Abstract
Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE/CRF07_BC superinfected putative donor and diverse CRF01_AE/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on env, and shared 4–7 breakpoints with each other. Moreover, 3’ half-genomes of recombinant strains from five recipients had identical/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.
Highlights
Human immunodeficiency virus type 1 (HIV-1) is characterized by extensive genetic diversity
Recombination is a major mechanism for rapid evolution and diversification of human immunodeficiency virus type 1 (HIV-1)
Multiple HIV-1 infection is believed to be a prerequisite for generating new recombinant strains
Summary
Human immunodeficiency virus type 1 (HIV-1) is characterized by extensive genetic diversity. Recombination is a major mechanism for the rapid evolution and diversification of HIV-1 [1]. More than 100 circulating recombinant forms (CRFs), along with massive unique recombinant forms (URFs) in HIV-1 group M have been identified worldwide [2] (www.hiv.lanl.gov). Some recombinants have recombined further with other subtypes or CRFs to generate secondgeneration recombinants [3]. It has been estimated that HIV-1 recombinants, including CRFs (16.7%) and URFs (6.1%), accounted for 22.8% of epidemics globally between 2010 and 2015 [4]. Recombination of HIV-1 can potentially change biological characteristics, fitness, susceptibility to antiretroviral drugs, disease progression, as well as the diagnostic accuracy of serology- and molecular- based assays [5,6,7,8]
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