ANALYSIS OF SARS-COV-2 VARIANTS AND BACTERIAL COMMUNITY PROFILE FROM NASOPHARINGEAL AND OROPHARINGEAL OF COVID-19 REINFECTION PATIENTS FROM WEST JAVA

• Main Author: Rifdah Sativa, Alvira
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/67368
• Institution: Institut Teknologi Bandung

Coronavirus diseases 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) with several symptoms such as fever, cough, dyspnea, myalgia, and even diarrhea. In the case of COVID-19, it is known that naturally acquired immunity will not be the same in all cases in providing protection after the first infection so that reinfection cases can occur in COVID-19 patients. One of the factors is a new variant of the SARS-CoV 2 virus which can change over time so that it affect the transmission process, severity, vaccine performance and immunity of infected patients. In addition to the SARS- CoV-2 variant that is increasingly developing and affecting the severity of COVID-19 patients, there are also several reports of co-infection due to the discovery of bacterial communities in SARS-CoV-2 patients. Therefore, this study was conducted to determine the SARS-CoV-2 variant and its key mutations and to obtain a bacterial community profile from nasopharyngeal and oropharyngeal swab samples of COVID-19 reinfected patients in West Java. Analysis of virus variants was carried out on 42 samples of patients who were confirmed positive for COVID-19. Whole Genome Sequencing Analysis was carried out using Oxford Nanopore Technologies (ONT) at the Biosafety Level-3 (BSL-3) Laboratory of the National Research and Innovation Agency (BRIN) Cibinong Science Center – Botanical Garden (CSC-BG). The raw data sequencing results in the form of Fast5 and FastQ were basecalling using Guppy (ONT). Furthermore, analysis using Nexstrain and Pangolin was carrid out to determine the virus variants that infects the patient. The phylogenetic tree was created using IQ-Tree and visualization with FigTree v.1.4.4. Key mutation analysis was performed using the cov.glue webserver. Then for the analysis of the abundance profile of bacterial community was carried out with 16S rRNA on 9 reinfected samples that had been obtained and 9 samples of patients who were not reinfected with positive patient ages in the productive age range (24-59 years). Analysis of the SARS-CoV-2 genome was performed using the EPI2ME workflow (ONT) and Microbiomeanalyst (microbiomeanalyst.ca) for stacked bar plot visualization, analysis of alpha and beta diversity and metagenomeSeq. The results showed that the variants found for the entire sample were delta variants with lineages AY.23, AY.24 and AY.109. In addition, most of the mutations that occurred in the reinfected samples were NSP3_V220A; S_T676I ; ORF7a_V82A and ORF7a_T120I. The results of the analysis alpha diversity and beta diversity showed that the level of diversity is relatively was not significantly different in the groups of patients with reinfection patients and COVID-19 patients who were not reinfected. The metagenomseq results showed that Haemophilus parainfluenzae, Fusobacterium periodonticum, Fusobacterium nucleatum, and Leptotrichia buccalis had an abundance value that increased significantly (p<0.05) based on the category of reinfected patients, whereas if based on age category it shows that there are several species, namely Haemophilus influenzae, Streptococcus mitis, Streptococcus pneumoniae, Streptococcus pseudopneumoniae and Prevotella denticola increased significantly in the age category of 35-60 years. So from this study it can be concluded that there is no difference in the SARS-CoV-2 variant that infects reinfected and non-reinfected patients, but there are differences in the abundance of bacterial communities found in these categories of patients.