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Updated: Jun 2, 2026
Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays
Published on: September 26, 2011
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples
Izumi Yoshida1, Wataru Sugiura, Junko Shibata
1School of Biomedical Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Abstract:
HIV-1 infection has been on the rise in Japan recently, and the main transmission route has changed from blood transmission in the 1980s to homo- and/or hetero-sexual transmission in the 2000s. The lack of early viral samples with clinical information made it difficult to investigate the possible virological changes over time. In this study, we sequenced 142 full-length env genes collected from 16 Japanese subjects infected with HIV-1 in the 1980s and in the 2000s. We examined the diversity change in sequences and potential adaptive evolution of the virus to the host population. We used a codon-based likelihood method under the branch-site and clade models to detect positive selection operating on the virus. The clade model was extended to account for different positive selection pressures in different viral populations. The result showed that the selection pressure was weaker in the 2000s than in the 1980s, indicating that it might have become easier for the HIV to infect a new host and to develop into AIDS now than 20 years ago and that the HIV may be becoming more virulent in the Japanese population. The study provides useful information on the surveillance of HIV infection and highlights the utility of the extended clade models in analysis of virus populations which may be under different selection pressures.
Insights
Human Immunodeficiency Virus type 1 (HIV-1) in Japan shows decreased selection pressure, suggesting increased virulence and easier transmission over two decades. This evolution may impact public health surveillance strategies.
Area of Science:
- Virology
- Evolutionary Biology
- Epidemiology
Background:
- HIV-1 transmission routes in Japan shifted from blood to sexual contact between the 1980s and 2000s.
- Limited early viral samples hindered investigations into HIV-1 virological evolution.
- Understanding viral adaptation is crucial for effective HIV-1 surveillance.
Purpose of the Study:
- To investigate changes in HIV-1 sequence diversity and adaptive evolution in Japan.
- To analyze shifts in viral selection pressure over time.
- To assess potential increases in HIV-1 virulence in the Japanese population.
Main Methods:
- Sequencing of 142 full-length env genes from Japanese HIV-1 infected individuals (1980s and 2000s).
- Application of codon-based likelihood methods (branch-site and clade models) to detect positive selection.
- Extension of the clade model to analyze differential selection pressures across viral populations.
Main Results:
- HIV-1 exhibited weaker selection pressure in the 2000s compared to the 1980s.
- Evidence suggests HIV-1 may be becoming more virulent and transmissible in Japan.
- The extended clade model effectively analyzed varying selection pressures.
Conclusions:
- HIV-1 evolution in Japan indicates a potential increase in virulence and transmissibility.
- Findings provide critical insights for HIV-1 infection surveillance and control.
- The utility of extended clade models in analyzing viral evolution under diverse selection pressures is highlighted.
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