Malaria risk and receptivity: Continuing development of insecticide resistance in the major malaria vector Anopheles arabiensis in northern KwaZulu-Natal, South Africa

Malaria incidence in South Africa is highest in the three endemic provinces: KwaZulu-Natal, Mpumalanga and Limpopo. The contribution to malaria transmission by several mosquito species, variation in their resting behaviours and low levels of insecticide resistance makes it necessary to periodically monitor Anopheles species assemblages and resistance phenotypes in vector populations. The aim of this study was therefore to assess Anopheles species assemblage in northern KwaZulu-Natal and to collect insecticide susceptibility data for An. arabiensis, the primary vector of malaria in that province. Anopheles specimens were collected from Mamfene, Jozini, northern KwaZulu-Natal from November 2019 to April 2021. Progeny of wild-collected An. arabiensis females were used for standard insecticide susceptibility tests and synergist bioassays. Anopheles arabiensis contributed 85.6% (n=11 062) of the total catches. Samples for subsequent insecticide susceptibility bioassays were selected from 212 An. arabiensis families. These showed low-level resistance to DDT, permethrin, deltamethrin, and bendiocarb, as well as full susceptibility to pirimiphos-methyl. Synergist bioassays using piperonyl butoxide and triphenyl phosphate suggest oxygenase-based pyrethroid and esterase-mediated sequestration of bendiocarb. These low levels of resistance are unlikely to be operationally significant at present. It is concluded that northern KwaZulu-Natal Province remains receptive to malaria transmission despite ongoing control and elimination interventions. This is due to the perennial presence of the major vector An. arabiensis and other secondary vector species. The continued detection of low-frequency insecticide resistance phenotypes in An. arabiensis is cause for concern and requires periodic monitoring for changes in resistance frequency and intensity.Significance:• Insecticide resistance in the major malaria vector Anopheles arabiensis in northern KwaZulu-Natal Province is cause for concern in terms of resistance management and ongoing vector control leading toward malaria elimination.• Despite ongoing control interventions, northern KwaZulu-Natal remains receptive to malaria owing to the perennial presence of several Anopheles vector species

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

Mating competitiveness of sterile genetic sexing strain males (GAMA) under laboratory and semi-field conditions: Steps towards the use of the Sterile Insect Technique to control the major malaria vector Anopheles arabiensis in South Africa

BACKGROUND : Anopheles arabiensis Patton is primarily responsible for malaria transmission in South Africa after successful suppression of other major vector species using indoor spraying of residual insecticides. Control of An. arabiensis using current insecticide based approaches is proving difficult owing to the development of insecticide resistance, and variable feeding and resting behaviours. The use of the sterile insect technique as an area-wide integrated pest management system to supplement the control of An. arabiensis was proposed for South Africa and is currently under investigation. The success of this technique is dependent on the ability of laboratory-reared sterile males to compete with wild males for mates. As part of the research and development of the SIT technique for use against An. arabiensis in South Africa, radio-sensitivity and mating competitiveness of a local An. arabiensis sexing strain were assessed. METHODS : The optimal irradiation dose inducing male sterility without compromising mating vigour was tested using Cobalt 60 irradiation doses ranging from 70-100 Gy. Relative mating competitiveness of sterile laboratory-reared males (GAMA strain) compared to fertile wild-type males (AMAL strain) for virgin wild-type females (AMAL) was investigated under laboratory and semi-field conditions using large outdoor cages. Three different sterile male to fertile male to wild-type female ratios were evaluated [1:1:1, 5:1:1 and 10:1:1 (sterile males: fertile, wild-type males: fertile, wild-type females)]. RESULTS : Irradiation at the doses tested did not affect adult emergence but had a moderate effect on adult survivorship and mating vigour. A dose of 75 Gy was selected for the competitiveness assays. Mating competitiveness experiments showed that irradiated GAMA male mosquitoes are a third as competitive as their fertile AMAL counterparts under semi-field conditions. However, they were not as competitive under laboratory conditions. An inundative ratio of 10:1 induced the highest sterility in the representative wild-type population, with potential to effectively suppress reproduction. CONCLUSION : Laboratory-reared and sterilised GAMA male An. arabiensis at a release ratio of 3:1 (3 sterile males to 1 wild, fertile male) can successfully compete for insemination of wild-type females. These results will be used to inform subsequent small-scale pilot field releases in South Africa.The Nuclear Technologies in Medicine and the Bioscience Initiatives (NTeMBI), a national platform developed and managed by the South African Nuclear Energy Corporation and supported by the Department of Science and Technology. Funding was also provided in part from the National Research Foundation, the International Atomic Energy Agency (Contracts 17904, SAF5013 and SAF16780/ under the G34002) and a Global Diseases Detection/CDC grant (U19GH000622-01 MAL01).http://www.parasitesandvectors.comam2016Paraclinical Science

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Optimization of Mass-Rearing Methods for Anopheles arabiensis Larval Stages: Effects of Rearing Water Temperature and Larval Density on Mosquito Life-History Traits.

Insect mass-rearing is an essential requirement for the sterile insect technique. Production at a large scale requires the development of standardized rearing procedures to produce good quality males able to compete with wild males to mate with wild females. Three sets of experiments (using trays placed on the table, the whole tray-rack system, and climate-controlled chambers) have been conducted aiming to determine the optimal water temperature and number of eggs to aliquot into each larval rearing tray to achieve the highest production of pupae. No difference was found in time to pupation, sex ratio, or male body size as a result of altering larval density. However, higher larval densities resulted in decreased emergence rate and female body size. A constant water temperature of 22°C delayed hatching and did not allow Anopheles arabiensis to complete larval development. Hatching eggs in water at 22°C and then increasing water temperature to 27°C resulted in decreased pupae production compared to eggs hatched and larvae maintained at a water temperature of 27°C throughout. Water temperature and larval density affected the production parameters of An. arabiensis mosquitoes, which has implications for mass release programs. We conclude that 4,000 eggs per 4 liter and a water temperature of 27°C were the optimal conditions for mass-rearing this mosquito species which yielded 105,000 pupae/larval rearing unit. These results are valuable information in the development of standard operation procedures for the efficient large-scale rearing of An. arabiensis mosquitoes

Malaria risk and receptivity: Continuing development of insecticide resistance in the major malaria vector Anopheles arabiensis in northern KwaZulu-Natal, South Africa

Malaria incidence in South Africa is highest in the three endemic provinces: KwaZulu-Natal, Mpumalanga and Limpopo. The contribution to malaria transmission by several mosquito species, variation in their resting behaviours and low levels of insecticide resistance makes it necessary to periodically monitor Anopheles species assemblages and resistance phenotypes in vector populations. The aim of this study was therefore to assess Anopheles species assemblage in northern KwaZulu-Natal and to collect insecticide susceptibility data for An. arabiensis, the primary vector of malaria in that province. Anopheles specimens were collected from Mamfene, Jozini, northern KwaZulu-Natal from November 2019 to April 2021. Progeny of wild-collected An. arabiensis females were used for standard insecticide susceptibility tests and synergist bioassays. Anopheles arabiensis contributed 85.6% (n=11 062) of the total catches. Samples for subsequent insecticide susceptibility bioassays were selected from 212 An. arabiensis families. These showed low-level resistance to DDT, permethrin, deltamethrin, and bendiocarb, as well as full susceptibility to pirimiphos-methyl. Synergist bioassays using piperonyl butoxide and triphenyl phosphate suggest oxygenase-based pyrethroid and esterase-mediated sequestration of bendiocarb. These low levels of resistance are unlikely to be operationally significant at present. It is concluded that northern KwaZulu-Natal Province remains receptive to malaria transmission despite ongoing control and elimination interventions. This is due to the perennial presence of the major vector An. arabiensis and other secondary vector species. The continued detection of low-frequency insecticide resistance phenotypes in An. arabiensis is cause for concern and requires periodic monitoring for changes in resistance frequency and intensity. Significance: Insecticide resistance in the major malaria vector Anophelesarabiensis in northern KwaZulu-Natal Province is cause for concern in terms of resistance management and ongoing vector control leading toward malaria elimination. Despite ongoing control interventions, northern KwaZulu-Natal remains receptive to malaria owing to the perennial presence of several Anophelesvector species