Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Phylogenetic taxonomy of the Zambian Anopheles coustani group using a mitogenomics approach

Background

Mosquito species belonging to the Anopheles coustani group have been implicated in driving residual malaria transmission in sub-Saharan Africa and are regarded as an established primary vector in Madagascar. The morphological identification of mosquitoes in this group is challenging due to cryptic features and their molecular confirmation is difficult due to a paucity of reference sequence data representing all members of the group. Conventional molecular barcoding with the cytochrome oxidase I (COI) gene and the internal transcribed spacer 2 (ITS2) region targets is limited in their discrimination and conclusive identification of members of species complexes. In contrast, complete mitochondrial genomes (mitogenomes) have demonstrated much improved power over barcodes to be useful in rectifying taxonomic discrepancies in Culicidae.

Methods

We utilized a genome skimming approach via shallow shotgun sequencing on individual mosquito specimens to generate sequence reads for mitogenome assembly. Bayesian inferred phylogenies and molecular dating estimations were perfomed on the concatenated protein coding genes using the Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST 2) platform. Divergence estimates were calibrated on published calucations for Anopheles-Aedes.

Results

This study generated 17 new complete mitogenomes which were comprable to reference An. coustani mitogenomes in the GenBank repository by having 13 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, with an average length of 15,400 bp and AT content of 78.3%. Bayesian inference using the concatenated protein coding genes from the generated and publicly available mitogenomes yielded six clades: one for each of the four taxa targeted in this study, the GenBank references, and a currently unknown species. Divergence times estimated that the An. coustani group separated from the An. gambiae complex approximately 110 million years ago (MYA), and members within the complex diverged at times points ranging from~34 MYA to as recent as ~7 MYA.

Conclusions

These findings demonstrate the value of mitochondrial genomes in differentiating cryptic taxa and help to confirm morphological identities of An. coustani s.s., An. paludis, An. zeimanni and An. tenebrosus. Divergence estimates with the An. coustani group are similar to those for well-studied anopheline vector groups. These analyses also highlight the likely prescence of other cryptic An. coustani group members circulating in Zambia.

A Comprehensive Review: Biology of Anopheles squamosus, an Understudied Malaria Vector in Africa

With ongoing global efforts to eliminate malaria, several countries have entered a pre-elimination stage, in which populations of the primary mosquito vector are reduced and the rates of malaria transmission are low. Efforts to eliminate malaria have changed the dynamics of disease transmission, causing a shift in anopheline community composition in some regions. One of the most abundant species of Anopheles found in pre-elimination areas, such as southern Africa, is Anopheles squamosus (Theobald, 1901; Diptera: Culicidae). Although An. squamosus has been documented across the African continent, limited information is available about its biology. Knowing what, when, and where the malaria vector bites humans can help develop effective malaria control strategies. The aim of this review is to compile the information available on An. squamosus's biology, ecology, distribution, behavior, and potential role in disease transmission. The review of current literature suggested that An. squamosus is abundant throughout the African continent. Studies indicate that this species occupies the same range and exhibits similar behaviors to primary malaria vectors in southern and eastern African countries, like Zambia. In conclusion, An. squamosus continues to be an understudied species that has circumvented disease control measures and further studies are needed to develop effective control strategies.

Evaluation of Anopheline Diversity and Abundance across Outdoor Collection Schemes Utilizing CDC Light Traps in Nchelenge District, Zambia

In the global fight against malaria, standard vector control methods such as indoor residual spraying (IRS) and insecticide-treated nets (ITNs) are intended to protect inside residential structures and sleeping spaces. However, these methods can still leave individuals vulnerable to residual transmission from vectors that they may be exposed to outdoors. Nchelenge District in northern Zambia experiences persistently high malaria transmission even with ITNs and IRS in place. However, very few studies have examined outdoor vector activity. To assess the diversity and abundance of outdoor foraging female anopheline mosquitoes, CDC light traps were used as proxy measures for mosquito host-seeking, set in three outdoor trapping schemes randomly assigned on different nights: (1) locations where people congregate at night outside of the house within the peri-domestic space, (2) animal pens or shelters, and (3) high-human-traffic areas, such as paths to latrines, where traps were baited with BG-Lure®. A total of 1087 total female anophelines were collected over a total of 74 trap nights. Anopheles funestus s.s. comprised the majority of the collection (86%), with An. gambiae s.s. (2%) and a highly diverse sampling of other anophelines (12%) making up the remainder. Plasmodium falciparum parasites were only detected in An. funestus (1%). No significant difference in species diversity or female anopheline abundance was detected between trapping schemes. Outdoor foraging anopheline mosquitoes, including a number of infectious An. funestus, may partially explain the difficulty of controlling malaria transmission in Nchelenge District, where vector control is only targeted indoors. BG-Lure® shows some promise as an alternative to human-baited landing catch collections in this resource-poor setting.

The first genome sequence of Anopheles squamous from Macha, Zambia

Despite efforts to minimize the impacts of malaria and reduce the number of primary vectors, malaria has yet to be eliminated in Zambia. Understudied vector species may perpetuate malaria transmission in pre-elimination settings. Anopheles squamosus is one of the most abundantly caught mosquito species in southern Zambia and has previously been found with Plasmodium falciparum sporozoites, a causal agent of human malaria. This species may be a critical vector of malaria transmission, however, there is a lack of genetic information available for An. squamosus. We report the first genome data and the first complete mitogenome (Mt) sequence of An. squamosus. The sequence was extracted from one individual mosquito from the Chidakwa area in Macha, Zambia. The raw reads were obtained using Illumina Novaseq 6000 and assembled through NOVOplasty alignment with related species. The length of the An. squamosus Mt was 15,351 bp, with 77.9 % AT content. The closest match to the whole mitochondrial genome in the phylogenetic tree is the African malaria mosquito, Anopheles gambiae. Its genome data is available through National Center for Biotechnology Information (NCBI) Sequencing Reads Archive (SRA) with accession number SRR22114392. The mitochondrial genome was deposited in NCBI GenBank with the accession number OP776919. The ITS2 containing contig sequence was deposited in GenBank with the accession number OQ241725. Mitogenome annotation and a phylogenetic tree with related Anopheles mosquito species are provided.

Expanded geographic distribution and host preference of Anopheles gibbinsi (Anopheles species 6) in northern Zambia

BACKGROUND

Nchelenge District in northern Zambia suffers from holoendemic malaria transmission despite a decade of yearly indoor residual spraying (IRS) and insecticide-treated net (ITN) distributions. One hypothesis for this lack of impact is that some vectors in the area may forage in the early evening or outdoors. Anopheles gibbinsi specimens were identified in early evening mosquito collections performed in this study area, and further insight was gleaned into this taxon, including characterizing its genetic identity, feeding preferences, and potential role as a malaria vector.

METHODS

Mosquitoes were collected in July and August 2019 by CDC light traps in Nchelenge District in indoor sitting rooms, outdoor gathering spaces, and animal pens from 16:00-22:00. Host detection by PCR, COI and ITS2 PCR, and circumsporozoite (CSP) ELISA were performed on all samples morphologically identified as An. gibbinsi, and a subset of specimens were selected for COI and ITS2 sequencing. To determine risk factors for increased abundance of An. gibbinsi, a negative binomial generalized linear mixed-effects model was performed with household-level variables of interest.

RESULTS

Comparison of COI and ITS2 An. gibbinsi reference sequences to the NCBI database revealed > 99% identity to "Anopheles sp. 6" from Kenya. More than 97% of specimens were morphologically and molecularly consistent with An. gibbinsi. Specimens were primarily collected in animal pen traps (59.2%), followed by traps outdoors near where humans gather (24.3%), and traps set indoors (16.5%). Host DNA detection revealed a high propensity for goats, but 5% of specimens with detected host DNA had fed on humans. No specimens were positive for Plasmodium falciparum sporozoites. Animal pens and inland households > 3 km from Lake Mweru were both associated with increased An. gibbinsi abundance.

CONCLUSIONS

This is the first report of An. gibbinsi in Nchelenge District, Zambia. This study provided a species identity for unknown "An. sp. 6" in the NCBI database, which has been implicated in malaria transmission in Kenya. Composite data suggest that this species is largely zoophilic and exophilic, but comes into contact with humans and the malaria parasites they carry. This species should continue to be monitored in Zambia and neighbouring countries as a potential malaria vector.