Viral Rna Sequencing
Viral Rna Sequencing - Related Videos
09:36
Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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Cited by 50 •
2016
This protocol describes a rapid and broadly applicable method for unbiased RNA-sequencing of viral samples from human clinical isolates.
03:20
Nested-PCR to Detect a Specific Viral Genomic Sequence
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2025
This video describes nested polymerase chain reaction, a technique that consists of two sequential PCR amplification processes using two primer sets. The first set of primers is intended to anneal to sequences upstream of the second set, resulting in selective amplification of specific gene sequences. This PCR is more sensitive and specific than a normal PCR and is widely used as a detection technique for various diseases.
10:16
Detection of Viral RNA by Fluorescence in situ Hybridization (FISH)
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Cited by 35 •
2012
A fluorescence in situ hybridization (FISH) method was developed to visually detect viral genomic RNA using fluorescence microscopy. A probe is made with specificity to the viral RNA that can then be identified using a combination of hybridization and immunofluorescence techniques. This technique offers the advantage of identifying the localization of the viral RNA or DNA at steady-state, providing information on the control of intracellular virus trafficking events.
07:30
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
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Cited by 19 •
2020
This method describes the steps to improve the quality and quantity of sequence data that can be obtained from formalin-fixed paraffin-embedded (FFPE) RNA samples. We describe the methodology to more accurately assess the quality of FFPE-RNA samples, prepare sequencing libraries, and analyze the data from FFPE-RNA samples.
02:59
Extraction of Viral RNA from Surface-Bound Virions Using a Silica Spin Column
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2026
Source: Klaus, J. P. et al. Highly Sensitive Assay for Measurement of Arenavirus-cell Attachment. J. Vis. Exp. (2016)This video demonstrates the extraction of viral RNA from surface-bound virions on epithelial cells using silica spin columns. The method includes chemical lysis, RNA stabilization, and membrane-based purification for downstream quantification of virus-cell attachment.
FAQs
Most sequencing platforms cannot read viral RNA directly, so researchers first use reverse transcription to produce complementary DNA, or cDNA. This conversion creates a DNA form that can be amplified and incorporated into a sequencing library. The quality of this step influences whether viral genetic material is represented adequately in the data and whether important sequence differences can be examined.
Amplification increases the amount of target viral material available for analysis, while library preparation organizes the resulting cDNA into a form compatible with high-throughput sequencing. Together, these steps help generate sufficient, sequence-ready material from an RNA-virus sample. Their placement between reverse transcription and sequencing connects the original viral genome to the data used for downstream interpretation.
Comparing viral sequences allows researchers to identify mutations and patterns of diversity that arise as viruses change over time. Some mutations may be associated with replication or with reduced recognition by host immune responses, described as immune escape. In infection research, these observations help connect genetic variation with viral behavior and host-virus interactions.
A typical workflow begins with viral RNA, converts it to complementary DNA by reverse transcription, and amplifies selected target material. Researchers then prepare a sequencing library and analyze it with a high-throughput platform. This sequence of steps transforms unstable RNA into an interpretable genetic dataset while preserving information needed to identify the virus and assess variation.
Sequence data can distinguish viral variants and reveal genetic relationships among samples collected during an outbreak. Those relationships help researchers track transmission and monitor the appearance of emerging variants. The method therefore adds genetic evidence to infection surveillance, supporting efforts to follow how viral populations change and spread across an affected setting.
In this field, sequence information helps researchers examine how viral mutations relate to replication, host immune recognition, and possible immune escape. These findings can inform diagnostic development and vaccine design while clarifying virus-host dynamics. The same data also provide a molecular basis for studying viral diversity during infection rather than viewing infection only through clinical or epidemiological measurements.