Emergence of HIV-1 Unique DG Recombinant Form in Pakistan

Tariq, Uroosa; Mahmood, Faisal; Naeem, Sadaf; Ali, Syed; Abidi, Syed Hani

doi:10.1089/aid.2019.0183

Cited by 7 publications

(15 citation statements)

References 6 publications

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“…The mixing of strains facilitates the complex diversification of the virus and can also favor drug resistance by bringing multiple DMRs together into a recombinant virus; while on the contrary, it can also interfere with drug resistance by breaking the association between DRMs [9]. Several circulating recombinant forms (CRF), unique recombinant forms (URF), and complex recombinant forms (Cpx) have been reported globally, and two of them were also evident in Pakistan recently [3,5].…”

Section: Discussionmentioning

confidence: 99%

“…Multidrug resistance and a lack of response ART limit the treatment options for the patient [14]. Several studies have linked the genotype diversity with the specific drug resistance patterns [3,5,9,10,15]. It was observed in an earlier study in Malaysia that 44.4% of children with CRF33_01B failed to respond to the treatment [4].…”

Section: Discussionmentioning

confidence: 99%

“…The amplification was performed using a nested PCR involving two sets of primers. These primers have previously been used in our studies for genotyping viruses in patients and for simultaneous identification of HIV strains [3,5]. The first round was performed using BesTaq Abm Mastermix (G464) with primers Pol OF (5'-CAG CAT GYC AGG GAG TRG GRG GAC C-3'; nt 1832 → nt 1856, with reference to the HXB2 genome) and IBR1 (5'-AAC TTC TGT ATA TCA TTG ACA GTC CA-3'; nt 3303 ← nt 3328, with reference to the HXB2 genome), whereas the second round involved HotStart Abm Mastermix (G906) with primers PolIF (5'-AGG CTA ATT TTT TAG GGA ARA TYT GGC CTT CC-3'; nt 2078 → nt 2109, with reference to the HXB2 genome) and RTout3 (5'-TAT GTC ATT GAC AGT CCA GCT-3', nt 3300 ← nt 3320, with reference to the HXB2 genome).…”

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The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual

et al. 2020

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In Pakistan, the HIV situation has gone from an outbreak to a concentrated epidemic, and the virus has now crossed into the low-risk population. In addition, several new HIV outbreaks have occurred in different parts of the country. HIV-1 subtype A has been the major epidemic subtype in Pakistan; however, as the epidemic has grown, the emergence of several new subtypes and recombinant forms has been observed. Here, we present the first case and genetic analysis of an unassigned, complex recombinant form in a Pakistani HIV-infected individual with virological failure. Genetic analysis of the sequence indicated that this recombinant form is multi-drug resistant, harboring drug resistance mutations against more than one class of antiretroviral drugs.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual

et al. 2020

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“…The HIV-1 epidemic in Pakistan has been expanding rapidly and a large increase (57%) in new HIV-1 infections has been observed during the last ten years [ 17 , 18 ]. These infections have now bridged from high-risk groups, such as people who inject drugs (PWID) and men who have sex with men (MSM), into the low-risk communities, including women and children [ 19 , 20 ]. The HIV-1 epidemic in Pakistan is mainly driven by HIV-1 sub-subtype A1.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan

Tariq

Nazziwa

Sasinovich

et al. 2022

Viruses

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(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented. We performed a detailed characterization of the HIV-1 sub-subtype A1 epidemic in Pakistan using state-of-the-art molecular epidemiology and phylodynamics. (2) Methods: A total of 143 HIV-1 sub-subtype A1 gag sequences, including 61 sequences generated specifically for this study from PLHIVs part of our cohort, representing all sub-subtype A1 gag sequences from Pakistan, were analyzed. Maximum-likelihood phylogenetic cluster analysis was used to determine the relationship between Pakistani sub-subtype A1 strains and pandemic sub-subtype A1 strains. Furthermore, we used signature variation, charge distribution, selection pressures, and epitope prediction analyses to characterize variations unique to Pakistani HIV-1 strains and establish the association between signature variations and Gag epitope profile. (3) Results: The HIV-1 sub-subtype A1 sequences from Pakistan formed three main clusters: two that clustered with Kenyan sequences (7 and 10 sequences, respectively) and one that formed a Pakistan-specific cluster of 123 sequences that were much less related to other sub-subtype A1 sequences available in the database. The sequences in the Pakistan-specific cluster and the Kenyan reference strains exhibited several signature variations, especially at amino acid positions 312, 319, 331, 372, 373, 383, and 402. Structural protein modeling suggested that amino acid changes in these positions result in alterations of the Gag protein structure as well as in Gag-specific T-cell epitopes. (4) Conclusions: Our results suggest that the majority of the Pakistan HIV-1 sub-subtype A1 strains were unique to Pakistan and with a specific mutation pattern in Gag.

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“…The first case of HIV in Pakistan was documented in 1987 in Karachi (1). Following this first recorded case, multiple subtypes and circulating recombinant forms (CRFs) have been identified and are currently circulating in the country (2)(3)(4). Still, before the implementation of integrated biological and behavioral surveillance (IBBS) of key populations in Pakistan in 2005 (5), little was known about the prevalence and associated risk behaviors of HIV in the country (6).…”

Section: Introductionmentioning

confidence: 99%

HIV Phylogenetics Reveals Overlapping Transmission Networks among Cities and Key Populations in Pakistan

Schneider

Cholette

Pelcat

et al. 2021

Preprint

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The first case of HIV in Pakistan was documented in 1987, with multiple subtypes and circulating recombinant forms being introduced and currently circulating in the country. Since then, there has been a shift in the country from a low prevalence/high risk to a high-risk concentrated epidemic. Pakistan’s epidemic is concentrated among key populations at greater risk of HIV infection including people who inject drugs (PWID), Hijra sex workers (HSW), female sex workers (FSW), male sex workers (MSW), and men who have sex with men (MSM). This study focused on the geographical aspect as well as on the interactions between key populations at higher risk of contracting HIV. We aimed at understanding the behavior of these key populations at a molecular level with high granularity as well as investigating the possibility of multiple HIV-1 introductions in Pakistan. In this cross-sectional biological and behavioral survey, we collected dried blood spots (DBS) for the purposes of seroprevalence estimates and molecular epidemiology from individuals in 17 cities in Pakistan representing four key populations: PWID, HSW, MSW, and FSW. A total of 1153 envelope sequences (reference positions in HXB2: 7860-8274) of HIV were sequenced using a Sanger-based sequencing approach. To identify clusters based on the introduction of the virus in Pakistan from foreign countries we added 3623 publicly available HIV envelope sequences to our dataset. Phylogeographic inference suggests at least 15 independent introductions of the virus into Pakistan, with a total of 12 clusters ranging from 3 to 675 sequences in size containing sequences from Pakistan and neighboring countries exclusively. Our phylogenetic analysis shows a significant degree of connectivity and directionality suggesting broad and overlapping networks of HIV-1 transmission among cities and key populations in Pakistan.

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Emergence of HIV-1 Unique DG Recombinant Form in Pakistan

Cited by 7 publications

References 6 publications

The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual

The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual

Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan

HIV Phylogenetics Reveals Overlapping Transmission Networks among Cities and Key Populations in Pakistan

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