Israir flight between Tel Aviv and Eilat, May 13, 2020. (Yossi Zeliger/Flash90)
Illustrative image. A worker wearing protective clothing on a plane at Ben Gurion Airport, May 13, 2020. (Yossi Zeliger/Flash90)

A team of Israeli scientists have concluded that America was Israel’s biggest source of coronavirus by far, after running genomic sequencing on the virus.

The research team, which was drawn from nine institutions, also found that once the virus reached Israel, a small number of “super spreaders” were responsible for the large majority of infections.

Seven out of every 10 Israelis who caught the virus to date were infected with a haplotype — variant — that arrived in the country from the United States, Tel Aviv University evolutionary virologist Adi Stern, who led the study, told The Times of Israel.

She said that just 30 percent of people who arrived in Israel during the crisis came from America, so she was “very surprised” by how widely their haplotypes of the virus spread. She thinks it may reflect, in part, the unusually high level of interaction that Jewish visitors from the Diaspora have with Israeli citizens.

The pattern of the spread was also surprising, she said. “We think that about 5% of the infected population spread the virus in 80% of cases,” Stern revealed, explaining this means that just 800 people are believed to be responsible for four out of five Israeli virus cases.

This is suggested by the fact that numerous patients have genomes of the virus that are 100% identical, “and we would expect far more variety if there was a more varied transmission chain,” Stern said.

Adi Stern of Tel Aviv University’s School of Molecular Cell Biology and Biotechnology (courtesy, Tel Aviv University)

“We know that everyone isn’t equal in terms of how much people spread viruses, and normally there’s an assumption that 20% of people spread 80% of the virus,” she said. “But this thinking cannot explain what we’re seeing here.”

Genomic sequencing has also allowed her to estimate how many Israelis have been infected by the coronavirus. She believes it is several times higher than the number of reported cases, which stands at 16,621, but fewer than 100,000. She said this is good news, in the sense that it indicates that the lockdown worked and the spread of the virus was limited, but the downside is that “it indicates there really isn’t any herd immunity in Israel.”

The Tel Aviv University-led study was a collaboration with Emory University, the Gertner Institute, the Holon Institute of Technology, the Genome Center at the Technion Institute of Technology, and five Israeli hospitals. It focused on so-called neutral mutations of the virus.

While a much-feared mutation that could change the novel coronavirus’s behavior has not happened, there have been other mutations that did not change its conduct, and do allow scientists to trace the chain of infection. In Israel’s first major exercise to conduct genomic sequencing on the virus, Stern’s team studied genetic material from 212 Israelis, who together constitute a representative sample of the general population.

Stern said she does not know why people arriving from America were such a major source of Israel’s virus cases, but made two suggestions.

There were some much-publicized failures in enforced quarantining of new arrivals, and Stern said it may reflect poor enforcement with regard to American flights in particular.

She said that the figures may also reflect the “behavior patterns” of people who land in Israel from America.

While people landing from elsewhere are often foreign tourists who have limited contact with Israeli citizens, those arriving from America often have lots of interactions, she said. Many are Israeli citizens returning home, or Jews who live in the Diaspora and have family and social connections in Israel.

After America, coronavirus haplotypes that infected Israelis came from Belgium (8%), France (6%), England (5%), Spain (3%), Italy (2%), the Philippines (2%), Australia (2%) and Russia (2%), according to the study.

Stern said that her team will continue its genomic sequencing research, and, as it becomes more precise, expects it to yield detailed information on the rate of infection in a household, in an apartment building, in a school, in a neighborhood, and in other settings.

She hopes that the picture of how and where the virus spreads will allow authorities to effectively target their preventative measures in the case of a second wave, knowing better where to apply closures and other measures. She said: “It will allow the government to focus future lockdowns on particular areas or shut down specific types of institutions,” as well as give it information on how long such shutdowns should last.

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