Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes

Geographical and Molecular Analysis of Haplotype Variations in Leishmania major Among Infected Iranian Phlebotomus papatasi

PURPOSE

Leishmania major is main causative agent and Phlebotomus papatasi is only proven vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Iran. Human leishmaniasis is mostly susceptible to climatic conditions and molecular variations of Leishmania parasites within sandflies.

METHODS

L. major was analyzed based on geographical, environmental, climatic changes and haplotype variations within P. papatasi. Molecular tools and different geographical aspects were employed using Arc-GIS software for mapping the geographic distribution of samples and other statistics tests. Fragments of ITS-rDNA, k-DNA, and microsatellite genes of Leishmania were used for PCR, RFLP, sequencing, and phylogenetic analyses.

RESULTS

Totally 81 out of 1083 female P. papatasi were detected with Leishmania parasites: 70 and five were L. major and L. turanica, respectively. Golestan and Fars provinces had the highest (13.64%) and lowest (4.55%) infection rates, respectively. The infection rate among female P. papatasi collected from gerbil burrows was significantly higher (15.15%) than animal shelters, yards, and inside houses (4.48%) (P < 0.0%). Microsatellite was more sensitive (22.72%) than k-DNA (18.8%) and ITS-rDNA (7.48%). More molecular variations of L. major were found in Isfahan province.

CONCLUSIONS

Arc-GIS software and other statistics tests were employed to find Leishmania positive and haplotype variations among sand flies. Geographical situations, altitude, climate, precipitation, humidity, temperature, urbanization, migrations, regional divergences, deforestation, global warming, genome instability, ecology, and biology of the sand flies intrinsically, and the reservoir hosts and neighboring infected locations could be reasons for increasing or decreasing the rate of Leishmania infection and haplotype variations.

Genetic diversity and phylogeography of Phlebotomus argentipes (Diptera: Psychodidae, Phlebotominae), using COI and ND4 mitochondrial gene sequences

BACKGROUND

Phlebotomus argentipes complex is the primary vector for cutaneous leishmaniasis, a burgeoning health concern in contemporary Sri Lanka, where effective vector control is important for proper disease management. Understanding the genetic diversity of the P. argentipes population in Sri Lanka is vital before implementing a successful vector control program. Various studies have indicated that genetic divergence, caused by genetic drift or selection, can significantly influence the vector capacity of arthropod species. To devise innovative control strategies for P. argentipes, exploring genetic diversity and phylogeography can offer valuable insights into vector competence, key genetic trait transfer, and impact on disease epidemiology. The primary objective is to analyze the genetic diversity and phylogeography of the P. argentipes complex in Sri Lanka, based on two mitochondrial genomic regions in modern representatives of P. argentipes populations.

METHODOLOGY

A total of 159 P. argentipes specimens were collected from five endemic areas of cutaneous leishmaniasis and identified morphologically. Two mitochondrial regions (Cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) were amplified using the total DNA and subsequently sequenced. Partial sequences of those mitochondrial genes were utilized to analyze genetic diversity indices and to explore phylogenetic and phylogeographic relationships.

PRINCIPAL FINDINGS

Among five sampling locations, the highest genetic diversity for COI and ND4 was observed in Hambantota (Hd-0.749, π-0.00417) and Medirigiriya (Hd-0.977, π-0.01055), respectively. Phylogeographic analyses conducted using COI sequences and GenBank retrieved sequences demonstrated a significant divergence of P. argentipes haplotypes found in Sri Lanka. Results revealed that they have evolved from the Indian ancestral haplotype due to historical- geographical connections of the Indian subcontinent with Sri Lanka.

CONCLUSIONS

Utilizing high-mutation-rate mitochondrial genes, such as ND4, can enhance the accuracy of genetic variability analysis in P. argentipes populations in Sri Lanka. The phylogeographical analysis of COI gene markers in this study provides insights into the historical geographical relationship between India and P. argentipes in Sri Lanka. Both COI and ND4 genes exhibited consistent genetic homogeneity in P. argentipes in Sri Lanka, suggesting minimal impact on gene flow. This homogeneity also implies the potential for horizontal gene transfer across populations, facilitating the transmission of genes associated with traits like insecticide resistance. This dynamic undermines disease control efforts reliant on vector control strategies.

Susceptibility of Phlebotomus papatasi (Diptera: Psychodidae) against DDT and Deltamethrin in an Endemic Focus of Zoonotic Cutaneous Leishmaniasis in Iran

Background

Phlebotomus papatasi (Diptera: Psychodidae) is the main vector of zoonotic cutaneous leishmaniasis (ZCL) in Iran. The nonstandard use of pesticides against pests, particularly in agriculture, indirectly has caused the development of resistance and, consequently, the threat of control measures in ZCL endemic areas. Up to 2023, several reports of resistance in Ph. papatasi have been declared in the Old World. The purpose of this study was to measure the lethal time (LT50 and LT90) of Ph. papatasi sand flies in the ZCL endemic center of Esfahan to DDT and deltamethrin insecticides.

Methods

Sand flies were collected in Borkhar and were tested using WHO adult mosquito test kit against DDT 4% and deltamethrin 0.0002%. The sand fly's survival was recorded during exposure time in 225, 450|, 900, 1800, and 3600-seconds' intervals for DDT and Deltamethrin and they were allowed to recover for 24 hours. Then LT50 and LT90 were analyzed using probit software. Phlebotomus papatasi were identified using morphological keys and other sand flies' species were excluded from the analysis.

Results

The insecticide against female Ph. papatasi revealed hundred percent mortality when exposed to DDT 4% and deltamethrin 0.0002%. The LT50 and LT90 were 19.32 and 22.74 minutes for DDT 4% and 39.92 and 51.33 minutes for deltamethrin 0.0002% respectively.

Conclusion

Results of this study revealed that Ph. papatasi is still susceptible to DDT and deltamethrin. This data provides valuable knowledge to implement effective control strategies against ZCL main vector and help to manage insecticide resistance in the region.

Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.

Population Genetic Structure of Phlebotomus sergenti (Diptera: Psychodidae) Collected in Four Regions of Morocco Based on the Analysis of Cyt b and EF-1α Genes

Phlebotomus (Ph.) sergenti is the main vector of Leishmania (L.) tropica (Trypanosomatida: Trypanosomatidae), the causative agent of anthroponotic cutaneous leishmaniasis in Morocco. This species has an extended geographical distribution, wider than that of the parasite. The main objective of our study was to analyze the genetic diversity of Ph. sergenti collected in four foci in Morocco: Taza, Foum Jemâa, El Hanchane, and Ouarzazate. We studied a set of diversity and population structure indices by sequencing two markers; nuclear EF-1α and mitochondrial Cyt b from 175 individual sand flies. Our results showed a considerable degree of intraspecific polymorphism with a high number of haplotypes identified in both genes. Many polymorphic sites detected in the Cyt b sequences (SCyt b = 45) indicate that it is the most polymorphic marker showing a distinct distribution of haplotypes according to their geographical origin, whereas the EF-1α marker showed no geographical isolation. Analysis by Tajima's D and Fu's Fs tests revealed a possible recent expansion of the populations, especially with the EF-1α marker, showing significant values in Taza and Ouarzazate sequences. The present study revealed significant genetic diversity within Ph. sergenti populations in Morocco. The results warrant further research using a combination of more than two markers including mitochondrial and non-mitochondrial markers, which may provide more information to clarify the genetic status of Ph. sergenti.

Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review

The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.

A 50-year-old redescription: molecular and morphometric characterization of Hepatozoon carinicauda Pessôa and Cavalheiro, 1969 in the brown-banded water snake Helicops angulatus (Linnaeus, 1758)

The combined use of molecular and microscopic techniques has become an increasingly common and efficient practice for the taxonomic and evolutionary understanding of single-celled parasites such as haemogregarines. Based on this integrative approach, we characterized Hepatozoon found in Helicops angulatus snakes from the Eastern Amazonia, Brazil. The gamonts observed caused cell hypertrophy and were extremely elongated and, in some cases, piriform (mean dimensions: 25.3 ± 1.9 × 8.6 ± 1.3 μm). These morphological features correspond to Hepatozoon carinicauda, described 50 years ago in the snake Helicops carinicaudus in the southeast region of Brazil. Phylogenetic and genetic divergence analyses, performed with the sequence obtained from the amplification of a 590 bp fragment of the 18S rRNA gene, revealed that Hepatozoon in He. angulatus differed from the other lineages retrieved from GenBank, and was clustered singly in both the phylogenetic tree and the haplotype network. The integration of these data allowed the identification of H. carinicauda in a new aquatic host, and increased the knowledge of its geographical distribution. Therefore, the present study included the first redescription of a Hepatozoon species in a snake from the Brazilian Amazon.

Niche divergence and paleo-distributions of Lutzomyia longipalpis mitochondrial haplogroups (Diptera: Psychodidae)

Lutzomyia longipalpis is a complex of species which has a wide but discontinuous distribution from southeastern Mexico to northern Argentina and Uruguay. To date, eight mitochondrial haplogroups have been identified along its distribution although key environmental tolerances and ecological niche models have been analyzed only at the complex level. The aim of the present study was to analyze whether genetic diversification using three mitochondrial genes of the Lu. longipalpis complex is associated with niche divergence and to explore evolution of distributional projections of all haplogroups between the Last Glacial Maximum (LGM; 21,000 yrs ago) and the present. Current occurrence of all haplogroups was used to develop ecological niche models (ENM) and these were projected in both periods to quantify and identify geographic area shifts. Environmental space was used to estimate niche similarity between major clades and pairwise between individual haplogroups. The two major Lu. longipalpis clades (Mex, CA, Col and Ven vs Arg and Bra) had significantly different environmental space, indicating niche divergence. Environmental space overlap of southern haplogroups was variable, with divergent niche, except between Arg and ArgBra. The most suitable regions for the ArgBra haplogroup were northeastern and southeastern Brazil, and the Gran Chaco region. In contrast, ENM of haplogroups within the northern major clade have significantly similar niche, with highest geographic ENM suitability along both the Caribbean and Pacific coasts. The intensity and coverage of high suitability areas in the LGM decreased for most haplogroups in the present. Integrating ENM and phylogenetic analyses has allowed us to test hypotheses of niche similarity between Lu. longipalpis haplogroups and major clades, and to identify conserved distributional areas of haplogroups since the LGM, with the exception of Arg. Evidence for distributional shifts and overlap of haplogroups is important to analyze Leishmaniasis´ eco-epidemiology and to successfully monitor and control transmission.

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations

Phlebotomus papatasi sand flies inject their hosts with a myriad of pharmacologically active salivary proteins to assist with blood feeding and to modulate host defenses. In addition, salivary proteins can influence cutaneous leishmaniasis disease outcome, highlighting the potential of the salivary components to be used as a vaccine. Variability of vaccine targets in natural populations influences antigen choice for vaccine development. Therefore, the objective of this study was to investigate the variability in the predicted protein sequences of nine of the most abundantly expressed salivary proteins from field populations, testing the hypothesis that salivary proteins appropriate to target for vaccination strategies will be possible. PpSP12, PpSP14, PpSP28, PpSP29, PpSP30, PpSP32, PpSP36, PpSP42, and PpSP44 mature cDNAs from field collected P. papatasi from three distinct ecotopes in the Middle East and North Africa were amplified, sequenced, and in silico translated to assess the predicted amino acid variability. Two of the predicted sequences, PpSP12 and PpSP14, demonstrated low genetic variability across the three geographic isolated sand fly populations, with conserved multiple predicted MHCII epitope binding sites suggestive of their potential application in vaccination approaches. The other seven predicted salivary proteins revealed greater allelic variation across the same sand fly populations, possibly precluding their use as vaccine targets.

Population Genetics of Phlebotomus papatasi from Endemic and Nonendemic Areas for Zoonotic Cutaneous Leishmaniasis in Morocco, as Revealed by Cytochrome Oxidase Gene Subunit I Sequencing

Zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania major Yakimoff & Shokhor and transmitted by Phlebotomus papatasi (Scopoli) is a public health concern in Morocco. The disease is endemic mainly in pre-Saharan regions on the southern slope of the High Atlas Mountains. The northern slope of the High Atlas Mountains and the arid plains of central Morocco remain non-endemic and are currently considered high risk for ZCL. Here we investigate and compare the population genetic structure of P. papatasi populations sampled in various habitats in historical foci and non-endemic ZCL areas. A fragment of the mtDNA cytochrome oxidase I (COI) gene was amplified and sequenced in 59 individuals from 10 P. papatasi populations. Haplotype diversity was probed, a median-joining network was generated (F_ST) and molecular variance (AMOVA) were analyzed. Overall, we identified 28 haplotypes with 32 distinct segregating sites, of which seven are parsimony informative. The rate of private haplotypes was high; 20 haplotypes (71.4%) are private ones and exclusive to a single population. The phylogenetic tree and the network reconstructed highlight a genetic structuration of these populations in two well defined groups: Ouarzazate (or endemic areas) and Non-Ouarzazate (or nonendemic areas). These groups are separated by the High Atlas Mountains. Overall, our study highlights differences in terms of population genetics between ZCL endemic and non-endemic areas. To what extent such differences would impact the transmission of L. major by natural P. papatasi population remains to be investigated.

Mitochondrial Gene Heterogeneity and Population Genetics of Haemaphysalis longicornis (Acari: Ixodidae) in China

INTRODUCTION

Haemaphysalis longicornis is an important ectoparasite of domestic and wild animals that can transmit many pathogens including viruses, fungi, bacteria and protozoa.

MATERIALS AND METHODS

In this study, we examined genetic variation and population genetics in three mitochondrial (mt) genes [cox1 (cytochrome c subunit 1), rrnL (large subunit ribosomal RNA) and nad5 (NADH dehydrogenase 5)] among four H. longicornis populations from China.

RESULTS

The sizes of the partial sequences of cox1, rrnL and nad5 were 776 bp, 409 bp, 510 bp, respectively. Among the obtained sequences, we identified 22 haplotypes for cox1, 2 haplotypes for rrnL and 17 haplotypes for nad5. Low gene flow and significant genetic differentiation (66.2%) were detected among H. longicornis populations. There was no rapid expansion event in the demographic history of four H. longicornis populations in China. In addition, phylogenetic analyses confirmed that all the Haemaphysalis isolates were H. longicornis which were segregated into two major clades.

CONCLUSION

The mt DNA genes provide a potential novel genetic marker for molecular epidemiology of H. longicornis and assist in the control of tick and tick-borne diseases in humans and animals.

Genetic diversity, phylogeography and molecular clock of the Lutzomyia longipalpis complex (Diptera: Psychodidae)

BACKGROUND

The Lutzomyia longipalpis complex has a wide but discontinuous distribution in Latin America, extending throughout the Neotropical realm between Mexico and northern Argentina and Uruguay. In the Americas, this sandfly is the main vector of Leishmania infantum, the parasite responsible for Visceral Leishmaniasis (VL). The Lu. longipalpis complex consists of at least four sibling species, however, there is no current consensus on the number of haplogroups, or on their divergence. Particularly in Argentina, there have been few genetic analyses of Lu. longipalpis, despite its southern expansion and recent colonization of urban environments. The aim of this study was to analyze the genetic diversity and structure of Lu. longipalpis from Argentina, and to integrate these data to re-evaluate the phylogeography of the Lu. longipalpis complex using mitochondrial markers at a Latin American scale.

METHODOLOGY/PRINCIPAL FINDINGS

Genetic diversity was estimated from six sites in Argentina, using a fragment of the ND4 and the 3´ extreme of the cyt b genes. Greatest genetic diversity was found in Tartagal, Santo Tomé and San Ignacio. There was high genetic differentiation of Lu. longipalpis in Argentina using both markers: ND4 (FST = 0.452, p < 0.0001), cyt b (FST = 0.201, p < 0.0001). Genetic and spatial Geneland analyses reveal the existence of two primary genetic clusters in Argentina, cluster 1: Tartagal, Santo Tomé, and San Ignacio; cluster 2: Puerto Iguazú, Clorinda, and Corrientes city. Phylogeographic analyses using ND4 and cyt b gene sequences available in GenBank from diverse geographic sites suggest greater divergence than previously reported. At least eight haplogroups (three of these identified in Argentina), each separated by multiple mutational steps using the ND4, are differentiated across the Neotropical realm. The divergence of the Lu. longipalpis complex from its most recent common ancestor (MRCA) was estimated to have occurred 0.70 MYA (95% HPD interval = 0.48-0.99 MYA).

CONCLUSIONS/SIGNIFICANCE

This study provides new evidence supporting two Lu. longipalpis genetic clusters and three of the total eight haplogroups circulating in Argentina. There was a high level of phylogeographic divergence among the eight haplogroups of the Lu. longipalpis complex across the Neotropical realm. These findings suggest the need to analyze vector competence, among other parameters intrinsic to a zoonosis, according to vector haplogroup, and to consider these in the design and surveillance of vector and transmission control strategies.