To detect Covid-19 causing viruses, an inspection is required called Polymerase Chain Reaction (PCR) and Rapid Test Antigen and Antibodies. Both types of checks aim to determine whether someone is infected with the SARS COV-2 virus or not. PCR tests that are still widely used can detect infection, including omicron infections, as observed in other variants. For the Rapid test antigen and antibodies are still in the research stage in its ability to detect omicron variants.
Detection and identification of the SARS-COV-2 virus variant can be done through several stages and methods. The beginning of the screening process was carried out, with an examination of RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) / naat examination (Nucleic Acid Amplification Test), using 2 (two) reagent types, namely:
1. Reagents that can detect direct mutations (mutation-detecting naat assays) with the target of mutation detection that has been known to certain variants.
2. Reagent with Gene target failure; Namely RT-PCR reagent, one of the target genes is proven to be affected by mutations to certain variants, but other target genes are still detected so that they still give positive results. Due to the SARS-COV-2 virus mutation is known to have the most common in genes that cause certain reagent failure to detect the target s; which is known as S-Gene Target Failure (SGTF).
For this reason, screening checks must use the naat reagents that have been officially tested or validated on the current variants. In addition, this screening examination also must still be confirmed by Whole Genome Sequencing (WGS), because
WGS is an examination that can identify and specifically determine the type of SARS-COV-2 variant.
The Screening Examination Strategy for the Omicron variant can be done through 4 (four) strategies, namely:
Strategy 1.
The examination uses routinely used NAAT / PCR reagents (not affected by mutations / non-SGTF). When obtained positive results SARS COV-2 and fulfill the WGS inspection requirements, the specimen is sent to the WGS reference laboratory.
Strategy 2.
Examination and screening variant using the affected Naat / PCR reagent (SGTF):
A. Positive specimens of SARS-COV-2 but Gen S is not detected (SGTF) and fulfills the WGS inspection requirements sent to the WGS reference laboratory as a priority specimen.
b. SARS-COV-2 positive specimens with genes are detected >> can be sent to the WGS reference laboratory if you meet the WGS inspection requirements.
Strategy 3.
Examination using the affected Naat / PCR reagent (SGTF) with the limitations of reagent inventory.

Stage 1 >> Examination using the Naat / PCR reagent which is routinely used (non-SGTF) → if the results are positive, it can be continued to stage 2.
Stage 2 >> Variant Examination Screening Using Naat / PCR Released Reagent Mutation (SGTF):
A. Positive results of SARS-COV-2 with G genes are not detected (SGTF) and meet the WGS inspection requirements sent to the WGS reference laboratory as priority specimens;
b. SARS-COV-2 positive results with detected genes can be sent to the WGS reference laboratory if you meet the WGS inspection requirements.
Strategy 4.
Laboratories have special naat / PCR reagents that can
Detect Mutations
Stage 1 >> Examination using routinely used naat reagents (non-SGTF) → if positive results, can be continued to stage 2.
Stage 2 >> Variant inspection screening using special naat reagents that can detect mutations.
A. Positive results and detected certain mutations and meet the WGS inspection requirements are sent to WGS reference laboratories as priority specimens;
b. Positive results without detecting certain mutations can be sent to the WGS reference laboratory if you meet the WGS inspection requirements.
Terms of Examination of Whole Genome Sequencing (WGS):

Specimens / sample checks used for WGS examination are specimens / covid-19 patient samples that meet the requirements in accordance with the guidelines of the Balitbangkes, which are the main requirements, namely:

▪ The results of the positive RT-PCR examination with low Cycle Threshold (CT value) values ​​(generally <30 on examinations using reagents with cut off around 40)
▪︎ Specimen volume of at least 600 μL.
Additional conditions for WGS examination, namely patients are included in one of the following case criteria:
A. International travel or migrant workers who arrived in Indonesia;
b. People from the Indonesian border area with neighboring countries;
c. Area where there is an increase in cases and clusters / fast transmission;
. People who participate in vaccine trials and / or have been vaccinated in full dose;
e. People with a history of infection and re-infection;
f. People with immune disorders (autoimmune disorder) and comorbid diseases (HIV, TB, etc.)
g. Children with <18 years old in areas that have increased cases in children
h. People with clinical symptoms of severe pain that are <60 year and do not have accompanying diseases;
i. All SARS-COV-2 positive cases contacted the Sarscov-2 case of VOC (Variants of Concern) and VOI (Variants of Interest).
If there are only a few positive cases with low CT Value, then all the specimens with low CT value results can be sent to do WGS without seeing the criteria above, as a step to keep monitoring the SARS-COV-2 variants).
Patient preparation and inspection material
▪︎ Pulmonary panel examination does not require special preparation before.
▪ The examination material used is wipe the nose and throat.
Further information, please contact the clinic Laboratory of the Nearest Pramita Branch in your city.
Author: S.M.Susianna., Dr., sp.pk (Doctor in charge of the Pramita Clinic Laboratory Jl. Martadinata No. 135 Bandung)