Usutu Virus Sequencing
Usutu Virus Sequencing - Related Videos
05:45
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
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Cited by 12 •
2020
We previously validated a protocol for amplicon-based whole genome Usutu virus (USUV) sequencing on a nanopore sequencing platform. Here, we describe the methods used in more detail and determine the error rate of the nanopore R10 flow cell.
09:36
Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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Cited by 46 •
2016
This protocol describes a rapid and broadly applicable method for unbiased RNA-sequencing of viral samples from human clinical isolates.
10:26
Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology
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Cited by 10 •
2023
Here, we present a rapid and cost-effective workflow for characterizing rabies virus (RABV) genomes using nanopore technology. The workflow is intended to support genomics-informed surveillance at a local level, providing information on circulating RABV lineages and their placement within regional phylogenies to guide rabies control measures.
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Cited by 40 •
2011
The present article describes the steps required to isolate and characterize RNA polymerase fidelity variants of RNA viruses and how to use mutation frequency data to confirm fidelity changes in tissue culture.
04:41
Plaquing of Herpes Simplex Viruses
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Cited by 1 •
2021
Plaquing is a routine method used to quantify live viruses in a population. Though plaquing is frequently taught in various microbiology curricula with bacteria and bacteriophages, plaquing of mammalian viruses is more complex and time-consuming. This protocol describes the procedures that function reliably for regular work with herpes simplex viruses.
FAQs
The RNA genome is converted into complementary DNA so the resulting material can be amplified and read as DNA fragments. This conversion connects the original viral genetic material to downstream sequencing and assembly steps. It allows researchers to analyze RNA-virus genomes using a workflow centered on amplified DNA regions and their nucleotide sequences.
Comparing nucleotide sequences reveals differences and similarities among viral samples. Shared sequence patterns can indicate close relationships, while observed variation helps distinguish lineages that may otherwise appear similar. After sequence assembly, these comparisons support genetic characterization and help clarify how samples are related to one another.
Assembly organizes the DNA fragments that were read during sequencing into a sequence representing the analyzed viral genome or selected region. This provides a coherent basis for comparing samples, identifying genetic variation, and examining relationships among viruses. The resulting sequence information is more useful for interpretation than isolated fragments considered independently.
A typical workflow begins with viral RNA, converts it to complementary DNA, and amplifies either selected regions or genome-wide material. Sequencing then reads the resulting DNA fragments, which are assembled and compared with sequences from other samples. Each stage contributes to turning viral genetic material into interpretable information about variation and relatedness.
The workflow can focus on selected viral regions or examine genome-wide material. Selected-region analysis concentrates comparisons on particular parts of the genome, whereas genome-wide sequencing provides sequence information across a broader extent of the viral genome. The choice therefore affects the scope of genetic characterization and the comparisons possible among samples.
Sequence data support surveillance, studies of viral distribution, and investigations of transmission patterns. Researchers can also use genetic comparisons to examine evolutionary change and explore associations between viral samples, hosts, or geographic locations. These applications make sequencing useful for connecting nucleotide-level variation with broader patterns in infectious-disease research.