Dual-Database Improvement of Metagenomic Viral Read Classification: A Respiratory Virus Case Study Restricted; Files Only

Abstract

The COVID-19 pandemic has underscored the necessity for precise identification of viral pathogens to inform clinical and public health responses effectively, especially with respiratory viruses with overlapping clinical presentations. Metagenomics, a powerful tool for the genetic profiling of complex microbial communities, has emerged as a promising solution. Utilizing high-throughput sequencing, metagenomics enables the unbiased identification of pathogens in clinical samples, offering a broad-spectrum diagnostic approach that transcends the capabilities of targeted PCR tests. This study introduces a metagenomic pipeline designed to enhance the detection and classification of viral samples, employing a combination of Kraken for initial viral read classification and BLASTN for subsequent validation. This project’s objectives were twofold: first to develop and test the dual database approach, and second to assess the efficacy of this pipeline in identifying known respiratory viruses in samples previously tested negative for COVID-19 using BinaxNOW antigen tests. The results revealed that the pipeline successfully identified the presence of various respiratory viruses in the samples, including parainfluenza viruses 2 and 3, rhinoviruses A and C, and influenza B, showcasing its superior performance over traditional diagnostic methods. Notably, the pipeline reduced false classifications, a critical advantage in the clinical setting where accurate pathogen identification directly influences treatment decisions and infection control measures.

Table of Contents

Introduction 1

Methods 6

Results 12

Discussion 16

References 18

Table 1 22

Table 2 24

Table 3 25

Table 4 28 Figure 1 29

Figure 2 31

Figure 3 32

Figure 4 33

Figure 5 34

Figure 6 35

Figure 7 36

Figure 8 37

Figure 9 38

Figure 10 39

About this Honors Thesis

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Emory College
Department	Biology
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Biology, Virology
Keyword	metagenomics
Committee Chair / Thesis Advisor	Piantadosi, Anne, Emory University
Committee Members	Read, Timothy, Emory University Koelle, Katia, Emory University

Last modified

Primary PDF

Thumbnail	Title	Date Uploaded	Actions
	File download under embargo until 24 May 2025	2024-04-10 09:23:47 -0400	File download under embargo until 24 May 2025

Supplemental Files

Thumbnail	Title	Date Uploaded	Actions