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Coronavirus

Indonesia ramps up effort to spot elusive COVID variants

'Genomic surveillance' effort to sequence 10,000 samples under fire over strategy

A healthcare worker injects a dose of the Sinovac COVID-19 vaccine during a mass vaccination drive for vendors and shop keepers at Tanah Abang textile market in Jakarta on Feb 17.   © EPA/Jiji

JAKARTA -- Indonesian scientists are planning to sequence 10,000 samples of COVID-19 this year to detect variants of the virus that may be circulating around the vast archipelago.

Last month, Health Minister Budi Gunadi Sadikin signed a memorandum of understanding with Minister of Research and Technology (RISTEK) Bambang Brodjonegoro to collaborate on "genomic surveillance" -- the process of identifying virus variants by sequencing genetic materials collected from infected patients.

The two ministers acknowledged that emerging variants from places such as the U.K., Brazil and South Africa may have "infiltrated" the country without detection. "I realize that we need to build defense system against them," Sadikin told reporters.

The World Health Organization issued a report on Tuesday that said the number of new cases continues to fall globally, but variants have spread to more than 100 countries. More than 82,000 cases of the new U.K. strain had been detected in 85 nations as of Feb. 19, according to data compiled by GISAID, an open access global database for virus genomes. The South African variant had infected 1,440 people in 42 countries.

The longer the disease is allowed to thrive, the higher the chance it will mutate into variants resistant to the vaccines being rolled out at different speeds across the world.

In Indonesia, 392 whole genome sequences from 27 provinces were submitted to GISAID between the signing of the MoU and Feb. 14. Slamet, head of the National Institute of Health Research and Development (Balitbangkes), said at least 14 institutions have contributed, each of which has capable people and cutting-edge devices for genomic research.

But critics say the program should set a clear strategy to determine which samples to sequence rather than simply boosting numbers. For example, the B.1.1.7 variant from the U.K. has not yet been detected in the country.

In a RISTEK webinar on Feb. 15, Peter Borgen, the president of GISAID, said the existence of these variants "cannot be proven or disproved" at the moment due to the size of the archipelago.

"It maybe because we are not creating enough data," he said, urging the Indonesian government to accelerate surveillance efforts. "It's time for collecting [samples] in a broad range" from metropolitan areas to remote regions to get a good picture of the situation."

Slamet admitted there is an unequal distribution of sequenced samples, but said this may be due to factors such as the "high mobility of people and the increasing number of COVID-19 cases in several areas."

Amien Soebandrio, the head of the Eijkman Institute of Molecular Biology in Jakarta -- the most prominent institution in the surveillance effort -- said Borgen's statement was included in the MoU.

The more the data we have, the more information we can get about the strains of the SARS-2 virus in Indonesia, he said. "We need widen the net so that the chance to catch the target is bigger."

Eijkman plans to sequence 5,000 samples this year and Balitbangkes is targeting 10,000 samples from all participating institutions.

Critics also say that speed is a crucial factor in genomic surveillance.

The number of new COVID-19 infections in Indonesia continues to rise. Officially, the virus has infected about 1.3 million people and killed around 35,000 in the country. But scientists say this number is far from the reality due to the limited number of testing and data discrepancies between local and central government. They say this means the virus is replicating rapidly, and likely creating undetected variants -- potentially affecting the country's mass vaccination program.

While Soumya Swaminathan, chief scientist at the World Health Organization, says that current vaccines are likely protecting people against new variants, scientists are researching whether the strains have made inoculations outdated. Companies such as Pfizer and Astra Zeneca are looking at potentially modifying their vaccines. China's Sinovac, whose vaccines have been rolled out in Indonesia, also reports their shots are effective against new variants.

Riza Putranto, head of the Indonesian Society for Bioinformatics and Biodiversity, said that Indonesia should set a surveillance strategy to determine which samples to sequence.

Based on his observation in GISAID, Putranto noted that the Philippines, which has sequenced fewer samples than Indonesia but has already detected the B.1.1.7 (U.K.) variant, because its scientists focus on sequencing samples from patients arriving from Britain.

"Indonesia needs to set up a strategy," he tweeted. "So even with a limited resource, we do it right on target."

Ahmad Utomo, a molecular biologist at YARSI University in Jakarta, is critical of how Indonesian scientists randomly select virus samples for genome sequencing.

Masdalina Pane, an epidemiologist at the Association of Indonesian Epidemiologists, said sequencing samples from unusual clusters of infections, such as large ones and those with fast transmission, could be a good strategy.

Soebandrio at Eijkman said that his team at Eijkman and other labs only sequenced samples that arrived in their lab -- none of them coming after consultation with epidemiologists.

"In the beginning, we didn't really look at mutations and it was not easy to get good samples," he said. "So far, we only sequenced samples available in our labs because it was difficult for us to get ones with enough quality."

The Eijkman Institute and Balitbangkes have started to coordinate with doctors at hospitals and local health agencies to obtain samples from unusual clusters, reinfections, and any suspicious cases.

Soebandrio said that before sending samples to be sequenced, every lab and hospital must submit clinical and demographical data to an online portal managed by Balitbangkes.

"We're going to put attention on those details," he said.

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