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Rapid CD4 cell loss is caused by specific CRF01_AE cluster with V3 signatures favoring CXCR4 usage

By Hongshuo Song, Weidong Ou, Yi Feng, Junli Zhang, Guei-Sheung Liu, Jing Hu, Hong Peng, Hui Xing, Liying Ma, Qiuxiang Tan, Beili Wu, Yiming Shao

Posted 26 Sep 2018
bioRxiv DOI: 10.1101/427625

HIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic, with the same subtype or CRF usually having similar phenotype. Being one of the major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the national HIV molecular epidemiology survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 count (391 vs. 470, p < 0.0001) and higher prevalence of predicted X4-using viruses (17.1% vs. 4.4%, p < 0.0001) compared to those infected by cluster 5. In a MSM cohort, X4-using viruses were only isolated from sero-convertors infected by cluster 4, which associated with rapid CD4 loss within the first year of infection (141 vs. 440, p = 0.01). Using co-receptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 usage. We demonstrate for the first time that HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in a single subtype. Since its initial spread to human from chimpanzee in 1930s, HIV-1 remains undergoing rapid evolution in larger and more diverse population. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance in monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning for the appearance of more pathogenic strains such as CRF01_AE cluster 4.

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