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ORIGINAL RESEARCH article
Front. Genet.
Sec. Applied Genetic Epidemiology
Volume 15 - 2024 |
doi: 10.3389/fgene.2024.1456644
This article is part of the Research Topic Advanced Genetic and Genomic Methods and Applications for Malaria Surveillance View all articles
Improved species assignments across the entire Anopheles genus using targeted sequencing
Provisionally accepted
Marilou Boddé
1,2,3*
Alex Makunin
3
Fiona Teltscher
3*
Jewelna Akorli
4
Nana Efua Andoh
4,5*
Amy K. Bei
6
Victor Chaumeau
7,8*
Ife Desamours
6*
Uwem F. Ekpo
9*
Nicodem J. Govella
10
Jonathan Kayondo
11*
Kevin Kobylinski
12*
Elhadji Malick Ngom
13*
El Hadji Amadou Niang
14*
Fredros Okumu
10*
Olaitan O. Omitola
9*
Alongkot Ponlawat
12*
Malala Nirina Rakotomanga
2
Mialy Tatamo Rasolonjatovoniaina
2*
Diego Ayala
15,2
Mara Lawniczak
3*- 1 Center for Molecular Biodiversity Research, LIB Leibniz Insitute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
- 2 Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- 3 Tree of Life, Wellcome Sanger Institute (WT), Hinxton, United Kingdom
- 4 Department of Parasitology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
- 5 Department of Pathology, University of Cambridge, Cambridge, England, United Kingdom
- 6 School of Public Health, Yale University, New Haven, Connecticut, United States
- 7 Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Research, Mahidol University, Salaya, Thailand
- 8 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
- 9 Federal University of Agriculture, Abeokuta, Abeokuta, Ogun, Nigeria
- 10 Ifakara Health Institute, Ifakara, Tanzania
- 11 Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- 12 Armed Forces Research Institute of Medical Science, Bangkok, Thailand
- 13 Institut Pasteur de Dakar, Dakar, Senegal
- 14 Laboratory of Vector and Parasity Ecology, Cheikh Anta Diop University, Dakar, Senegal
- 15 MIVEGEC, Institut de Recherche Pour le Développement (IRD), Montpellier, Languedoc-Roussillon, France
Accurate species identification of the mosquitoes in the genus Anopheles is of crucial importance to implement malaria control measures and monitor their effectiveness. We use a previously developed amplicon panel (ANOSPP) that retrieves sequence data from multiple short nuclear loci for any species in the genus. Species assignment is based on comparison of samples to a reference index using k-mer distance. Here, we provide a protocol to generate version controlled updates of the reference index and present its latest release, NNv2, which contains 91 species, compared to 56 species represented in its predecessor NNv1. With the updated reference index, we are able to assign samples to species level that previously could not be assigned. We discuss what happens if a species is not represented in the reference index and how this can be addressed in a future update. To demonstrate the increased power of NNv2, we showcase the assignments of 1789 wild-caught mosquitoes from Madagascar and demonstrate that we can detect within species population structure from the amplicon sequencing data.
Keywords: vector monitoring, Malaria vector, Species assignment, Anopheles, amplicon panel
Received: 28 Jun 2024; Accepted: 12 Aug 2024.
Copyright: © 2024 Boddé, Makunin, Teltscher, Akorli, Andoh, Bei, Chaumeau, Desamours, Ekpo, Govella, Kayondo, Kobylinski, Ngom, Niang, Okumu, Omitola, Ponlawat, Rakotomanga, Rasolonjatovoniaina, Ayala and Lawniczak. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Marilou Boddé, Center for Molecular Biodiversity Research, LIB Leibniz Insitute for the Analysis of Biodiversity Change, Bonn, 53113, North Rhine-Westphalia, Germany
Fiona Teltscher, Tree of Life, Wellcome Sanger Institute (WT), Hinxton, United Kingdom
Nana Efua Andoh, Department of Parasitology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
Victor Chaumeau, Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Research, Mahidol University, Salaya, Thailand
Ife Desamours, School of Public Health, Yale University, New Haven, 06520-8034, Connecticut, United States
Uwem F. Ekpo, Federal University of Agriculture, Abeokuta, Abeokuta, 110282, Ogun, Nigeria
Jonathan Kayondo, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
Kevin Kobylinski, Armed Forces Research Institute of Medical Science, Bangkok, Thailand
Elhadji Malick Ngom, Institut Pasteur de Dakar, Dakar, Senegal
El Hadji Amadou Niang, Laboratory of Vector and Parasity Ecology, Cheikh Anta Diop University, Dakar, BP 5005, Senegal
Fredros Okumu, Ifakara Health Institute, Ifakara, 78 373, Tanzania
Olaitan O. Omitola, Federal University of Agriculture, Abeokuta, Abeokuta, 110282, Ogun, Nigeria
Alongkot Ponlawat, Armed Forces Research Institute of Medical Science, Bangkok, Thailand
Mialy Tatamo Rasolonjatovoniaina, Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Mara Lawniczak, Tree of Life, Wellcome Sanger Institute (WT), Hinxton, United Kingdom
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