Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P. vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long- and short-read sequence technologies 2 new P. vivax-like reference genomes and 9 additional P. vivax-like genotypes. Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and colinear within the core regions. Phylogenetic analyses clearly show that P. vivax-like parasites form a genetically distinct clade from P. vivax. Concerning the relative divergence dating, we show that the evolution of P. vivax in humans did not occur at the same time as the other agents of human malaria, thus suggesting that the transfer of Plasmodium parasites to humans happened several times independently over the history of the Homo genus. We further identify several key genes that exhibit signatures of positive selection exclusively in the human P. vivax parasites. Two of these genes have been identified to also be under positive selection in the other main human malaria agent, P. falciparum, thus suggesting their key role in the evolution of the ability of these parasites to infect humans or their anthropophilic vectors. Finally, we demonstrate that some gene families important for red blood cell (RBC) invasion (a key step of the life cycle of these parasites) have undergone lineage-specific evolution in the human parasite (e.g., reticulocyte-binding proteins [RBPs])

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers, as well as convergent evolution, were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor, shows a host-specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate the timing of the beginning of speciation to be 40,000–60,000 years ago followed by a population bottleneck around 4,000–6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans

S1FigData_PvlkRAFdataset_2 samples Pvl07 to Pvl09

This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl07 to Pvl09. Please see the Materials and methods section for a detailed description

S1FigData_PvlkRAFdataset_3 samples Pvl10 and Pvl11

This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl10 and Pvl11. Please see the Materials and methods section for a detailed description

High Rate of Simian Immunodeficiency Virus (SIV) Infections in Wild Chimpanzees in Northeastern Gabon

The emergence of HIV-1 groups M, N, O, and P is the result of four independent cross-species transmissions between chimpanzees (cpz) and gorillas (gor) from central/south Cameroon and humans respectively. Although the first two SIVcpz were identified in wild-born captive chimpanzees in Gabon in 1989, no study has been conducted so far in wild chimpanzees in Gabon. To document the SIVcpz infection rate, genetic diversity, and routes of virus transmission, we analyzed 1458 faecal samples collected in 16 different locations across the country, and we conducted follow-up missions in two of them. We found 380 SIV antibody positive samples in 6 different locations in the north and northeast. We determined the number of individuals collected by microsatellite analysis and obtained an adjusted SIV prevalence of 39.45%. We performed parental analysis to investigate viral spread between and within communities and found that SIVs were epidemiologically linked and were transmitted by both horizontal and vertical routes. We amplified pol and gp41 fragments and obtained 57 new SIVcpzPtt strains from three sites. All strains, but one, clustered together within a specific phylogeographic clade. Given that these SIV positive samples have been collected nearby villages and that humans continue to encroach in ape’s territories, the emergence of a new HIV in this area needs to be considered

Data from: Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, Plasmodium vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long and short read sequence technologies two new P. vivax-like reference genomes and 9 additional P. vivax-like genotypes. Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and co-linear within the core regions. Phylogenetic analyses clearly show that P. vivax-like parasites form a genetically distinct clade from P. vivax. Concerning the relative divergence dating, we show that the evolution of P. vivax in humans did not occur at the same time as the other agents of human malaria, thus suggesting that the transfer of Plasmodium parasites to humans happened several times independently over the history of the Homo genus. We further identify several key genes that exhibit signatures of positive selection exclusively in the human P. vivax parasites. Interestingly, two of these genes have been identified to also be under positive selection in the other main human malaria agent, Plasmodium falciparum, thus suggesting their key role in the evolution of the ability of these parasites to infect humans or their anthropophilic vectors. We finally demonstrate that some gene families important for red blood cell (RBC) invasion (a key step of the life cycle of these parasites) have undergone lineage-specific evolution in the human parasite (e.g. Reticulocyte Binding Proteins)

S1FigData_PvlkRAFdataset_1 samples Pvl01 to Pvl06

This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl01 to Pvl06. Please see the Materials and methods section for a detailed description

Knowledge, attitudes, and practices of mothers regarding childhood malaria in southeastern Gabon

Abstract Background In Gabon, children under 5 years of age and pregnant women are the populations who are most at risk of malaria. Despite the presence of accessible health facilities, the community-based management of childhood fever remains a very common practice in Gabon, which may have serious consequences on child health. As such, the objective of this descriptive cross-sectional survey is to assess the mothers’ perception and knowledge of malaria and its severity. Methods Different households were selected using the simple random sampling method. Results A total of 146 mothers from different households were interviewed in the city of Franceville, in southern Gabon. Among the households interviewed, 75.3% had a low monthly income (below the minimum monthly income of $272.73). Among the respondents, 98.6% of mothers had heard of malaria and 55.5% had heard of severe malaria. Regarding preventive measures, 83.6% of mothers used an insecticide-treated net as a means of protection. Self-medication was practiced by 68.5% of women (100/146). Discussion The use of health facilities was motivated by better care, the decision of the head of the family, but above all by the severity of the disease. Women identified fever as the main symptom of malaria, which could be beneficial for a quicker and more efficient management of the disease in children. Malaria educational campaigns should also increase awareness of severe forms of malaria and its manifestations. This study shows that Gabonese mothers react quickly when their children have fever. However, several external factors lead them to practice self-medication as a first resort. In this survey population, the practice of self-medication did not depend on social status, marital status, level of education, on the young age or inexperience of mothers (p > 0.05). Conclusions The data revealed that mothers may underestimate severe malaria and delay medical care by self-medicating, which can have detrimental effects for children and hinder the regression of the disease