Displaying all 4 publications

  1. MalariaGEN, Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, et al.
    Wellcome Open Res, 2022;7:136.
    PMID: 35651694 DOI: 10.12688/wellcomeopenres.17795.1
    This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
  2. Commons RJ, Simpson JA, Thriemer K, Abreha T, Adam I, Anstey NM, et al.
    PLoS Med, 2019 Oct;16(10):e1002928.
    PMID: 31584960 DOI: 10.1371/journal.pmed.1002928
    BACKGROUND: Artemisinin-based combination therapy (ACT) is recommended for uncomplicated Plasmodium vivax malaria in areas of emerging chloroquine resistance. We undertook a systematic review and individual patient data meta-analysis to compare the efficacies of dihydroartemisinin-piperaquine (DP) and artemether-lumefantrine (AL) with or without primaquine (PQ) on the risk of recurrent P. vivax.

    METHODS AND FINDINGS: Clinical efficacy studies of uncomplicated P. vivax treated with DP or AL and published between January 1, 2000, and January 31, 2018, were identified by conducting a systematic review registered with the International Prospective Register of Systematic Reviews (PROSPERO): CRD42016053310. Investigators of eligible studies were invited to contribute individual patient data that were pooled using standardised methodology. The effect of mg/kg dose of piperaquine/lumefantrine, ACT administered, and PQ on the rate of P. vivax recurrence between days 7 and 42 after starting treatment were investigated by Cox regression analyses according to an a priori analysis plan. Secondary outcomes were the risk of recurrence assessed on days 28 and 63. Nineteen studies enrolling 2,017 patients were included in the analysis. The risk of recurrent P. vivax at day 42 was significantly higher in the 384 patients treated with AL alone (44.0%, 95% confidence interval [CI] 38.7-49.8) compared with the 812 patients treated with DP alone (9.3%, 95% CI 7.1-12.2): adjusted hazard ratio (AHR) 12.63 (95% CI 6.40-24.92), p < 0.001. The rates of recurrence assessed at days 42 and 63 were associated inversely with the dose of piperaquine: AHRs (95% CI) for every 5-mg/kg increase 0.63 (0.48-0.84), p = 0.0013 and 0.83 (0.73-0.94), p = 0.0033, respectively. The dose of lumefantrine was not significantly associated with the rate of recurrence (1.07 for every 5-mg/kg increase, 95% CI 0.99-1.16, p = 0.0869). In a post hoc analysis, in patients with symptomatic recurrence after AL, the mean haemoglobin increased 0.13 g/dL (95% CI 0.01-0.26) for every 5 days that recurrence was delayed, p = 0.0407. Coadministration of PQ reduced substantially the rate of recurrence assessed at day 42 after AL (AHR = 0.20, 95% CI 0.10-0.41, p < 0.001) and at day 63 after DP (AHR = 0.08, 95% CI 0.01-0.70, p = 0.0233). Results were limited by follow-up of patients to 63 days or less and nonrandomised treatment groups.

    CONCLUSIONS: In this study, we observed the risk of P. vivax recurrence at day 42 to be significantly lower following treatment with DP compared with AL, reflecting the longer period of post-treatment prophylaxis; this risk was reduced substantially by coadministration with PQ. We found that delaying P. vivax recurrence was associated with a small but significant improvement in haemoglobin. These results highlight the benefits of PQ radical cure and also the provision of blood-stage antimalarial agents with prolonged post-treatment prophylaxis.

  3. Trimarsanto H, Amato R, Pearson RD, Sutanto E, Noviyanti R, Trianty L, et al.
    Commun Biol, 2022 Dec 23;5(1):1411.
    PMID: 36564617 DOI: 10.1038/s42003-022-04352-2
    Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.
  4. Yassin Ibrahim, Rosnah Sutan, Khalib Bin Abdul Latif, Al - Abed A. Al - Abed, Amara, Ahmed, Adam, Ishag
    Adherence to antiretroviral therapy (ART) plays an important role in the treatment outcomes of human immunodeficiency virus (HIV) infection. Poor adherence would result in failure to prevent viral replication as well as an increased risk of developing drug resistance. Adherence to a life long treatment such as antiretroviral therapy is usually a complicated issue that requires careful and continuous collaboration of patient, family and healthcare provider. The objective of this study was to assess adherence to antiretroviral therapy and its associated factors among people living with HIV. This is a health facility-based cross sectional study conducted among adults’ people living with HIV in Omdurman HIV/AIDS centre, Sudan. Data was collected through direct interview using semi-structured questionnaire. There were only 144/846 (17.02%) who adhered to antiretroviral therapy as prescribed by their doctors. The remaining 51.18% were taking the therapy but not regularly, 31.21% were taking it but currently not and 0.59% stated that they have never taken any antiretroviral therapy. Factors associated with poor adherence that have been identified include female gender (Adj. OR = 3.46 (95%CI: 1.46-8.21), P = 0.005), younger age (Adj. OR = 1.14 (95%CI: 1.02-1.28), P = 0.022), being unemployed (Adj. OR = 5.94 (95%CI: 1.51-23.40), P = 0.011), those who were divorced, separated or widowed (Adj. OR = 11.35 (95%CI: 1.74-73.96), P = 0.011) and respondents who perceived that their health status is poor (Adj. OR = 5.21 (95%CI: 1.44-18.81), P = 0.012) or very poor (Adj. OR = 4.04 (95%CI: 1.27-12.81), P = 0.018). Educational level and social support against HIV-related stigma and discrimination were not significantly associated with adherence. Adherence to antiretroviral therapy among the respondents is very poor. Urgent interventions based on modifiable factors and mainly targeting females and younger age group are needed to improve adherence to antiretroviral therapy among people living with HIV.
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