The polyphyly of Plasmodium: comprehensive phylogenetic analyses of the malaria parasites (order Haemosporida) reveal widespread taxonomic conflict

New member of Plasmodium (Vinckeia) and Plasmodium cyclopsi discovered in bats in Sierra Leone - nuclear sequence and complete mitochondrial genome analyses

Malaria remains the most important arthropod-borne infectious disease globally. The causative agent, Plasmodium, is a unicellular eukaryote that develops inside red blood cells. Identifying new Plasmodium parasite species that infect mammalian hosts can shed light on the complex evolution and diversity of malaria parasites. Bats feature a high diversity of microorganisms including seven separate genera of malarial parasites. Three species of Plasmodium have been reported so far, for which scarce reports exist. Here we present data from an investigation of Plasmodium infections in bats in the western Guinean lowland forest in Sierra Leone. We discovered a new Plasmodium parasite in the horseshoe bat Rhinolophus landeri. Plasmodium cyclopsi infections in a member of leaf-nosed bats, Doryrhina cyclops, exhibited a high prevalence of 100%. Phylogenetic analysis of complete mitochondrial genomes and nine nuclear markers recovered a close relationship between P. cyclopsi and the new Plasmodium parasite with the rodent species Plasmodium berghei, a widely used in vivo model to study malaria in humans. The data suggests that the "rodent/bat" Plasmodium (Vinckeia) clade represents a diverse group of malarial parasites that would likely expand with a systematic sampling of small mammals in tropical Africa. Identifying the bat Plasmodium repertoire is central to our understanding of the evolution of Plasmodium parasites in mammals.

Unresolved haemosporidia of the Australian skink, Egernia stokesii

The Australian skink Egernia stokesii had been recognised as a host of two species of Plasmodium, Plasmodium mackerrasae and P. circularis; nevertheless, molecular data are available for only a single haemosporidian species of this host. Its sequences are labelled as "Plasmodium sp." or "Plasmodium mackerrasae", but morphological characteristics of this isolate are unavailable. Phylogenetic analyses of these sequences placed them into the clade of the genus Haemocystidium. In this study, blood samples of six E. stokesii were analysed by both, molecular and microscopic methods to clarify the haemosporidia of this lizard. Application of these approaches offered discordant results. Whereas sequence analysis clustered our isolates with lizard species of Haemocystidium, morphology of blood stages is more akin to Plasmodium than Haemocystidium. However, limited sampling, indistinguishable nuclei/merozoites and risk of possible hidden presence of mixed infection prevent reliable species identification of detected parasites or their description as new species of Haemocystidium.

Phylogenetic congruence of Plasmodium spp. and wild ungulate hosts in the Peruvian Amazon

Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%, 1/2). We performed PCR-based analysis of blood samples from 47 ungulates of five different species collected during subsistence hunting by an indigenous community in the Peruvian Amazon. We detected Plasmodium malariae/brasilianum lineage in a sample from red-brocket deer. However, no parasite DNA was detected in collared peccary (Pecari tajacu; 0.0%, 0/10), white-lipped peccary (Tayassu pecari; 0.0%, 0/15), and tapir (Tapirus terrestris; 0.0%, 0/11). Concordant phylogenetic analyses suggested a possible co-evolutionary relationship between the Plasmodium lineages found in American deer and their hosts.

Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Avian haemosporidian parasites (order Haemosporida, phylum Apicomplexa) are blood and tissue parasites transmitted by blood-sucking dipteran insects. Three genera (Plasmodium, Haemoproteus and Leucocytozoon) have been most often found in birds, with over 270 species described and named in avian hosts based mainly on the morphological characters of blood stages. A broad diversity of Haemoproteus parasites remains to be identified and characterized morphologically and molecularly, especially those infecting birds of prey, an underrepresented bird group in haemosporidian parasite studies. The aim of this study was to investigate and identify Haemoproteus parasites from a large sample comprising accipitriform raptors of 16 species combining morphological and new molecular protocols targeting the cytb genes of this parasite group. This study provides morphological descriptions and molecular characterizations of two Haemoproteus species, H. multivacuolatus n. sp. and H. nisi Peirce and Marquiss, 1983. Haemoproteus parasites of this group were so far found in accipitriform raptors only and might be classified into a separate subgenus or even genus. Cytb sequences of these parasites diverge by more than 15% from those of all others known avian haemosporidian genera and form a unique phylogenetic clade. This study underlines the importance of developing new diagnostic tools to detect molecularly highly divergent parasites that might be undetectable by commonly used conventional tools.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.

The association between haemosporidian infection and non-breeding moult location in great reed warblers revisited by combining feather stable isotope profiles and geolocator data

Stable isotope analysis provides valuable insights into the ecology of long-distance migratory birds during periods spent away from a specific study site. In a previous study, Swedish great reed warblers (Acrocephalus arundinaceus) infected with haemosporidian parasites differed in feather isotope ratios compared to non-infected birds, suggesting that infected and non-infected birds spent the non-breeding season in different locations or habitats. Here, we use a novel dataset comprising geolocator data, isotopes, and haemosporidian infection status of 92 individuals from four Eurasian populations to investigate whether parasite transmission varies with geography or habitats. We found that the probability of harbouring Plasmodium and Leucocytozoon parasites was higher in birds moulting in the eastern region of the non-breeding grounds. However, no geographic pattern occurred for Haemoproteus infections or overall infection status. In contrast to the previous study, we did not find any relationship between feather isotope ratios and overall haemosporidian infection for the entire current dataset. Plasmodium-infected birds had lower feather δ15N values indicating that they occupied more mesic habitats. Leucocytozoon-infected birds had higher feather δ34S values suggesting more coastal sites or wetlands with anoxic sulphate reduction. As the composition and prevalence of haemosporidian parasites differed between the old and the current dataset, we suggest that the differences might be a consequence of temporal dynamics of haemosporidian parasites. Our results emphasize the importance of replicating studies conducted on a single population over a restricted time period, as the patterns can become more complex for data from wider geographical areas and different time periods.

Simian malaria: a narrative review on emergence, epidemiology and threat to global malaria elimination

Simian malaria from wild non-human primate populations is increasingly recognised as a public health threat and is now the main cause of human malaria in Malaysia and some regions of Brazil. In 2022, Malaysia became the first country not to achieve malaria elimination due to zoonotic simian malaria. We review the global distribution and drivers of simian malaria and identify priorities for diagnosis, treatment, surveillance, and control. Environmental change is driving closer interactions between humans and wildlife, with malaria parasites from non-human primates spilling over into human populations and human malaria parasites spilling back into wild non-human primate populations. These complex transmission cycles require new molecular and epidemiological approaches to track parasite spread. Current methods of malaria control are ineffective, with wildlife reservoirs and primarily outdoor-biting mosquito vectors urgently requiring the development of novel control strategies. Without these, simian malaria has the potential to undermine malaria elimination globally.

First investigation of blood parasites of bats in Burkina Faso detects Hepatocystis parasites and infections with diverse Trypanosoma spp

Bats are hosts to a large diversity of eukaryotic protozoan blood parasites that comprise species of Trypanosoma and different haemosporidian parasite taxa and bats have played an important role in the evolutionary history of both parasite groups. However, bats in several geographical areas have not been investigated, including in Burkina Faso, where no information about malaria parasites and trypanosomes of bats exists to date.In this study, we collected data on the prevalence and the phylogenetic relationships of protozoan blood parasites in nine different bat species in Burkina Faso. Hepatocystis parasites were detected in two species of epauletted fruit bats, and a relatively high diversity of trypanosome parasites was identified in five bat species. The phylogenetic analyses recovered the trypanosome parasites of the bat species Rhinolophus alcyone and Nycteris hispida as close relatives of T. livingstonei, the trypanosome infections in Scotophilus leucogaster as closely related to the species T. vespertilionis and the trypanosomes from Pipistrellus nanulus and Epomophorus gambianus might present the species T. dionisii. These findings of the first investigation in Burkina Faso present a first snapshot of the diversity of protozoan blood parasites in bats in this country.

Leucocytozoon cariamae n. sp. and Haemoproteus pulcher coinfection in Cariama cristata (Aves: Cariamiformes): first mitochondrial genome analysis and morphological description of a leucocytozoid in Brazil

The distribution of avian haemosporidians of the genus Leucocytozoon in the Neotropics remains poorly understood. Recent studies confirmed their presence in the region using molecular techniques alone, but evidence for gametocytes and data on putative competent hosts for Leucocytozoon are still lacking outside highland areas. We combined morphological and molecular data to characterize a new Leucocytozoon species infecting a non-migratory red-legged seriema (Cariama cristata), the first report of a competent host for Leucocytozoon in Brazil. Leucocytozoon cariamae n. sp. is distinguished from the Leucocytozoon fringillinarum group by its microgametocytes that are not strongly appressed to the host cell nucleus. The bird studied was coinfected with Haemoproteus pulcher, and we present a Bayesian phylogenetic analysis based on nearly complete mitochondrial genomes of these 2 parasites. Leucocytozoon cariamae n. sp. morphology is consistent with our phylogenetic analysis indicating that it does not share a recent common ancestor with the L. fringillinarum group. Haemoproteus pulcher and Haemoproteus catharti form a monophyletic group with Haemocystidium parasites of Reptilia, supporting the polyphyly of the genus Haemoproteus. We also discussed the hypothesis that H. pulcher and H. catharti may be avian Haemocystidium, highlighting the need to study non-passerine parasites to untangle the systematics of Haemosporida.

Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

In recent phylogenetic studies, bat Polychromophilus and ungulate Plasmodium, two relatively understudied haemosporidian parasites within the Apicomplexa phylum, have often been overlooked. Instead, the focus has been primarily on haemosporidian parasites in primates, rodents, and birds. Several phylogenetic analyses of bat Polychromophilus have relied on limited datasets and short informative DNA sequences. As a result of these inherent limitations, the substantiation of their evolutionary stance has encountered a diminished degree of robust validation. This study successfully obtained complete mitochondrial genome sequences from 11 Polychromophilus parasites originating from Hipposideros gentilis and Myotis siligoensis bats for the first time. Additionally, the authors have sequenced the apicoplast caseinolytic protease C genes from Polychromophilus murinus and a potentially new Polychromophilus species. These mitochondrial genomes range in length from 5994 to 6001 bp and consist of three protein-coding genes (PCGs), seven small subunit ribosomal RNA genes (SSU rRNA), 12 large subunit ribosomal RNA genes (LSU rRNA), and seven miscellaneous RNA genes. Phylogenetic analyses using Bayesian Inference and Maximum Likelihood methods indicated robust support for the grouping of ungulate Plasmodium and bat Polychromophilus in a single clade separate from other Plasmodium spp., confirming previous reports, albeit with stronger evidence in this study. The divergence between Polychromophilus in bats and Plasmodium in ungulates occurred approximately 29.61 to 55.77 million years ago (Mya), with a node age estimated at 40.63 Mya. These findings highlight that the genus Plasmodium, which includes species found in ungulates, birds, reptiles, and other mammals, does not form a monophyletic group. By incorporating Polychromophilus in bats and Plasmodium in ungulates, this study contributes significantly to understanding the phylogenetic relationships within the Haemosporida order. It provides valuable insights into the evolutionary history and interconnections among these diverse parasites, thereby expanding knowledge in this field.

Co-infection with Leucocytozoon and Other Haemosporidian Parasites Increases with Latitude and Altitude in New World Bird Communities

Establishing how environmental gradients and host ecology drive spatial variation in infection rates and diversity of pathogenic organisms is one of the central goals in disease ecology. Here, we identified the predictors of concomitant infection and lineage richness of blood parasites in New Word bird communities. Our multi-level Bayesian models revealed that higher latitudes and elevations played a determinant role in increasing the probability of a bird being co-infected with Leucocytozoon and other haemosporidian parasites. The heterogeneity in both single and co-infection rates was similarly driven by host attributes and temperature, with higher probabilities of infection in heavier migratory host species and at cooler localities. Latitude, elevation, host body mass, migratory behavior, and climate were also predictors of Leucocytozoon lineage richness across the New World avian communities, with decreasing parasite richness at higher elevations, rainy and warmer localities, and in heavier and resident host species. Increased parasite richness was found farther from the equator, confirming a reverse Latitudinal Diversity Gradient pattern for this parasite group. The increased rates of Leucocytozoon co-infection and lineage richness with increased latitude are in opposition with the pervasive assumption that pathogen infection rates and diversity are higher in tropical host communities.

Host genetic backgrounds: the key to determining parasite-host adaptation

Parasitic diseases pose a significant threat to global public health, particularly in developing countries. Host genetic factors play a crucial role in determining susceptibility and resistance to infection. Recent advances in molecular and biological technologies have enabled significant breakthroughs in understanding the impact of host genes on parasite adaptation. In this comprehensive review, we analyze the host genetic factors that influence parasite adaptation, including hormones, nitric oxide, immune cells, cytokine gene polymorphisms, parasite-specific receptors, and metabolites. We also establish an interactive network to better illustrate the complex relationship between host genetic factors and parasite-host adaptation. Additionally, we discuss future directions and collaborative research priorities in the parasite-host adaptation field, including investigating the impact of host genes on the microbiome, developing more sophisticated models, identifying and characterizing parasite-specific receptors, utilizing patient-derived sera as diagnostic and therapeutic tools, and developing novel treatments and management strategies targeting specific host genetic factors. This review highlights the need for a comprehensive and systematic approach to investigating the underlying mechanisms of parasite-host adaptation, which requires interdisciplinary collaborations among biologists, geneticists, immunologists, and clinicians. By deepening our understanding of the complex interactions between host genetics and parasite adaptation, we can develop more effective and targeted interventions to prevent and treat parasitic diseases. Overall, this review provides a valuable resource for researchers and clinicians working in the parasitology field and offers insights into the future directions of this critical research area.

Origin and diversity of malaria parasites and other Haemosporida

Symbionts, including parasites, are ubiquitous in all world ecosystems. Understanding the diversity of symbiont species addresses diverse questions, from the origin of infectious diseases to inferring processes shaping regional biotas. Here, we review the current approaches to studying Haemosporida's species diversity and evolutionary history. Despite the solid knowledge of species linked to diseases, such as the agents of human malaria, studies on haemosporidian phylogeny, diversity, ecology, and evolution are still limited. The available data, however, indicate that Haemosporida is an extraordinarily diverse and cosmopolitan clade of symbionts. Furthermore, this clade seems to have originated with their vertebrate hosts, particularly birds, as part of complex community level processes that we are still characterizing.

Distinct biogeographic processes and areas of endemism contributed differentially to Plasmodium and Parahaemoproteus community assembly on Marajó Island

Amazonia is the primary source of haemosporidian diversity for South American biomes. Yet, our understanding of the contribution of each area of endemism and the biogeographical processes that generated such diversity in this group of vector transmitted parasites remains incomplete. For example, a recently formed fluvial island in the Amazon delta - Marajó Island, is composed of avian lineages from adjacent Amazonian areas of endemism, but also from open habitats, such as Cerrado. This raises the question: Is the parasite assemblage found in avian hosts on this island formed by parasite lineages from adjacent Amazonian areas of endemism or Cerrado? Here, we assessed the spatiotemporal evolution of Plasmodium and Parahaemoproteus parasites. Our biogeographic analysis showed that dispersal dominated Plasmodium diversification, whereas duplication was more frequent for the genus Parahaemoproteus. We show that the Inambari area of endemism was the primary source for Plasmodium diversity on Marajó Island, but that this island received more Parahaemoproteus lineages from Cerrado than any Amazonian area of endemism. The unique patterns of dispersal for each parasite genus coupled with their propensity to shift hosts locally may have facilitated their diversification across Amazonia, suggesting that differences in deep evolutionary history may have constrained their colonization of Marajó Island.

Insights into the Biology of Leucocytozoon Species (Haemosporida, Leucocytozoidae): Why Is There Slow Research Progress on Agents of Leucocytozoonosis?

Blood parasites of the genus Leucocytozoon (Leucocytozoidae) only inhabit birds and represent a readily distinct evolutionary branch of the haemosporidians (Haemosporida, Apicomplexa). Some species cause pathology and even severe leucocytozoonosis in avian hosts, including poultry. The diversity of Leucocytozoon pathogens is remarkable, with over 1400 genetic lineages detected, most of which, however, have not been identified to the species level. At most, approximately 45 morphologically distinct species of Leucocytozoon have been described, but only a few have associated molecular data. This is unfortunate because basic information about named and morphologically recognized Leucocytozoon species is essential for a better understanding of phylogenetically closely related leucocytozoids that are known only by DNA sequence. Despite much research on haemosporidian parasites during the past 30 years, there has not been much progress in taxonomy, vectors, patterns of transmission, pathogenicity, and other aspects of the biology of these cosmopolitan bird pathogens. This study reviewed the available basic information on avian Leucocytozoon species, with particular attention to some obstacles that prevent progress to better understanding the biology of leucocytozoids. Major gaps in current Leucocytozoon species research are discussed, and possible approaches are suggested to resolve some issues that have limited practical parasitological studies of these pathogens.

Let’s end taxonomic blank slates with molecular morphology

Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.

Beta diversity, prevalence, and specificity of avian haemosporidian parasites throughout the annual cycle of Chilean Elaenia (Elaenia chilensis), a Neotropical austral migrant

Migratory birds are implicated in dispersing haemosporidian parasites over great geographic distances. However, their role in sharing these vector-transmitted blood parasites with resident avian host species along their migration flyway is not well understood. We studied avian haemosporidian parasites in 10 localities where Chilean Elaenia, a long-distance Neotropical austral migrant species, spends part of its annual cycle to determine local parasite transmission among resident sympatric host species in the elaenia's distributional range across South America. We sampled 371 Chilean Elaenias and 1,818 birds representing 243 additional sympatric species from Brazilian wintering grounds to Argentinian breeding grounds. The 23 haemosporidian lineages found in Chilean Elaenias exhibited considerable variation in distribution, specialization, and turnover across the 10 avian communities in South America. Parasite lineage dissimilarity increased with geographic distance, and infection probability by Parahaemoproteus decreased in localities harbouring a more diverse haemosporidian fauna. Furthermore, blood smears from migrating Chilean Elaenias and local resident avian host species did not contain infective stages of Leucocytozoon, suggesting that transmission did not take place in the Brazilian stopover site. Our analyses confirm that this Neotropical austral migrant connects avian host communities and transports haemosporidian parasites along its distributional range in South America. However, the lack of transmissive stages at stopover site and the infrequent parasite lineage sharing between migratory host populations and residents at breeding and wintering grounds suggest that Chilean Elaenias do not play a significant role in dispersing haemosporidian parasites, nor do they influence local transmission across South America.

Host life-history traits predict haemosporidian parasite prevalence in tanagers (Aves: Thraupidae)

Vector-borne parasites are important ecological drivers influencing life-history evolution in birds by increasing host mortality or susceptibility to new diseases. Therefore, understanding why vulnerability to infection varies within a host clade is a crucial task for conservation biology and for understanding macroecological life-history patterns. Here, we studied the relationship of avian life-history traits and climate on the prevalence of Plasmodium and Parahaemoproteus parasites. We sampled 3569 individual birds belonging to 53 species of the family Thraupidae. Individuals were captured from 2007 to 2018 at 92 locations. We created 2 phylogenetic generalized least-squares models with Plasmodium and Parahaemoproteus prevalence as our response variables, and with the following predictor variables: climate PC1, climate PC2, body size, mixed-species flock participation, incubation period, migration, nest height, foraging height, forest cover, and diet. We found that Parahaemoproteus and Plasmodium prevalence was higher in species inhabiting open habitats. Tanager species with longer incubation periods had higher Parahaemoproteus prevalence as well, and we hypothesize that these longer incubation periods overlap with maximum vector abundances, resulting in a higher probability of infection among adult hosts during their incubation period and among chicks. Lastly, we found that Plasmodium prevalence was higher in species without migratory behaviour, with mixed-species flock participation, and with an omnivorous or animal-derived diet. We discuss the consequences of higher infection prevalence in relation to life-history traits in tanagers.

Keys to the avian Haemoproteus parasites (Haemosporida, Haemoproteidae)

Background

Haemoproteus is a sister genus to malaria parasites (Plasmodium), which both belong to the order Haemosporida (Apicomplexa). Parasites of both genera are flourishing in birds, however, Haemoproteus species are noticeably less investigated. This is unfortunate because knowledge about close relatives of malaria pathogens is important for better understanding the evolutionary origin and basic biological features of the entire group of haemosporidian infections. Moreover, recent findings show that Haemoproteus species can cause severe damage of various bird organs due to megalomeronts and other exo-erythrocytic stages. These haemosporidians are remarkably diverse, but remain neglected partly due to difficulties in species identification. Hundreds of Haemoproteus genetic lineages have been reported in birds, and numerous new lineages are found each year, but most remain unidentified to the species level. Numerous new Haemoproteus pathogens were described during the past 20 years. However, keys for their identification are absent. Identification of Haemoproteus species remains a difficult task and is an obstacle for better understanding of the distribution and epidemiology of these parasites. This study aimed to develop comprehensive keys for the identification of described avian Haemoproteus species using morphological features of their blood stages (gametocytes).

Methods

Type and voucher preparations of avian Haemoproteus species were accessed in museums in Europe, Australia and the USA. Gametocytes of most described species were examined, and these data formed a background for this study. The data also were considered from published articles containing parasite species descriptions. The method of dichotomous keys was applied. The most difficult steps in the keys were accompanied with references to the corresponding parasite pictures.

Results

In all, 201 published articles were included in this review. Morphological diagnostic features of gametocytes of all described Haemoproteus species were analysed and compared. Illustrated keys for identification of these parasite species were developed. Available information about the molecular characterization of Haemoproteus parasites was provided.

Conclusion

This review shows that 177 described species of avian Haemoproteus can be distinguished and identified in blood films using morphological characters of their gametocytes and host cells. These species were incorporated in the keys. Information about possible morphologically cryptic parasites was provided. Molecular markers are available for only 42% of the described Haemoproteus parasites, calling for researchers to fill this gap.

A new haemosporidian parasite from the Red-legged Seriema Cariama cristata (Cariamiformes, Cariamidae)

Haemoproteids (Haemosporida, Haemoproteidae) are a diverse group of avian blood parasites that are transmitted by hematophagous dipterans. In this study, we describe Haemoproteus pulcher sp. nov. from a Red-legged Seriema (Cariama cristata) in southeast Brazil. Analysis of the mitochondrial cytb gene indicates this parasite is closely related to Haemoproteus catharti (from Turkey Vulture, Cathartes aura) and the unidentified haemosporidian lineages PSOOCH01 (from Pale-winged Trumpeter, Psophia leucoptera) and MYCAME08 (from Wood Stork, Mycteria americana). This group of parasites appears to represent an evolutionary lineage that is distinct from other Haemoproteus spp., being instead more closely related to Haemocystidium spp. (from reptiles), Plasmodium spp. (from reptiles, birds, and mammals) and other mammal-infecting haemosporidians (Nycteria, Polychromophilus, and Hepatocystis). Current evidence suggests that parasites of this newly discovered evolutionary lineage may be endemic to the Americas, but further studies are necessary to clarify their taxonomy, life cycle, vectors, hosts, geographic distribution and host health effects. Additionally, it should be borne in mind that some PCR protocols targeting the cytb gene might not reliably detect H. pulcher due to low primer affinity.

First report of haemosporidia and associated risk factors in red junglefowl (Gallus gallus) in China

Background

Avian haemosporidia infect both domestic and wild birds, causing anemia, acute tissue degeneration, and depopulation in wild birds. Poultry and wild birds have been reported as common reservoirs of haemosporidia, but limited information is available for red junglefowl (Gallus gallus) in China. The present study investigated the prevalence and molecular characterization of haemosporidia in red junglefowl.

Methods

Blood samples were collected from 234 red junglefowl from Jinghong City of Yunnan Province, and genomic DNA was extracted from these samples. The prevalence of haemosporidia was determined by nested PCR targeting the mitochondrial cytochrome b (cytb) gene. Molecular characterization was investigated based on phylogenetic analysis of cytb sequences, and associated risk factors were analyzed using the Chi-square (χ²) test.

Results

The overall prevalence of haemosporidia was 74.8% (175/234), and three species were identified, namely Haemoproteus enucleator, Leucocytozoon californicus, and Plasmodium juxtanucleare. The prevalence of haemosporidia in adult fowl (81.1%, 107/132) was significantly higher (χ² = 6.32, df = 1, P = 0.012) than that in juveniles (66.7%, 68/102). Three novel haemosporidian lineages were revealed.

Conclusions

This study examined the prevalence and identified species of avian haemosporidians in red junglefowl, providing new information on the molecular epidemiology and geographical distribution of haemosporidian parasites. Our results indicated high prevalence and diverse species distribution of these haemosporidians in red junglefowl. To the best of our knowledge, this is the first record of haemosporidian infection in red junglefowl in China.

Graphical Abstract

Molecular detection of Trypanosoma spp. and Hepatocystis parasite infections of bats in Northern Nigeria

Bats are mammalian hosts to a large diversity of eukaryotic protozoan blood parasites, including different genera of haemosporidians and diverse species of trypanosomes. Phylogenetic studies suggest that bats, particularly in Africa, have played an important role in the evolutionary histories of these parasite groups. However, our understanding of the diversity and distribution of chiropteran haemosporidians and trypanosomes in Africa remains tenuous. We investigated the prevalence and phylogenetic relationships of the blood parasites in different bat species in Northern Nigeria using molecular methods. A low prevalence of Hepatocystis parasites was detected in a potentially rare host species, the African straw-coloured fruit bat (Eidolon helvum) confirming yet another fruit bat species in the diverse range of African bat hosts. Trypanosome infections were identified in 3 different bat species. The trypanosomes of Mops cf. pumilus were recovered as a distinct lineage that is related to Trypanosoma erneyi, a species which is closely related to Trypanosoma dionisii and Trypanosoma cruzi. Nycteris cf. macrotis bats were infected with trypanosomes that are related to the distinct lineage of Trypanosoma cf. livingstonei parasites. Further, 2 different lineages of trypanosomes in E. helvum bats share highest nucleotide identities with Trypanosoma livingstonei and a group of Trypanosoma sp. parasites that are closely related to T. cf. livingstonei and T. livingstonei, respectively. The findings of this study confirm the notion that trypanosomes of African bats are phylogenetically diverse and that African bats might harbour a variety of yet undescribed trypanosome species.

Isolation and molecular characterization of Polychromophilus spp. (Haemosporida: Plasmodiidae) from the Asian long-fingered bat (Miniopterus fuliginosus) and Japanese large-footed bat (Myotis macrodactylus) in Japan

Bats (order, Chiroptera) account for more than one-fifth of all mammalian species in the world and are infected by various intra-erythrocytic parasites of the family Plasmodiidae (Apicomplexa: Haemosporida), including Polychromophilus Dionisi, 1899. Recent advance in the molecular characterization of haemosporidian isolates has enabled their accurate identification, particularly in the last decade. Studies are actively conducted in tropical regions, Europe, and Australia; however, data on haemosporidian infection in bats in Asian temperate areas, including Japan, remain limited. In this study, 75 bats of 4 species (Miniopterus fuliginosus, Myotis macrodactylus, Rhinolophus nippon, and Rhinolophus cornutus) were captured at three sites in western Japan (Yamaguchi Prefecture), and haemosporidian parasites were screened microscopically and molecularly via nested polymerase chain reaction (PCR) targeting the cytochrome b (cytb), cytochrome c oxidase subunit I (cox-1), apicoplast caseinolytic protease C (clpc), and nuclear elongation factor 2 (EF2) genes. The survey detected Polychromophilus melanipherus in 15 (40.5%) miniopterid bats (M. fuliginosus) and Polychromophilus murinus in 6 (46.2%) vespertilionid bats (M. macrodactylus), whereas none of the 25 rhinolophid bats (R. nippon and R. cornutus) was infected, indicating the robust host specificity for miniopterid (P. melanipherus) and vespertilionid (P. murinus) bats regardless of orthotopic nesting. The 15 Polychromophilus cytb sequences obtained from 11 miniopterid and 4 vespertilionid bats were classified into six cytb haplotypes (three for each species), showing no region-specific variation in a phylogenetic tree of Polychromophilus isolates in the Old World. Similarly, multiple haplotypes (seven for cox-1 and nine for clpc) and genotypes (three for EF2) were characterized for the Japanese isolates of Polychromophilus, and the results were consistent with those based on a haemosporidian cytb analysis. Bat flies (Nycteribia allotopa and another undetermined Nycteribia sp.) collected from the body surface of bats harbored Polychromophilus oocysts on the external surface of the midgut. This is the first study to report the isolation and molecular characterization of Polychromophilus spp. in miniopterid and vespertilionid bats in the temperate area of Asia (western Japan). Future studies should evaluate the global prevalence of haemosporidian infections in bats.

A novel one-step multiplex PCR protocol to detect avian haemosporidian parasites in the subgenus Haemoproteus (Kruse, 1890) used to quantify parasite prevalence in domestic pigeons (Columba livia) in Turkey

Infections of avian haemosporidian parasites are regularly identified by molecular methods including multiplex PCR, which allows researchers to distinguish mixed infections of parasites from multiple genera. Here we extend the utility of a previously designed multiplex PCR by designing a primer set specific to parasites of the subgenus Haemoproteus (genus: Haemoproteus). The updated one-step multiplex PCR protocol we describe here allows for the detection of the genera Plasmodium and Leucocytozoon and the two subgenera (Haemoproteus and Parahaemoproteus) of the genus Haemoproteus. A sensitivity analysis showed that the multiplex PCR could amplify DNA of parasites in the subgenus Haemoproteus at very low levels of infection. We used this multiplex PCR to identify haemosporidian infections in 250 adult domestic pigeons (Columba livia) in Turkey. All samples were also screened by microscopy and a widely used nested PCR to compare with the results of multiplex PCR, to detect low levels of parasitemia, and to identify possible abortive infections. In total, 71 pigeons (28.4%) were found to be infected by all three methods. The multiplex PCR protocol successfully detected and discriminated both subgenera Haemoproteus and Parahaemoproteus infections. We compared our results with previous host species records to assess the host specificity of the parasite lineages we found. Our findings provide novel data on the prevalence of avian haemosporidians in domestic pigeons and demonstrate the utility of the new one-step multiplex PCR protocol for the determination of mixed avian haemosporidian infections. We expect that this protocol will contribute to a better understanding of the distribution, epizootiology, and ecology of avian haemosporidians.

The evolution of primate malaria parasites: A study on the origin and diversification of Plasmodium in lemurs

Among the primate malaria parasites, those found in lemurs have been neglected. Here, six Plasmodium lineages were detected in 169 lemurs. Nearly complete mitochondrial genomes (mtDNA, ≈6Kb) and apicoplast loci (≈6Kb) were obtained from these parasites and other Haemosporida species. Plasmodium spp. in lemurs are a diverse clade that shares a common ancestor with other primate parasites from continental Africa. Time-trees for the mtDNA were estimated under different scenarios, and the origin of the lemur clade coincides with the proposed time of their host species' most recent common ancestor (Lemuridae-Indriidae). A time tree with fewer taxa was estimated with mtDNA + Apicoplast loci. Those time estimates overlapped but were younger and had narrower credibility intervals than those from mtDNA alone. Importantly, the mtDNA + Apicoplast estimates that the clade including the most lethal malaria parasite in humans, Plasmodium falciparum, may have originated with Homininae (African apes). Finally, the phylogenetic congruence of the lemurs and their parasites was explored. A statistically significant scenario identified four cospeciation, two duplications, four transfer (host-switches), and zero loss events. Thus, the parasite species sampled in lemurs seem to be radiating with their hosts.

Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities

The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current phylogeny using genome-level data, some specific molecular features will be discussed as examples of how these parasites have diverged. The two subgenera of malaria parasites found in primates, Plasmodium and Laverania, reflect extant monophyletic groups that originated in Africa. However, the subgenus Plasmodium involves species in Southeast Asia that were likely the result of adaptive radiation. Such events led to the Plasmodium vivax lineage. Although the Laverania species, including P. falciparum, has been considered to share “avian characteristics,” molecular traits that were likely in the common ancestor of primate and avian parasites are sometimes kept in the Plasmodium subgenus while being lost in Laverania. Assessing how molecular traits in the primate malaria clades originated is a fundamental science problem that will likely provide new targets for interventions. However, given that the genus Plasmodium is paraphyletic (some descendant groups are in other genera), understanding the evolution of malaria parasites will benefit from studying “non-Plasmodium” Haemosporida.

Parasite-associated mortality in birds: the roles of specialist parasites and host evolutionary distance

The factors that influence whether a parasite is likely to cause death in a given host species are not well known. Generalist parasites with high local abundances, broad distributions and the ability to infect a wide phylogenetic diversity of hosts are often considered especially dangerous for host populations, though comparatively little research has been done on the potential for specialist parasites to cause host mortality. Here, using a novel database of avian mortality records, we tested whether phylogenetic host specialist or host generalist haemosporidian blood parasites were associated with avian host deaths based on infection records from over 81 000 examined hosts. In support of the hypothesis that host specialist parasites can be highly virulent in novel hosts, we found that the parasites that were associated with avian host mortality predominantly infected more closely related host species than expected under a null model. Hosts that died tended to be distantly related to the host species that a parasite lineage typically infects, illustrating that specialist parasites can cause death outside of their limited host range. Overall, this study highlights the overlooked potential for host specialist parasites to cause host mortality despite their constrained ecological niches.

PMRT1, a Plasmodium -Specific Parasite Plasma Membrane Transporter, Is Essential for Asexual and Sexual Blood Stage Development

Plasmodium falciparum -infected erythrocytes possess multiple compartments with designated membranes. Transporter proteins embedded in these membranes not only facilitate movement of nutrients, metabolites, and other molecules between these compartments, but also are common therapeutic targets and can confer antimalarial drug resistance.

Primate malarias as a model for cross-species parasite transmission

Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.

Description and molecular characterization of novel Leucocytozoon parasite (Apicomplexa: Haemosporida: Leucocytozoidae), Leucocytozoon polynuclearis n. sp. found in North American woodpeckers

We describe Leucocytozoon polynuclearis n. sp. (Haemosporida: Leucocytozoidae) from two North American woodpeckers, the northern flicker (Colaptes auratus Linnaeus) and white-headed woodpecker (Dryobates albolarvatus Boie, 1826), based on the morphology of its blood stages and portions of the mitochondrial cytochrome b gene. The most distinctive features of Leucocytozoon polynuclearis n. sp. development are the triangular-shaped host cell nuclei and position of host cell nuclei above gametocytes. This parasite inhabits thrombocytes. Leucocytozoon squamatus Nandi, 1986, the only other Leucocytozoon species detected from Picidae birds, lacks features that are commonly found with L. polynuclearis n. sp. infections. Phylogenetic analysis identified DNA lineages associated with L. polynuclearis n. sp. and showed that this parasite is more closely related to other North American Leucocytozoon species than to L. squamatus, whose initial description was from infected Old World Picidae species. Although there are reports of L. squamatus in North American Picidae species, these detections were based only on microscopic examinations, remain genetically non-characterized, and might be misidentifications with regards to L. polynuclearis n. sp. Available parasite distribution data indicate that L. polynuclearis n. sp. infects Picidae species throughout North America and L. squamatus distribution probably is restricted to Old World Piciformes birds.

Haemosporidia of grey crowned cranes in Rwanda

Grey crowned cranes (Balearica regulorum) have been facing significant and long-term population declines in East Africa. Studies of Haemosporidian infections are essential to gain insight into pathogenic threats and help infer vector-host relationships, resolve parasite relationships, and support conservation efforts. As part of a program to reintroduce captive cranes in Rwanda back to their natural habitats, through health checks and initial microscopic examination, 120 grey crowned cranes were selected under suspicion of harboring Haemosporidian infections following initial peripheral blood smear examinations. Of these, 104 were infected with Haemoproteus and 3 were coinfected with Leucocytozoon as detected by PCR and microscopy. Sequencing allowed us to identify 2 distinct unreported lineages of Haemoproteus antigonis and one lineage of Leucocytozoon in the subspecies of Grey Crowned Cranes endemic to East Africa, B. r. gibbericeps. Molecularly, our two lineages of Haemoproteus antigonis differ by 32 base pairs and matched with about 95 percent identity to previously reported sequences of H. antigonis found in other species of cranes. No visible morphologic differences were found when compared to images of H. antigonis from previous studies. Our work demonstrates not only a need for increased testing within the family Gruidae, but also to investigate the possibility of cryptic speciation within the morphospecies Haemoproteus antigonis.

The vectors of Plasmodium knowlesi and other simian malarias Southeast Asia: challenges in malaria elimination

Plasmodium knowlesi, a simian malaria parasite of great public health concern has been reported from most countries in Southeast Asia and exported to various countries around the world. Currently P. knowlesi is the predominant species infecting humans in Malaysia. Besides this species, other simian malaria parasites such as P. cynomolgi and P. inui are also infecting humans in the region. The vectors of P. knowlesi and other Asian simian malarias belong to the Leucosphyrus Group of Anopheles mosquitoes which are generally forest dwelling species. Continual deforestation has resulted in these species moving into forest fringes, farms, plantations and human settlements along with their macaque hosts. Limited studies have shown that mosquito vectors are attracted to both humans and macaque hosts, preferring to bite outdoors and in the early part of the night. We here review the current status of simian malaria vectors and their parasites, knowledge of vector competence from experimental infections and discuss possible vector control measures. The challenges encountered in simian malaria elimination are also discussed. We highlight key knowledge gaps on vector distribution and ecology that may impede effective control strategies.

A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax

Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).

Hepatocystis and Nycteria (Haemosporida) parasite infections of bats in the Central Region of Cameroon

Mammalian haemosporidian parasites are classified in ten genera, including Plasmodium, Hepatocystis and Nycteria. A high diversity of haemosporidian parasites has been described from bats, but our understanding of their prevalence, distribution and use of hosts remain fragmented. The haemosporidian parasites of bats in Cameroon have been largely understudied, but here, bats, sampled from different habitat types of the Central Region of Cameroon, were investigated for haemosporidian infections with a combination of microscopic and molecular phylogenetic analysis. An overall prevalence of 18.1% of haemosporidian infections was detected in a total of 155 investigated bats belonging to 14 bat species. For the first time Hepatocystis and Nycteria parasites were detected in bats from Cameroon and molecularly characterized. Hepatocystis infections were exclusively identified in the epauletted fruit bat host species Epomophorus pusillus with a high prevalence of 65.5%, whereas Nycteria infections could be detected in several hosts, namely: Doryrhina cyclops (60.0%), Rhinolophus landeri (20.0%) and one Nycteris grandis. This study unveils evidence that habitat types may play a role in transmission of Hepatocystis parasites on a local scale and it adds important information on the distribution and host specificity of the neglected haemosporidian genus Nycteria.

Contrasting drivers of diversity in hosts and parasites across the tropical Andes

Geographic turnover in community composition is created and maintained by eco-evolutionary forces that limit the ranges of species. One such force may be antagonistic interactions among hosts and parasites, but its general importance is unknown. Understanding the processes that underpin turnover requires distinguishing the contributions of key abiotic and biotic drivers over a range of spatial and temporal scales. Here, we address these challenges using flexible, nonlinear models to identify the factors that underlie richness (alpha diversity) and turnover (beta diversity) patterns of interacting host and parasite communities in a global biodiversity hot spot. We sampled 18 communities in the Peruvian Andes, encompassing ∼1,350 bird species and ∼400 hemosporidian parasite lineages, and spanning broad ranges of elevation, climate, primary productivity, and species richness. Turnover in both parasite and host communities was most strongly predicted by variation in precipitation, but secondary predictors differed between parasites and hosts, and between contemporary and phylogenetic timescales. Host communities shaped parasite diversity patterns, but there was little evidence for reciprocal effects. The results for parasite communities contradicted the prevailing view that biotic interactions filter communities at local scales while environmental filtering and dispersal barriers shape regional communities. Rather, subtle differences in precipitation had strong, fine-scale effects on parasite turnover while host-community effects only manifested at broad scales. We used these models to map bird and parasite turnover onto the ecological gradients of the Andean landscape, illustrating beta-diversity hot spots and their mechanistic underpinnings.

Genetic diversity and expression profile of Plasmodium falciparum Pf34 gene supports its immunogenicity

PURPOSE OF THE STUDY

Genetic variation is one of the major obstacles in the development of effective vaccines. A multivalent malaria vaccine is required to increase efficacy and confer long term protection. In this context, we analysed the genetic diversity, expression profile, and immune response against Pf34.

METHODS

Phylogenetic analysis was carried out using Pf34 orthologues sequences of various Plasmodium species. Genetic diversity was analysed by PCR amplification and Sanger dideoxy sequencing of Pf34 gene from Plasmodium falciparum positive human blood samples. The expression level of Pf34 gene was studied during erythrocytic stage by real time qPCR at four-hour interval, and immune response against synthetic peptides of Pf34 (P1 and P2) was analysed using ELISA.

RESULTS

Phylogenetic analysis revealed the conserved nature of Pf34 gene. Genetic diversity analysis showed that majority (92%) of Plasmodium falciparum isolates in available database bore wild type Pf34 gene (Hd = 0.160 ± 0.030, π = 0.00021), including the present study (89.3%). The P. falciparum specific amino acid repeats (NNDK, NNDLK, and NNNNNN) in the B cell epitope regions were conserved. Furthermore, Pf34 gene is expressed throughout the erythrocytic cycle and comparatively high expression was observed in early ring and schizont stage. High IgG response was observed against both the peptides P1 and P2 of Pf34 containing asparagine NNNNNN and NNDLK repeat respectively.

CONCLUSION

The limited genetic diversity, presence of conserved amino acid repeats within B cell epitope and high IgG response suggests that Pf34 may be a potential vaccine candidate for malaria. However, further validation studies are required.

Rediscovery of Plasmodium (Huffia) huffi (Apicomplexa, Haemosporida): a lost lineage from toucans

Literature data on toucans haemosporidians are scarce and all reports come from investigations in Brazil. Muniz et al. (Rev Bras Malariol 3: 339-356, Muniz et al., Rev Bras Malariol 3:339-356, 1951) and Muniz and Soares (Rev Bras Malar 611-617, Muniz J, Soares R de RL (1954) Nota sôbre um parasita do gênero Plasmodium encontrado no Ramphastos toco Müller, 1776, "Tucano-Açu", e diferente do Plasmodium huffi: Plasmodium pinottii n. sp. Rev Bras Malar 611 - 617.) described two Plasmodium species, P. huffi and P. pinottii, in Ramphastos toco. Later, Manwell and Sessler (J Protozol 18: 570-574, Manwell and Sessler, Malaria Parasites of Toucans J Protozol 18:570-574, 1971) established a new subspecies, P. nucleophilum toucani. In the last review on avian haemosporidians, Valkiūnas (Valkiūnas, Avian malaria parasites and other haemosporidia, CRC Press, New York, 2005) highlighted that P. huffi was insufficiently characterized, considering it a lost lineage. Also, the original description of P. huffi was considered insufficiently clear, due to a possible co-infection of the toucan hosts with a Novyella-like species. Here, we redescribed the species Plasmodium (Huffia) huffi based on morphological and molecular data, which were found in two toucan species, Ramphastos toco and Pteroglossus aracari from Brazil. Morphological features of the specimens are markedly the same as the original description. In R. toco, we observe two individuals infected, one infected only with P. huffi and one co-infected with P. huffi and the Novyella-like species, as observed in the original description. Also, we observe one R. toco infected only with the Novyella-like species, identified by morphological and molecular data as Plasmodium (Novyella) nucleophilum nucleophilum. In this way, it was possible to redescribe Plasmodium huffi in detail, without the doubt characters observed in the original description. Moreover, by applying species delimitation algorithms to a large Plasmodium phylogeny, we were able to identify new possible hosts for P. huffi and extend its geographic distribution to include North America.

Advances and opportunities in malaria population genomics

Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.

Evolution of transcriptional control of antigenic variation and virulence in human and ape malaria parasites

Background

The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. This unicellular organism is a member of a subgenus of Plasmodium called the Laverania that infects apes, with P. falciparum being the only member that infects humans. The exceptional virulence of this species to humans can be largely attributed to a family of variant surface antigens placed by the parasites onto the surface of infected red blood cells that mediate adherence to the vascular endothelium. These proteins are encoded by a large, multicopy gene family called var, with each var gene encoding a different form of the protein. By changing which var gene is expressed, parasites avoid immune recognition, a process called antigenic variation that underlies the chronic nature of malaria infections.

Results

Here we show that the common ancestor of the branch of the Laverania lineage that includes the human parasite underwent a remarkable change in the organization and structure of elements linked to the complex transcriptional regulation displayed by the var gene family. Unlike the other members of the Laverania, the clade that gave rise to P. falciparum evolved distinct subsets of var genes distinguishable by different upstream transcriptional regulatory regions that have been associated with different expression profiles and virulence properties. In addition, two uniquely conserved var genes that have been proposed to play a role in coordinating transcriptional switching similarly arose uniquely within this clade. We hypothesize that these changes originated at a time of dramatic climatic change on the African continent that is predicted to have led to significant changes in transmission dynamics, thus selecting for patterns of antigenic variation that enabled lengthier, more chronic infections.

Conclusions

These observations suggest that changes in transmission dynamics selected for significant alterations in the transcriptional regulatory mechanisms that mediate antigenic variation in the parasite lineage that includes P. falciparum. These changes likely underlie the chronic nature of these infections as well as their exceptional virulence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01872-z.

An Ecologically Framed Comparison of The Potential for Zoonotic Transmission of Non-Human and Human-Infecting Species of Malaria Parasite

The threats, both real and perceived, surrounding the development of new and emerging infectious diseases of humans are of critical concern to public health and well-being. Among these risks is the potential for zoonotic transmission to humans of species of the malaria parasite, Plasmodium, that have been considered historically to infect exclusively non-human hosts. Recently observed shifts in the mode, transmission, and presentation of malaria among several species studied are evidenced by shared vectors, atypical symptoms, and novel host-seeking behavior. Collectively, these changes indicate the presence of environmental and ecological pressures that are likely to influence the dynamics of these parasite life cycles and physiological make-up. These may be further affected and amplified by such factors as increased urban development and accelerated rate of climate change. In particular, the extended host-seeking behavior of what were once considered non-human malaria species indicates the specialist niche of human malaria parasites is not a limiting factor that drives the success of blood-borne parasites. While zoonotic transmission of non-human malaria parasites is generally considered to not be possible for the vast majority of Plasmodium species, failure to consider the feasibility of its occurrence may lead to the emergence of a potentially life-threatening blood-borne disease of humans. Here, we argue that recent trends in behavior among what were hitherto considered to be non-human malaria parasites to infect humans call for a cross-disciplinary, ecologically-focused approach to understanding the complexities of the vertebrate host/mosquito vector/malaria parasite triangular relationship. This highlights a pressing need to conduct a multi-species investigation for which we recommend the construction of a database to determine ecological differences among all known Plasmodium species, vectors, and hosts. Closing this knowledge gap may help to inform alternative means of malaria prevention and control.

Identification of a protein unique to the genus Plasmodium that contains a WD40 repeat domain and extensive low-complexity sequence

Proteins containing WD40 domains play important roles in the formation of multiprotein complexes. Little is known about WD40 proteins in the malaria parasite. This report contains the initial description of a WD40 protein that is unique to the genus Plasmodium and possibly closely related genera. The N-terminal portion of this protein consists of seven WD40 repeats that are highly conserved in all Plasmodium species. Following the N-terminal region is a central region that is conserved within the major Plasmodium clades, such as parasites of great apes, monkeys, rodents, and birds, but partially conserved across all Plasmodium species. This central region contains extensive low-complexity sequence and is predicted to have a disordered structure. Proteins with disordered structure generally function in molecular interactions. The C-terminal region is semi-conserved across all Plasmodium species and has no notable features. This WD40 repeat protein likely functions in some aspect of parasite biology that is unique to Plasmodium and this uniqueness makes the protein a possible target for therapeutic intervention.

Malaria in the 'Omics Era'

Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.

The apicoplast of Haemoproteus columbae: A comparative study of this organelle genome in Haemosporida

Apicomplexa is a phylum of parasitic protozoa; among them are the order Haemosporida, vector-borne parasites that include those that cause malaria (genus Plasmodium). Most Apicomplexa species have a non-photosynthetic plastid or apicoplast. Given its unique metabolic pathways, this organelle is considered a target for malaria therapeutics. Regardless of its importance, there is a paucity of complete apicoplast genome data hindering comparative studies. Here, the Haemoproteus (Haemoproteus) columbae apicoplast genome (lineage HAECOL1) was obtained using next-generation sequencing. This genome was included in a comparative analysis with other plastids. This 29.8 kb circular genome shares the same structure found in Plasmodium parasites. It is A + T rich (87.7%), comparable but at the higher end of A + T content observed in Plasmodium species (85.5-87.2%). As expected, considering its high A + T content, the synonymous codon usage (RSCU) and the effective number of codons (ENc) showed a moderate codon bias. Several apicoplast genes have a phylogenetic signal. However, unlike mitochondrial genes, single-gene phylogenies have low support in haemosporidian clades that diverged recently. The H. columbae apicoplast genome suggests that the apicoplast function may be conserved across Haemosporida. This parasite could be a model to study this organelle in a non-mammalian system.

A cornucopia of research resources for the fourth rodent malaria parasite species

The study of human malaria caused by species of Plasmodium has undoubtedly been enriched by the use of model systems, such as the rodent malaria parasites originally isolated from African thicket rats. A significant gap in the arsenal of resources of the species that make up the rodent malaria parasites has been the lack of any such tools for the fourth of the species, Plasmodium vinckei. This has recently been rectified by Abhinay Ramaprasad and colleagues, whose pivotal paper published in BMC Biology describes a cornucopia of new P. vinckei 'omics datasets, mosquito transmission experiments, transfection protocols, and virulence phenotypes, to propel this species firmly into the twenty-first century.

Host specificity of Hepatocystis infection in short-nosed fruit bats (Cynopterus brachyotis) in Singapore

Haemosporidians infect a wide diversity of bat genera and species, yet little is known about their transmission cycles or epidemiology. Though several recent studies have focused on the genus Hepatocystis, an Old World parasite primarily infecting bats, monkeys, and squirrels, this group is still understudied with little known about its transmission and molecular ecology. These parasites lack an asexual erythrocytic stage, making them unique from the Plasmodium vertebrate life cycle. In this study, we detected a prevalence of 31% of Hepatocystis in short-nosed fruit bats (Cynopterus brachyotis) in Singapore. Phylogenetic reconstruction with a partial cytochrome b sequence revealed a monophyletic group of Hepatocystis from C. brachyotis in Malaysia, Singapore, and Thailand. There was no relationship with infection and bat age, sex, location, body condition or monsoon season. The absence of this parasite in the five other bat species sampled in Singapore indicates this Hepatocystis species may be host restricted.

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A bat haemosporidian (Hepatocystis) was detected in short nose fruit bats (Cynopterus brachyotis) in Singapore.

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Infection was not associated with bat age, sex, sample location, body condition or monsoon season.

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Infection was detected in only one bat species, indicating this Hepatocystis species may be host specific.