We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Background: Since malaria is one of the foremost public health problems in Ethiopia, assessment of situation of the disease, and communities’ knowledge and perceptions about malaria is necesary to institute appropriate preventive and control measures. Thus, the aim of this study was to assess malaria prevalence and knowledge, attitude and practice (KAP) about the disease among ShewaRobit Town community, northeastern Ethiopia. Methods: A community-based cross-sectional study was conducted in Shewa Robit Town from October to November 2011. A multi-stage random sampling technique was used to select the study participants. A total of 425 individuals were examined for malaria using thin and thick Giemsa stained blood film, and 284 of the participants were interviewed to assess their KAP about malaria. Logistic regression analysis was used to assess predictor factors for malaria prevalence. Results: All respondents had ever heard of malaria. Most of the respondents (85.2%) attributed the cause of malaria to mosquito bite. However, some of the respondents (>20%) mentioned lack of personal hygiene, exposure to cold weather, hunger, chewing maize stalk, body contact with malaria patient and flies as the causes of malaria. Sleeping under mosquito nets, draining stagnant water and indoor residual spraying were the most frequently mentioned malaria preventive measures perceived and practiced by the respondents. Among 425 individuals examined for malaria, only 2.8% were positive for Plasmodium parasites. Living in houses made of wall without hole, sprayed with insecticide within the last 12 hours and located at a distance of greater than 500 meters from potential mosquito breeding sites as well as knowing and using of mosquito net were significant predictors of low malaria prevalence among the study participants. Conclusions: A high level of knowledge about the cause, transmission and preventive methods of malaria was detected among the community in Shewa Robit Town. However, a considerable proportion had misconception about the cause and transmission of malaria suggesting the necessity of health education to raise the community’s awareness about the disease.

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Information about risk factors of undernutrition and anaemia is useful to design appropriate strategies to control the health problems. In this study, the prevalence and factors associated with undernutrition and anaemia were assessed among school children in Abchikeli and Ayalew Mekonnen Elementary Schools, northwest Ethiopia, in February and March 2010. A cross-sectional study was carried out among 384 school children. Stool samples were examined using single Kato-Katz slide and nutritional status was determined using anthropometry technique. A pre-tested standardized questionnaire was used to gather information on the socio-demographic and the socio-economic status of the school children. Multivariate logistic regression analysis was used to quantify the association of intestinal helminth infection and socio-demographic and socio-economic factors with undernutrition and anaemia. Out of 384 children examined, 32.3 % were undernourished (27.1 % underweight and 11.2 % stunted) and 10.7 % were anaemic. The odds of stunting were approximately seven times higher in children of ages 10 to 14 [Adjusted Odds Ratio (AOR) = 6.93, 95 % CI = 2.60, 18.46] and 2.5 times higher in males [AOR = 2.50, 95 % CI = 1.24, 5.07] than children of ages 5 to 9 and females, respectively. The odds of underweight was three times higher in children who did not wash their hands before eating compared to those who did wash their hands [AOR = 3.13, 95 % CI = 1.19, 8.17]. The chance of anaemia was nine times higher in children who were infected with hookworms compared to those who were not infected with any helminth species [AOR = 8.87, 95 % CI = 2.28, 34.58]. The odds of being undernourished and anemic were similar among children with different socio-economic status. Undernutrition and anaemia are public health problems of school-age children in Durbete Town. Health education and provision of additional food supplements would be important to reduce the problem of undernutrition among school-age children in the town. Deworming of children in the town would also have additional impact on reducing the level of anaemia.

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.