Detection of the SARS-CoV-2 Omicron Variant in COVID-19 Patients from South Tangerang Using SNP-Probes S371L and K417N

The COVID-19 pandemic caused by the SARS-CoV-2 virus has posed a global challenge. Experts from various branches of science have endeavoured to find solutions to control its spread, one of which has been the quick and precise detection of the virus and its variants in patients. This study aimed to detect the presence of SARS-CoV-2, notably the rapidly spreading Omicron variant, using the spike (S)-gene target failure (SGTF) and S-gene target positive (SGTP) with the principle of the single nucleotide polymorphism (SNP)-probe test. Our descriptive experimental approach detected Omicron variants with the SNP-probe technique using samples of SARS-CoV-2 patients and controls. The probes were designed to recognize the nucleotide code of the amino acids in positions 371 and 417 of SARS-CoV-2. The existence of variants was monitored by the presence or absence of a fluorescence signal, which was translated into a sigmoidal graph using a real-time (RT)-PCR machine. One hundred and twelve samples that had tested positive for SARS-CoV-2 and the Omicron variant using a registered commercial kit showed a similar result to our in-house-developed SNP-probe 371 and 417 assays. The results of this study indicate that the SNP-probe we designed can be used in the detection of the SARS-CoV-2 Omicron variant

Added Value of Bleach for Tuberculosis Microscopy Diagnostic in Limited Resources Setting

Indonesia is one of the high burden tuberculosis (TB) countries. The utilization of molecular diagnostic has been setting over the country, however there are still a lot of remote areas that only depend on microscopic smear. Bleach might be used to increase the value of microscopy diagnos- tic. The study aimed to evaluate the added value of 1% bleach to increase the positivity rate of TB compared to conventional stain. This study was conducted on 70 subjects who were suspected as TB from various pri- mary care centers in West Java and Banten, Indonesia. The sputum was 2-3 mL, and divided into two parts, both of them were stained using Ziehl-Neelsen (ZN), however the first was only stained and the second added 1% bleach. Bleach was added in same volume with sputum and incubated for 10 minutes. After 10 minutes, the spu- tum was stained with ZN. The positivity rate for ZN only was 39 (55.7%) compared to 1% bleach was 63 (90%), and significant- ly different (P=0.000) using Mann-Whitney U test. Bleach can be used as an alternative agent to improve the TB smear in setting that only depends on microscopy diagnostic

The Identification of the SARS-CoV-2 Whole Genome: Nine Cases Among Patients in Banten Province, Indonesia

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the current pandemic. Viral genome sequencing has been widely applied during outbreaks to study the relatedness of this virus to other viruses, its transmission mode, pace, evolution and geographical spread, and also its adaptation to human hosts. To date, more than 90,000 SARS-CoV-2 genome sequences have been uploaded to the GISAID database. The availability of sequencing data along with clinical and geographical data may be useful for epidemiological investigations. In this study, we aimed to analyse the genetic background of SARS-CoV-2 from patients in Indonesia by whole genome sequencing. We examined nine samples from COVID-19 patients with RT-PCR cycle threshold (Ct) of less than 25 using ARTIC Network protocols for Oxford Nanopore’s Gridi On sequencer. The analytical methods were based on the ARTIC multiplex PCR sequencing protocol for COVID-19. In this study, we found that several genetic variants within the nine COVID-19 patient samples. We identified a mutation at position 614 P323L mutation in the ORF1ab gene often found in our severe patient samples. The number of SNPs and their location within the SARS-CoV-2 genome seems to vary. This diversity might be responsible for the virulence of the virus and its clinical manifestation