Related Experiment Video
Updated: Mar 31, 2026
10:18
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
12.8K
Analysis of temporal virus evolution and intra-host diversity in long-term non-progressors by bulk next-generation
Rongfeng Chen1,2, Jianwen Mo1, Yuanting Li1
1Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
Microbiology Spectrum
|March 30, 2026
Summary
Long-term non-progressors (LTNPs) show limited HIV-1 evolution and greater proviral DNA diversity than plasma RNA. CTL escape mutations are frequent and sustained, indicating a balance between viral persistence and immune control.
Area of Science:
- Virology
- Immunology
- Genetics
Background:
- Long-term non-progressors (LTNPs) offer insights into HIV-1 pathogenesis and functional cure strategies.
- Understanding viral evolution and immune control mechanisms in LTNPs is crucial for developing new therapies.
- Previous studies on viral evolution in LTNPs were limited by focusing on partial genome fragments.
Purpose of the Study:
- To investigate viral quasispecies evolution, diversity, and CTL-associated mutations in LTNPs using near full-length genome sequencing.
- To compare viral evolution and diversity between HIV-1 plasma RNA and proviral DNA in LTNPs.
- To analyze intra-host viral dynamics at the nucleotide level in LTNPs over time.
Main Methods:
- Employed near full-length bulk next-generation sequencing (NGS) on plasma RNA and proviral DNA from two LTNPs across four time points over two years.
- Performed phylogenetic analysis, divergence calculation, and analysis of intra-host single-nucleotide variants (iSNVs) and amino acid variations.
- Identified and analyzed mutations within CTL epitopes to assess their frequency and changes over time.
Main Results:
- Limited viral evolution and genetic distance were observed in both LTNPs over the study period.
- Proviral DNA sequences exhibited higher divergence and greater intra-host diversity (iSNVs, Shannon entropy) compared to plasma RNA sequences.
- A substantial number of high-frequency mutations in CTL epitopes were consistently identified in both DNA and RNA, with minor temporal frequency changes.
Conclusions:
- HIV-1 evolution is limited in LTNPs, with proviral DNA showing greater diversity than plasma RNA.
- Sustained, high-frequency CTL escape mutations suggest a dynamic interplay between viral persistence and immune containment in LTNPs.
- These findings challenge the notion of viral stasis and provide critical insights for HIV vaccine design and reservoir-targeting therapies.
Related Concept Videos
00:36Viral Mutations
40.7K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
40.7K
01:08Evolution of Microbial Genome
46
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
46
03:00Next-generation Sequencing
101.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
101.0K
01:26Size and Structure of Viral Genomes
1.1K
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
1.1K
01:29Viruses with RNA Genomes
1.3K
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
1.3K
02:54Evolutionary Relationships through Genome Comparisons
7.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K