Tweaked Israeli sewage test can check spread of coronavirus variants

New strains of COVID are extra-catchy or weaken vaccine defense, but their prevalence is unclear; an upgrade to an existing monitoring system provides vital health intelligence

Nathan Jeffay is The Times of Israel's health and science correspondent

Ziv hospital team members wearing safety gear as they work on a coronavirus ward on February 04, 2021. (David Cohen/Flash90)
Ziv hospital team members wearing safety gear as they work on a coronavirus ward on February 04, 2021. (David Cohen/Flash90)

New Israeli technology can give health authorities around the world advance warning before populations are swept by coronavirus variants that are extra-transmissible or more likely to breach vaccine protection.

There is deep concern in the US and elsewhere that the British variant, catchier than regular COVID-19, is gaining a significant foothold.

And in Israel, where that strain already accounts for 95 percent of cases, there are worries about the South African variant, which has been diagnosed in more than 450 people and is thought to weaken vaccine efficiency. Meanwhile, on Tuesday the Health Ministry announced it had detected the first three cases of the New York variant, which is also feared to be less efficiently halted by vaccines.

But authorities worldwide are struggling to get a picture of how fast variants are spreading. That is because such data normally relies on the sequencing of genetic material from individual test samples — a costly and lengthy process that is usually only performed on a subset of swabs.

A technician collects nasal swab samples for COVID-19 at the coronavirus lab, at the Ben-Gurion International Airport on February 28, 2021. (Yossi Aloni/Flash90)

Researchers at Ben Gurion University say they have found a way to easily and cheaply get a big-picture view of the variants’ spread, with an “upgrade” to the coronavirus sewage monitoring programs that many countries already use. It is a test kit that looks exactly like those currently used to assess COVID levels in sewage, but it screens for variants.

The researchers are submitting a paper on their tech for peer review, but have already published it online.

The scientists developed their test for the British variant, then made a version of the technology that works on the South African variant, and are optimistic that it can be adapted for other mutations as they emerge.

“This could be a game-changer in alerting authorities to the spread of these variants in the population, and enabling them to take the relevant steps that can help in the face of more transmissible strains,” microbiologist Prof. Ariel Kushmaro, who headed the research, told The Times of Israel.

Hadassah Ein Kerem Hospital team members wearing safety gear as they work in a coronavirus ward on February 01, 2021. (Olivier Fitoussi/Flash90)

Given that the British variant is estimated to be 45 percent more transmissible than regular coronavirus, its prevalence is vital health intelligence for authorities, said Kushmaro. And in view of concerns that vaccines may prove less effective against the South African variant, it is important that officials have the chance to reassess the easing of restrictions for vaccinated people if it is making inroads, he added.

Kushmaro said that if authorities see either strain spread, they will have options to implement policies including local lockdowns and testing drives; reassess the functioning of schools, where they spreads more than regular COVID; and call on the public for vigilant social distancing.

Sewage monitoring currently provides a regional picture of coronavirus levels to health officials in parts of the US, Europe, Australia and Israel, but it doesn’t tell them whether variants are on the rise.

Illustrative image: the installation of sewage-monitoring stations at the Technion-Israel Institute of Technology (courtesy of the Technion-Israel Institute of Technology)

Kushmaro’s team has created new primers and probes — two key aspects of testing systems — that detail the level of the British and South African variants.

While the invention involves complex adjustments to the regular design, instructions to produce the new test can be easily detailed to genomics companies worldwide as part of a licensing arrangement, Kushmaro said.

The British variant has quickly spread in Israel and today accounts for almost all COVID-19 cases, but in other countries is spreading more slowly.

“There are many countries where the British variant has not yet spread widely, including the US, but for the most part they are only monitoring whether or not there is coronavirus, and getting a sense of the viral load,” said Kushmaro. “This test can help us to face the major challenge of variants.”

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