| 1. |
- Abidi, Syed Hani, et al.
(author)
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Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan
- 2021
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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Journal article (peer-reviewed)abstract
- 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.
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| 2. |
- Mahmood, Saqib, et al.
(author)
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Divergent path: isolating land use and climate change impact on river runoff
- 2024
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In: Frontiers in Environmental Science. - : Frontiers Media Sa. - 2296-665X. ; 12
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Journal article (peer-reviewed)abstract
- Water resource management requires a thorough examination of how land use and climate change affect streamflow; however, the potential impacts of land-use changes are frequently ignored. Therefore, the principal goal of this study is to isolate the effects of anticipated climate and land-use changes on streamflow at the Indus River, Besham, Pakistan, using the Soil and Water Assessment Tool (SWAT). The multimodal ensemble (MME) of 11 general circulation models (GCMs) under two shared socioeconomic pathways (SSPs) 245 and 585 was computed using the Taylor skill score (TSS) and rating metric (RM). Future land use was predicted using the cellular automata artificial neural network (CA-ANN). The impacts of climate change and land-use change were assessed on streamflow under various SSPs and land-use scenarios. To calibrate and validate the SWAT model, the historical record (1991-2013) was divided into the following two parts: calibration (1991-2006) and validation (2007-2013). The SWAT model performed well in simulating streamflow with NSE, R2, and RSR values during the calibration and validation phases, which are 0.77, 0.79, and 0.48 and 0.76, 0.78, and 0.49, respectively. The results show that climate change (97.47%) has a greater effect on river runoff than land-use change (2.53%). Moreover, the impact of SSP585 (5.84%-19.42%) is higher than that of SSP245 (1.58%-4%). The computed impacts of climate and land-use changes are recommended to be incorporated into water policies to bring sustainability to the water environment.
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| 3. |
- Abbafati, Cristiana, et al.
(author)
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- 2020
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Journal article (peer-reviewed)
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