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Phylogenetic and Dr...
Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan
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- Abidi, Syed Hani (författare)
- Aga Khan University, Pakistan
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- Nduva, George Makau (författare)
- Lund University,Lunds universitet,Systemvirologi,Forskargrupper vid Lunds universitet,Systems Virology,Lund University Research Groups,Kenya Medical Research Institute (KEMRI)
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- Siddiqui, Dilsha (författare)
- Aga Khan University, Pakistan
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- Rafaqat, Wardah (författare)
- Aga Khan University, Pakistan
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- Mahmood, Syed Faisal (författare)
- Aga Khan University, Pakistan
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- Siddiqui, Amna Rehana (författare)
- Aga Khan University, Pakistan
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- Nathwani, Apsara Ali (författare)
- Aga Khan University, Pakistan
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- Hotwani, Aneeta (författare)
- Aga Khan University, Pakistan
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- Shah, Sharaf Ali (författare)
- Bridge Consultants Foundation
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- Memon, Sikander (författare)
- Ministry of Health, Pakistan
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- Sheikh, Saqib Ali (författare)
- Ministry of Health, Pakistan
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- Khan, Palwasha (författare)
- London School of Hygiene and Tropical Medicine
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- Esbjörnsson, Joakim (författare)
- Lund University,Lunds universitet,Systemvirologi,Forskargrupper vid Lunds universitet,Systems Virology,Lund University Research Groups,University of Oxford
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- Ferrand, Rashida Abbas (författare)
- Aga Khan University, Pakistan,London School of Hygiene and Tropical Medicine
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- Mir, Fatima (författare)
- Aga Khan University, Pakistan
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(creator_code:org_t)
- 2021-08-17
- 2021
- Engelska.
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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http://dx.doi.org/10... (free)
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https://www.frontier...
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https://doi.org/10.3...
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Abstract
Ämnesord
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- Introduction: In 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. Methods: A 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. Results: The 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. Conclusion: The 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.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
Nyckelord
- drug resistance
- HIV-1
- outbreak investigation
- paediatric [MeSH]
- phylogenetic analysis
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Abidi, Syed Hani
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Nduva, George Ma ...
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Siddiqui, Dilsha
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Rafaqat, Wardah
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Mahmood, Syed Fa ...
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Siddiqui, Amna R ...
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visa fler...
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Nathwani, Apsara ...
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Hotwani, Aneeta
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Shah, Sharaf Ali
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Memon, Sikander
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Sheikh, Saqib Al ...
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Khan, Palwasha
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Esbjörnsson, Joa ...
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Ferrand, Rashida ...
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Mir, Fatima
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