Genome Sequence of a Novel HIV-1 Circulating Recombinant Form 54_01B from Malaysia

Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
Journal of Virology (Impact Factor: 4.44). 10/2012; 86(20):11405-6. DOI: 10.1128/JVI.01949-12
Source: PubMed


We report here the first novel HIV-1 circulating recombinant form (CRF) 54_01B (CRF54_01B) isolated from three epidemiologically
unlinked subjects of different risk groups in Malaysia. These recently sampled recombinants showed a complex genome organization
composed of parental subtype B′ and CRF01_AE, with identical recombination breakpoints observed in the gag, pol, and vif genes. Such a discovery highlights the ongoing active generation and spread of intersubtype recombinants involving the subtype
B′ and CRF01_AE lineages and indicates the potential of the new CRF in bridging HIV-1 transmission among different risk groups
in Southeast Asia.

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Available from: Adeeba Kamarulzaman, Oct 21, 2014
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    • "Recombination breakpoint analysis revealed that these six NFLG sequences shared identical recombinant structures in which two subtype B regions (nucleotide position 2570–2718 in the pol region and 6149–8243 nt in the region relative to the HXB2 genome) were located in a CRF01_AE backbone (Figure 3). The recombinant structure is distinct from any other known CRFs comprising CRF01_AE and subtype B, including CRF15_01B [22], CRF33_01B [23], CRF34_01B [24], CRF48_01B [25], CRF51_01B [3], CRF52_01B [4], CRF53_01B [5], CRF54_01B [6], and CRF55 01B [7]. Subregion tree analyses further confirmed the parental origins of each region of the recombinant genome as follows (Figure 3C): Region I (HXB2: 790–2569) = CRF01_AE; Region II (HXB2: 2570–2718) = B; Region III (HXB2: 2719–6148) = CRF01_AE; Region IV (HXB2: 6149–8243) = B; Region V (HXB2: 8244–9600) = CRF01_AE. "
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    ABSTRACT: The HIV-1 epidemic among men-who-have-sex-with-men (MSM) continues to expand in China. A large-scale national survey we conducted on HIV-1 strains among MSM in 11 provinces in China from 2008 to 2013 (n = 920) identified a novel transmission cluster consisting of six strains (0.7%) that belonged to a new circulating recombinant form (designated CRF59_01B). CRF59_01B contains two subtype B segments of U.S.-European origin (in the pol and vpu-env regions) in a CRF01_AE backbone. CRF59_01B is the second CRF (after CRF55_01B) circulating primarily among MSM in China. CRF59_01B occurs at a low frequency (less than 1%), but it was detected in four different provinces/regions in China: Liaoning (northeast China) (n = 3); Hunan (central China) (n = 1); Guangdong (south China) (n = 1); Yunnan (southwest China) (n = 1). One additional recombinant strain was detected in a heterosexual individual in Liaoning province but is not the focus of this paper. Bayesian molecular clock analyses indicate that CRF59_01B emerged as a result of recombination between CRF01_AE and subtype B around the year 2001. The emergence of multiple forms of recombinants and CRFs reflects the ever-increasing contribution of homosexual transmission in China's HIV epidemic and indicates an active HIV transmission network among MSM in China.
    Full-text · Article · Jun 2014 · PLoS ONE
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    • "This phenomenon has been demonstrated by the emergence of several CRFs that are derived from unique HIV-1 subtype B and F-like URFs in South America.28,29,31,54 The most recent occurrence is evident in the discovery of an URF strain 07MYKLD49, which was first reported in 2007 by our group,25 and later classified with two other URFs as a new CRF in 2012.55 More second generation recombinants have emerged due to the recombination of CRFs with other HIV-1 strains, indicating the up-coming of new recombinant strains. "
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    ABSTRACT: One of the major characteristics of HIV-1 is its high genetic variability and extensive heterogeneity. This characteristic is due to its molecular traits, which in turn allows it to vary, recombine, and diversify at a high frequency. As such, it generates complex molecular forms, termed recombinants, which evade the human immune system and so survive. There is no sequence constraint to the recombination pattern as it appears to occur at inter-group (between groups M and O), as well as interand intra-subtype within group M. Rapid emergence and active global transmission of HIV-1 recombinants, known as circulating recombinant forms (CRFs) and unique recombinant forms (URFs), requires urgent attention. To date, 55 CRFs have been reported around the world. The first CRF01_AE originated from Central Africa but spread widely in Asia. The most recent CRF; CRF55_01B is a recombinant form of CRF01_AE and subtype B, although its origin is yet to be publicly disclosed. HIV-1 recombination is an ongoing event and plays an indispensable role in HIV epidemics in different regions. Africa, Asia and South America are identified as recombination hot-spots. They are affected by continual emergence and cocirculation of newly emerging CRFs and URFs, which are now responsible for almost 20% of HIV-1 infections worldwide. Better understanding of recombinants is necessary to determine their biological and molecular attributes.
    Full-text · Article · Jun 2013 · Infectious disease reports
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    • "The main hallmark of the HIV-1 is an extraordinary evolution rate, which results in high molecular diversity and dynamism of the AIDS epidemic [1]. HIV-1 is classified in four groups and the group M, currently estimated to infect around 33 million people around the world, is subdivided in 9 subtypes (A–D, F–H, J, and K) and 54 circulating recombinant forms (CRFs) [1-3]. "
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    ABSTRACT: Background The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal dynamics of HIV-1 subtypes circulating in patients from distinct exposure categories in Southern Brazil. For this purpose 166 HIV-1 samples collected at the years of 1998 (group I) and 2005–2008 (group II) were analyzed. Results Analysis of group I revealed statistically significant (p < 0.05) associations between MSM and subtype B as well as between IDU and subtype C; while no statistical significant association between HIV-1 subtypes and exposure category was verified for group II. An overall temporal increase in the prevalence of subtype C and BC recombinants was observed in both HET and MSM populations, accompanied by a proportional decrease in the prevalence of the pure subtype B. Conclusions The present study shows an association between HIV subtypes and exposure categories at the middle 1990s in Southern Brazil. Our findings suggest that MSM and IDU populations might have played a major role in the introduction and initial dissemination of subtypes B and C, respectively, in Southern Brazil. This study also suggests a trend towards homogenization of HIV-1 strains across distinct exposure categories as a consequence of an overall increase in the prevalence of subtype C and BC recombinants in both HET and MSM populations.
    Full-text · Article · Dec 2012 · Virology Journal
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