A PROBABILISTIC ASSESSMENT OF SARS-COV-2 HOST INTERACTIONS IN THE CONTEXT OF META-COMMUNITY AND URBAN ECOLOGY

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2021-6-29

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Nehri, Leman Nur

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Coronavirus disease 2019 (COVID-19) is an ongoing pandemic that was detected in Wuhan, China, in December 2019 and spread all around the world. COVID-19 is caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spreads through close contact. Many studies have been conducted on the transmission, virulence, and immune response of SARS-CoV-2. The intracellular mechanism of action of the virus and various host interaction pathways are also known. In addition, there are many studies on the mutant types of the virus. However, no study has been found on the microbial host interactions of the specific mutants of the Spike protein, which is one of the most important structural proteins of the virus. This protein allows the virus to enter the cell and is the main target of the ongoing vaccine studies. In this study, interactions between Spike protein variants and bacteria of gut microbiota were analyzed with a probabilistic programming language (PPL), WebPPL. It is preferred since it is an expressive and generative language that can infer from small data sets. The relationship between the three Spike protein mutants and the two SARS-CoV-2 variants with the intestinal microbiota was also investigated. As a result, it was found that different variants of Spike protein exist in the hosts that have dissimilar intestinal microbial compositions. Because of the fact that the microbe interplays are very dynamic systems, laboratory applications turn to be quite costly, time-consuming, and difficult in microbial interaction studies. This study is expected to be helpful for the applications of interactions between virus variants and microbiomes for laboratory environments.

Subject Keywords

Probabilistic Programming, Spike protein, SARS-CoV-2, Microbial Meta-Community, Microbiome

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https://hdl.handle.net/11511/91439

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Graduate School of Natural and Applied Sciences, Thesis

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Citation Formats

L. N. Nehri, “A PROBABILISTIC ASSESSMENT OF SARS-COV-2 HOST INTERACTIONS IN THE CONTEXT OF META-COMMUNITY AND URBAN ECOLOGY,” M.S. - Master of Science, Middle East Technical University, 2021.