Indonesia: Raging pandemic offers fertile ground for new variants

The speed and scale of the coronavirus outbreak in Indonesia has created a perfect breeding ground for a potential new super-strain that could be even more contagious and deadly than the Delta variant, infectious disease experts from around the world are warning.

Last week Indonesia surpassed India and Brazil to become the country reporting the world’s highest number of daily cases. On Thursday, the archipelago reported more than 49,500 new cases and 1,449 deaths.

“New variants always appear in regions or countries that cannot control outbreaks,” said Dicky Budiman, an Indonesian epidemiologist researching coronavirus variants at Australia’s Griffith University. “The World Health Organization [WHO] says if more than 5 percent of tests come back positive, the outbreak is uncontrollable. In Indonesia, it’s been higher than 10 percent for 16 months at the start of the pandemic. Now it’s higher than 30 percent. So you can imagine how high the possibility is for Indonesia to create a new variant or a super variant of COVID-19.”

Amin Soebandrio, a director at of the Eijkman Institute, a government organisation studying tropical and emerging infectious diseases, says while no new variants have yet surfaced in Indonesia vigilance is crucial.

“With the increasing number of cases, we cannot deny that it’s possible and have to carefully observe to identify new variants as soon as they emerge,” he said.

Variants of Concern

Viruses constantly change through mutations to their genes, creating more advanced variants.

Dr Stuart Ray, the vice chair of medicine for data integrity and analytics at the Johns Hopkins University School of Medicine, says new COVID-19 variants are being detected around the world every week but “it is in the nature of RNA viruses such as the coronavirus to evolve and change – gradually”.

He says “most come and go – some persist but don’t become more common; some increase in the population for a while and then fizzle out.”

Only when a variant displays a jump in its ability to transmit, increased severity based on hospital admissions or deaths, or reduced effectiveness of treatments and vaccines, does WHO classify the strain as a ‘variant of concern‘.

Globally, there are four variants of concern: the so-called Alpha variant, first identified in the UK; the Beta variant, first identified in South Africa, the Delta variant, first identified in India; and the Gamma variant, first identified in Brazil.

Soebandrio says all but the Gamma variant have been detected in Indonesia, and that the country now has the diagnostic capacity to detect new strains within short time frames. More than 3,000 genome strings have been sequenced since the start of the year in Indonesia compared with only 200 to 300 last year. The results show the Alpha variant is still spreading but Delta is dominant.

The Delta variant is “four to five times more infectious than the original virus,” said Shahid Jameel, India’s top virologist who until recently led the advisory group at the Indian SARS-CoV-2 Genomics Consortia, which monitors variants of COVID-19.

Jameel says the situation in Indonesia is now “very similar” to India’s second wave due to “poor rates” of vaccination. Only 8 percent of Indonesians are fully vaccinated according to the Ministry of Health.

Opportunity to run wild

Representatives of two of the world’s leading coronavirus research groups in the United States worry conditions in Indonesia are ripe for the emergence of a new COVID-19 variant of concern.

“The more infections in a community, the more a chance for a new variant,” said Ali Mokdad, a professor of Health Metrics Sciences at the Institute for Health Metrics and Evaluation in Seattle. He also expressed concern about Indonesia’s Eid al-Adha festival, which took place this week and “activity around it”.

Indonesia’s COVID-19 task force issued a special directive for the holiday week, banning public travel nationwide. It also extended an emergency partial lockdown, introduced on July 3, until next Monday.

Thousands of security personnel have been deployed around the country to enforce the travel ban, after a similar order at Eid al-Fitr, the end of the fasting month of Ramadan, did little to stop people travelling.

But last weekend, police and army at the port of Gilimanuk in west Bali looked on as thousands of migrant workers boarded overcrowded ferries to return to their families in Java, the epicentre of the outbreak in Indonesia, to celebrate the holiday. I Nengah Tamba, the head of the regency in which Gilimanuk is found, is refusing to enforce the extension of the emergency partial lockdown.

Dr Robert Bollinger, a professor of infectious diseases at Johns Hopkins University School of Medicine, warns COVID-19 “has the potential to mutate into a new variant every time it infects a new person. So the risk of new variants is highest in communities and countries with the highest number of new cases, which includes Indonesia.”

But predicting where and when a new variant of concern will emerge, is currently beyond the ability of today’s scientists.

“All I can say is that when you give an RNA virus like this the opportunity to run wild, it will accumulate random mutations more frequently and the chances of a new variant will increase,” said Indian virologist Shahid Jameel.

“They should learn from India’s experience, the foremost being a very quick surge in hospital capacity and oxygen availability. Because unfortunately, the worst is yet to come for the region.”