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Cosme LV, Corley M, Johnson T, Severson DW, Yan G, Wang X, Beebe N, Maynard A, Bonizzoni M, Khorramnejad A, Martins AJ, Lima JBP, Munstermann LE, Surendran SN, Chen CH, Maringer K, Wahid I, Mukherjee S, Xu J, Fontaine MC, Estallo EL, Stein M, Livdahl T, Scaraffia PY, Carter BH, Mogi M, Tuno N, Mains JW, Medley KA, Bowles DE, Gill RJ, Eritja R, González-Obando R, Trang HTT, Boyer S, Abunyewa AM, Hackett K, Wu T, Nguyễn J, Shen J, Zhao H, Crawford JE, Armbruster P, Caccone A. A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasit Vectors 2024; 17:106. [PMID: 38439081 PMCID: PMC10910840 DOI: 10.1186/s13071-024-06158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. METHODS We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. RESULTS Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. CONCLUSIONS The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS.
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Affiliation(s)
- Luciano Veiga Cosme
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA.
| | - Margaret Corley
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Dave W Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Guiyun Yan
- Department of Population Health and Disease Prevention, University of California, Irvine, CA, USA
| | - Xiaoming Wang
- Department of Population Health and Disease Prevention, University of California, Irvine, CA, USA
| | - Nigel Beebe
- School of the Environment, University of Queensland Australia, St Lucia, Australia
| | - Andrew Maynard
- School of the Environment, University of Queensland Australia, St Lucia, Australia
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Ayda Khorramnejad
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - José Bento Pereira Lima
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Leonard E Munstermann
- Yale School of Public Health and Yale Peabody Museum, Yale University, New Haven, CT, USA
| | | | - Chun-Hong Chen
- National Health Research Institutes, National Mosquito-Borne Disease Control Research Center & National Institute of Infectious Diseases and Vaccinology, Miaoli, Taiwan
| | | | - Isra Wahid
- Center for Zoonotic and Emerging Diseases, Hasanuddin University Medical Research Centre (HUMRC), Makassar, Indonesia
| | - Shomen Mukherjee
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Jiannon Xu
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Michael C Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- University of Groningen, Groningen Institute for Evolutionary Life Sciences, Groningen, The Netherlands
| | - Elizabet L Estallo
- Facultad de Ciencias Exactas, Físicas y Naturales, Centro de Investigaciones Entomológicas de Córdoba, Universidad Nacional de Córdoba, Córdoba, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Marina Stein
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, CONICET CCT Nordeste, Resistencia, Argentina
| | | | - Patricia Y Scaraffia
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Brendan H Carter
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Motoyoshi Mogi
- Division of Parasitology, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Nobuko Tuno
- Laboratory of Ecology, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | | | - Kim A Medley
- Tyson Research Center, Washington University in St. Louis, St. Louis, USA
| | | | - Richard J Gill
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Berkshire, UK
| | - Roger Eritja
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Spain
| | | | - Huynh T T Trang
- Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Sébastien Boyer
- Medical Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Ann-Marie Abunyewa
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Kayleigh Hackett
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Tina Wu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Justin Nguyễn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
| | - Jiangnan Shen
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | | | - Peter Armbruster
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA
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Gloria-Soria A, Faraji A, Hamik J, White G, Amsberry S, Donahue M, Buss B, Pless E, Cosme LV, Powell JR. Origins of high latitude introductions of Aedes aegypti to Nebraska and Utah during 2019. Infect Genet Evol 2022; 103:105333. [PMID: 35817397 DOI: 10.1016/j.meegid.2022.105333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Aedes aegypti (L.), the yellow fever mosquito, is also an important vector of dengue and Zika viruses, and an invasive species in North America. Aedes aegypti inhabits tropical and sub-tropical areas of the world and in North America is primarily distributed throughout the southern US states and Mexico. The northern range of Ae. aegypti is limited by cold winter months and establishment in these areas has been mostly unsuccessful. However, frequent introductions of Ae. aegypti to temperate, non-endemic areas during the warmer months can lead to seasonal activity and disease outbreaks. Two Ae. aegypti incursions were reported in the late summer of 2019 into York, Nebraska and Moab, Utah. These states had no history of established populations of this mosquito and no evidence of previous seasonal activity. We genotyped a subset of individuals from each location at 12 microsatellite loci and ~ 14,000 single nucleotide polymorphic markers to determine their genetic affinities to other populations worldwide and investigate their potential source of introduction. Our results support a single origin for each of the introductions from different sources. Aedes aegypti from Utah likely derived from Tucson, Arizona, or a nearby location. Nebraska specimen results were not as conclusive, but point to an origin from southcentral or southeastern US. In addition to an effective, efficient, and sustainable control of invasive mosquitoes, such as Ae. aegypti, identifying the potential routes of introduction will be key to prevent future incursions and assess their potential health threat based on the ability of the source population to transmit a particular virus and its insecticide resistance profile, which may complicate vector control.
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Affiliation(s)
- Andrea Gloria-Soria
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, P.O. Box 1106, New Haven, CT 06511, USA; Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Ary Faraji
- Salt Lake City Mosquito Abatement District, 2215 North 2200 West, Salt Lake City, UT 84116-1108, USA.
| | - Jeff Hamik
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; University of Nebraska-Lincoln, Department of Educational Psychology, 114 Teachers College Hall, Lincoln, NE 68588, USA.
| | - Gregory White
- Salt Lake City Mosquito Abatement District, 2215 North 2200 West, Salt Lake City, UT 84116-1108, USA.
| | - Shanon Amsberry
- Moab Mosquito Abatement District, 1000 Sand Flats Rd, Moab, UT 84532, USA.
| | - Matthew Donahue
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; Epidemic Intelligence Service, CDC, USA.
| | - Bryan Buss
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; Career Epidemiology Field Officer Program, Division of State and Local Readiness, Center for Preparedness and Response, CDC, USA.
| | | | - Luciano Veiga Cosme
- Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Jeffrey R Powell
- Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
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Rahman RU, Cosme LV, Costa MM, Carrara L, Lima JBP, Martins AJ. Insecticide resistance and genetic structure of Aedes aegypti populations from Rio de Janeiro State, Brazil. PLoS Negl Trop Dis 2021; 15:e0008492. [PMID: 33591988 PMCID: PMC7909666 DOI: 10.1371/journal.pntd.0008492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 02/26/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Vector control largely relies on neurotoxic chemicals, and insecticide resistance (IR) directly threatens their effectiveness. In some cases, specific alleles cause IR, and knowledge of the genetic diversity and gene flow among mosquito populations is crucial to track their arrival, rise, and spread. Here we evaluated Aedes aegypti populations’ susceptibility status, collected in 2016 from six different municipalities of Rio de Janeiro state (RJ), to temephos, pyriproxyfen, malathion, and deltamethrin. We collected eggs of Ae. aegypti in Campos dos Goytacazes (Cgy), Itaperuna (Ipn), Iguaba Grande (Igg), Itaboraí (Ibr), Mangaratiba (Mgr), and Vassouras (Vsr). We followed the World Health Organization (WHO) guidelines and investigated the degree of susceptibility/resistance of mosquitoes to these insecticides. We used the Rockefeller strain as a susceptible positive control. We genotyped the V1016I and F1534C knockdown resistance (kdr) alleles using qPCR TaqMan SNP genotyping assay. Besides, with the use of Ae. aegypti SNP-chip, we performed genomic population analyses by genotyping more than 15,000 biallelic SNPs in mosquitoes from each population. We added previous data from populations from other countries to evaluate the ancestry of RJ populations. All RJ Ae. aegypti populations were susceptible to pyriproxyfen and malathion and highly resistant to deltamethrin. The resistance ratios for temephos was below 3,0 in Cgy, Ibr, and Igg populations, representing the lowest rates since IR monitoring started in this Brazilian region. We found the kdr alleles in high frequencies in all populations, partially justifying the observed resistance to pyrethroid. Population genetics analysis showed that Ae. aegypti revealed potential higher migration among some RJ localities and low genetic structure for most of them. Future population genetic studies, together with IR data in Ae aegypti on a broader scale, can help us predict the gene flow within and among the Brazilian States, allowing us to track the dynamics of arrival and changes in the frequency of IR alleles, and providing critical information to improving vector control program. Monitoring of insecticide resistance (IR) is mandatory for the effectiveness of vector control programs. We investigate six populations of Aedes aegypti regarding their IR status towards insecticides previously or currently in use, their frequency of IR alleles and resistance ratio, their genetic ancestry and structure, and the gene flow. We observed that Ae. aegypti populations from RJ are becoming susceptible to the larvicide organophosphate temephos. The resistance ratios of temephos are lower among populations where gene flow might be occurring. All RJ populations are highly resistant to deltamethrin, partially explained by the high frequency of kdr alleles. Besides, all populations are susceptible to pyriproxyfen’s insect growth regulator and the organophosphate malathion. Population genomic analyses using more than 15,000 SNPs identified three potential genetic clusters within RJ populations, with higher gene flow to and out of the touristic region called Região dos Lagos. IR data, together with knowledge of the genetic structure and gene flow among different mosquito populations, can help with vector control program decisions.
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Affiliation(s)
- Rafi Ur Rahman
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
| | - Luciano Veiga Cosme
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - Monique Melo Costa
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
| | - Luana Carrara
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
| | - José Bento Pereira Lima
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
| | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
- * E-mail:
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Cosme LV, Gloria-Soria A, Caccone A, Powell JR, Martins AJ. Evolution of kdr haplotypes in worldwide populations of Aedes aegypti: Independent origins of the F1534C kdr mutation. PLoS Negl Trop Dis 2020; 14:e0008219. [PMID: 32298261 PMCID: PMC7188295 DOI: 10.1371/journal.pntd.0008219] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/28/2020] [Accepted: 03/13/2020] [Indexed: 01/30/2023] Open
Abstract
Aedes aegypti is the primary vector of dengue, chikungunya, Zika, and urban yellow fever. Insecticides are often the most effective tools to rapidly decrease the density of vector populations, especially during arbovirus disease outbreaks. However, the intense use of insecticides, particularly pyrethroids, has selected for resistant mosquito populations worldwide. Mutations in the voltage gated sodium channel (NaV) are among the principal mechanisms of resistance to pyrethroids and DDT, also known as “knockdown resistance,” kdr. Here we report studies on the origin and dispersion of kdr haplotypes in samples of Ae. aegypti from its worldwide distribution. We amplified the IIS6 and IIIS6 NaV segments from pools of Ae. aegypti populations from 15 countries, in South and North America, Africa, Asia, Pacific, and Australia. The amplicons were barcoded and sequenced using NGS Ion Torrent. Output data were filtered and analyzed using the bioinformatic pipeline Seekdeep to determine frequencies of the IIS6 and IIIS6 haplotypes per population. Phylogenetic relationships among the haplotypes were used to infer whether the kdr mutations have a single or multiple origin. We found 26 and 18 haplotypes, respectively for the IIS6 and IIIS6 segments, among which were the known kdr mutations 989P, 1011M, 1016I and 1016G (IIS6), 1520I, and 1534C (IIIS6). The highest diversity of haplotypes was found in African samples. Kdr mutations 1011M and 1016I were found only in American and African populations, 989P + 1016G and 1520I + 1534C in Asia, while 1534C was present in samples from all continents, except Australia. Based primarily on the intron sequence, IIS6 haplotypes were subdivided into two well-defined clades (A and B). Subsequent phasing of the IIS6 + IIIS6 haplotypes indicates two distinct origins for the 1534C kdr mutation. These results provide evidence of kdr mutations arising de novo at specific locations within the Ae. aegypti geographic distribution. In addition, our results suggest that the 1534C kdr mutation had at least two independent origins. We can thus conclude that insecticide selection pressure with DDT and more recently with pyrethroids is selecting for independent convergent mutations in NaV. Insecticide resistance is a global threat for the control of Aedes aegypti, the mosquito vector of aboviruses such as dengue, chikungunya and Zika. Mutations in the voltage gated sodium channel (NaV), known as kdr, are one of the principal mechanisms related to resistance to pyrethroids, the class of insecticide most employed worldwide inside and around residences. We investigate whether the same kdr mutations found in Ae. aegypti populations from distinct regions of the world have a common origin and subsequently dispersed or if they emerged in unrelated populations at distinct moments. By evaluating the sequences of two fragments of the NaV gene, obtained from DNA collections of Ae. aegypti from several countries, we found at least two independent origins for the F1534C kdr mutation in American, African and Asian populations. There was no evidence for multiple origins of the common kdr mutations V1016I and P989S + V1016G, which were exclusive to American and Asian populations. Our results increase our knowledge of insecticide resistance evolution in one of the main arboviral mosquito vectors of major global diseases.
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Affiliation(s)
| | - Andrea Gloria-Soria
- Yale University, New Haven, CT, United States of America
- Center for Vector Biology & Zoonotic Diseases. The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | | | | | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Av Brasil, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, UFRJ, Rio de Janeiro, RJ, Brazil
- * E-mail:
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