Identification of New CRF51_01B in Singapore Using Full Genome Analysis of Three HIV Type 1 Isolates

Johns Hopkins School of Medicine, Johns Hopkins Medical Institution, Baltimore, MD, USA.
AIDS research and human retroviruses (Impact Factor: 2.33). 09/2011; 28(5):527-30. DOI: 10.1089/AID.2011.0177
Source: PubMed


A recent HIV-1 molecular epidemiology survey in Singapore identified a novel CRF01_AE/B recombinant form, which accounted for 13 (11.9%) of 109 patient samples. Peripheral blood mononuclear cell DNA from three of these 13 patients was used to generate near full-length sequences to characterize the novel CRF01_AE/B recombinant form. The three isolates had a recombinant structure composed of CRF01_AE and subtype B, and shared identical breakpoints. As the three patients were not epidemiologically linked, this recombinant form has been designated CRF51_01B. Identification of the novel recombinant forms indicates ongoing active HIV-1 transmission in Singapore.

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Available from: Kk Chew, Mar 31, 2015
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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.
    PLoS ONE 06/2014; 9(6):e99693. DOI:10.1371/journal.pone.0099693 · 3.23 Impact Factor
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    • "A more recent study further confirmed that HIV-1 subtype B and CRF01_AE continue to be the predominant genotypes circulating in Singapore, with a higher CRF01_AE prevalence among MSM [8]. In addition, Ng et al. [9] reported the emergence of a novel HIV-1 CRF51_01B lineage among MSM in Singapore which is genetically distinct from other previously established subtypes or recombinants. Despite the significant clinical and epidemiological impact attributed to HIV-1 subtype B, CRF01_AE and CRF51_01B in Singapore [10], the genetic history, population dynamics and pattern of transmission networks of these genotypes remains largely unexplored. "
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    ABSTRACT: HIV-1 subtype B and CRF01_AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatment-naïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01_AE and one within CRF51_01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01_AE. Exponential increase in effective population size for both subtype B and CRF01_AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51_01B lineages were probably generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and CRF51_01B viral strains circulating among MSM in Singapore.
    PLoS ONE 12/2013; 8(12):e80884. DOI:10.1371/journal.pone.0080884 · 3.23 Impact Factor
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    • "In many regions around the world, there is a significant displacement of the existing HIV-1 subtype by other new strains, for instance subtype B and CRF01_AE in Southern China,12,13 Southeast Asia,23-27 and subtype B and F in Brazil.28-31 It is likely that the initial predominance of a certain HIV subtype is attributable to its specific mode of transmission within a given geographical region, for instance displacement of subtype C by subtype B.32 However, there is no substantial evidence to suggest that HIV-1 strains such as CRF01_AE and subtypes A, B, C and D are more or less transmissible by a specific route, in a specific ethnic group, or in a specific cell type.33-39 "
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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.
    Infectious disease reports 06/2013; 5(Suppl 1):e4. DOI:10.4081/idr.2013.s1.e4
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