The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.DOI: http://dx.doi.org/10.7554/eLife.08714.001

For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to measure the spatial spread of malaria parasites in southeast Bangladesh. We developed a genetic mixing index to estimate the likelihood of samples being local or imported from parasite genetic data and inferred the direction and intensity of parasite flow between locations using an epidemiological model integrating the travel survey and mobile phone calling data. Our approach indicates that, contrary to dogma, frequent mixing occurs in low transmission regions in the southwest, and elimination will require interventions in addition to reducing imported infections from forested regions. Unlike risk maps generated from clinical case counts alone, therefore, our approach distinguishes areas of frequent importation as well as high transmission.

Events associated with NPfIT reinforce that the use of IT does create hazardous circumstances and can lead to patient harm or death. Large-scale patient safety events have the potential to affect many patients and clinicians, and this suggests that addressing them should be a priority for all major IT implementations.

Background Measures of malaria burden using microscopy and rapid diagnostic tests (RDTs) in cross-sectional household surveys may incompletely describe the burden of malaria in low-transmission settings. This study describes the pattern of malaria transmission in Ethiopia using serological antibody estimates derived from a nationwide household survey completed in 2015. Methods Dried blood spot (DBS) samples were collected during the Ethiopian Malaria Indicator Survey in 2015 from malarious areas across Ethiopia. Samples were analysed using bead-based multiplex assays for IgG antibodies for six Plasmodium antigens: four human malaria species-specific merozoite surface protein-1 19kD antigens (MSP-1) and Apical Membrane Antigen-1 (AMA-1) for Plasmodium falciparum and Plasmodium vivax . Seroprevalence was estimated by age, elevation and region. The seroconversion rate was estimated using a reversible catalytic model fitted with maximum likelihood methods. Results Of the 10,278 DBS samples available, 93.6% (9622/10,278) had valid serological results. The mean age of participants was 15.8 years and 53.3% were female. National seroprevalence for antibodies to P. falciparum was 32.1% (95% confidence interval (CI) 29.8–34.4) and 25.0% (95% CI 22.7–27.3) to P. vivax . Estimated seroprevalences for Plasmodium malariae and Plasmodium ovale were 8.6% (95% CI 7.6–9.7) and 3.1% (95% CI 2.5–3.8), respectively. For P. falciparum seroprevalence estimates were significantly higher at lower elevations (< 2000 m) compared to higher (2000–2500 m) (aOR 4.4; p < 0.01). Among regions, P. falciparum seroprevalence ranged from 11.0% (95% CI 8.8–13.7) in Somali to 65.0% (95% CI 58.0–71.4) in Gambela Region and for P. vivax from 4.0% (95% CI 2.6–6.2) in Somali to 36.7% (95% CI 30.0–44.1) in Amhara Region. Models fitted to measure seroconversion rates showed variation nationally and by elevation, region, antigen type, and within species. Conclusion Using multiplex serology assays, this study explored the cumulative malaria burden and regional dynamics of the four human malarias in Ethiopia. High malaria burden was observed in the northwest compared to the east. High transmission in the Gambela and Benishangul-Gumuz Regions and the neglected presence of P. malariae and P. ovale may require programmatic attention. The use of a multiplex assay for antibody detection in low transmission settings has the potential to act as a more sensitive biomarker. Electronic supplementary material The online version of this article (10.1186/s12936-019-2874-z) contains supplementary material, which is available ...

Scrub and murine typhus are common, treatable causes of undifferentiated febrile illnesses in hospitalized patients.

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Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa.We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. IntroductionArtemisinin combination therapy (ACT), the frontline treatment for P. falciparum infection, has played a major part in reducing the number of deaths due to malaria over the past decade (World Health Organization 2014). However artemisinin resistant P. falciparum, which has recently spread across large parts of Southeast Asia, now threatens to destabilise malaria control worldwide (Dondorp et al. 2009;Hien et al. 2012;Phyo et al. 2012;Kyaw et al. 2013;Ashley et al. 2014; World Health Organization 2014). One of the main contemporary challenges in global health is to prevent artemisinin resistance from becoming established in Africa, where the consequences for childhood mortality could be disastrous (Dondorp and Ringwald 2013).. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/019737 doi: bioRxiv preprint first posted online May. 22, 2015; Genomic epidemiology of the current wave of artemisinin resistant malaria Page 2Understanding the epidemiological and evolutionary processes that are driving the current wave of artemisinin resistance is essential to develop effective strategies to stop it spreading. At the molecular level, artemisinin resistance is caused by mutations in a kelch protein encoded by PF3D7_1343700 on P. falciparum chromosome 13, referred to here as kelch13. More specifically, non-synonymous mutations in the kelch13 propeller and BTB-POZ domains (KPBD) result in reduced sensitivity of P. falciparum to artemisinin, as demonstrated by multiple lines of evidence including laboratory studies of artificially acquired resistance, genetic association studies of natural resistance and allelic replacement experiments (Ariey et al. 2014;Ghorbal et al. 2014;Miotto et al. 2015; Straimer et al. 2015; Takala-Harrison et al. 2015). The precise biological function of kelch13 is still not fully understood, but parasites with KBPD mut...

Background: Spread of malaria and antimalarial resistance through human movement present major threats to current goals to eliminate the disease. Bordering the Greater Mekong Subregion, southeast Bangladesh is a potentially important route of spread to India and beyond, but information on travel patterns in this area are lacking.Methods: Using a standardised short survey tool, 2090 patients with malaria were interviewed at 57 study sites in 2015-2016 about their demographics and travel patterns in the preceding 2 months. Results: Most travel was in the south of the study region between Cox's Bazar district (coastal region) to forested areas in Bandarban (31% by days and 45% by nights), forming a source-sink route. Less than 1% of travel reported was between the north and south forested areas of the study area. Farmers (21%) and students (19%) were the top two occupations recorded, with 67 and 47% reporting travel to the forest respectively. Males aged 25-49 years accounted for 43% of cases visiting forests but only 24% of the study population. Children did not travel. Women, forest dwellers and farmers did not travel beyond union boundaries. Military personnel travelled the furthest especially to remote forested areas. Conclusions:The approach demonstrated here provides a framework for identifying key traveller groups and their origins and destinations of travel in combination with knowledge of local epidemiology to inform malaria control and elimination efforts. Working with the NMEP, the findings were used to derive a set of policy recommendations to guide targeting of interventions for elimination.