Viral Genome Sequencing
Viral Genome Sequencing - Related Videos
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.
06:57
Dot Blot Assay to Quantify Viral Genome
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2025
In this video, we describe the dot blot assay to quantify a viral genome. The signal intensity is directly related to the amount of viral DNA in the sample.
12:36
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
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Cited by 2 •
2011
We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.
08:31
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Cited by 2 •
2013
Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Cited by 10 •
2012
Pooled DNA sequencing is a fast and cost-effective strategy to detect rare variants associated with complex phenotypes in large cohorts. Here we describe the computational analysis of pooled, next-generation sequencing of 32 cancer-related genes using the SPLINTER software package. This method is scalable, and applicable to any phenotype of interest.
FAQs
Sequence data provide a detailed nucleotide-level record that can be compared with reference genomes. Differences and similarities across genomes help distinguish viral identities, characterize diversity, and examine how viral populations change over time. This comparative perspective supports infection research by linking genetic variation with surveillance findings and broader patterns of viral evolution.
When a virus has an RNA genome, the workflow converts that RNA into complementary DNA before sequencing. This creates a DNA form that can enter the subsequent amplification and high-throughput reading steps described in the workflow. The conversion is therefore a necessary preparation stage for obtaining sequence information from RNA viruses.
Mutations provide genetic clues about changes that may influence interactions between a virus and immune defenses or antiviral treatments. Sequencing can therefore help identify mutations linked to immune escape or antiviral resistance. These findings support closer surveillance and can inform vaccine design, diagnostic development, and responses to changing infection patterns.
A typical workflow begins with nucleic acid extraction from a clinical or environmental sample. The material may then be amplified, while RNA genomes are converted to complementary DNA, followed by high-throughput sequencing. Computational assembly organizes the resulting reads, and comparison with reference genomes helps interpret viral identity, variation, and evolution.
Viral nucleic acid can be obtained from either clinical or environmental samples, allowing the same broad approach to address different infection and surveillance questions. After extraction, amplification or complementary DNA conversion may prepare the material for sequencing. The resulting data can then support pathogen surveillance, outbreak investigation, or other infection research.
During an outbreak, genome sequences can be compared across viral samples and against reference genomes to examine their relationships. These comparisons provide genetic evidence for surveillance and transmission tracking, helping characterize how viral variation is distributed during an infectious event. The findings can contribute to public health responses alongside other available information.
The data can guide several connected activities, including pathogen surveillance, outbreak investigation, transmission tracking, vaccine design, and diagnostic development. They can also support detection of mutations associated with immune escape or antiviral resistance. Together, these uses make sequencing relevant to both laboratory studies of infection and public health responses to evolving viruses.