Genetic differentiation in the yellow fever virus vector, Aedes simpsoni complex, in Africa: sequence variation in the ribosomal DNA internal transcribed spacers of anthropophilic and non-anthropophilic populations

Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification

Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens-the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.

Analysis of genetic diversity and phylogeny of Philosamia ricini (Lepidoptera: Saturniidae) by using RAPD and internal transcribed spacer DNA1

The Indian Eri silkworm, Philosamia ricini Hutt, a commercial silk producing insect, is believed to have originated in the Brahmaputra valley of Assam. In this study, the genetic diversity and phylogenetic relationships of six morphs of Eri silkworm viz. white plain, white zebra, white spotted, blue plain, blue zebra and blue spotted collected from different geographical locations of North-East India were investigated by using random amplified polymorphic DNA (RAPD) and the first internal transcribed spacer region (ITS1). This study revealed a low genetic diversity among the morphs of Eri silkworm. Twenty-eight random primers generated 199 bands. Out of these, 112 were polymorphic (56.28%) with an average of 7.1 bands per primer. The genetic similarity matrix ranged from 0.56 to 0.99. The morphs collected from same geographical area shared the same cluster in the dendrogram. The genetic diversity in case of ITS1 sequences (2.19%) was found to be less as compared to RAPD. The ITS1 sequences of the morphs collected from same geographical area were found to be identical. The information generated in this study will help in conservation and effective breeding program to improve its productivity.

A community-level investigation following a yellow fever virus outbreak in South Omo Zone, South-West Ethiopia

Background

Despite the availability of a highly effective vaccine, yellow fever virus (YFV) remains an important public health problem across Africa and South America due to its high case-fatality rate. This study investigated the historical epidemiology and contemporary entomological and social determinants of a YFV outbreak in South Omo Zone (SOZ), Ethiopia.

Methods

A YFV outbreak occurred in SOZ, Ethiopia in 2012–2014. Historical epidemiological data were retrieved from the SOZ Health Department and analyzed. Entomological sampling was undertaken in 2017, including mosquito species identification and molecular screening for arboviruses to understand mosquito habitat distribution, and finally current knowledge, attitudes and preventative practices within the affected communities were assessed.

Results

From October 2012 to March 2014, 165 suspected cases and 62 deaths were reported, principally in rural areas of South Ari region (83.6%). The majority of patients were 15–44 years old (75.8%) and most case deaths were males (76%). Between June and August 2017, 688 containers were sampled across 180 households to identify key breeding sites for Aedes mosquitoes. Ensete ventricosum (“false banana”) and clay pots outside the home were the most productive natural and artificial breeding sites, respectively. Entomological risk indices classified most sites as “high risk” for future outbreaks under current World Health Organization criteria. Adult mosquitoes in houses were identified as members of the Aedes simpsoni complex but no YFV or other arboviruses were detected by PCR. The majority of community members had heard of YFV, however few activities were undertaken to actively reduce mosquito breeding sites.

Discussion

Study results highlight the potential role vector control could play in mitigating local disease transmission and emphasize the urgent need to strengthen disease surveillance systems and in-country laboratory capacity to facilitate more rapid responses to future YFV outbreaks.

Vector competence of Aedes bromeliae and Aedes vitattus mosquito populations from Kenya for chikungunya virus

Background

Kenya has experienced outbreaks of chikungunya in the past years with the most recent outbreak occurring in Mandera in the northern region in May 2016 and in Mombasa in the coastal region from November 2017 to February 2018. Despite the outbreaks in Kenya, studies on vector competence have only been conducted on Aedes aegypti. However, the role played by other mosquito species in transmission and maintenance of the virus in endemic areas remains unclear. This study sought to determine the possible role of rural Aedes bromeliae and Aedes vittatus in the transmission of chikungunya virus, focusing on Kilifi and West Pokot regions of Kenya.

Methods

Four day old female mosquitoes were orally fed on chikungunya virus-infected blood at a dilution of 1:1 of the viral isolate and blood (10^6.4 plaque-forming units [PFU]/ml) using artificial membrane feeder (Hemotek system) for 45 minutes. The engorged mosquitoes were picked and incubated at 29–30°C ambient temperature and 70–80% humidity in the insectary. At days 5, 7 and 10 post-infection, the mosquitoes were carefully dissected to separate the legs and wings from the body and their proboscis individually inserted in the capillary tube containing minimum essential media (MEM) to collect salivary expectorate. The resultant homogenates and the salivary expectorates were tested by plaque assay to determine virus infection, dissemination and transmission potential of the mosquitoes.

Results

A total of 515 female mosquitoes (311 Ae. bromeliae and 204 Ae. vittatus) were exposed to the East/Central/South Africa (ECSA) lineage of chikungunya virus. Aedes vittatus showed high susceptibility to the virus ranging between 75–90% and moderate dissemination and transmission rates ranging from 35–50%. Aedes bromeliae had moderate susceptibility ranging between 26–40% with moderate dissemination and transmission rates ranging from 27–55%.

Conclusion

This study demonstrates that both Ae. vittatus and Ae. bromeliae populations from West Pokot and Kilifi counties in Kenya are competent vectors of chikungunya virus. Based on these results, the two areas are at risk of virus transmission in the event of an outbreak. This study underscores the need to institute vector competence studies for populations of potential vector species as a means of evaluating risk of transmission of the emerging and re-emerging arboviruses in diverse regions of Kenya.

Kenya experienced its first chikungunya outbreak in 2004/2005 along the coastal area, followed by sporadic outbreaks in Mandera in 2016, and subsequently in Mombasa city in late 2017 and early 2018. Despite the rising risk of transmission of the virus in the country based on evidence of outbreaks in Kenya, vector competence studies have only been limited to Ae. aegypti, while the role played by other Aedes species largely remain unknown. This study demonstrated the ability of Ae. bromeliae and Ae. vittatus to transmit chikungunya virus under controlled laboratory conditions. Vector competence remains the most important approach in disease risk assessment that provides knowledge to the public health sector in developing vector control guideline.

Evaluation of collection methods for Culex quinquefasciatus, Aedes aegypti, and Aedes simpsoni in northeastern Tanzania

In East Africa, significant morbidity and mortality are caused by infections spread by Culex quinquefasciatus and Aedes aegypti. Sticky traps have been shown to be effective tools for sampling populations of Aedes mosquitoes and have been found to catch Cx. quinquefasciatus. Thus, they could potentially be used to sample populations of this species. This study compared Sticky ovitraps (SO) and MosquiTraps (MQT) with the CDC Gravid trap (CDC-GT) for collection of Culex and Aedes mosquito populations in Tanzania. A follow-up experiment was carried out using traps set for a 24-h period to accommodate the oviposition habits of Aedes aegypti and Ae. simpsoni s.l. mosquitoes. The results showed that the CDC-GT caught significantly more Cx. quinquefasciatus and Ae. aegypti than the SO or MQT, but there was no significant difference in the number of mosquitoes caught between the two sticky traps or of Ae. simpsoni s.l. caught among the three trap types. The results suggest that CDC-GTs are the most appropriate in sampling of Cx. quinquefasciatus. Although CDC-GTs collected more Ae. aegypti than the sticky traps, the simplicity and cost benefit of sticky traps facilitates large scale studies. All three trap types should be considered for monitoring Aedes mosquitoes.

Molecular Differentiation of the African Yellow Fever Vector Aedes bromeliae (Diptera: Culicidae) from Its Sympatric Non-vector Sister Species, Aedes lilii

INTRODUCTION

Yellow fever continues to be a problem in sub-Saharan Africa with repeated epidemics occurring. The mosquito Aedes bromeliae is a major vector of yellow fever, but it cannot be readily differentiated from its non-vector zoophilic sister species Ae. lilii using morphological characters. Genetic differences have been reported between anthropophilic Ae. bromeliae and zoophilic Ae. lilii and between forest and domestic populations. However, due to the application of different molecular markers and non-overlapping populations employed in previous studies, interpretation of species delimitation is unclear.

METHODOLOGY/PRINCIPLE FINDINGS

DNA sequences were generated from specimens of Ae. simpsoni s.l. from the Republic of Benin, Tanzania and Uganda for two nuclear genes apolipophorin 2 (apoLp2) and cytochrome p450 (CYPJ92), the ribosomal internal transcribed spacer region (ITS) and the mitochondrial cytochrome c oxidase (COI) barcoding region. Nuclear genes apoLp2 and CYPJ92 were unable to differentiate between species Ae. bromeliae and Ae. lilii due to ancestral lineage sorting, while ITS sequence data provided clear topological separation on a phylogeny. The standard COI barcoding region was shown to be subject to species introgression and unable to clearly distinguish the two taxa. Here we present a reliable direct PCR-based method for differentiation of the vector species Ae. bromeliae from its isomorphic, sympatric and non-biomedically important sister taxon, Ae. lilii, based on the ITS region. Using molecular species verification, we describe novel immature habitats for Ae. lilii and report both sympatric and allopatric populations. Whereas only Ae. lilii is found in the Republic of Benin and only Ae. bromeliae in Tanzania, both species are sympatric in Uganda.

CONCLUSIONS/SIGNIFICANCE

Our accurate identification method will allow informed distribution and detailed ecological studies that will facilitate assessment of arboviral disease risk and development of future targeted vector control.

Microhabitat partitioning of Aedes simpsoni (Diptera: Culicidae)

Yellow fever virus is a reemerging infection responsible for widespread, sporadic outbreaks across Africa. Although Aedes aegypti (L.) is the most important vector globally, in East Africa, epidemics may be vectored by Aedes bromeliae (Theobald), a member of the Aedes simpsoni (Theobald) species complex. The Ae. simpsoni complex contains 10 subspecies, of which Ae. bromeliae alone has been incriminated as a vector of yellow fever virus. However, morphological markers cannot distinguish Ae. bromeliae from conspecifics, including the sympatric and non-anthropophilic Aedes lilii (Theobald). Here, we used three sequenced nuclear markers to examine the population structure of Ae. simpsoni complex mosquitoes collected from diverse habitats in Rabai, Kenya. Gene trees consistently show strong support for the existence of two clades in Rabai, with segregation by habitat. Domestic mosquitoes segregate separately from forest-collected mosquitoes, providing evidence of habitat partitioning on a small spatial scale (< 5 km). Although speculative, these likely represent what have been described as Ae. bromeliae and Ae. lilii, respectively. The observation of high levels of diversity within Rabai indicates that this species complex may exhibit significant genetic differentiation across East Africa. The genetic structure, ecology, and range of this important disease vector are surprisingly understudied and need to be further characterized.

Stegomyia mosquitoes in Mayotte, taxonomic study and description of Stegomyia pia n. sp

Four mosquito species, including a new species of the genus Stegomyia, are reported from Mayotte in the western Indian Ocean. The most abundant species were Stegomyia aegypti and St. albopicta. Only one species of the St. simpsoni group was observed, St. bromeliae. The fourth species is Stegomyia pia Le Goff & Robert n. sp. of which the larva, pupa, male and female are here described. The larval stages of St. pia n. sp. are morphologically similar to St. aegypti but differ in the number of branches of the seta 1-X; the adult is morphologically distinct for a number of characters, for instance the scutal ornamentation. Stegomyia pia n. sp. is uncommon but not rare, and largely distributed across Mayotte. Its larval habitats are natural and diverse including rock pools, tree holes, and cut and severed bamboos. The biology of adults remains unknown, especially female biting behaviour. Both morphological characters and nucleotide sequences of the ITS2 and COI genes indicate that this species is best placed in the genus Stegomyia. Dichotomous keys to the four species of Mayotte Stegomyia are presented for adults and fourth-instar larvae. The potential vector role of these mosquitoes is hypothesised. This paper underlines advances in knowledge of the biodiversity in the French overseas departments and territories.

Spatiotemporal distribution of diurnal yellow fever vectors (Diptera: Culicidae) at two sylvan interfaces in Kenya, East Africa

Yellow fever virus (YFV) remains a significant public health threat in sub-Saharan Africa in which 90% of the estimated 200,000 cases occur annually. In East Africa, human cases of YFV are characterized by unpredictable focal periodicity, lengthy inter-epidemic periods, and a precarious potential for large epidemics. YFV had remained undetected in this region for nearly 40 years until emerging in Kenya in 1992-93 and more recently in Sudan during 2003 and 2005. From an ecological perspective the emergence and epidemiological outcomes associated with YFV, and related vector-borne diseases, are critically dependent upon the underlying vector ecology at a local scale. The study here was aimed at defining the dynamics of important vector interactions at two important sites in Kenya with previous YFV or related arbovirus activity. The temporal abundance, spatial distribution, and human host seeking behavior of diurnal man-landing mosquito species along sylvan interfaces were investigated. A number of YFV vectors were identified including their abundances for the duration of the main rainy season. Spatially, results indicated that the greatest human-mosquito interactions occurred within the forest and decreased across more domesticated biotopes. A discussion of significant differences, ecological associations, and epidemiological implications is included.

Genetic structure of Anopheles gambiae populations on islands in northwestern Lake Victoria, Uganda

Background

Alternative means of malaria control are urgently needed. Evaluating the effectiveness of measures that involve genetic manipulation of vector populations will be facilitated by identifying small, genetically isolated vector populations. The study was designed to use variation in microsatellite markers to look at genetic structure across four Lake Victoria islands and two surrounding mainland populations and for evidence of any restriction to free gene flow.

Methods

Four Islands (from 20–50 km apart) and two surrounding mainland populations (96 km apart) were studied. Samples of indoor resting adult mosquitoes, collected over two consecutive years, were genotyped at microsatellite loci distributed broadly throughout the genome and analysed for genetic structure, effective migration (Nem) and effective population size (Ne).

Results

Ne estimates showed island populations to consist of smaller demes compared to the mainland ones. Most populations were significantly differentiated geographically, and from one year to the other. Average geographic pair-wise FST ranged from 0.014–0.105 and several pairs of populations had Ne m < 3. The loci showed broad heterogeneity at capturing or estimating population differences.

Conclusion

These island populations are significantly genetically differentiated. Differences reoccurred over the study period, between the two mainland populations and between each other. This appears to be the product of their separation by water, dynamics of small populations and local adaptation. With further characterisation these islands could become possible sites for applying measures evaluating effectiveness of control by genetic manipulation.

The epidemiology of yellow fever in Africa

Yellow fever (YF) is still a major public heath problem, particularly in Africa, despite the availability of a very efficacious vaccine. The World Health Organization estimates that there are 200,000 cases of YF annually, including 30,000 deaths, of which over 90% occur in Africa. In the past 15 years, the number of YF cases has increased tremendously, with most of the YF activity in West Africa. This increase in YF activity is in part due to a breakdown in YF vaccination and mosquito control programs. Five genotypes of YF virus have been found in Africa, and each genotype circulates in a distinct geographical region. West Africa genotype I, found in Nigeria and surrounding areas, is associated with frequent epidemics, whereas the three genotypes in East and Central Africa are in regions where YF outbreaks are rare. Other factors, including genetic and behavioral variation among vector species, are also thought to play a role in the epidemiology of YF in Africa.

Laboratory vector competence experiments with yellow fever virus and five South African mosquito species including Aedes aegypti

Three domestic and peridomestic mosquito species, selected because their prevalence, distribution and ecology favoured them as potential urban vectors of yellow fever (YF) in South Africa, were submitted to numerous tests for infectivity [measured as dose needed to infect 50% of the mosquitoes (MID50)], mainly with a Kenyan strain (BC7914) of the virus. Use of a Nigerian virus strain (TVP1617) did not significantly alter infectivity. After artificial infective blood meals with titres of 7.0-8.0 log10MID50/mL, head squash infection rates (HSIRs) determined by the indirect fluorescent antibody test were 0-4% (Eretmapodites quinquevittatus), 0-29% (Aedes simpsoni s. s.) and 0-21% (5 populations of Aedes aegypti). For some populations of Ae. aegypti tests were repeated with blood meals incorporating freshly prepared rather than frozen mouse brain but HSIRs did not increase. HSIRs did increase when a high infecting titre of 9.0 log10MID50/mL was used with the Richards Bay population (67-90%). It is concluded that these 3 mosquito species are potentially poor YF vectors but that Ae. simpsoni and Richards Bay Ae. aegypti are the most susceptible to the virus. However, the latter 2 species could support person-to-person transmission only if they were present at very high densities. This rarely occurs with Ae. simpsoni in South Africa but Ae. aegypti may occur at high densities although only in discrete foci. The feral Ae. furcifer and Ae. cordellieri had HSIRs of 29% and 3% respectively and Ae. furcifer 'transmitted' the virus in vitro at a transmission rate of 25%. This suggests that Ae. furcifer would be more important than Ae. cordellieri in transmission between monkeys in West Africa.

Investigation of the aedes (Stegomyia) flavopictus complex (Diptera: Culicidae) in Japan by sequence analysis of the internal transcribed spacers of ribosomal DNA

Aedes (Stegomyia) flavopictus Yamada is widely distributed in Japan and Korea. The species comprises three subspecies based on current morphological taxonomy: Aedes flavopictus in the Palearctic region of Japan, Ae. f downsi Bohart & Ingram from Amami and Okinawa Islands, and Ae. f miyarai Tanaka, Mizusawa & Ingram from Ishigaki and Iriomote Islands of the Ryukyu Archipelago. These subspecies designations are based on observations of a combination of several morphological characters, none of which, by itself is diagnostic for discriminating among the three subspecies. To further study the relationships in this group, we examined the nucleic acid sequence divergence in the internal transcribed spacer regions (ITSI and ITS2) of the ribosomal DNA gene array of Ae. flavopictus individuals collected at five sites from three geographic regions in Japan. Analysis of sequence data by distance and maximum parsimony methods produced phylogenetic trees that showed separation of the specimens into three major clades, corresponding to both subspecies and geographic region. These results were consistent with and support the current classification and geographic distribution of the three subspecies.

Genetic and physical mapping in mosquitoes: molecular approaches

The genetic background of individual mosquito species and populations within those species influences the transmission of mosquito-borne pathogens to humans. Technical advances in contemporary genomics are contributing significantly to the detailed genetic analysis of this mosquito-pathogen interaction as well as all other aspects of mosquito biology, ecology, and evolution. A variety of DNA-based marker types are being used to develop genetic maps for a number of mosquito species. Complex phenotypic traits such as vector competence are being dissected into their discrete genetic components, with the intention of eventually using this information to develop new methods to prevent disease transmission. Both genetic- and physical-mapping techniques are being used to define and compare genome architecture among and within mosquito species. The integration of genetic- and physical-map information is providing a sound framework for map-based positional cloning of target genes of interest. This review focuses on advances in genome-based analysis and their specific applications to mosquitoes.