Emergence of Circulating Recombinant Form 56_cpx in Pakistan

Tariq, Uroosa; Parveen, Azra; Akhtar, Furqana; Mahmood, Faisal; Ali, Syed; Abidi, Syed Hani

doi:10.1089/aid.2018.0128

Cited by 11 publications

(21 citation statements)

References 4 publications

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“…This falls in line with our findings, implying that the origin of these strains could have been in the eastern Mediterranean region. In addition, CRF56_cpx has been observed in Pakistan and the Philippines, thus reaching global diffusion [45].…”

Section: Discussionmentioning

confidence: 99%

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Lunar

Mlakar

Zorec

et al. 2020

Viruses

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Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.

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Section: Discussionmentioning

confidence: 99%

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Lunar

Mlakar

Zorec

et al. 2020

Viruses

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“…nt 2078-2109, amino acid PR: 1-9; HXB2) and reverse (RTOUT3 5 -TATGTCATT GACAGTCCAGCT-3 . nt 3300-3320, amino acid RT: 251-257 HXB2) (Tariq et al, 2018). PCR Mastermix (ABM) Bestaq (2X) cat# G464 and Hotstart (2X) cat# G906 were used to prepare a 25 ul reaction mixture, and 0.8 pmol and 0.6 pmol primer used for the first and second round, respectively.…”

Section: Dna Amplification and Hiv-1 Genotypingmentioning

confidence: 99%

Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan

et al. 2021

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IntroductionIn April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan.MethodsA total of 401 blood samples were collected between April–June 2019, from children infected with HIV-1 aged 0–15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters.ResultsThe HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan.ConclusionThe presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan.

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“…However, as the epidemic grows, the emergence of several new subtypes and recombinant forms is being observed [4]. Recently, we reported the first case (the seventh case worldwide) of a unique recombinant form, CRF 56_cpx, in an HIV-1-infected Pakistani individual [3]. Pakistani strain 56_cpx was 1) possibly acquired during the HIV-infected individual's travel to UAE, 2) was multi-drug resistant, and 3) had more DRMs compared to other 56_cpx strains reported worldwide [3].…”

Section: Introductionmentioning

confidence: 99%

“…The high rate of evolution, combined with other features, such as error-prone reverse transcription, natural polymorphisms, drug resistance mutations (DRMs), immune escape mutations and inter-subtype recombination, facilitates HIV-1 diversification within the host milieu [2]. Multiple viral introductions during transmission and subtype mixing promote the recombination between HIV-1 variants, resulting in the generation of unique recombinant forms with the capacity to harbor complex patterns of drug resistance or immune escape mutations, which can complicate therapeutic interventions, and enhance viral transmission [3].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we reported the first case (the seventh case worldwide) of a unique recombinant form, CRF 56_cpx, in an HIV-1-infected Pakistani individual [3]. Pakistani strain 56_cpx was 1) possibly acquired during the HIV-infected individual's travel to UAE, 2) was multi-drug resistant, and 3) had more DRMs compared to other 56_cpx strains reported worldwide [3]. Here, we present the first report an unassigned complex recombinant form of HIV-1 subtype A1.…”

Section: Introductionmentioning

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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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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Emergence of Circulating Recombinant Form 56_cpx in Pakistan

Cited by 11 publications

References 4 publications

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan

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

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