METAGENOMIC STUDY ON NASOPHARYNGEAL SAMPLES OF SEVERELY SYMPTOMATIC COVID-19 PATIENTS IN WEST JAVA, INDONESIA

• Main Author: Suryo Santoso, Vincentius
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/77411
• Institution: Institut Teknologi Bandung

Nasopharyngeal dysbiosis is one of the causes that may decrease the quality of human health because it increases the risk of opportunistic pathogen infections. Numerous studies have reported that SARS-CoV-2 virus infection has been to cause nasopharyngeal dysbiosis in severe COVID-19 patients. However, research related to nasopharyngeal dysbiosis due to SARS-CoV-2 infection in the Indonesian population, especially in West Java, is still limited. Therefore, in this study, an analysis of the taxonomic and functional composition of microbes in the nasopharyngeal microbiome was carried out in severe COVID-19 patients in West Java. Data was acquired from metagenomic whole-genome shotgun sequencing of COVID-19 patients with severe symptoms (n=8) and control (n=3) at the West Java Health Laboratory. Identification of microbial abundance and diversity were done using Kraken2 software and functional identification was performed using HUMAnN3. Statistical testing and data visualization were carried out on RStudio with Vegan and DESeq2 packages. Based on the results of the study, the alpha diversity analysis showed that the group of patients with severe COVID-19 symptoms had a lower Shannon index (Mdn=2.6) compared to the control group (Mdn=3.6; p<0.05). Beta diversity analysis showed that the group of patients with severe COVID-19 symptoms and the control group formed separate clusters. Bacterial taxonomy abundance at the genus level suggests that there is a dominance of the Burkholderia genus in 75% of COVID-19 patients with severe symptoms, while in the control group there is no domination of a specific genus. Based on the results of a comparative analysis of the diversity of the control and severely affected patients, the species of bacteria whose abundance is significantly lower in the COVID-19 with severe symptoms is Ralstonia picketti, while species with significantly higher abundance are Burkholderia spp and Pseudomonas spp. (p<0.01 and log2FC>2). Based on functional analysis, significantly higher metabolic pathways expressed in the COVID-19 group includes the category of biosynthesis pathways (sugar, amino acids, cell walls, nucleotides, fats, and fatty acids), degradation/assimilation pathways, metabolite precursor formation, and macromolecular modification (p<0.01 and log2FC>2), all of which play a role in bacterial survival. Thus, it can be concluded that in this study, the nasopharyngeal microbiome in the group of patients with severe COVID-19 symptoms had a higher abundance of opportunistic pathogens with metabolic pathways that played a role in its survival and pathogenicity in the human nasopharynx so that it could potentially worsen the symptoms of COVID-19.