While the Omicron COVID-19 variant appears to be diminishing, it is possible that there could be a resurgence of the Delta variant in the coming months in some countries, according to a team of researchers from Ben-Gurion University (BGU) of the Negev studying the prevalence of SARS-CoV2 virus variants in sewage.

The warning comes following last month’s peak in new cases in China, followed by rising coronavirus cases now in South Africa as it heads into chilly weather, while uptake of COVID vaccines remains sluggish.

“Of course, there are a lot of factors involved, but our model indicates there could be another outbreak of Delta or another coronavirus variant this summer,” said BGU’s Prof Ariel Kushmaro, last author on the study.

The study monitoring sewage in Beersheba – Israel’s fourth-most populous metropolitan area – between December 2021 and January 2022 found that while Delta had wiped out the variants that preceded it, Omicron did not eliminate Delta even at the height of the Omicron wave. They then built a model that predicts that while Omicron is burning itself out, Delta is just biding its time.

The findings were published recently in the peer-reviewed journal Science of the Total Environment.

“If the essence of the model predictions … will be proven accurate, the Delta variant has the potential of becoming far more problematic than the Omicron,” the researchers wrote in their paper. “With the expected significant decline in morbidity from all the recovered Omicron cases, the Israeli government and Ministry of Health will most likely remove various restrictions. In the meantime, the Delta, which is still circulating in a population with waning immunity and under fewer restrictions, may reemerge in larger numbers or even produce a new, different variant to generate infections in Israel.”

Sewage – ‘An early indicator’

South Africa is already seeing a surge in new cases in recent weeks. According to Foster Mohale, director of media relations for the Johannesburg, South Africa National Department of Health, there have been peaks of up to 10,000 new cases daily, although the average is somewhat lower.

South Africa also has a wastewater surveillance program – the SAMRC Wastewater Surveillance and Research Programme – which has been monitoring sewage for the virus.

“By testing wastewater weekly, we can measure the SARS-CoV-2 RNA signal and see whether it is increasing or decreasing,” states SAMRC. Added Mohale, “This can be used as an early indicator of COVID-19 case trends within a community.”

However, so far, the predominant variants identified seem to be two Omicron subvariants – BA.4 and BA.5 – and not Delta.  But health officials are still urging people to get vaccinated to ward off possible future threats.

“For now, we are not detecting other variants,” stressed Mohale. “So, we are saying there is no need to panic, and no new variants found in the country. The thing is that it can mutate and change in a short period of time. “We need to raise awareness and encourage the public to continue vaccinating and to get those who are vaccinated [at least five months ago] to take a booster shot.”

‘Gigabytes of data running just under the city’

Israel and South Africa are two among several dozen of countries around the world engaging in cutting-edge wastewater surveillance for COVID-19. The novel results of Kushmaro’s study are that it now appears that surveillance can be used not only to track the virus in real-time but to help predict the future.

“The idea behind this publication is to show how the data that we can generate from the wastewater can be used later on for predictions,” Kushmaro said. “So, this is the novel thing when we look at the scientific point of view of the publication.”

His team, which specializes in wastewater epidemiology, has been identifying different pathogens in wastewater for decades. The latest study is part of the research they started in March 2020 ton track coronavirus via sewage.

Towns of more than 20,000 people are monitored twice a week using a series of sensors and control units placed in municipal sewage systems, in a model surveillance system. The samples are sent to laboratories where PCR tests suitable for wastewater are conducted. In the event that the results received are positive, an additional test is carried out to quantify the prevalence of Omicron  and other variants. Sample results are fed into a national computer database that can analyze the results based on big data models and AI. The entire process takes about 24 hours.

‘Omicron levels will decrease until eliminated, while Delta variant will maintain its cryptic circulation’

Modeling of future trends was enabled by the development of a new RT-qPCR primers-probe set for even faster and more precise detection of the Omicron variant.

“Characterized as highly specific and sensitive, the new Omicron detection set was deployed on clinical and wastewater samples. In contrast to the expected dynamics, whereupon the Delta variant diminishes as Omicron variant increases, representative results received from wastewater detection indicated a cryptic circulation of the Delta variant even with the increased levels of Omicron variant,” the authors state in their study.

“Based on the initial results, a double susceptible-infected-recovered model was developed for the Delta and Omicron variants,” the paper continued. “According to the developed model, it can be expected that the Omicron levels will decrease until eliminated, while the Delta variant will maintain its cryptic circulation. If this comes to pass, the mentioned cryptic circulation may result in the reemergence of a Delta morbidity wave or in the possible generation of a new threatening variant.

“In conclusion, the deployment of wastewater-based epidemiology is recommended as a convenient and representative tool for pandemic containment.”

The Delta variant was considered “cryptic” because it did not diminish as expected but also did not remain dominant, only circulating enough to exist but not to cause an increase in morbidity levels.

“Resulting wastewater data illustrated the very initial Delta-Omicron dynamics occurring in real-time. Despite this, the future development and dynamics of the two variants side-by-side are still mainly unknown,” the authors conclude.

Kushmaro noted to Health Policy Watch, however, that the team’s latest samples were in mid-February. But he said that rising case numbers in parts of the world “hint that coronavirus is still with us… and we have to be prepared.”

‘Vaccination remains the most effective weapon against COVID-19’

Mohale said that South Africa is actively deploying a multi-pronged vaccination strategy to help ensure more of the population gets vaccinated.

According to Our World in Data, only 31% of the South African population is fully vaccinated and less than 5% of eligible individuals have opted for a booster shot – despite new data published this week, which showed the much greater benefits of a third shot.

“We are integrating vaccination services into normal health services. So, for example, you can access vaccination services at dedicated vaccination sites, but also in your general health facility,” Mohale said.

In addition, the country has added COVID-19 vaccination to its school health program for children ages 12 and older. And it is offering the shots at large events; unvaccinated people who would otherwise need to present a negative PCR test to enter a sporting event, for example, can forgo the swab and take a jab instead, Mohale added, saying:

“Aside from all other preventative measures, vaccination remains the most effective weapon against COVID-19.”

Image Credits: Kando , Our World in Data, Screenshot.