A cocktail polymerase chain reaction assay to identify members of the Anopheles funestus (Diptera: Culicidae) group

Malaria vectors in Angola: distribution of species and molecular forms of the Anopheles gambiae complex, their pyrethroid insecticide knockdown resistance (kdr) status and Plasmodium falciparum sporozoite rates

Background

Malaria is by far the greatest cause of morbidity and mortality in Angola, being responsible for 50% of all outpatient attendance and around 22% of all hospital deaths, yet by 2003 only 2% of under-5s used insecticide-treated nets. Entomological studies are an essential foundation for rational malaria control using insecticide-treated nets and indoor residual spraying, but there have been no published studies of malaria vectors in Angola over the 27 years of the civil war, to its end in 2002. This paper describes studies arising from a WHO-sponsored visit in support of the National Malaria Control Programme.

Methods

During April 2001, mosquitoes were sampled by indoor pyrethrum spray collection from four sites in the semi-arid coastal provinces of Luanda and Benguela and two sites in Huambo province, in the humid tropical highlands. Collections took place towards the end of the rainy season and were used to determine the Anopheles species present, their sporozoite rates and the frequency of a kdr allele conferring resistance to pyrethroid insecticides.

Results

A PCR test for the Anopheles gambiae complex showed a preponderance of An. gambiae, with indoor resting densities ranging from 0.9 to 23.5 per house. Of 403 An. gambiae identified to molecular form, 93.5% were M-form and 6.5% S-form. M and S were sympatric at 4 sites but no M/S hybrids were detected. The highest proportion of S-form (20%) was in samples from Huambo, in the humid highlands. Anopheles funestus was found at one site near Luanda. The sporozoite rate of mosquitoes, determined by an ELISA test, was 1.9% for An. gambiae (n = 580) and 0.7% for An. funestus (n = 140). Of 218 An. gambiae (195 M-form and 23 S-form) genotyped for the West African kdr-resistance allele, all were homozygous susceptible.

Conclusion

An. gambiae M-form is the most important and widespread malaria vector in the areas studied but more extensive studies of malaria vectors are required to support the malaria control programme in Angola. These should include standard insecticide resistance biossays and molecular assays that can detect both metabolic resistance and target site insensitivity.

An unusual distribution of the kdr gene among populations of Anopheles gambiae on the island of Bioko, Equatorial Guinea

In West Africa, Anopheles gambiae exists in discrete subpopulations known as the M and S molecular forms. Although these forms occur in sympatry, pyrethroid knock-down resistance (kdr) is strongly associated with the S molecular form. On the island of Bioko, Equatorial Guinea we found high frequencies of the kdr mutation in M form individuals (55.8%) and a complete absence of kdr in the S form. We also report the absence of the kdr allele in M and S specimens from the harbour town of Tiko in Cameroon, representing the nearest continental population to Bioko. The kdr allele had previously been reported as absent in populations of An. gambiae on Bioko. Contrary to earlier reports, sequencing of intron-1 of this sodium channel gene revealed no fixed differences between M form resistant and susceptible individuals. The mutation may have recently arisen independently in the M form on Bioko due to recent and intensive pyrethroid application.

Identification of three members of the Anopheles funestus (Diptera: Culicidae) group and their role in malaria transmission in two ecological zones in Nigeria

The role of the Anopheles funestus group in malaria transmission was investigated in two ecological zones in Nigeria. Sampling was carried out at four sites each around Ibadan (forest) and Ilorin (savanna). Human landing catches were supplemented with indoor and outdoor resting collections. PCR was used to identify 1848 A. funestus group mosquitoes to species level (749 in the savanna, 1099 in the forest) and three species were identified. In the forest, A. funestus s.s. predominated (55.4%), followed by A. rivulorum (27.6%) and A. leesoni (17.0%). Anopheles funestus was found mostly indoors. Anopheles rivulorum and A. leesoni predominated in outdoor collections (P<0.001). Only Anopheles funestus s.s. was found in the savanna. ELISA analysis of 803 blood meal-positive specimens showed that over half of the blood meals were taken from humans in both ecotypes. The human blood index in A. funestus from the two study areas was similar. Anopheles funestus s.s. was the only species found positive for Plasmodium falciparum using ELISA, with overall infection rates of 2.3% and 1.0% in the forest and savanna respectively. The presence of three A. funestus species in Nigeria emphasizes the desirability of correct species identification within a malaria vector control programme.

Molecular differentiation between chromosomally defined incipient species of Anopheles funestus

Anopheles funestus Giles is one of the most important vectors of malaria in sub-Saharan Africa. The population structure of this mosquito in Burkina Faso, West Africa based on chromosomal inversion data led to the description of two chromosomal forms, Kiribina and Folonzo. Because both forms co-occur in the same locales yet differ significantly, both in the frequency of inverted arrangements on chromosome arms 3R and 2R and in vectorial capacity, they were hypothesized to be emerging species with at least partial barriers to gene flow. This hypothesis would be strengthened by molecular evidence of differentiation between Kiribina and Folonzo at loci outside chromosomal inversions. We surveyed molecular variation in sympatric populations of the two forms using sequences from the mitochondrial ND5 gene and genotypes at sixteen microsatellite loci distributed across the genome. Both classes of marker revealed slight but significant differentiation between the two forms (mtDNA F(ST) = 0.023, P < 0.001; microsatellite F(ST) = 0.004, P < 0.001; R(st) = 0.009, P = 0.002). Locus-by-locus analysis of the microsatellite data showed that significant differentiation was not genome-wide, but could be attributed to five loci on chromosome 3R (F(ST) = 0.010, P < 0.001; R(st) = 0.016, P = 0.002). Importantly, three of these loci are outside of, and in linkage equilibrium with, chromosomal inversions, suggesting that differentiation between chromosomal forms extends beyond the inversions themselves. The slight overall degree of differentiation indicated by both marker classes is likely an underestimate because of recent population expansion inferred for both Folonzo and Kiribina. The molecular evidence from this study is consistent with the hypothesis of incipient speciation between Kiribina and Folonzo.

Integration of Anopheles beklemishevi (Diptera: Culicidae) in a PCR assay diagnostic for palaearctic Anopheles maculipennis sibling species

A few years ago a PCR-based assay for a quick and reliable identification of six palaearctic sibling species of the Anopheles maculipennis complex was presented making use of differences in the nucleotide sequence of the ITS2 ribosomal mosquito DNA. An. beklemishevi, which is distributed in Scandinavia and Russia only, has now been integrated into this test after analysis of its ITS2 region which turned out to be much longer than those of the other sibling species. Three oligonucleotides putatively specific for An. beklemishevi were constructed and tested in combination with a universal genus-specific primer for the amplification of an An. beklemishevi-specific ITS2 DNA-fragment. Two of the three oligos generated accurate and specific PCR products, even when used in a multiplex PCR together with the specific primers for the other six sibling species. Cross-hybridization of the primers to heterologous culicid DNA was never observed. The amplicons that identify An. beklemishevi consist of 554 and 735 bp, respectively, and are easily distinguished from those specific for the other sibling species after gel electrophoresis.

Gene flow between chromosomal forms of the malaria vector Anopheles funestus in Cameroon, Central Africa, and its relevance in malaria fighting

Knowledge of population structure in a major vector species is fundamental to an understanding of malaria epidemiology and becomes crucial in the context of genetic control strategies that are being developed. Despite its epidemiological importance, the major African malaria vector Anopheles funestus has received far less attention than members of the Anopheles gambiae complex. Previous chromosomal data have shown a high degree of structuring within populations from West Africa and have led to the characterization of two chromosomal forms, "Kiribina" and "Folonzo." In Central Africa, few data were available. We thus undertook assessment of genetic structure of An. funestus populations from Cameroon using chromosomal inversions and microsatellite markers. Microsatellite markers revealed no particular departure from panmixia within each local population and a genetic structure consistent with isolation by distance. However, cytogenetic studies demonstrated high levels of chromosomal heterogeneity, both within and between populations. Distribution of chromosomal inversions was not random and a cline of frequency was observed, according to ecotypic conditions. Strong deficiency of heterokaryotypes was found in certain localities in the transition area, indicating a subdivision of An. funestus in chromosomal forms. An. funestus microsatellite genetic markers located within the breakpoints of inversions are not differentiated in populations, whereas in An. gambiae inversions can affect gene flow at marker loci. These results are relevant to strategies for control of malaria by introduction of transgenes into populations of vectors.

Vecteurs de paludisme : du terrain à la génétique moléculaire Recherches en Afrique

Only about 60 Anopheline species transmit malaria among more than 3,000 mosquito species recorded in the world. In Africa, the major vectors are Anopheles gambiae,An. arabiensis, An. funestus, An. nili and An. moucheti. They all belong to species complexes or groups of closely related species that are very difficult to set apart on morphological grounds, but which may have highly variable behaviours and vectorial capacities. Understanding this complexity is of major importance in vector control programs or for implementing any public health intervention program such as drugs or vaccine trials. Among the seven species of the complex,Anopheles gambiaes.s. shows a huge chromosomal polymorphism related to adaptation to specific natural or anthropic environments, from equatorial forested Africa to dry sahelian areas. Recent studies conducted in West and Central Africa suggest an incipient speciation into 2 molecular forms provisionally called M and S. A similar evolutionary phenomenon is observed in An. funestus, in which sympatric populations carrying specific chromosomal paracentric inversions showed restricted gene flow. Distribution of species from An. nili group and An. moucheti complex is restricted to more humid regions of Africa. However in some areas these species play the major role in malaria transmission. Comprehensive knowledge of transmission cycles and of behavioural and underlying genetic heterogeneities that exist within and among natural vector populations will thus benefit the whole area of malaria control and epidemiology. Molecular and genetic studies, as well as in depth monitoring of vector biology, have been recently facilitated by advances in functional and comparative genomics, including recent publication of the nearly complete genome sequence of An. gambiae. Challenge for the next years is to answer to the very simple question: why is an insect a vector?

Plasmodium species mixed infections in two areas of Manhiça district, Mozambique

We compared the distribution patterns of individual Plasmodium species and mixed-species infections in two geographically close endemic areas, but showing environmental differences. Comparisons concerned circulating Plasmodium infections in both human and mosquito vector populations in the dry and wet seasons, at a micro-epidemiological level (households). Both areas revealed a very high overall prevalence of infection, all year-round and in all age groups. Plasmodium falciparum was the predominant species, being found in the vast majority of infected individuals regardless of the presence of other species. Plasmodium malariae and Plasmodium ovale occurred almost exclusively in mixed infections. Seasonal variation in P. malariae prevalence was observed in one area but not in the other. A decrease in P. malariae prevalence concurred with a marked increase of P. falciparum prevalence. However this was strongly dependent on age and when analysing infections at the individual level, a different pattern between co-infecting species was unveiled. Regarding transmission patterns, in both areas, P. falciparum gametocytes predominated in single infections regardless of age and P. malariae gametocyte carriage increased when its overall prevalence decreased.

Systematics and biogeographical implications of the phylogenetic relationships between members of the funestus and minimus groups of Anopheles (Diptera: Culicidae)

The Afrotropical Funestus and the Oriental-African Minimus Groups of the Myzomyia Series of Anopheles subgenus Cellia are considered distinct only because of their geographical separation. For the first time, a phylogenetic study was done on six Oriental and four Afrotropical species based on the comparison of ribosomal (ITS2, D3) and mitochondrial (COI) nucleotide sequences. Both maximum parsimony (MP) and maximum likelihood (ML) analyses revealed that the groups form a monophyletic assemblage containing four clades. The inclusion of Afrotropical An. leesoni with the Oriental species was confirmed, whereas An. rivulorum, also an Afrotropical species, was placed in a basal position relative to the African and Oriental species. The biogeography of the Afrotropical and Oriental species was examined in relation to the phylogeny and estimates of divergence time. Divergence events correspond to periods of major tectonic movement as well as periods of great aridity or humidity.

Spatial distribution patterns of malaria vectors and sample size determination in spatially heterogeneous environments: a case study in the west Kenyan highland

The current study examined temporal and spatial distribution patterns of anopheline malaria vectors in a highland site and determined the number of houses to be sampled to achieve the targeted precision level. Adult mosquito sampling was conducted seasonally in May and August 2002 in a 3 by 3-km2 area, and in November 2002 and February 2003 in an expanded 4 by 4-km2 area in Kakamega District, western Kenya. Anopheles gambiae Giles was the predominant malaria vector species, constituting 84.6% of the specimens, whereas Anopheles funestus Giles constituted 15.4% of the vector populations. An. gambiae abundance increased by six- to eight-fold in the long rainy season over the dry seasons, but An. funestus abundance peaked 3 mo after the long rainy season. For both species, the coefficient of variation was larger than 1, suggesting that the distribution of mosquito adults was aggregated. Mosquito clustering occurred in houses <400 m from a valley bottom. The negative binomial distribution was accepted in one sample period (August 2002) for An. gambiae and in two sampling periods (May and August 2002) for An. funestus. Taylor's power law analyses indicated that An. gambiae distribution was more aggregated in the wet seasons than in the dry seasons, whereas the degree of aggregation of An. funestus was similar in all four seasons. The minimum number of houses required to estimate anopheline female abundance within the commonly acceptable precision level (0.2) should be 17 houses per km2 for An. gambiae and 42 houses per km2 for An. funestus. The potential factors causing aggregated anopheline mosquito distribution are discussed.

Unravelling complexities in human malaria transmission dynamics in Africa through a comprehensive knowledge of vector populations

Malaria transmission dynamics is highly variable throughout Africa: inoculation rates vary from almost null to more than a 1000 infective bites per year, transmission can occur throughout the year or only during a couple of months, and heterogeneities are also observed between years within the same locale. Depending on the area, as much as five different anophelines species can transmit parasites to the human population. Major vectors are Anopheles gambiae, Anopheles arabiensis, Anopheles funestus, Anopheles nili and Anopheles moucheti. They all belong to species complexes or groups of closely related species that are very difficult to set apart on morphological grounds. Recent research on the bionomics, morphology and genetics of these mosquito species and populations produced innovative results. New species were described and straightforward molecular identification tools were implemented. We review here these recent findings and discuss research opportunities in light of recent advances in molecular entomology and genomics.

High malaria transmission intensity due to Anopheles funestus (Diptera: Culicidae) in a village of savannah-forest transition area in Cameroon

An entomological survey was conducted on vectors of malaria in a village of the forest-savannah transition area in Cameroon from February 1999 to October 2000. A total of 2,050 anopheline mosquitoes belonging to eight species were caught 1) after landing on human volunteers, 2) by using pyrethrum spray collections in human dwellings, and 3) in resting sites outdoors. Anopheles funestus Giles was the most abundant species (accounting for 91% of anophelines caught) followed by Anopheles gambiae Giles (7%). Applying polymerase chain reaction led to the identification of all specimens of the An. funestus group as An. funestus sensu stricto and mosquitoes from the An. gambiae complex were mostly An. gambiae sensu stricto of the S molecular form. Malaria transmission was perennial with an entomological inoculation rate estimated at 172 infective bites per person during the period of study. An. funestus was responsible for 88% of the total malaria transmission, with a Plasmodium falciparum circumsporozoite rate of 6.8% and an anthropophilic rate of 99.3%. These results confirm that in high agricultural activity areas, An. funestus can be, by far, the major malaria vector.

Advances in the study of Anopheles funestus, a major vector of malaria in Africa

The recent literature on cytogenetic and molecular studies of Anopheles funestus, a major vector of malaria in Africa, is reviewed. Molecular data from West and Central Africa suggest a new species in the group closely allied to Anopheles rivulorum. Cytogenetic and molecular studies of populations from West, Central, East and southern Africa indicate considerable genetic structuring within An. funestus itself, which may well restrict the spread of pyrethroid resistance that has been demonstrated in southern Africa.

Population structure of the malaria vector Anopheles funestus in Senegal based on microsatellite and cytogenetic data

The study of chromosomal inversions distribution within natural Anopheles funestus populations from West Africa revealed high levels of genetic structuring. In Burkina Faso, this was interpreted as evidence for incipient speciation, and two chromosomal forms were described, namely 'Folonzo' and 'Kiribina'. Assignation of field collected specimens to one chromosomal form depends upon application of an algorithm based on chromosomal inversions. We assessed relevance and applicability of this algorithm on An. funestus populations from Senegal, where both forms occur. Furthermore, we estimated the level of genetic differentiation between populations using microsatellite loci spread over the whole genome. Significant genetic differentiation was revealed between geographical populations of An. funestus, and the pattern observed suggested isolation by distance. Chromosomal heterogeneity was not detected by microsatellite markers. Thus, although incipient speciation could not be ruled out by our data, our results suggest that differential environmental selection pressure acting on inversions should be considered a major factor in shaping their distribution in wild An. funestus populations.

Microsatellite DNA polymorphism and heterozygosity in the malaria vector mosquito Anopheles funestus (Diptera: Culicidae) in east and southern Africa

There has been an increase in malaria cases in southern African countries in recent years due to the presence of populations of Anopheles funestus that are resistant to the pyrethroid class of insecticides. Since A. funestus is one of the major African malaria vectors, knowledge of its genetic structure will benefit control strategies, such as the management of insecticide resistance, by allowing predictions to be made of possible spread of the resistance. This study uses microsatellite DNA markers to analyze samples from five countries in east (Kenya and Uganda), central (Malawi) and southern (South Africa and Mozambique) Africa. There were deviations from Hardy-Weinberg expectations for some loci in all population samples but this was probably due to the presence of null alleles. High levels of genetic diversity were observed (mean alleles per locus = 6.5-10; unbiased H=0.23-0.89). Low differentiation was observed between Kenya and Uganda (average F(ST)=0.002, R(ST)=0.0001) and between Mozambique and South Africa (F(ST)=0.0004, R(ST)=0.02), contrary to high differentiation among the central and southern Africa samples (average F(ST)=0.023, R(ST)=0.027). High differentiation was measured across the region (mean F(ST)=0.04, R(ST)=0.08), east versus Malawi (F(ST)=0.067, R(ST)=0.089) or southern Africa populations (F(ST)=0.068, R(ST)=0.15). A test of isolation by distance along the east-central-south transect gave evidence (R(2)=0.50, P<0.001) that geographic distance limits gene flow in A. funestus.

Evaluation of a species-specific PCR assay for the Anopheles funestus group from eleven African countries and Madagascar

A newly published cocktail polymerase chain reaction (PCR) assay can identify five members of the Anopheles funestus group: An. funestus, An. vaneedeni, An. parensis, An. leesoni and An. rivulorum. The assay was evaluated on specimens from 11 African countries: Angola, Cote d'Ivoire, Ethiopia, Kenya, Malawi, Mozambique, Namibia, South Africa, Tanzania, Uganda and Zambia; and the island of Madagascar. The polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) and the internal transcribed spacer PCR (ITS2-PCR) assays were used as a priori identification methods on 900 specimens. Of these, 96.4% were correctly identified using the new cocktail PCR method. The remaining 3.5% (32) from Malawi failed to amplify. The failure to identify these samples was not significantly different from the samples from the other countries (Chi-square; P > 0.05). The results suggest that the new species-specific PCR assay is an efficient and effective means of identifying 5 members of the An. funestus group in a single reaction. It is also less time-consuming than the molecular methods previously used on the group.

A survey of the Anopheles funestus (Diptera: Culicidae) group of mosquitoes from 10 sites in Kenya with special emphasis on population genetic structure based on chromosomal inversion karyotypes

We sampled Anopheles funestus Giles mosquitoes from 10 sites in Kenya to determine (1) the different members of this group present at these sites and (2) the population genetic structure of these species based on chromosomal inversion karyotypes with particular reference to the role of the Eastern arm of the Great Rift Valley and geographical distance as barriers to gene flow. Four members of this species group, namely An. funestus s.s., An. parensis, An. leesoni, and An. rivulorum, were found. An. funestus was found almost exclusively inside human dwellings while An. rivulorum was found almost exclusively outdoors. An. parensis was found both indoors and outdoors in comparable proportions. Earlier attempts to collect this group of mosquitoes from two of the sites yielded no mosquitoes, suggesting that numbers of mosquitoes change during the year, sometime reaching zero or very near zero. Significant levels of differentiation were observed among some An. funestus s.s. populations studied. Results suggest that the Rift Valley acts as a barrier to gene flow for An. funestus, but that levels of differentiation are not associated with the geographical distance between populations. The results are discussed in the light of the fact that inversions may have some adaptive significance to differences in environmental conditions.

Molecular systematics of Anopheles: from subgenera to subpopulations

The century-old discovery of the role of Anopheles in human malaria transmission precipitated intense study of this genus at the alpha taxonomy level, but until recently little attention was focused on the systematics of this group. The application of molecular approaches to systematic problems ranging from subgeneric relationships to relationships at and below the species level is helping to address questions such as anopheline phylogenetics and biogeography, the nature of species boundaries, and the forces that have structured genetic variation within species. Current knowledge in these areas is reviewed, with an emphasis on the Anopheles gambiae model. The recent publication of the genome of this anopheline mosquito will have a profound impact on inquiries at all taxonomic levels, supplying better tools for estimating phylogeny and population structure in the short term, and ultimately allowing the identification of genes and/or regulatory networks underlying ecological differentiation, speciation, and vectorial capacity.