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Molecular evidence for historical presence of knock-down resistance in Anopheles albimanus, a key malaria vector in Latin America

  • 1,
  • 1,
  • 2,
  • 2,
  • 1 and
  • 1Email author
Parasites & Vectors20136:268

  • Received: 18 July 2013
  • Accepted: 12 September 2013
  • Published:



Anopheles albimanus is a key malaria vector in the northern neotropics. Current vector control measures in the region are based on mass distributions of long-lasting insecticidal nets (LLINs) and focal indoor residual spraying (IRS) with pyrethroids. Resistance to pyrethroid insecticides can be mediated by increased esterase and/or multi-function oxidase activity and/or mutations in the voltage-gated sodium channel gene. The aim of this work was to characterize the homologous kdr region of the voltage-gated sodium channel gene in An. albimanus and to conduct a preliminary retrospective analysis of field samples collected in the 1990’s, coinciding with a time of intense pyrethroid application related to agricultural and public health insect control in the region.


Degenerate primers were designed to amplify the homologous kdr region in a pyrethroid-susceptible laboratory strain (Sanarate) of An. albimanus. Subsequently, a more specific primer pair was used to amplify and sequence the region that contains the 1014 codon associated with pyrethroid resistance in other Anopheles spp. (L1014F, L1014S or L1014C).


Direct sequencing of the PCR products confirmed the presence of the susceptible kdr allele in the Sanarate strain (L1014) and the presence of homozygous-resistant kdr alleles in field-collected individuals from Mexico (L1014F), Nicaragua (L1014C) and Costa Rica (L1014C).


For the first time, the kdr region in An. albimanus is described. Furthermore, molecular evidence suggests the presence of kdr-type resistance in field-collected An. albimanus in Mesoamerica in the 1990s. Further research is needed to conclusively determine an association between the genotypes and resistant phenotypes, and to what extent they may compromise current vector control efforts.


  • Anopheles albimanus
  • Pyrethroid resistance
  • Voltage-gated sodium channel gene
  • kdr mutations


Anopheles albimanus is one of the key malaria vectors of Latin America and is widely distributed throughout the region [1, 2]. In recent years, insecticide resistance has emerged in malaria vectors worldwide as a result of increased intensity of insecticide use, principally via the widespread use of indoor residual spraying (IRS) and long-lasting insecticidal nets (LLINs) in malaria endemic areas [35]. Malaria control in the region currently relies heavily on the use of LLINs, which are treated with pyrethroid insecticides [6]. The widespread use of insecticide treated nets (ITNs) [711], LLINs [1214] and both the historical and ongoing use of DDT and pyrethroid insecticides for IRS [13, 1517] elicit selection pressures on local vector populations. As such, the routine surveillance of insecticide resistance must be implemented in the context of vector control programs to verify that control tools are maintaining their efficacy. The timely detection of insecticide resistance and the characterization of the mechanisms underlying insecticide resistance in a vector population can provide valuable data regarding which insecticides should be used to maintain maximum vector control impact.

Resistance to pyrethroid insecticides in malaria vectors can be primarily mediated by either metabolic mechanisms or target site insensitivity, such as mutations on the voltage-gated sodium channel (VGSC) gene [3, 18]. Despite reports of pyrethroid resistance throughout the region, none of these mechanisms have been well-described at the molecular level for malaria vectors in Latin America [19]. Previous studies using biochemical assays and bioassays with synergists on pyrethroid resistant An. albimanus from Guatemala and Mexico suggest that an increase in the activity levels of esterases and multi-function oxidases are at least partially responsible for the resistance detected in these populations [2024]. Elevated oxidase activity has been associated with cross-resistance to pyrethroids and DDT in An. albimanus[23]. One previous study carried out on An. albimanus from Mexico suggested that a target-site mechanism may be involved in cross-resistance between pyrethroids and DDT [25]. Knock-down resistance (kdr) is a target-site mechanism reported in other anopheline species that results in cross-resistance to both pyrethroids and DDT [26, 27]. In anophelines, kdr is linked to single nucleotide polymorphisms on transmembrane segment 6 of domain II of the VGSC gene. The mutations previously reported for anophelines occur on codon 1014, resulting in an amino acid change of leucine to phenylalanine, serine or cysteine [2834]. To date, similar mutations have not been described in An. albimanus.

The present study describes for the first time the homologous kdr region of the VGSC gene in An. albimanus where mutations in other anopheline species have been detected that are associated with kdr-type resistance. Further, we report molecular evidence of kdr resistant-type alleles in field mosquitoes collected in Mexico, Nicaragua and Costa Rica in the 1990s.


Primer design

DNA and cDNA sequences of the VGSC gene of different Anopheles spp. were retrieved from GenBank (Table 1). Conserved regions were identified from a multiple alignment (MEGA 5.0 [35]) and degenerate primers were designed based on conserved codons using An. punctipennis as a basis [GenBank: AY283039-AY283041]. The strategy used to design the primers to amplify the VGSC gene in An. albimanus is presented in Figure 1A.
Figure 1
Figure 1

Strategy to amplify segment 6 of domain II of the VGSC gene in Anopheles albimanus . (A) Diagrammatic representation of the design of degenerate and specific primers for An. albimanus [GenBank: KF137581] based on An. gambiae [GenBank: Y13592] and An. punctipennis [GenBank: AY283041]. The identical positions are indicated by an asterisk and mutation site is enclosed by a box. Intron position is indicated by a black line below the sequence. AAKDRF (5′-AGATGGAAYTTYACNGAYTTC-′3); AAKDRF2 (5′-CATTCATTTATGATTGTGTTTCGTG-′3); AAKDRR (5′-GCAANGCTAAGAANAGRTTNAG-′3). (B) PCR products using degenerate and specific primers. The PCR products were separated on a 2% agarose gel containing ethidium bromide. Lane 1: 50 bp DNA ladder (Novagen); Lane 2: degenerate PCR products (using AAKDRF and AAKDRR primers); Lane 3: negative control of degenerate PCR (H2O); Lane 4: specific PCR product (using AAKDRF2 and AAKDRR primers); Lane 5: negative control of specific PCR (H2O).

Table 1

DNA sequences of the VGSC gene from different Anopheles spp. used in the primer design

Specie (subgenus)

Sequence identification

Anopheles aconitus (Cellia)

GenBank: EU155388

An. annularis (Cellia)

GenBank: DQ026443

An. arabiensis (Cellia)

GenBank: DQ263749

An. culicifacies (Cellia)

GenBank: GQ279245

GenBank: GQ279246

GenBank: GQ279247

An. dirus (Cellia)

GenBank: DQ026439

GenBank: DQ026440

GenBank: DQ026441

GenBank: DQ026442

An. epiroticus (Cellia)

GenBank: EU155384

An. funestus (Cellia)

GenBank: DQ399296

GenBank: DQ399298

An. gambiae (Cellia)

GenBank: Y13592

GenBank: DQ263748

An. harrisoni (Cellia)

GenBank: EU155387

An. jeyporiensis (Cellia)

GenBank: EU155389

An. kochi (Cellia)

GenBank: DQ026446

An. maculatus (Cellia)

GenBank: DQ026445

An. minimus (Cellia)

GenBank: GU064930

GenBank: EU155386

An. paraliae (Anopheles)

GenBank: GQ225104

An. peditaeniatus (Anopheles)

GenBank: GQ225106

An. punctipennis (Anopheles)

GenBank: AY283041

GenBank: AY283039

GenBank: AY283040

An. sinensis (Anopheles)

GenBank: JN002364

GenBank: GQ225102

An. stephensi (Cellia)

GenBank: JF304953

An. subpictus (Cellia)

GenBank: EU155385

GenBank: DQ333331

An. tessellatus (Cellia)

GenBank: DQ075250

An. vagus (Cellia)

GenBank: GQ225100

Mosquito population

The An. albimanus Sanarate laboratory strain, maintained in the insectary of Center for Health Studies (CHS) of Universidad del Valle de Guatemala (Guatemala, Guatemala) was used to validate the designed primers. The Sanarate strain is susceptible to DDT, deltamethrin, permethrin, bendiocarb and malathion (unpublished observations) according to bottle bioassay susceptibility tests [36]. Genomic DNA from individual mosquitoes was isolated following the method described by Collins et al. [37].

Amplification, cloning and sequencing of the VGSC gene

The amplification of segment 6 of domain II of the VGSC gene with degenerate primers was carried out in a 50 μl reaction mixture containing 1X Colorless GoTaq® Flexi Buffer, 1.5 mM MgCl2, 0.2 mM dNTPs, 2.5 μM of each degenerate primer (AAKDRF and AAKDRR), 1 unit of GoTaq® HotStart Polymerase (Promega, Fitchburg, Wisconsin) and 10 to 30 ng of genomic DNA. The degenerate PCR conditions were 95°C for 3 min, followed by 35 cycles of 95°C for 45 sec, 40.5°C for 45 sec and 72°C for 1 min with a final extension step at 72°C for 5 min in a Px2 Thermal Cycler (Thermo Fisher Scientific, Waltham, Massachusetts).

Non-specific amplification was obtained in An. albimanus from the Sanarate strain using the degenerate primers (Figure 1B). Four different-sized PCR products were isolated for specific amplification using the band-stab PCR technique [38]. These purified PCR products were directly sequenced by Macrogen Inc. (Korea) using AAKDRF and AAKDRR as sequencing primers. BLAST analysis showed that a fragment of approximately 250 bp corresponded to the VGSC gene in An. albimanus. To confirm these findings and to obtain a high-quality DNA sequence of this fragment, PCR products were cloned using a TA Cloning® Kit (Invitrogen, Carlsbad, California) according to the manufacturer’s instructions. The plasmids of the positive clones that contained the fragment of VGSC gene were isolated with the PureLink™ HQ Mini Plasmid Purification Kit (Invitrogen, Carlsbad, California) according to the manufacturer’s instructions. Plasmids were sequenced with M13 universal primers using 3500XL Genetic Analyzer (Applied Biosystems, Foster City, California) with BigDye® Terminator v1.1.

PCR assay to detect kdr-type resistance

A second, non-degenerate forward primer (AAKDRF2) was designed based on the sequence of the VGSC gene of An. albimanus (GenBank: KF137581) obtained with the degenerate primers (Figure 1A). The amplification with the specific forward (AAKDRF2) and AAKDRR primer was performed using the same reaction specifications as in the degenerate PCR, except that 0.5 μM of each primer were used. The PCR conditions consisted of an initial denaturation at 95°C for 3 min, followed by 40 cycles at 95°C for 45 sec, 51.5°C for 45 sec and 72°C for 1 min, with a final extension step at 72°C for 5 min in an iCycler (BioRad, Hercules, California). The PCR assay with AAKDRF2 and AAKDRR primers amplified a single band of 225 bp in An. albimanus from the Sanarate strain (Figure 1B), which corresponds to the VGSC gene of An. albimanus. These primers were used to amplify the VGSC gene in DNA samples of An. albimanus from Guatemala (collected in 1995), Mexico (collected in 1991), Nicaragua (collected in 1995), Costa Rica (collected in 1995), Ecuador (collected in 1991) and Colombia (collected in 1992) previously used in population genetic studies [39, 40]. The PCR products were sequenced by Macrogen Inc. (Korea) using AAKDRF2 and AAKDRR primers.

Results and discussion

Sequence analysis showed that segment 6 of domain II of the VGSC gene (excluding the intron sequence) of An. albimanus has a sequence identity of 92% with An. gambiae and 83% with An. punctipennis at the nucleotide level. Variations in the nucleotide sequence of An. albimanus did not produce changes in the amino acid sequence (100% identity with An. gambiae and An. punctipennis, Figure 2). The position of intron II was established through comparison with the VGSC cDNA sequence from An. gambiae [GenBank: Y13592]. The size of intron II in An. albimanus (71 bp) was greater than in An. gambiae (57 bp) and An. punctipennis (68 bp). Variation in the size of intron II has been detected in An. vestitipennis and An. pseudopunctipennis (unpublished observations), and may potentially be used for taxonomic identification of malaria vectors from Latin America, as proposed for other anopheline species [41].
Figure 2
Figure 2

Amino acid sequence comparison of kdr region of Anopheles albimanus with other anopheline species. The sequence of the segment 6 of domain II of the VGSC gene of An. albimanus was compared to An. gambiae [GenBank: CAA73920] and An. punctipennis [GenBank: AAP60053]. Identical positions are indicated by an asterisk and mutation site (codon 1014) is enclosed by a red box. The amino acid at the mutation site corresponds to the pyrethroid and DDT susceptible (wild-type) genotypes.

Sequence results from the Sanarate strain of An. albimanus showed that the individuals contained the susceptible/wild type kdr allele, TTG (L1014), previously reported in An. sacharovi, An. sinensis and other anopheline species from the Mekong region [34, 42, 43]. In the field-collected mosquitoes from Latin America, polymorphisms at codon 1014 were detected in several of the samples (Figure 3A). The field samples from Guatemala, Ecuador and Colombia also contained the susceptible TTG (L1014) allele. A non-synonymous homozygous mutation, TGT (cysteine, L1014C), was detected in field samples from Mexico and Nicaragua. This mutation has previously been associated with permethrin, deltamethrin and beta-cypermethrin resistance in An. sinensis[34, 44, 45]. A field sample from Costa Rica contained a homozygous TTC polymorphism (phenylalanine, L1014F), previously reported in populations of An. gambiae resistant to permethrin and DDT, An. sinensis resistant to deltamethrin and An. peditaeniatus resistant to DDT, permethrin, alpha-cypermethrin, lambda-cyhalothrin and etofenprox [28, 43, 45]. With the exception of certain individuals from Nicaragua and Guatemala, all kdr alleles were found to be homozygous (Figure 3B). The heterozygote alleles from Nicaragua were TKY and from Guatemala were TKK. Interestingly, the kdr allele reported in An. gambiae from East Africa (L1014S) [29] was not detected.
Figure 3
Figure 3

Kdr alleles detected on the segment 6 of domain II of the VGSC gene of Anopheles albimanus. (A) DNA alignment of the VGSC gene of An. albimanus from different regions of Latin America. The identical positions are indicated by an asterisk and polymorphic site (codon 1014) is enclosed by a red box. (B) Electropherograms for kdr alleles detected on the VGSC gene of An. albimanus.

An. albimanus populations are panmictic over at least 600 km in Central America, West of Panama [46]. In this region, insecticide resistance in An. albimanus has been reported and the main source of its selection has been the extensive use of pesticides in large scale agricultural activities [4750]. During the nineties, populations in the area in continued exposure to agricultural insecticides plus pressures from the use of insecticides for vector control could have maintained a constant selection pressure on Mesoamerican An. albimanus populations, possibly explaining the finding of three homozygous kdr variants in Mexico, Nicaragua and Costa Rica with mutations that have been associated with pyrethroid and DDT resistance in other anopheline species. Even though to date the role of kdr has not been directly implicated in the insecticide resistance documented in the region, it is highly likely that kdr is an important resistance mechanism in Latin American malaria vectors.


Our findings describe for the first time the kdr region in An. albimanus, including the presence of polymorphisms associated with insecticide resistance in other anopheline species. We have documented the presence of homozygous kdr alleles associated with resistance in other anopheline species in An. albimanus individuals collected across Mesoamerica at a time of intense agricultural and public health insecticide use. This suggests that pyrethroid and DDT resistance in the region could have been mediated in the past by a kdr mechanism. Future work will endeavor to link resistant phenotypes with the kdr polymorphisms described here, as well as lead to the development of allele-specific diagnostic assays for An. albimanus and other malaria vectors across the region.



Partial funding for this work was provided by the US Agency for International Development (USAID) under Amazon Malaria Initiative, Cooperative Agreement Guatemala Public Health/No. 1U51GH000011 and the Center for Health Studies, Universidad del Valle de Guatemala. Ana María de Mérida and Álvaro Molina for providing historic mosquito samples. We also thank Ellen Dotson from CDC (MR4) for providing the kdr positive controls and primers, and William Brogdon for his helpful comments.

Authors’ Affiliations

Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), 18 avenida 11-95 zona 15 Vista Hermosa 3, Guatemala, Guatemala
Centers for Disease Control and Prevention (CDC), Center for Global Health, Division of Parasitic Disease and Malaria, Entomology Branch, 1600 Clifton Road, Atlanta, GA 30329, USA


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