The government officially confirmed the case of the first Omicron variant of Covid-19 in Indonesia on Thursday (December 16). This variant is said to be five times more contagious than the first variant of the coronavirus.
In order to anticipate the spread of the Omicron variant in the country, Health Minister Budi Gunadi Sadikin will step up the tests to detect the Covid-19 variant in positively confirmed cases. One type of test that is improving, namely Sequencing the entire genome (WGS) also known as whole genomic data sequencing.
Budi announced that the test would be increased from 5% to 10% of the total confirmed cases. Meanwhile, confirmed cases are currently in the 200-300 cases per day range.
What is WGS?
Quoted from Genecraft Labs, WGS is a comprehensive technique used in sequencing DNA sequences into a complete genome image (entire genome sequence), through the use of technology Next generation sequencing (NGS).
Sequencing and piecing together the genome sequence is like putting together a puzzle made up of billions or billions of image pieces. proceedings Sequencing the entire genome This is done with the help of complex calculations and algorithms or is called bioinformatics.
Genome is a complete set of genetic material (DNA / RNA) of an organism that contains important data (stored in genes) to carry out the functions of organisms in life. Physically, the genome is divided into several different nucleic acid molecules, while the genome is functionally divided into genes.
Every organism contains the biological information needed to build body tissue, sustain life, and pass on to the next generation. Most genomes are made up of DNA, but some viruses are made up of RNA in their genomes.
Comparing the genomes of organisms can provide information about the properties of organisms, their evolution and various biological processes that take place in the body of these living things. The human genome (homo sapiens) consists of 23 paired chromosomes with more than 3 billion DNA base pairs (base pairs). There are 3 million pairs of DNA in the human body, all of which are located in the nucleus of every cell.
Roles and functions of WGS
Given the conditions of the Covid-19 pandemic, WGS also plays an important role as a tool for creating genetic blueprints (genetic blueprint) of the virus genome of SARS-CoV-2, identification of new mutations, tracing of the virus origin and prevention of virus transmission.
Specific SARS-CoV-2 genomic data will form the basis for vaccine research and formulate appropriate treatments for the treatment of Covid-19 cases in a country by researchers and medical staff. In addition, the SARS-CoV-2 genomic data can also be used to map and study the course of the spread of Covid-19, enabling policy makers (governments and related agencies) in a country to adopt strategies to contain the spread of Covid-19. 19 can develop the virus.
The working methods or techniques of the WGS can be divided into traditional techniques and modern techniques (new methods). Whereby for traditional techniques based on the fragmentation and reassembly of pieces of sequence, ie method hierarchical order and Shotgun Sequencing.
In the meantime, modern techniques in the WGS method have been developed from the existing sequencing, such as: Nanopore sequencing, HiSeq and NGS.
WGS development in Indonesia
The 2019 World Health Organization (WHO) report found that WGS is a relatively new concept in genome technology. In which the skills and knowledge of the country in WGS laboratory work and data analysis can be improved.
The Genome Surveillance Team is based in Indonesia SARS-CoV-2 from the Indonesian Institute of Sciences alias LIPI (Venomcov Team), has the platform of. used successfully Oxford Nanopore Technologies (ONT) to identify COVID19 variants.
University of Indonesia health expert Prof. Tjandra Yoga Aditama had previously stated that WGS in Indonesia needs further improvement. This must be done in order to prevent the entry of new variants of SARS-CoV-2 from abroad as well as domestic mutations.
In addition to actively reporting on the WGS sample, the former director general of P2P and head of Balitbangkes promotes social restrictions as well as the use of 3T such as testing, tracking and therapy. This step needs to be implemented so that Indonesia can avoid the attack of another wave of Covid-19 cases.
As of November 1, 2021, Indonesia sent 8,350 samples, according to a report by the genome data collection agency GISAID. Singapore has now sent 8,970 samples, the Philippines 12,681 samples and India 72,325 WGS samples to GSID.
“Of course, a comparison (Indonesia) with developed countries isn’t very accurate, but the United States has submitted 1.46 million WGS samples to GISAID and the UK has 1.11 million samples,” said Tjandra Yoga, quoted by Antara. Between, Thursday (4/11).
Previously, the GISAID report showed that as of Thursday, December 9, 2021, there were 48 cases of the Omicron variant of the Covid-19 virus (B.1.1.529) in 11 countries in Asia. The majority or 13 cases Covid-19 The Omicron variant comes from Hong Kong.
Israel ranks second in Asia with the most cases of Covid-19, the Omicron variant with 12 cases. At the time, Singapore and India had 6 cases and 5 cases of the Omicron variant of Covid-19, respectively.
Then up to 3 cases of the Omicron variant of Covid-19 were discovered in Japan and South Korea. Then Russia discovered 2 cases of the Omicron variant of Covid-19.
Sri Lanka, Thailand, Maldives and Malaysia each have recorded 1 case of COVID-19, the Omicron variant. According to the Ministry of Health, no cases of the Omicron variant of Covid-19 have so far occurred in Indonesia.
The GISAID report also states that there are 41 countries worldwide that have discovered cases of Covid-19 Omicron. A total of 1,109 cases of the Omicron variant of Covid-19 were detected.
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