Precise Mapping of Recombination Breakpoints Suggests a Common Parent of Two BC Recombinant HIV Type 1 Strains Circulating in China

Abstract

Two different BC recombinant HIV-1 strains have arisen and begun to circulate among intravenous drug users in China. The recombinants are mostly subtype C with a few small subtype B segments. Additional full-genome sequences of the two recombinants, termed CRF07_BC and CRFO&_BC, are now available for analysis. Four CRF07_BC strains, including c54, 97CNU01, 98CN009, and a new strain CNGL-179, described here, and four CRF08_BC strains, including 97CNGX-6, 97CNGX-7, 97CNGX-9, and 98CN006, were compared for their recombination breakpoints by bootscanning and software for fine mapping of recombinants. The four CRF07_BC strains shared an identical recombination structure and the four CRF08_BC strains shared an identical, but different, recombination structure. The two CRFs share five precise subtype B/C boundaries, although although other segments differ between them, suggesting that they shared a common ancestor, itself a BC recombinant that separately "back-crossed" onto different subtype C strains. Both CRFs are broadly distributed from north to south in western China and have maintained low interpatient diversity.

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

“…An interesting feature of the URFs in Thailand is that most of them share common recombination breakpoints. Molecular epidemiological studies support the hypothesis that these similarities reflect common ancestry (28,(77)(78)(79), though some common breakpoints may represent independent and convergent events (80). In RV148, 1 out of 15 sequenced B/CRF01_AE recombinants belonged to a CRF, CRF15_01B, which is the CRF that has spread among different provinces and social networks throughout Thai- land (32,59).…”

Temporal and Spatial Dynamics of Human Immunodeficiency Virus Type 1 Circulating Recombinant Forms 08_BC and 07_BC in Asia

“…Evolutionary analysis of subtype C. HIV-1 subtype C, probably of Indian origin, was identified as a major circulating strain in China in the early 1990s and is believed to be the putative parent for CRF08_BC and CRF07_BC (19,20). To assess the divergence times of subtype C in both India and China, "pure" nonrecombinant subtype C genetic regions from 12 nearly full-length subtype C sequences of Indian origin (including a nearly full-length sequence from Myanmar [41]) were retrieved from the HIV Sequence Database.…”

“…HIV-1 CRF08_BC, a descendant of the parental subtypes BЈ and C, was first described in the Guangxi province in southern China around 1997 (26). CRF08_BC is thought to have originated in Yunnan province (20,49) and has spread to other regions of China, particularly in the south (26,51). HIV-1 CRF07_BC is a related but distinct BЈ/C recombinant that was first reported in 1997 in Xinjiang and is predominant in the north of China; its origin has also been traced to Yunnan province (38).…”

Worldwide molecular epidemiology of HIV

“…117 In order to make easier the vaccine design and evaluation, several programs for typing the HIV-1 isolates have been implemented mainly for countries suitable as sites for conducting the phase III vaccine efficacy trials. 35 For these proposals, the employed techniques include serotyping, 137 heteroduplex mobility assay (HMA), 14,30,31 RT-polymerase chain reaction (RT-PCR)-gag fingerprinting 50,73,85,118,145 and lately DNA microarray assays have been introduced for this purpose. 124 The HIV subtyping has been an important molecular tool for monitoring the geographic changes in worldwide AIDS epidemic.…”

“…As the two CRFs became dispersed geographically, moving away from the main concentrations of both subtype C and subtype B, further backcrossing may have been curtailed, fixing these strains in the population. 85,132,145,155 In Thailand, the frequency of subtype B increased in early-1990s mainly among IDUs and, by the end of that decade, its decrease was observed just when the prevalence of subtype C began to increase and, at the same time, the emergence of Indian subtypes E and F was recog-Molecular epidemiology of HIV Requejo HIZ nized, thereof the new recombinants BC, BE and BF became predominant. 83 In Portugal, there has been a potential spreading of multiple CRFs owing to the return of native Portuguese people from former Portuguese colonies in Africa, where they lived or worked.…”