The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity

Genome wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Awash Sebat Kilo in Ethiopia

Since the detection of the Asian mosquito Anopheles stephensi in Dijbouti in 2012, it has spread throughout the Horn of Africa. This invasive vector continues to expand across the continent and is a significant threat to malaria control programs. Vector control methods, including insecticide-treated nets and indoor residual spraying, have substantially reduced the malaria burden. However, the increasing prevalence of mosquitoes resistant to insecticides, including An. stephensi populations, undermines ongoing malaria elimination efforts. Understanding population structure, gene flow between populations, and the distribution of insecticide resistance mutations is essential for guiding effective malaria control strategies. Here, we generated whole genome sequencing data for An. stephensi sourced from Awash Sebat Kilo, Ethiopia (n = 27) and compared with South Asian populations (n = 45; India and Pakistan) to assess genomic diversity, population structure, and uncovering insecticide resistance mutations. Population structure analysis using genome-wide single nucleotide polymorphisms (n = 15,533,476) revealed Ethiopian isolates clustering as a distinct ancestral group, separate from South Asian isolates. Three insecticide resistance-associated SNPs (gaba gene: A296S and V327I; vgsc L1014F) were detected. Evidence of ongoing selection was found in several loci, including genes previously associated with neonicotinoids, ivermectin, DDT, and pyrethroid resistance. This study represents the first whole genome population genetics study of invasive An. stephensi, revealing genomic differences from South Asian populations, which can be used for future assessments of vector population dispersal and detection of insecticide resistance mechanisms.

Phylogeographic Patterns and Genetic Diversity of Anopheles stephensi: Implications for Global Malaria Transmission

Background: Anopheles stephensi, a primary malaria vector in South Asia, is expanding its geographic range, raising concerns about increased malaria transmission. However, critical aspects of its genetic diversity, population structure, and evolutionary dynamics remain poorly understood in Khyber Pakhtunkhwa (KP), Pakistan, an endemic malaria region where An. stephensi is adapting to urban settings, posing challenges for the development of targeted vector control strategies. This study addresses this gap by analyzing COI, COII (cytochrome oxidase subunit I and II), and ITS2 (internal transcribed spacer 2) sequences from An. stephensi populations in KP and comparing them with global isolates. Additionally, egg morphology analysis was conducted to identify the biological form. Methods: Mosquitoes were collected from malaria-endemic districts (Nowshera, Charsadda, and Peshawar) using ovitraps. Eggs were characterized morphologically, and DNA was extracted for PCR amplification of COI, COII, and ITS2 markers. Sequences from 17 Pakistani isolates, along with global sequences, were analyzed. Phylogenetic relationships, haplotype networks, genetic diversity, and neutrality tests (Tajima's D and Fu's Fs) were assessed. Results: Egg morphology confirmed the mysorensis form (13-15 ridges per egg) in KP. COI sequences clustered into two subclades (Punjab and KP), with >99% similarity to global isolates. COII and ITS2 sequences showed high similarity (99.46-100%) with populations from China, Iran, India, and Brazil, reflecting strong genetic connectivity rather than distinct regional clustering. Haplotype analysis identified six COI, ten COII, and ten ITS2 haplotypes, with Hap_2 (50.7%) and Hap_1 (43.3%) being the most prevalent in COI, Hap_7 (29.4%) in COII, and Hap_3 (80.8%) in ITS2. Population genetic analysis revealed higher COI diversity in Pakistan and India, with moderate diversity in COII. Neutrality tests suggested balancing selection in COI for both countries, while COII and ITS2 indicated population contraction in Iran. Conclusions: The findings reveal strong genetic connectivity within regions (e.g., Pakistan) and differentiation across global populations of An. stephensi, highlighting its potential for further expansion and adaptation. These insights are critical for informing global malaria control strategies, particularly in regions vulnerable to vector invasion.

Genetic surveillance of Plasmodium-Anopheles compatibility markers during Anopheles stephensi associated malaria outbreak

Despite previous decline of malaria in Ethiopia, an outbreak in Dire Dawa in 2022 implicated invasive vector An. stephensi as responsible. The transmission of Plasmodium by invasive An. stephensi raises questions about the molecular basis of compatibility, and the origin of the Plasmodium being transmitted. The Plasmodium P47 gene is a parasite-vector interaction gene in Anopheles , and along with corresponding mosquito P47 receptor ( P47Rec ), can be critical in establishment of Plasmodium infections in anophelines. Here, we analyzed P47 and P47Rec sequences to determine the origin of Plasmodium detected in An. stephensi during the outbreak and evaluate markers of compatibility. Analysis of geographically informative SNPs in Pfs47 revealed that these P. falciparum exhibit the African haplotype. We also identified a single amino acid change in P47Rec within these An. stephensi, which could act as a marker for the propensity of An. stephensi populations to outbreaks. Together, we provide the basis for further study to deepen the understanding of invasive An. stephensi -African Plasmodium interactions to better control transmission of malaria and prevent further outbreaks.

The origin, invasion history and resistance architecture of Anopheles stephensi in Africa

The invasion of Africa by the Asian urban malaria vector, Anopheles stephensi, endangers 126 million people across a rapidly urbanising continent where malaria is primarily a rural disease. Control of An. stephensi requires greater understanding of its origin, invasion dynamics, and mechanisms of widespread resistance to vector control insecticides. We present a genomic surveillance study of 551 An. stephensi sampled across the invasive and native ranges in Africa and Asia. Our findings support a hypothesis that an initial invasion from Asia to Djibouti seeded separate incursions to Sudan, Ethiopia, and Yemen before spreading inland, aided by favourable temperature, vegetation cover, and human transit conditions. Insecticide resistance in invasive An. stephensi is conferred by detoxification genes introduced from Asia. These findings, and a companion genomic data catalogue, will form the foundation of an evidence base for surveillance and management strategies for An. stephensi.

Two Nested Inversions in the X Chromosome Differentiate the Dominant Malaria Vectors in Europe, Anopheles atroparvus and Anopheles messeae

The Maculipennis subgroup of malaria mosquitoes includes both dominant malaria vectors and non-vectors in Eurasia. Understanding the genetic factors, particularly chromosomal inversions, that differentiate Anopheles species can provide valuable insights for vector control strategies. Although autosomal inversions between the species in this subgroup have been characterized based on the chromosomal banding patterns, the number and positions of rearrangements in the X chromosome remain unclear due to the divergent banding patterns. Here, we identified two large X chromosomal inversions, approximately 13 Mb and 10 Mb in size, using fluorescence in situ hybridization. The inversion breakpoint regions were mapped by hybridizing 53 gene markers with polytene chromosomes of An. messeae. The DNA probes were designed based on gene sequences from the annotated An. atroparvus genome. The two nested inversions resulted in five syntenic blocks. Only two small syntenic blocks, which encompass 181 annotated genes in the An. atroparvus genome, changed their position and orientation in the X chromosome. The analysis of the An. atroparvus genome revealed an enrichment of gene ontology terms associated with immune system and mating behavior in the rearranged syntenic blocks. Additionally, the enrichment of DNA transposons was found in sequences homologous to three of the four breakpoint regions. This study demonstrates the successful application of the physical genome mapping approach to identify rearrangements that differentiate species in insects with polytene chromosomes.

Aeroplane wing, a new recessive autosomal phenotypic marker in the malaria vector, Anopheles stephensi Liston

A novel and distinct mutant with a phenotype, aeroplane wing (ae) is reported for the first time in the urban malaria vector Anopheles stephensi. The main aim of this study was to establish the mode of inheritance of the ae gene performing genetic crossings between the mutants and wild types. These mutants show extended open wings that are visible to naked eyes in both the sexes. Mutants were first noticed in a nutritionally stressed isofemale colony. Strategic genetic crosses revealed that the ae gene is a recessive, autosomal, and monogenic trait having full penetrance with uniform expression in its adult stage. Egg morphometric analysis confirmed that these mutants were intermediate variant. No significant differences were observed in the wing venation and size of ae mutants compared to their control parental lines. Further cytogenetic analysis on the ovarian polytene chromosome of ae mutant showed an inversion (3Li) on the 3L arm like its parental line. This ae mutant would be a prominent marker and could be useful to study the functions of related specific genes within its genome.

S, Joshi SG, Ramanjini CK, Alalamath T, Srinivasan S, Subramani S, Kumar S, Swain S. Enrichment of phenotype among biological forms of Anopheles stephensi Liston through establishment of isofemale lines

BACKGROUND

Vector management programs rely on knowledge of the biology and genetic make-up of mosquitoes. Anopheles stephensi is a major invasive urban malaria vector, distributed throughout the Indian subcontinent and Middle East, and has recently been expanding its range in Africa. With the existence of three biological forms, distinctly identifiable based on the number of ridges on eggs and varying vectorial competence, An. stephensi is a perfect species for developing isofemale lines, which can be tested for insecticide susceptibility and vectorial competence of various biological forms.

METHODS

We describe key steps involved in establishment and validation of isofemale lines. Isofemale colonies were further used for the characterization of insecticide susceptibility and differential vector competence. The results were statistically evaluated through descriptive and inferential statistics using Vassar Stat and Prism GraphPad software packages.

RESULTS

Through a meticulous selection process, we overcame an initial inbreeding depression and found no significant morphometric differences in wings and egg size between the parental and respective isofemale lines in later generations. IndCh and IndInt strains showed variations in resistance to different insecticides belonging to all four major classes. We observed a significant change in vectorial competence between the respective isofemale and parental lines.

CONCLUSIONS

Isofemale lines can be a valuable resource for characterizing and enhancing several genotypic and phenotypic traits. This is the first detailed report of the establishment of two isofemale lines of type and intermediate biological forms in Anopheles stephensi. The work encompasses characterization of fitness traits among two lines through a transgenerational study. Furthermore, isofemale colonies were established and used to characterize insecticide susceptibility and vector competence. The study provides valuable insights into differential susceptibility status of the parental and isofemale lines to different insecticides belonging to the same class. Corroborating an earlier hypothesis, we demonstrate the high vector competence of the type form relative to the intermediate form using homozygous lines. Using these lines, it is now possible to study host-parasite interactions and identify factors that might be responsible for altered susceptibility and increased vector competence in An. stephensi biological forms that would also pave the way for developing better vector management strategies.

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. Anopheles stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, were reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in the IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a tumor necrosis factor-alpha (TNF-alpha) like gene, which is the homolog of the Eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of Wengen (Wgn) and Grindelwald (Grnd) genes, which are known to be the receptors for Eiger in Drosophila. We have identified all the genes in IndInt required for Eiger-mediated signaling by analogy to the TNF-alpha system, suggesting the presence of a functionally-active Eiger signaling pathway in IndInt. Comparative genomics of the three type-forms with that of IndInt, reveals structurally disruptive mutations in Eiger gene in all three strains of the type-form, suggesting compromised innate immunity in the type-form as the likely cause of high vectorial capacity in these strains. This is the first report of the presence of a homolog of Eiger in malaria vectors, known to be involved in cell death in Drosophila, within an inversion region in IndInt syntenic to an inversion associated with Plasmodium resistance in An. gambiae.

Tandem duplication of a genomic region encoding glutathione S-transferase epsilon-2 and -4 genes in DDT-resistant Anopheles stephensi strain from India

The glutathione S-transferases (GST) genes are a multigene family of enzymes involved in the metabolism of endogenous and xenobiotic compounds by catalysing the conjugation of the reduced form of glutathione to the substrate. The epsilon class of GST (GSTe), unique to arthropods, is known to be involved in the detoxification process of several classes of insecticides, and GSTe2 in particular is known to have DDT dehydrochlorinase activity. This communication reports a tandem duplication of a genomic region encoding GSTe2 and GSTe4 genes in a laboratory-colonized DDT-resistant Anopheles stephensi. We identified duplication breakpoints and the organization of gene duplication through Sanger sequencing performed on long-PCR products. Manual annotation of sequences revealed a tandemly-arrayed duplication of a 3.62 kb segment of GST epsilon gene clusters comprised of five genes: a partial GSTe1, GSTe2, GSTe2-pseudogene, GSTe4 and partial GSTe5, interconnected by a conserved 2.42 kb DNA insert segment major part of which is homologous to a genomic region located on a different chromosome. The tandemly duplicated array contained a total of two GSTe2 and three GSTe4 functional paralog genes. Read-depth coverage and split-read analysis of Illumina-based whole-genome sequence reads confirmed the presence of duplication in the corresponding region of the genome. The increased gene dose in mosquitoes as a result of the GSTe gene-duplication may be an adaptive process to increase levels of detoxifying enzymes to counter insecticide pressure.

Global water quality changes posing threat of increasing infectious diseases, a case study on malaria vector Anopheles stephensi coping with the water pollutants using age-stage, two-sex life table method

Background

Water pollution due to uncontrolled release of chemical pollutants is an important global problem. Its effect on medically important insects, especially mosquitoes, is a critical issue in the epidemiology of mosquito-borne diseases.

Methods

In order to understand the effect of water pollutants on the demography of Anopheles stephensi, colonies were reared in clean, moderately and highly polluted water for three consecutive generations at 27 °C, 75% RH, and a photoperiod of 12:12 h (L:D). The demographic data of the 4th generation of An. stephensi were collected and analysed using the age-stage, two-sex life table.

Results

The intrinsic rate of increase (r), finite rate of increase (λ), mean fecundity (F) and net reproductive rate (R₀) of An. stephensi in clean water were 0.2568 d⁻¹, 1.2927 d⁻¹, 251.72 eggs, and 109.08 offspring, respectively. These values were significantly higher than those obtained in moderately polluted water (r = 0.2302 d⁻¹, λ = 1.2589 d⁻¹, 196.04 eggs, and R₀ = 65.35 offspring) and highly polluted water (r = 0.2282 d⁻¹, λ = 1.2564 d⁻¹, 182.45 eggs, and R₀ = 62.03 offspring). Female adult longevity in moderately polluted (9.38 days) and highly polluted water (9.88 days) were significantly shorter than those reared in clean water (12.43 days), while no significant difference in the male adult longevity was observed among treatments.

Conclusions

The results of this study showed that An. stephensi can partially adapt to water pollution and this may be sufficient to extend the range of mosquito-borne diseases.