Mutations in the Plasmodium falciparum K13-propeller domain have recently been shown to be important determinants of artemisinin resistance in Southeast Asia. This study investigated the prevalence of K13-propeller polymorphisms across sub-Saharan Africa. A total of 1212 P. falciparum samples collected from 12 countries were sequenced. None of the K13-propeller mutations previously reported in Southeast Asia were found, but 22 unique mutations were detected, of which 7 were nonsynonymous. Allele frequencies ranged between 1% and 3%. Three mutations were observed in >1 country, and the A578S was present in parasites from 5 countries. This study provides the baseline prevalence of K13-propeller mutations in sub-Saharan Africa.

Elucidation of the evolutionary history and interrelatedness of Plasmodium species that infect humans has been hampered by a lack of genetic information for three human-infective species: P. malariae and two P. ovale species (P. o. curtisi and P. o. wallikeri)1. These species are prevalent across most regions in which malaria is endemic2,3 and are often undetectable by light microscopy4, rendering their study in human populations difficult5. The exact evolutionary relationship of these species to the other human-infective species has been contested6,7. Using a new reference genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to accurately place these species within the Plasmodium phylogeny. Sequencing of a P. malariae relative that infects chimpanzees reveals similar signatures of selection in the P. malariae lineage to another Plasmodium lineage shown to be capable of colonization of both human and chimpanzee hosts. Molecular dating suggests that these host adaptations occurred over similar evolutionary timescales. In addition to the core genome that is conserved between species, differences in gene content can be linked to their specific biology. The genome suggests that P. malariae expresses a family of heterodimeric proteins on its surface that have structural similarities to a protein crucial for invasion of red blood cells. The data presented here provide insight into the evolution of the Plasmodium genus as a whole.

Plasmodium falciparum remains a relevant global health pathogen with high levels of genomic variation and gene flow that could undermine malaria elimination strategies, especially in the high burden regions of Africa. Infections with P. falciparum remain complex across most of sub-Saharan Africa. SNP variants from 2263 isolates from 24 malaria endemic settings within 15 African countries classified into western, central and eastern ancestry, plus a divergent Ethiopian population. The parasite populations are interbred and share genomic haplotypes especially across drug resistance loci. Haplotypes across drug resistance associated loci showed the strongest recent identity-by-descent between populations and endogenous haplotypes have spread to and from all populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives is evident in Ghana and Malawi. Such selection and emerging sub-structure may affect intervention strategies and the efficacy of drugs and vaccines for malaria elimination. Formatted: Font: +Body (Calibri) Formatted: Line spacing: Multiple 1.15 li

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.

Objectives Specific serological tests are mandatory for reliable SARS‐CoV‐2 diagnostics and seroprevalence studies. Here, we assess the specificities of four commercially available SARS‐CoV‐2 IgG ELISAs in serum/plasma panels originating from Africa, South America, and Europe. Methods 882 serum/plasma samples collected from symptom‐free donors before the COVID‐19 pandemic in three African countries (Ghana, Madagascar, Nigeria), Colombia, and Germany were analysed with three nucleocapsid‐based ELISAs (Euroimmun Anti‐SARS‐CoV‐2‐NCP IgG, EDI TM Novel Coronavirus COVID‐19 IgG, Mikrogen recom Well SARS‐CoV‐2 IgG), one spike/S1‐based ELISA (Euroimmun Anti‐SARS‐CoV‐2 IgG), and in‐house common cold CoV ELISAs. Results High specificity was confirmed for all SARS‐CoV‐2 IgG ELISAs for Madagascan (93.4%‐99.4%), Colombian (97.8%‐100.0%), and German (95.9%‐100.0%) samples. In contrast, specificity was much lower for the Ghanaian and Nigerian serum panels (Ghana: NCP‐based assays 77.7%‐89.7%, spike/S1‐based assay 94.3%; Nigeria: NCP‐based assays 39.3%‐82.7%, spike/S1‐based assay 90.7%). 15 of 600 African sera were concordantly classified as positive in both the NCP‐based and the spike/S1‐based Euroimmun ELISA, but did not inhibit spike/ACE2 binding in a surrogate virus neutralization test. IgG antibodies elicited by previous infections with common cold CoVs were found in all sample panels, including those from Madagascar, Colombia, and Germany and thus do not inevitably hamper assay specificity. Nevertheless, high levels of IgG antibodies interacting with OC43 NCP were found in all 15 SARS‐CoV‐2 NCP/spike/S1 ELISA positive sera. Conclusions Depending on the chosen antigen and assay protocol, SARS‐CoV‐2 IgG ELISA specificity may be significantly reduced in certain populations probably due to interference of immune responses to endemic pathogens like other viruses or parasites.

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.

BackgroundPlasmodium falciparum uncomplicated malaria can successfully be treated with an artemisinin-based combination therapy (ACT). However resistance is spreading to the different ACT compounds; the artemisinin derivative and the partner drug. Studies of P. falciparum polymorphisms associated with drug resistance can provide a useful tool to track resistance and guide treatment policy as well as an in-depth understanding of the development and spread of resistance.MethodsThe role of P. falciparum molecular markers in selection of reinfections was assessed in an efficacy trial comparing artesunate–amodiaquine fixed-dose combination with artemether–lumefantrine to treat malaria in Nimba County, Liberia 2008–2009. P. falciparum polymorphisms in pfcrt 76, pfmdr1 86, 184 and 1246, and pfmrp1 876 and 1466 were analysed by PCR-RFLP and pyrosequencing.ResultsHigh baseline prevalence of pfmdr1 1246Y was found in Nimba county (38 %). Pfmdr1 1246Y and pfmdr1 86+184+1246 haplotypes NYY and YYY were selected in reinfections in the artesunate–amodiaquine arm and pfcrt K76, pfmdr1 N86 and pfmdr1 haplotype NFD were selected in artemether–lumefantrine reinfections. Parasites harbouring pfmdr1 1246Y could reinfect earlier after treatment with artesunate–amodiaquine and parasites carrying pfmdr1 N86 could reinfect at higher lumefantrine concentrations in patients treated with artemether–lumefantrine.ConclusionsAlthough treatment is highly efficacious, selection of molecular markers in reinfections could indicate a decreased sensitivity or tolerance of parasites to the current treatments and the baseline prevalence of molecular markers should be closely monitored. Since individual drug levels and the day of reinfection were demonstrated to be key determinants for selection of reinfections, this data needs to be collected and taken into account for accurate evaluation of molecular markers for anti-malarial treatments.The protocols for the clinical trial was registered with Current Controlled Trials, under the Identifier Number ISRCTN51688713 on 9 October 2008

In malaria patients admitted to the study hospital, the likelihood of a co-diagnosis decreased with an increasing parasite count. In malaria-endemic settings, parasite densities provide important information for patient management, in particular for antimicrobial medication.