Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania

To keep ahead of the evolution of resistance to insecticides in mosquitoes, national malaria control programmes must make use of a range of insecticides, both old and new, while monitoring resistance mechanisms. Knowledge of the mechanisms of resistance remains limited in Anopheles arabiensis, which in many parts of Africa is of increasing importance because it is apparently less susceptible to many indoor control interventions. Furthermore, comparatively little is known in general about resistance to non-pyrethroid insecticides such as pirimiphos-methyl (PM), which are crucial for effective control in the context of resistance to pyrethroids. We performed a genome-wide association study to determine the molecular mechanisms of resistance to deltamethrin (commonly used in bednets) and PM, in An. arabiensis from two regions in Tanzania. Genomic regions of positive selection in these populations were largely driven by copy number variants (CNVs) in gene families involved in resistance to these two insecticides. We found evidence of a new gene cluster involved in resistance to PM, identifying a strong selective sweep tied to a CNV in the Coeae2g-Coeae6g cluster of carboxylesterase genes. Using complementary data from An. coluzzii in Ghana, we show that copy number at this locus is significantly associated with PM resistance. Similarly, for deltamethrin, resistance was strongly associated with a novel CNV allele in the Cyp6aa / Cyp6p cluster. Against this background of metabolic resistance, target site resistance was very rare or absent for both insecticides. Mutations in the pyrethroid target site Vgsc were at very low frequency in Tanzania, yet combining these samples with three An. arabiensis individuals from West Africa revealed a startling diversity of evolutionary origins of target site resistance, with up to 5 independent origins of Vgsc-995 mutations found within just 8 haplotypes. Thus, despite having been first recorded over 10 years ago, Vgsc resistance mutations in Tanzanian An. arabiensis have remained at stable low frequencies. Overall, our results provide a new copy number marker for monitoring resistance to PM in malaria mosquitoes, and reveal the complex picture of resistance patterns in An. arabiensis.

Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae s.l

Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of the most widespread tools currently used to control malaria. The genetic underpinnings of resistance are still only partially understood, with much of the variance in resistance phenotype left unexplained. We performed a multi-country large scale genome-wide association study of resistance to two insecticides widely used in malaria control: deltamethrin and pirimiphos-methyl. Using a bioassay methodology designed to maximise the phenotypic difference between resistant and susceptible samples, we sequenced 969 phenotyped female An. gambiae and An. coluzzii from ten locations across four countries in West Africa (Benin, Côte d'Ivoire, Ghana and Togo), identifying single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) segregating in the populations. The patterns of resistance association were highly multiallelic and variable between populations, with different genomic regions contributing to resistance, as well as different mutations within a given region. While the strongest and most consistent association with deltamethrin resistance came from the region around Cyp6aa1 , this resistance was based on a combination of several independent CNVs in An. coluzzii , and on a non-CNV bearing haplotype in An. gambiae . Further signals involved a range of cytochrome P450, mitochondrial, and immunity genes. Similarly, for pirimiphos-methyl, while the strongest signal came from the region of Ace1 , more widespread signals included cytochrome P450s, glutathione S-transferases, and a subunit of the nAChR target site of neonicotinoid insecticides. The regions around Cyp9k1 and the Tep family of immune genes were associated with resistance to both insecticide classes, suggesting possible cross-resistance mechanisms. These locally-varying, multigenic and multiallelic patterns highlight the challenges involved in genomic monitoring and surveillance of resistance, and form the basis for improvement of methods used to detect and predict resistance. Based on simulations of resistance variants, we recommend that yet larger scale studies, exceeding 500 phenotyped samples per population, are required to better identify associated genomic regions.

Surveillance of viral haemorrhagic fevers in ghana: entomological assessment of the risk of transmission in the northern regions

SUMMARY OBJECTIVES

To assess the risk of transmission of viral haemorrhagic fevers in northern Ghana.

DESIGN

A two-year cross-sectional entomological study was carried out in four communities in the northern part of Ghana. Standard WHO methods were used to collect adult and larvae of Aedes mosquitoes to estimate man-vector contact rates and larval indices.

RESULTS

A total of 2804 households were surveyed to estimate larval indices and man-vector contacts of potential vectors of viral haemorrhagic fevers such as Yellow fever and Dengue. Over 56% households in each study site were positive for Aedes larvae. Relatively higher Breteaux index (BI) and Container index (CI) were estimated in Damongo (BI: 180 and CI: 44.8) and Jirapa (BI: 149.7 and CI: 41.5) compared to Tumu (BI: 76.1 and CI: 19.5) and Bolgatanga (BI: 72.4 and CI: 20.6). Man-biting rates of 9.8 and 18.5 bites /man/hour were estimated for Damongo and Jirapa respectively whilst Bolgatanga recorded 10 B/M/H. Generally, man-vector contact rates in all the study sites were higher during the dry season than the wet season. Larval indices showed seasonal variations and the dry season was identified as the high-risk period for transmission of viral haemorrhagic fevers and possible disease outbreaks. No flavivirus was detected in the 2034 Aedes mosquitoes from the study sites by RT-PCR.

CONCLUSIONS

Aedes mosquito larval densities and adult biting rates, in all the study areas were sufficient to promote outbreaks of viral haemorrhagic fevers.

Delayed recovery of adrenocortical and testicular function after chemotherapy of human trypanosomiasis

The following indicators of pituitary, adreno-cortical and testicular function were measured in 58 male African trypanosomiasis patients from Western Kenya; plasma cortisol, luteinizing hormone (LH) and testosterone levels. The measurements were carried out by specific radioimmunoassay methods in early and late stage infected patients on admission to hospital and in both groups of patients after one month of chemotherapy. Packed cell volume (PCV) and hemoglobin levels were also measured in all the patients to determine the extent of their anaemia and success of recovery. High parasitaemia, anaemia and clinical symptoms of human trypanosomiasis were found in the infected patients and were eliminated with chemotherapy in the infected/treated patients. Increased levels of cortisol and decreased concentrations of testosterone without significant changes in LH levels were evident in the infected patients; this condition remained unchanged even after one month of chemotherapy. Evidence is thus provided of persistent hormonal perturbations which probably indicate residual endocrine organ damage.