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Updated: May 29, 2026

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
[Coreceptor usage of human immunodeficiency virus-1 in primary infection through sexual contact transmission]
Yan-hai Wang1, Xiao-xu Han, Ming-hui An
1China Medical University, Shenyang 110001, China.
Objective:
To evaluate the coreceptor usage characters and evolution of human immunodeficiency virus-1 (HIV-1) primary infection.
Methods:
A total of 12 HIV-1 primary infection cases were recruited from a high-risk population for this prospective cohort trial. The blood samples were collected at the earliest time after infection and after a viral setpoint respectively. RNA was extracted from plasma. The env genes were amplified through reverse transcription-PCR (RT-PCR) and nested PCR. And the env fragments were ligated to T vector and then sequenced. The pattern of coreceptor usage was predicted with five different online tools.
Results:
Among them, 11 were predicted as CCR5 virus transmission and 1 as CXCR4 virus transmission. The viruses in 1 case were detected as a switch of coreceptor usage from CCR5 to CXCR4. The consistency of five different prediction rules was 88.3%.
Conclusion:
Although the CCR5 usage virus is predominant in primary infection through sexual transmission, CXCR4 usage virus can also be detected. A switch of coreceptor usage may happen within the first year post-infection. Adopting multiple rules may improve the efficiency and validity for the prediction of coreceptor usage based on genotypes.
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