Dataset Information

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

ABSTRACT: The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identified in the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the five NFLG sequences of DG recombinants showed that all five NFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmed these sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff.

Importance

In Pakistan, the genetic diversity of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly complex, compared to the early years of the epidemic that started after the detection of the first cases of HIV-1 in 1987 in Karachi. Based on the available molecular studies, two dominant HIV-1 clades, sub-subtype A1 and CRF02_AG, have been found to co-circulate with other clades, namely B, C, D, G, CRF01_AE, CRF35_A1D, and CRF56_cpx, in various urban areas of Pakistan. Several novel recombinant forms have also been detected. This first report of CRF152_DG highlights the complex nature of the HIV epidemic in Pakistan and emphasizes the importance of continual molecular surveillance (ideally based on whole-genome sequences) of HIV.

SUBMITTER: Rashid A

PROVIDER: S-EPMC11218485 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

Rashid Abdur A Kang Li L Yi Feng F Getaneh Yimam Y Chu Qingfei Q Shah Sharaf Ali SA Abidi Syed Hani SH Shao Yiming Y

Microbiology spectrum 20240521 7

The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the <i>pol</i> gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses ...[more]

PMID: 38771033

Similar Datasets

Project description:(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.

Project description:BackgroundPsychosis is known to have an adverse impact on an individual's quality of life, social and occupational functioning. A lack of treatment options for psychotic disorders such as schizophrenia contributes to adverse outcomes for individuals. A significant proportion of people with psychosis consult both formal and traditional routes of care. This warrants a need to explore perceptions around treatment options provided by diverse care providers, as the identification of avenues for support can improve psychiatric, alternative treatment and social outcomes.MethodsFocus groups discussions (FGDs) and in-depth interviews (IDIs) were used. Interactive Research and Development (IRD) research staff conducted 20 IDIs and 2 FGDs to obtain information about the perspectives, treatment pathways and experiences of individuals with psychosis, their caregivers, and service providers. Questions for clinician care providers and faith healers revolved around perceptions of psychosis, service users' background, subject knowledge and treatment, feedback and referral mechanisms, and promotion of services. A thematic analysis was used to analyze the interviews and coding was conducted on NVivo.ResultsThe results were categorized into five themes: perception of psychosis, experience of seeking/receiving care, assessment and diagnosis methods, promotion of services, and living with psychosis. Across service providers and patients, there was a wide variety of causes attributed to psychosis, and an overall lack of awareness regarding severe mental health conditions from both formal and informal care-providers. Biomedical treatment received mixed reviews, while some reported it as beneficial, the limited number of institutes and clinicians to cater for patients, stigma within society and care providers, the burden of caregiving, and misinformation from faith healers were all significant barriers to treatment.ConclusionThe results highlight the use of traditional healing practices for psychosis in Pakistan, which, coupled with inadequate referral mechanisms, present an opportunity to bridge the treatment gap between clinical and traditional healing practices through integration of treatment within community structures and systems. Better awareness of psychosis and its treatment methods, alongside interventions that reduce stigma could help facilitate help-seeking behavior and reduce the burden of caregiving.

Dataset Information

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

Importance

Publications

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets