Molecular Viral Genotyping
Molecular Viral Genotyping - Related Videos
08:27
Mouse Genotyping
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2023
Even though the human genome was mapped over 10 years ago, scientists are still far from understanding the function of every human gene! One way to evaluate how a gene functions is to disrupt the sequence encoding it and then evaluate the impact of this change (the phenotype) on the animal’s biology. This approach is commonly used in the mouse (Mus musculus), since it shares a high degree of genetic similarity with humans. To track the animals bearing genetic changes over several generations,...
08:23
SNP Genotyping
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2023
Single nucleotide polymorphisms, or SNPs, are the most common form of genetic variation in humans. These differences at individual bases in the DNA often do not directly affect gene expression, but in many cases can still be useful for locating disease-associated genes or for diagnosing patients. Numerous methodologies have been established to identify, or “genotype”, SNPs.JoVE’s introduction to SNP Genotyping begins by discussing what SNPs are and how they can be used to identify...
11:00
Genotyping of Plant and Animal Samples without Prior DNA Purification
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Cited by 14 •
2012
The Direct PCR approach presented here facilitates PCR amplification directly from small amounts of unpurified plant and animal tissue.
13:06
Pyrosequencing: A Simple Method for Accurate Genotyping
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Cited by 22 •
2008
Pyrosequencing(R) is one of the most thorough yet simple methods to date used to analyze polymorphisms. This method has led to rapid and efficient single-nucleotide polymorphism evaluation including many clinically relevant polymorphisms. The technique and methodology of Pyrosequencing is explained.
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
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Cited by 15 •
2013
A protocol is described that uses Illumina's Infinium assays to perform large-scale genotyping. These assays can reliably genotype millions of SNPs across hundreds of individual DNA samples in three days. Once generated, these genotypes can be used to check for associations with a variety of different diseases or phenotypes.
FAQs
After viral nucleic acid is analyzed, diagnostic regions or whole-genome sequences are compared with reference sequences. Shared sequence patterns support assignment to a genotype, while differences reveal genetic variation among viral samples. This comparison provides a standardized way to classify related viruses and helps researchers examine diversity, transmission patterns, and evolutionary change.
Targeted analysis examines selected diagnostic regions, using approaches such as targeted amplification or hybridization, whereas whole-genome analysis evaluates genetic variation across the complete viral genome. The choice determines which differences can be detected and how broadly the virus can be characterized. Both approaches can support genotype assignment, but they provide different levels of genomic coverage.
Mutations can distinguish viral strains and indicate changes that may be associated with antiviral resistance or immune escape. Their interpretation depends on comparing sequences with appropriate reference information rather than viewing each difference in isolation. In infection research, this helps connect genetic variation with surveillance findings, treatment considerations, and questions about host immune recognition.
The workflow begins with nucleic acid extraction from the viral material, followed by targeted amplification, hybridization, or sequencing. The resulting genetic information is then compared with reference sequences to identify diagnostic patterns, assign genotypes, and detect mutations. This sequence of steps links sample preparation with molecular classification and downstream interpretation.
Genotyping can distinguish strains detected in different samples, allowing investigators to compare their genetic relatedness during epidemiological surveillance. These comparisons can help trace transmission patterns and monitor how viral populations change over time. The resulting molecular evidence complements infection data and supports investigation of outbreaks without relying solely on clinical or geographic information.
In immunology and infection research, sequence-based genotype data help examine viral diversity, evolution, immune escape, and changes associated with antiviral resistance. Researchers can use these findings to evaluate interventions, inform vaccine design, and support clinical decision-making. The method therefore connects molecular variation with both population-level surveillance and questions about host-pathogen interactions.