RSJMM Laboratory, the First Hospital Lab Capable of Detecting Omicron Variants in Bogor City
Starting from the city of Wuhan, Hubei Province, China, at the end of 2019, a new type of coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was identified and quickly spread to various countries, including Indonesia, which reported its first case on March 2, 2020. On March 11, 2020, the WHO declared Coronavirus Disease 2019 (COVID-19) as a pandemic. Common symptoms of COVID-19 include a fever of 38 degrees Celsius, dry cough, and shortness of breath. Other symptoms may include fatigue, muscle pain, headache, diarrhea, nausea, vomiting, loss of smell, and an inability to taste food.
The Coronavirus is an RNA (Ribonucleic Acid) virus type that naturally undergoes mutations to survive, resulting in the emergence of new variants. The Omicron B.1.1.529 variant of COVID-19 is currently drawing attention worldwide. The WHO has designated this variant as a Variant of Concern (VOC), meaning it is on the WHO's watchlist because it has a high transmission rate, high virulence, and reduces diagnostic and vaccine effectiveness. Some other variants classified as VOCs include Alpha, Beta, Gamma, and Delta. Additionally, there are other variants classified as Variants of Interest (VOIs), such as the MU and Kappa variants.
To control the spread of COVID-19 in the country, the government has been actively conducting mass diagnostic testing for COVID-19 using the Gold Standard, which is the Real-Time Polymerase Chain Reaction (RT-PCR) test. This follows WHO guidelines, which stipulate that the standard number of RT-PCR tests should be 1,000 per 1 million population per week. Therefore, the role of laboratories during this pandemic is crucial, including at RSJ dr. H. Marzoeki Mahdi.
Laboratory tests for diagnosing COVID-19 at RSJ MM include antibody and antigen tests, as well as RT-PCR for SARS-CoV-2. RT-PCR tests at the hospital's Emergency Room (IGD) are used as screening to determine the type of treatment room. Testing is conducted every day (24/7) twice a day at 11 AM and 6 PM. Since the beginning of the pandemic, the RSJ MM laboratory has been performing RT-PCR tests using both conventional equipment and rapid molecular tests. The test results are affiliated with the Ministry of Health's New All Record (NAR), which can be accessed through the Peduli Lindungi app. The quality of the test results is unquestionable because the RSJ MM laboratory has participated in the External Quality Assurance (EQA) for RT-PCR COVID-19 organized by the National Institute of Health Research and Development (Balitbangkes), with satisfactory results.
The SARS-CoV-2 Omicron variant is becoming dominant in Indonesia. To address the current COVID-19 phenomenon, the Ministry of Health is working to enhance early detection of new variants of the SARS-CoV-2 virus. The RSJ MM laboratory is one of the recipients of the SGTF kits from the Ministry of Health, branded as mBiofarma, with a total of 3 kits (each containing 50 tests). The RSJ MM laboratory became the first hospital laboratory capable of detecting the Omicron variant in Bogor City. The detection of the Omicron variant is intended for COVID-19 patients with worsening conditions.
The characteristic of the Omicron variant includes a unique mutation at amino acid position 69/70 in the S gene. This mutation can be identified by the failure of detection using the PCR method, or in other words, one of the three target genes is not detected. This condition is known as SGTF (S-Gene-Target-Failure) and has been used by the WHO as a guideline for screening variants/mutations. The SGTF method can detect genetic variants more quickly (4-6 hours after sample collection) compared to Whole Genome Sequencing (WGS), which takes at least 3-5 days. However, it can only identify known variants or specific variants like Omicron.
The SGTF detection technique, thus far, only determines probable status and is not yet confirmed as positive. Therefore, it needs to be validated again using WGS testing. Nevertheless, probable Omicron cases are monitored and quarantined. WGS can identify all mutations/variants, even those previously unknown. WGS is the process of determining the complete DNA sequence of the SARS-CoV2 genome (approximately 30,000 base pairs) using Next-Generation Sequencing technology. In addition to identifying variants, WGS can also be used for other purposes such as vaccine development, diagnostics, determining transmission patterns, and relationships.
RSJ MM not only provides mental health services but also non-mental health services. Therefore, the laboratory services at a mental hospital are quite competent. One reason for the stigma of people preferring to seek treatment at general hospitals rather than mental hospitals, even for mental health issues, is because they perceive mental hospitals as worse than general hospitals. "If you ask your neighbor where you've been, and you say, 'I've just been to the general hospital,' compare that to saying, 'I've just been to the mental hospital,' you might get even more questions later," said Sunjaya (quoted from health.detik.com).
Recently, RSJ MM was designated as the National Mental Health Center (PKJN), with the responsibility of providing comprehensive mental health services (promotive, preventive, curative, and rehabilitative) integrated with services in the community, complete specialist and subspecialist psychiatric services, non-psychiatric services as supporting mental health services, establishing mental health referral networks, and serving as a national referral hospital in the field of mental health.
With adequate facilities and infrastructure, the RSJ MM Laboratory is ready to be part of the National Mental Health Center!
Author: Arsita Setyani, A.Md.,AK
Bibliography:
https://www.litbang.kemkes.go.id/mengenal-cara-deteksi-varian-sars-cov-2-dengan-wgs-dan-pcr-sgtf/
https://sehatnegeriku.kemkes.go.id/baca/umum/20210305/0737135/mutasi-virus-corona-lebih-cepat-menular-masyarakat-dihimbau-perketat-disiplin-protokol-kesehatan/