V3 Region Sequencing
V3 Region Sequencing - Related Videos
11:10
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
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Cited by 20 •
2010
HIV tropism can be inferred from the V3 region of the viral envelope. V3 is PCR amplified in triplicate using nested RT-PCR, sequenced, and interpreted using bioinformatic software. Samples with with 1 or more sequence(s) with low g2P scores are classified as non-R5 virus.
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Cited by 10 •
2010
The crown region of different V3 loop sequences of the surface envelope glycoprotein (gp120) of HIV-1 can be structurally characterized in many cases by in silico folding of positions 10 to 22 of the loop using a state-of-the-art ab initio folding algorithm. Here we demonstrate the folding and evaluation of this region of the V3 loop from the R2 strain of HIV-1, a uniquely neutralization sensitive strain with puzzling functional properties.
06:40
G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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2018
We describe a technique for combining flow cytometry and high throughput sequencing to identify late replicating regions of the genome.
02:40
The Eukaryotic Promoter Region
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2020
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
01:03
IR Frequency Region: Fingerprint Region
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2024
IR spectra are divided into two main regions: the diagnostic region and the fingerprint region. The diagnostic region of the spectrum lies above 1500 cm−1. The absorptions resulting from single-bond vibrations of the N–H, C–H, and O–H stretch at higher wavenumbers and appear on the left side of the spectrum. The stretching absorptions of the C≡C and C≡N occur between 2100–2300 cm−1. In contrast, those arising from stretching absorptions of the C=O, C=N, and C=C occur between 1600–1850 cm−1. The...
FAQs
Changes in the V3 loop can be associated with differences in how HIV-1 interacts with host-cell coreceptors. After sequencing the env segment, researchers examine its amino acid patterns and compare them with reference information. This supports an estimate of coreceptor usage, helping relate viral sequence variation to entry-related properties without treating the sequence as a complete description of infection behavior.
A raw nucleotide sequence becomes more informative when evaluated against reference data. The comparison helps identify amino acid patterns linked with viral properties and places an individual sequence within a broader context of HIV-1 variation. This approach supports interpretation of sequence differences, rather than relying only on the presence of mutations or changes in the amplified segment.
V3 sequence profiles provide a way to track variation in a viral region shaped by interactions with host cells and the immune environment. Comparing profiles across samples can help investigators study immune selection and examine disease-related changes. These analyses connect molecular differences with larger questions about viral adaptation, pathogenesis, and infection progression.
The workflow begins by amplifying the relevant portion of the HIV-1 env gene. Researchers then sequence the resulting DNA and examine the sequence for informative nucleotide and amino acid patterns. Finally, they compare the profile with reference data to support interpretation of viral properties, diversity, and estimated coreceptor usage.
This method is useful when investigators need to characterize viral diversity or examine how sequence profiles relate to transmission and pathogenesis. It also supports epidemiological studies by allowing viral profiles to be compared across research samples. In immunology and infection research, the same information can help investigate changes associated with host responses and disease.
Sequence profiles can support treatment research focused on viral entry by identifying amino acid patterns associated with estimated coreceptor usage. This is relevant to strategies involving entry-targeting drugs, because the V3 region provides molecular information about a viral property connected to host-cell interaction. The method therefore contributes sequence-based context for evaluating treatment-related questions.