Limits...
Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters.

Chow WZ, Ong LY, Razak SH, Lee YM, Ng KT, Yong YK, Azmel A, Takebe Y, Al-Darraji HA, Kamarulzaman A, Tee KK - PLoS ONE (2013)

Bottom Line: Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s.Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population.The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

View Article: PubMed Central - PubMed

Affiliation: Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.

ABSTRACT
Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

Show MeSH

Related in: MedlinePlus

Bootscan analyses of HIV-1 unique recombinant forms (URFs) isolated from people who inject drugs (PWID) in Malaysia.A, Schematic representation of the full length recombinant structure of CRF33_01B with the four unique recombination breakpoints labelled as 1–4 (HXB2∶2053–2063 nt, 2375–2416 nt, 2538–2540 nt and 2841–2875 nt, respectively) in the gag-pol region [21]. B, Bootscanning plots of three novel CRF candidates (1 to 3) generated from the 1.6 kb gag-pol gene (HXB2∶1753–3440 nt) using SimPlot version 3.5.1 [36]. HIV-1 reference strains CRF01_CM240 (CRF01_AE) and B′_RL42 (Thai subtype B′) were selected as the putative parental genotypes by similarity plotting and C_95IN21068 (subtype C) as an outgroup, with a window size of 200 nucleotides moving along the alignment in increments of 50 nucleotides to define the recombination structures. The shared recombination breakpoints between the URFs were highlighted and in cases where the breakpoints were also shared with CRF33_01B, these breakpoints were further numbered (1 to 4). Each sub-region of these CRF candidates was also indicated and described further in Figure 3. C, Bootscanning plots of unique recombinant forms (URFs) –11MY1MR851 (sharing a similar recombination breakpoint with 07MYKLD49 [46]), 10MYKJ086, 11MY2NF831, 11MY3HA741 and 11MY1IM781 displaying distinct recombinant structures in the 1.6 kb gag-pol sequences amplified among the PWIDs study population. For clarity, bootscanning plots of partial RT and gag-PR sequences (11MY1JJ741 and 10MYKJ084, respectively) were not displayed here but their recombination structures have been discussed in detail in the text.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3646884&req=5

pone-0062560-g002: Bootscan analyses of HIV-1 unique recombinant forms (URFs) isolated from people who inject drugs (PWID) in Malaysia.A, Schematic representation of the full length recombinant structure of CRF33_01B with the four unique recombination breakpoints labelled as 1–4 (HXB2∶2053–2063 nt, 2375–2416 nt, 2538–2540 nt and 2841–2875 nt, respectively) in the gag-pol region [21]. B, Bootscanning plots of three novel CRF candidates (1 to 3) generated from the 1.6 kb gag-pol gene (HXB2∶1753–3440 nt) using SimPlot version 3.5.1 [36]. HIV-1 reference strains CRF01_CM240 (CRF01_AE) and B′_RL42 (Thai subtype B′) were selected as the putative parental genotypes by similarity plotting and C_95IN21068 (subtype C) as an outgroup, with a window size of 200 nucleotides moving along the alignment in increments of 50 nucleotides to define the recombination structures. The shared recombination breakpoints between the URFs were highlighted and in cases where the breakpoints were also shared with CRF33_01B, these breakpoints were further numbered (1 to 4). Each sub-region of these CRF candidates was also indicated and described further in Figure 3. C, Bootscanning plots of unique recombinant forms (URFs) –11MY1MR851 (sharing a similar recombination breakpoint with 07MYKLD49 [46]), 10MYKJ086, 11MY2NF831, 11MY3HA741 and 11MY1IM781 displaying distinct recombinant structures in the 1.6 kb gag-pol sequences amplified among the PWIDs study population. For clarity, bootscanning plots of partial RT and gag-PR sequences (11MY1JJ741 and 10MYKJ084, respectively) were not displayed here but their recombination structures have been discussed in detail in the text.

Mentions: Of note, four isolates (10MYKJ036, 11MY1RJ704, 11MY1ZK731 and 11MY1EP794) showed unique tree topology by grouping together with a previously reported CRF01_AE/B recombinant (06MYKLD46) [45] at the base of the CRF33_01B clade, supported by a bootstrap value of 71% in the neighbour-joining tree (Figure 1). The four isolates sequenced in this study seemed to have diverged from 06MYKLD46 lineage and formed a well-supported clade (98% bootstrap value). Nucleotide sequences of these five isolates were submitted to the RIP tool at the HIV database and later bootscanned (using HIV-1 CRF01_CM240 and B′_RL42 as the putative parental genotypes) by SimPlot, showing evidence of identical CRF01_AE/B mosaic genome structure shared among the four isolates except 06MYKLD46 (Figure 2Band Figure S2). Informative sites analyses revealed the recombination of two subtype B′ segments at HXB2 positions 2064–2665 and 3260–3440 nt shared by all four isolates (10MYKJ036, 11MY1RJ704, 11MY1ZK731 and 11MY1EP794) in addition to the CRF01_AE segments at positions 1753–2052 and 2690–3194 nt. In all four isolates, similar multiple recombination breakpoints were identified at positions 2053–2063, 2666–2689 and 3195–3259 nt.


Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters.

Chow WZ, Ong LY, Razak SH, Lee YM, Ng KT, Yong YK, Azmel A, Takebe Y, Al-Darraji HA, Kamarulzaman A, Tee KK - PLoS ONE (2013)

Bootscan analyses of HIV-1 unique recombinant forms (URFs) isolated from people who inject drugs (PWID) in Malaysia.A, Schematic representation of the full length recombinant structure of CRF33_01B with the four unique recombination breakpoints labelled as 1–4 (HXB2∶2053–2063 nt, 2375–2416 nt, 2538–2540 nt and 2841–2875 nt, respectively) in the gag-pol region [21]. B, Bootscanning plots of three novel CRF candidates (1 to 3) generated from the 1.6 kb gag-pol gene (HXB2∶1753–3440 nt) using SimPlot version 3.5.1 [36]. HIV-1 reference strains CRF01_CM240 (CRF01_AE) and B′_RL42 (Thai subtype B′) were selected as the putative parental genotypes by similarity plotting and C_95IN21068 (subtype C) as an outgroup, with a window size of 200 nucleotides moving along the alignment in increments of 50 nucleotides to define the recombination structures. The shared recombination breakpoints between the URFs were highlighted and in cases where the breakpoints were also shared with CRF33_01B, these breakpoints were further numbered (1 to 4). Each sub-region of these CRF candidates was also indicated and described further in Figure 3. C, Bootscanning plots of unique recombinant forms (URFs) –11MY1MR851 (sharing a similar recombination breakpoint with 07MYKLD49 [46]), 10MYKJ086, 11MY2NF831, 11MY3HA741 and 11MY1IM781 displaying distinct recombinant structures in the 1.6 kb gag-pol sequences amplified among the PWIDs study population. For clarity, bootscanning plots of partial RT and gag-PR sequences (11MY1JJ741 and 10MYKJ084, respectively) were not displayed here but their recombination structures have been discussed in detail in the text.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646884&req=5

pone-0062560-g002: Bootscan analyses of HIV-1 unique recombinant forms (URFs) isolated from people who inject drugs (PWID) in Malaysia.A, Schematic representation of the full length recombinant structure of CRF33_01B with the four unique recombination breakpoints labelled as 1–4 (HXB2∶2053–2063 nt, 2375–2416 nt, 2538–2540 nt and 2841–2875 nt, respectively) in the gag-pol region [21]. B, Bootscanning plots of three novel CRF candidates (1 to 3) generated from the 1.6 kb gag-pol gene (HXB2∶1753–3440 nt) using SimPlot version 3.5.1 [36]. HIV-1 reference strains CRF01_CM240 (CRF01_AE) and B′_RL42 (Thai subtype B′) were selected as the putative parental genotypes by similarity plotting and C_95IN21068 (subtype C) as an outgroup, with a window size of 200 nucleotides moving along the alignment in increments of 50 nucleotides to define the recombination structures. The shared recombination breakpoints between the URFs were highlighted and in cases where the breakpoints were also shared with CRF33_01B, these breakpoints were further numbered (1 to 4). Each sub-region of these CRF candidates was also indicated and described further in Figure 3. C, Bootscanning plots of unique recombinant forms (URFs) –11MY1MR851 (sharing a similar recombination breakpoint with 07MYKLD49 [46]), 10MYKJ086, 11MY2NF831, 11MY3HA741 and 11MY1IM781 displaying distinct recombinant structures in the 1.6 kb gag-pol sequences amplified among the PWIDs study population. For clarity, bootscanning plots of partial RT and gag-PR sequences (11MY1JJ741 and 10MYKJ084, respectively) were not displayed here but their recombination structures have been discussed in detail in the text.
Mentions: Of note, four isolates (10MYKJ036, 11MY1RJ704, 11MY1ZK731 and 11MY1EP794) showed unique tree topology by grouping together with a previously reported CRF01_AE/B recombinant (06MYKLD46) [45] at the base of the CRF33_01B clade, supported by a bootstrap value of 71% in the neighbour-joining tree (Figure 1). The four isolates sequenced in this study seemed to have diverged from 06MYKLD46 lineage and formed a well-supported clade (98% bootstrap value). Nucleotide sequences of these five isolates were submitted to the RIP tool at the HIV database and later bootscanned (using HIV-1 CRF01_CM240 and B′_RL42 as the putative parental genotypes) by SimPlot, showing evidence of identical CRF01_AE/B mosaic genome structure shared among the four isolates except 06MYKLD46 (Figure 2Band Figure S2). Informative sites analyses revealed the recombination of two subtype B′ segments at HXB2 positions 2064–2665 and 3260–3440 nt shared by all four isolates (10MYKJ036, 11MY1RJ704, 11MY1ZK731 and 11MY1EP794) in addition to the CRF01_AE segments at positions 1753–2052 and 2690–3194 nt. In all four isolates, similar multiple recombination breakpoints were identified at positions 2053–2063, 2666–2689 and 3195–3259 nt.

Bottom Line: Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s.Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population.The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

View Article: PubMed Central - PubMed

Affiliation: Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.

ABSTRACT
Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

Show MeSH
Related in: MedlinePlus