Identification of two novel HIV-1 circulating recombinant forms of CRF111_01C and CRF116_0108 in southwestern Yunnan, China

ABSTRACT

Yunnan, the region hardest hit by HIV/AIDS in China, is also an area with the most abundant HIV-1 genetic diversity. A large number of novel HIV-1 circulating recombinant forms (CRFs) and unique recombinants were identified among injection drug users in Yunnan; however, few were found among sexual contacts. Here, we obtained 15 near full-length genome sequences (NFLGs) from HIV-1 seropositive heterosexual contacts in Yunnan who received antiretroviral therapy during the period from 2014 to 2016. Phylogenetic analysis showed that six NFLGs belonged to CRF01_AE (n = 3) and CRF106_cpx (n = 3), and the other nine sequences were novel inter-subtype recombinants. Of the recombinants, two novel CRFs (CRF111_01 C (n = 4) and CRF116_0108 (n = 4)) and one CRF106_cpx variant (n = 1) were identified. CRF111_01 C had a CRF01_AE backbone with seven subtype C fragments inserted into the gag, pol, vif, env, nef and 3ʹLTR regions. CRF116_0108 had a CRF08_BC backbone with a CRF01_AE fragment inserted into the pol, tat, rev, vif, vpr, vpu and env regions. Phylogeographic analyses estimated that CRF111_01 C and CRF116_0108 originated approximately 1995.7–1998.6 and 1991.7–1993.7, respectively. These identifications of two novel HIV-1 CRFs highlighted the importance of continuous surveillance in heterosexual contacts and other high-risk groups in this region and the surrounding regions.

KEYWORDS:

• Human immunodeficiency virus type 1
• heterosexual contacts
• circulating recombinant forms
• China
• Yunnan

Acknowledgments

We would like to thank the staff of the Department of Infectious Diseases, Cangyuan Wa Autonomous County People’s Hospital, for their assistance in collecting the demographic data and blood samples. We also thank Dr. Yanpeng Li for his advice and help on NGS analysis and all the study participants for their donation of blood samples.

Author contributions

YZ and CZ conceived and designed the study. LD, XC and JM collected the samples. MY performed the experiments, analyzed the data and drafted the manuscript. LC performed the NGS analysis. YZ and CZ revised the manuscript. All authors reviewed and approved the final version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The datasets presented in this study can be found in online repositories. These data can be found here: https://www.ncbi.nlm.nih.gov/nuccore/MT624743.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This study was supported in part by grants from the National Natural Science Foundation of China [U1802284, U1302224, 81601802, 81271892], Project of Innovative Research Team of Yunnan Province [202005AE160005] and Yunnan Key Research and Development Program [202103AQ100001, 202102AA310055].