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Updated: Feb 27, 2026
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences
Xingguang Li1,2, Haizhou Liu3, Lu Liu4,5
1State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Insights
The Human Immunodeficiency Virus (HIV) circulating recombinant form CRF01_AE originated in Central Africa in the 1970s. This HIV strain later spread to Asia, leading to significant epidemics in Thailand and China.
Area of Science:
- Virology
- Epidemiology
- Population Genetics
Background:
- Human Immunodeficiency Virus (HIV) exists as various circulating recombinant forms (CRFs) resulting from subtype recombination.
- The first identified HIV-1 CRF was CRF01_AE, originating in Central Africa and now prevalent in Southeast and East Asia.
Purpose of the Study:
- To investigate the evolutionary history, timescale, and population genetics of HIV-1 CRF01_AE strains in Asia.
- To standardize nomenclature and provide reference sequences for CRF01_AE phylogenetic transmission clusters.
Main Methods:
- Analysis of 334 near-complete HIV-1 genome sequences from nine countries (1990-2011).
- Phylogenetic analyses using maximum likelihood and Bayesian methods.
- Bayesian skyline plot for population expansion analysis.
Main Results:
- HIV-1 CRF01_AE diversity originated in Central Africa (mid-1970s).
- Introduction to Thailand (1979-1982) with subsequent expansion (1982-1984).
- Multiple CRF01_AE clusters significantly contributed to China's epidemic, with rapid expansion around 1999-2000 and at least eight distinct clusters identified since the late 1980s.
Conclusions:
- Confirms Central African origin and Asian spread of HIV-1 CRF01_AE.
- Highlights the significant role of multiple CRF01_AE clusters in China's HIV epidemic.
- Provides a framework for standardized nomenclature and reference sequences for CRF01_AE research.
Abstract:
Human immunodeficiency virus (HIV) has a number of circulating recombinant forms that are the product of recombination between different HIV subtypes. The first circulating recombinant form of HIV-1 to be identified was CRF01_AE, which originated in Central Africa and is now most prevalent in Southeast and East Asia. In this study, we investigated the timescale, evolutionary history, and population genetics of the HIV-1 CRF01_AE strains primarily responsible for the epidemic in Asia. A further aim of our study was to define and standardize the nomenclature and provide well-characterized reference sequences for the phylogenetic transmission clusters of CRF01_AE. We analysed a data set of 334 near-complete genome sequences from various risk groups, sampled between 1990 and 2011 from nine countries. Phylogenetic analyses of these sequences were performed using maximum likelihood and Bayesian methods. Our study confirms that the diversity of HIV-1 CRF01_AE originated in Central Africa in the mid-1970s, was introduced into Thailand between 1979 and 1982, and began expanding there shortly afterwards (1982-1984). Subsequently, multiple clusters significantly contributed to China's HIV epidemic. A Bayesian skyline plot revealed the rapid expansion of CRF01_AE in China around 1999-2000. We identified at least eight different clusters of HIV-1 CRF01_AE formed by rapid expansion into different risk groups and geographic regions in China since the late 1980s.
