ANALISIS METAGENOMIK BAKTERI PADA SAMPEL USAP NASOFARING PASIEN COVID-19 TIDAK BERGEJALA DAN BERGEJALA BERAT

• Main Author: Marcheline Herman, Sonia
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/65962
• Institution: Institut Teknologi Bandung

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the new coronavirus that causes the disease Coronavirus 19 (COVID-19). This disease has been declared as pandemic by the WHO in 2020. Symptoms caused by COVID-19 range from asymptomatic (OTG), mild, moderate, severe, critical to causing death. It is known that the microbiota in the patient's body can also influence the severity of COVID-19 disease. However, until now there have not been many studies on the metagenomic profile of bacteria in COVID-19 patients in Indonesia. Therefore, in this study, we wanted to study the bacterial abundance profile and identify bacteria associated with severity in Indonesian COVID-19 nasopharyngeal swab samples, particularly in West Java. In this study, two categories of COVID-19 patients will be recruited, namely the OTG patient group consisting of four samples (A1, A2, A3, and A4) and the severe symptomatic patient group consisting of six samples (S3, S4, S8, S9, S10, S12). Nasopharyngeal swab samples were taken and then the RNA was extracted for Next Generation Sequencing with the metagenomic shotgun method. Furthermore, the quality of the data was analyzed using the FASTQC application and trimmed with Cutadapt for quality control. Abundance mapping was carried out with Kraken 2 based on the minikraken_8GB_20200312 database, then an analysis of the relative abundance of bacteria from the results of Kraken 2 will be carried out and visualized using piecharts and barplots. After that, analysis of alpha diversity was carried out by making the Shannon index and analysis of beta diversity by making Principal Component Analysis (PCA). The relative abundance of bacteria in the severe symptom category compared to asymptomatic as control using DESeq2 on R studio (ver 4.1.1). DESeq2 visualization was performed with an enhanced volcano plot with an LFC value of ±2.0 and a p-value of 0.01 and a heatmap. The results of the analysis of the abundance of bacterial reads showed that bacterial colonization was more common in samples of the severe symptom category but had a lower alpha diversity value than the asymptomatic sample. The results of beta diversity show that the diversity of samples in the same category is quite similar, but between different categories the diversity is also quite different, it's just that in the severe symptom category there are two samples (S3 and S12) that are outliers. The piechart results show that the bacterial species with the highest relative abundance in the OTG sample and the severe symptomatic sample, respectively, were Candidatus Koribacter versatilis (12.69%) and Corynebacterium segmentosum (27.19%). The results of the volcano plot showed that there were 31 bacterial species whose abundance was significantly higher in severe symptoms when compared to OTG, including Streptococcus mitis, Streptococcus sanguinis, and Pandoraea norimbergensis which were associated with the severity of the patient's illness. In addition, there is one bacterial species whose abundance is lower in the severe symptom category when compared to the control (OTG), namely Thermus scotoductus. Thus, it can be concluded that in patients in Indonesia, especially in West Java, the abundance of microorganisms can also affect the patient's disease outcome. In addition, the bacteria thought to be associated with the severity of COVID-19 patients with severe symptoms in West Java, Indonesia are Streptococcus mitis, Streptococcus sanguinis, and Pandoraea norimbergensis.