Omicron Case Deported To Indonesia Was Semenyih Immigration Detainee: Khairy

Khairy Jamaluddin also says the Covid-19 genome sequencing strategy to identify the Omicron variant will be expanded to include high-risk cases, besides international travellers.

KUALA LUMPUR, Dec 25 – An Omicron case recently reported as an imported infection in Indonesia was previously detained at the Semenyih immigration detention depot, Khairy Jamaluddin said today.

The health minister said the 20-year-old Indonesian man, an undocumented migrant worker, was arrested with three others.

The four tested negative for Covid-19 upon entry screening at the Semenyih immigration detention depot on September 23. Two of the man’s friends were released on September 24 because they had complete work documents, while the Omicron case and another were convicted of immigration offences and deported to Indonesia on December 10.

The man tested negative for Covid-19 upon arrival in Indonesia, but tested positive six days later for the virus on December 16 during quarantine in Indonesia. Indonesia’s Health Ministry said in a statement Thursday that the man’s Covid-19 infection was confirmed to be of the Omicron variant on December 21.

“To date, the companion of the case deported with him tested negative for Covid-19 in a second screening,” Khairy told a press conference.

“Further investigations are underway to get information on the close contacts of the case and the source of infection.”

When asked whether he was concerned about potential Omicron outbreaks in immigration detention centres, Khairy said the Ministry of Health (MOH) is working together with the Immigration Department to pick up any positive cases, where genotyping assay testing can be done to identify probable Omicron infections.

The health minister also explained that testing protocols are very stringent in these detention facilities, as detainees are tested before arrival and exit.

“We’ll have a word with the immigration department on the conditions in the depot itself.”

Numerous Covid-19 outbreaks at immigration detention centres were reported previously, attributed to poor and congested conditions in the facilities. The facilities are also not completely isolated from the community, as staff and officers working in the immigration detention centres go back to their homes.

On the suspected locally transmitted Omicron case in Kuching, Sarawak, Khairy clarified that the case is a 38-year-old male Chinese citizen. The Sarawak state government yesterday misidentified the case as a woman.

The fully vaccinated Chinese man, who has been working at an engineering firm in Sarawak for three years, did not travel overseas for the past three years.

He got tested for Covid-19 on December 18 after fever and cough symptoms since December 13. After testing positive, he was admitted into the Covid-19 quarantine and treatment centre (PKRC) at Sarawak General Hospital on December 20. The man is currently in stable condition.

The Institute of Health and Community Medicine (IHCM) at Universiti Malaysia Sarawak (Unimas) subsequently undertook genomic sequencing testing and confirmed the case to be an Omicron infection on December 23.

“The source of infection still has not been identified and investigations are ongoing at the Kuching state health department,” said Khairy.

Two of the man’s close contacts have been identified and directed to a quarantine station to self-isolate for 14 days. Their first Covid-19 tests showed negative results.

When asked whether he agreed with the US-based Institute for Health Metrics and Evaluation’s (IHME) projections of up to 300,000 daily Covid-19 cases in Malaysia by end January due to Omicron, Khairy said MOH has yet to make a prediction on the spread or severity of the new variant.

This, he said, depends on epidemiological analysis on confirmed Omicron cases, their close contacts, and severity of their infection. All of the 49 new Omicron cases reported in the past two days are asymptomatic or mild in Categories 1 or 2.

“I think it’s too early for us to project what will happen in Malaysia,” Khairy said.

“But based on what’s happening in other countries, we know Omicron is more transmissible. With the news of the possibility of the community case in Sarawak, it follows that there will be a spike of cases over the next few weeks. How much and how severe, we don’t know yet.”

Genome Sequencing Expanded to High-Risk Cases

Khairy announced that surveillance for coronavirus variants would be expanded to cover not just international travellers, but also high-risk cases. Four hospitals in the peninsula – Tuanku Jaafar Seremban Hospital in Negeri Sembilan, Sultanah Bahiyah Alor Setar Hospital in Kedah, Sungai Buloh Hospital in Selangor, and Raja Permaisuri Bainun Ipoh Hospital in Perak – have the capacity to test for variants, plus another four hospitals in Sarawak.

Whole genome sequencing to confirm variants is undertaken by the IMR-MOSTI-KPT-MGI consortium comprising seven institutes under MOH, the Higher Education Ministry (KPT), and the Ministry of Science, Technology and Innovation (MOSTI): Institute for Medical Research (IMR), the National Public Health Laboratory (MKAK), IHCM, UKM Medical Molecular Biology Institute’s (UMBI), University Malaya’s Tropical Infectious Diseases Research & Education Centre’s (Tidrec), UiTM’s iPromise Institute, and the Malaysian Genome Institute under MOSTI.

The sampling strategy for genomic sequencing of Covid-19 cases includes looking for the S-gene target failure in RT-PCR tests that can flag probable Omicron cases, or clinical cases that present like Covid-19 but repeatedly show negative RT-PCR test results.

Genomic surveillance covers:

  • cases from areas with high transmission or with a rapid spike in infections (cases should consist of different age groups, different severity from mild to severe or fatal cases; or different localities within the state);
  • international points of entry;
  • children in areas with increased incidence of paediatric Covid-19 cases;
  • severe cases among those aged below 60 years and without comorbidities;
  • patients with unusual manifestations like rapid deterioration, those in intensive care units (ICUs);
  • cases suspected of reinfection;
  • health care workers and those from the community with vaccine breakthrough infections;
  • deaths or brought-in-dead cases with positive PCR test results for Covid-19;
  • samples from severe acute respiratory infections, influenza-like illness, as well as sporadic or random cases will be taken for genomic sequencing.

High RNA concentration and stability are the key factors for whole-genome sequences of high quality. Therefore, recommended clinical samples based on laboratory diagnostics are as follows:

  • Samples with Ct values < 25;
  • Samples transported through an unbroken cold chain and storage under ultra-low temperatures conditions;
  • Avoid multiple freeze-thaw cycles of the sample.

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