In addition, 14 other people were believed to have contracted Omicron, based on their test results showing S gene target failure (SGTF).
By
Kompas Team
·5 minutes read
AFP/MOHD RASFAN
A passenger wearing a face mask queues to check-in for her flight at the Kuala Lumpur International Airport (KLIA) in Sepang on November 29, 2021, as countries across the globe shut borders and renewed travel curbs in response to the spread of a new, heavily mutated Covid-19 coronavirus variation dubbed Omicron.
JAKARTA, KOMPAS—The Omicron variant is believed to have entered Indonesia at the end of November 2021. This is according to the tracing results, which indicate that the first case of the Omicron variant of Covid-19 was presumably an Indonesia citizen arriving from Nigeria on 27 Nov. 2021.
The Health Ministry’s Covid-19 vaccination spokesperson, Siti Nadia Tarmizi, said in Jakarta on Sunday (19/12/2021) that the identification of the country’s first Omicron case was based on the mandatory quarantine for all travelers entering Indonesian territory. Through quarantine, health workers monitored all overseas arrivals. If a traveler tested positive for Covid-19, their close contacts were promptly traced. Infected travelers showing symptoms could also be treated directly.
A Health Ministry report on Sunday revealed that three cases of the Omicron variant had been detected in Indonesia. The first was N, a cleaner at the Athletes Village Covid-19 Emergency Hospital (RSDC) in Jakarta. The two other cases were confirmed on 17 Dec. as Indonesian citizens who had arrived from abroad and were quarantined at the Athletes Village.
In addition, 14 other people were believed to have contracted Omicron, based on their test results showing S gene target failure (SGTF).
KOMPAS/DEONISIA ARLINTA
Siti Nadia Tarmizi
SGTF, also called “S gene dropout”, refers to when the S gene is not detected in a PCR (polymerase chain reaction) test as an indicator of the presence of the Omicron variant. Seven cases were detected at the Entikong border checkpoint in West Kalimantan.
Earlier entrance
In tracing N’s close contacts to determine the chain of infection, 169 samples were tested, all taken from Indonesian citizens. The results of whole genome sequencing (WGS) tests showed that five samples were negative, 88 were not present with the Omicron variant, 51 had no specimens, and 24 tests failed due to high cycle threshold (CT) values. Meanwhile, one sample was still being processed. Forty people are receiving treatment and 129 people have been released and gone home.
Of the 70 people who were close contacts of N, 10 have tested positive for Covid-19. Their samples are being examined further for the Omicron variant.
“The tracing is intended to ascertain whether they were infected with Omicron from N or not,” said Nadia.
A partial lockdown of the Athletes Village RSDC is being imposed until 23 Dec. The head of the Indonesian Military Health Center, Maj. Gen. Budiman, said the lockdown was imposed pending the WGS test results of 10 other close contacts of N.
Nigeria origin
Tracing 169 people to discover the original source of N’s infection also found a possible Omicron case two weeks prior to N. The patient suspected of being infected with Omicron, TF, is a 21-year-old Indonesian citizen who had arrived from Nigeria on 27 Nov. and treated at the Athletes Village RSDC from 27 Nov. to 8 Dec.
AP/POOL/LEON NEAL
A medical staffer prepares a shot of Moderna COVID-19 vaccine, at a vaccination center in Ramsgate, England, Thursday, Dec. 16, 2021. Spiraling infections in Britain driven in part by the new omicron variant of the coronavirus sent shockwaves into the rest of Europe, fueling a familiar dread that tighter restrictions will scuttle holiday plans again this year. (Leon Neal, Pool via AP)
Previously, TF was quarantined at Wisma Pademangan in Jakarta. Tracing was now carried out among the health workers at Wisma Pademangan. On 28 Nov., TF’s sample was analyzed through WGS, but failed because of a high CT value of 38. A second sample was tested for SGTF on 18 Dec. and the results indicated that TF was a suspected Omicron case.
A high CT indicates a small number of viruses, so genome sequencing would be difficult. WGS needs all viral genetic materials.
Safarina G. Malik, a senior researcher at the Eijkman Institute for Molecular Biology under the National Research and Innovation Agency, said that WGS could not be done if the CT value was above 30. “A high CT indicates a small number of viruses, so genome sequencing would be difficult. WGS needs all viral genetic materials,” she said.
Meanwhile, not all laboratories have the capacity to conduct SGTF analyses. “SGTF is a special approach, not an ordinary PCR [test]. Not many PCR kits target the S gene because it mutates frequently,” she added.
Spreading fast
A report from the World Health Organization (WHO) on Saturday (18/12) revealed that the Omicron variant was spreading rapidly, even in countries with high rates of vaccination. The variant had been detected in 89 countries and the Omicron caseload was doubling in 1.5 days to 3 days in areas with community transmission.
The WHO has been investigating whether the rapid growth in Omicron cases was because the variant’s ability to evade immunity. It is also researching whether this variant has higher transmissibility than previous variants, or has a combination of both traits.
The former director of infectious diseases at WHO Southeast Asia, Tjandra Yoga Aditama, highlighted the need to immediately determine whether the variant was spreading in the community. This could begin by revealing the tracing results of N, including where N was infected and who else had been infected. In addition, tighter control should be imposed at entry points to Indonesia to anticipate a potential increase in cases imported from abroad.
“Health facilities should be prepared, including supplies of drugs and medical equipment,” he said.
AFP/GETTY IMAGES/JOE RAEDLE
MIAMI, FLORIDA - DECEMBER 03: People visit the Wynwood area on December 03, 2021 in Miami, Florida. Tourism economies around the country are concerned about the possible slowdown in business now that the COVID-19 Omicron variant is in the United States..
Dean of the University of Indonesia medical school, Ari Fahrial Syam, said the risk of Omicron entering the country would be very high if the authorities were relying only on PCR tests. On the other hand, WGS tests were not possible if a sample contained only a small quantity of the virus. Therefore, testing for SGTF should be optimized. (AIK/EVY/HLN/TAM/DAN)
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