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Advancing Genomic Sequencing Approach for Viruses to Address One Health /

Record Type:	Electronic resources : Monograph/item
Title/Author:	Advancing Genomic Sequencing Approach for Viruses to Address One Health // Katie Vigil.
Author:	Vigil, Katie,
Description:	1 electronic resource (244 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 85-11, Section: B.
Contained By:	Dissertations Abstracts International85-11B.
Subject:	Microbiology. -
Online resource:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=31236666
ISBN:	9798382742922

Advancing Genomic Sequencing Approach for Viruses to Address One Health /
Vigil, Katie,

Advancing Genomic Sequencing Approach for Viruses to Address One Health /Katie Vigil. - 1 electronic resource (244 pages)

Source: Dissertations Abstracts International, Volume: 85-11, Section: B.

One Health emphasizes the need to incorporate human, animal and environmental health when developing public health monitoring plans through collaborative efforts. Many viruses that infect humans originate from wildlife. By studying viruses in animals, we can detect new viruses that could jump species barriers and potentially prevent them from causing widespread infections. Marine mammals and bivalves are good sentinel species to monitor viruses in the environment, because they are sensitive indicators of environmental health and changes. Viruses can reach aquatic environments through urban stormwater runoff and wastewater run-off, potentially causing infectious-disease mass mortality events in sensitive species.In this dissertation project the long-read nanopore sequencing technology was explored for the detection and monitoring of viruses from marine organisms, seawater and wastewater for metagenomics and targeted whole genome sequencing. In paper 1, a systematic review on global zoonotic virus mortality events in marine mammals was conducted according to the Preferred Reporting Items for Systematic Reviews and MetaAnalysis (PRISMA) guidelines using PubMed, Web of Science and Scopus with a total 88 of 2883 studies meeting inclusion criteria with only 30 countries reporting marine mammal viral deaths. Harbor seals had the most viral mortalities at 92.2%, with Morbillivirus and Influenza A virus's being the most impactful and immunohistochemistry (IHC) being the most employed detection method (27%). This study underscores the importance of global surveillance efforts in understanding and mitigating the impact of viral infections on marine mammal populations thereby emphasizing the necessity of collaborative One Health approaches to address emerging threat at the human-animal-environment interface. In paper 2, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two long-read de novo assemblers Canu and Metaflye were utilized to study vertebrate viral sequences. Canu performed better over Metaflye by producing more vertebrate viral contigs including viruses from the Anelloviridae, Parvoviridae, and Circoviridae families. Some of the invertebrate and vertebrate viruses reported in paper 2 were known to potentially cause mortality events and/or diseases in seals, sea starts, fish, and bivalve species. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts. In paper 3, long-read metagenomic sequencing was used to sequence zoonotic viruses from oysters, mussels and seawater samples collected from Barataria Bay Louisiana and San Diego Bay California. Metagenomic analysis revealed distinct patterns in viral abundance and diversity across sample types, with adenoviruses and papillomaviruses being detected in all samples. Temporal analysis highlighted dynamic shifts in viral abundance and composition, suggesting environmental and host-specific influences. The presence of viruses associated with diverse marine mammal species underscores the potential for interspecies transmission and spillover events. In paper 4, a coordinated workflow using long-read nanopore sequencing and reverse transcription-droplet digital PCR (RT-ddPCR) was utilized to quantify SARS-CoV-2 RNA in wastewater samples to track the trends of viral activity levels while identifying emerging variants. This surveillance was conducted at 23 sewer maintenance hole sites and five wastewater treatment plants in Michigan from 2020 to 2022. In 2020, the wastewater samples were dominated by the parental variants, followed by 20I (Alpha, B.1.1.7) in early 2021, the Delta variant of concern (VOC) in late 2021, and Omicron dominated in 2022. The concordance rate between nanopore sequencing and RT-ddPCR assays in identifying SARS-CoV-2 variants to the clade-level was 76.9%. Notably, instances of disagreement between the two methods were most prominent in the identification of the parental and Omicron variants. The RT-ddPCR and nanopore sequencing methods reported here can be adopted as a reliable in-house analysis of SARS-CoV-2 in wastewater for rapid community level surveillance and public health response. This project contributes to a better understanding of how marine mammals, bivalves, seawater and wastewater can be utilized to monitor zoonotic viruses that could potentially spill-over to human environments. In addition, nanopore sequencing methods can be implemented in a collaborative One Health surveillance program for zoonotic viral surveillance in urban and marine aquatic environments.

English

ISBN: 9798382742922Subjects--Topical Terms:

536250
Microbiology.
Subjects--Index Terms:

Bivalves

Advancing Genomic Sequencing Approach for Viruses to Address One Health /
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