Identification and Characterization of a New Class of Human Immunodeficiency Virus Type 1 Recombinants Comprised of Two Circulating Recombinant Forms, CRF07_BC and CRF08_BC, in China

Abstract

We identified a new class of human immunodeficiency virus type 1 (HIV-1) recombinants (00CN-HH069 and 00CN-HH086) in which further recombination occurred between two established circulating recombinant forms (CRFs). These two isolates were found among 57 HIV-1 samples from a cohort of injecting drug users in eastern Yunnan Province of China. Informative-site analysis in conjunction with bootscanning plots and exploratory tree analysis revealed that these two strains were closely related mosaics comprised of CRF07_BC and CRF08_BC, which are found in China. The genotype screening based on gag-reverse transcriptase sequences of 57 samples from eastern Yunnan identified 47 CRF08_BC specimens (82.5%), 5 CRF07_BC specimens (8.8%), and 3 additional specimens with the novel recombinant structure. These new "secondgeneration" recombinants thus constitute a substantial proportion (5 of 57; 8.8%) of HIV-1 strains in this population and may belong to a new but yet-undefined class of CRF. This might be the first example of CRFs recombining with each other, leading to the evolution of second-generation inter-CRF recombinants.

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms

“…For instance, viruses carrying subtype G sequences at pol could be pure G subtypes or recombinants, and interestingly, 18 of the CRF described (http://www.hiv.lanl.gov/content/sequence /HIV/CRFs/CRFs.html) harbor clade G sequences in partial or complete pol coding regions. Therefore, it is not surprising that CRF may constitute at least 10 to 20% of new HIV-1 infections worldwide and that recombination involving different non-B subtypes is rising where diverse variants cocirculate, particularly in areas where distinct subtypes are highly prevalent (8,12,21,24).…”

Expansion of HIV/AIDS in China: Lessons from Yunnan Province

“…HIV subtype E was also identified in Yunnan in 1993 (Cheng, Zhang, Capizzi, Young, & Mastro, 1994). In early 2000, subtypes C, E, and B′ (B′ is a Thai variant of subtype B) were identified, as well as three recombinant forms of B and C (CRF07_BC, CRF08_BC, and a unique recombinant form of B′ and C) and a recombinant form of A and E (CRF01_AE) (Li et al, 2004;Yang et al, 2002;Yang et al, 2003;Yin et al, 2003). HIV viruses sequenced in Sichuan, Xinjiang, and Guangxi were found to have many gene sequences identical to those of the previously identified Yunnan strains but had somewhat lower genetic divergence, suggesting that viruses in these areas were likely introduced from Yunnan (Shao, Zhao, Yang, Zhang, & Gong, 1999;Yin et al, 2003).…”

Snapshot of HIV pathogenesis in China

“…Interestingly, subtype B' actively replaced the subtype B strains of American lineage, and increased from 20% in 1990 to 90% in 1996 [19]. Following this, HIV-1 subtype C strains were also identified in early 1990s among IDUs [21].…”

“…Other South East Asian (SEA) countries, proximal to China, have also experienced similar epidemiological shifts, for example Thailand [18]. China is also no exception to this phenomenon and currently the Chinese HIV epidemic is dominated by high prevalence of a variety CRFs [7,19].…”

“…Consequently new recombinant strains between these two CRFs have also been described [19], highlighting the ongoing evolution of strains in this region, which will make vaccine design progressively more complicated. The second and third generation recombinant CRFs in China harbor extensive variability in breakpoints, making vaccine design even more difficult.…”