Section 3. Studying Viral Pathogens with High Throughput Sequencing (HTS) (from DOI: 10.3390/v12020211)

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Article	Current Trends in Diagnostics of Viral Infections of Unknown Etiology (DOI: 10.3390/v12020211)
Sections in this Publication
Section	Section 1. Introduction (from DOI: 10.3390/v12020211)
Section	Section 2. Traditional Methods of Diagnosing Infections (from DOI: 10.3390/v12020211)
Section	Section 3. Studying Viral Pathogens with High Throughput Sequencing (HTS) (from DOI: 10.3390/v12020211)
Section	Section 3.1. Metagenomic Approach (from DOI: 10.3390/v12020211)
Section	Section 3.2. Problems of Metagenomic Approach (from DOI: 10.3390/v12020211)
Section	Section 3.3. Methods for Improving Sequencing Output (from DOI: 10.3390/v12020211)
Section	Section 3.3.1. Nucleic Acids Depletion (from DOI: 10.3390/v12020211)
Section	Section 3.3.2. Hybridization-Based Enrichment (from DOI: 10.3390/v12020211)
Section	Section 3.3.3. Target Amplification (from DOI: 10.3390/v12020211)
Section	Section 3.4. Whole Viral Genome Sequencing (from DOI: 10.3390/v12020211)
Section	Section 3.5. Methods of Sequencing Data Analysis (from DOI: 10.3390/v12020211)
Section	Section 4. Long Read Sequencing (from DOI: 10.3390/v12020211)
Section	Section 5. Obstacles to Overcome in the Nearest Future (from DOI: 10.3390/v12020211)
Section	Section 6. Conclusions (from DOI: 10.3390/v12020211)
Section	Author Contributions (from DOI: 10.3390/v12020211)
Section	Funding (from DOI: 10.3390/v12020211)
Section	Conflicts of Interest (from DOI: 10.3390/v12020211)
Section	References (from DOI: 10.3390/v12020211)
Named Entities in this Section

From publication: "Current Trends in Diagnostics of Viral Infections of Unknown Etiology" published as Viruses; 2020 Feb 14 ; 12 (2); DOI: https://doi.org/10.3390/v12020211

Section 3. Studying Viral Pathogens with High Throughput Sequencing (HTS)

The invention of HTS:alias next generation sequencing (NGS):has revolutionized research in biology and medical science, including virology, allowing new viruses to be genetically analyzed without prior cultivation. Sequencing of viral genomes has already become a pivotal part of virological research, aiding clinicians in identifying complex infections. It is gradually growing to become one of the main methods in molecular diagnostics, development of vaccines and searches for new therapeutic strategies. Over the years, it has pushed the frontiers of molecular epidemiology and evolutionary genomics.

Another type of NGS-based analysis is metagenomics, which was comprehensively defined by Chen and Pachter as "the application of modern genomics technique without the need for isolation and lab cultivation of individual species". In essence, it offers the means to investigate the taxonomic diversity of a microbial community in an environmental or biological sample as the entirety of present nucleic acids is studied. Further applications of this method extend to transcriptomics and proteomics, allowing for a deeper insight into several aspects of pathogens, such as drug resistance, adaptation mechanisms and vast communication networks between species.