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      Sand fly identification and screening for Leishmania spp. in six provinces of Thailand

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          Abstract

          Background

          Phlebotomine sand flies are vectors of Leishmania spp. At least 27 species of sand flies have been recorded in Thailand. Although human leishmaniasis cases in Thailand are mainly imported, autochthonous leishmaniasis has been increasingly reported in several regions of the country since 1999. Few studies have detected Leishmania infection in wild-caught sand flies, although these studies were carried out only in those areas reporting human leishmaniasis cases. The aim of this study was therefore to identity sand fly species and to investigate Leishmania infection across six provinces of Thailand.

          Methods

          Species of wild-caught sand flies were initially identified based on morphological characters. However, problems identifying cryptic species complexes necessitated molecular identification using DNA barcoding in parallel with identification based on morphological characters. The wild-caught sand flies were pooled and the DNA isolated prior to the detection of Leishmania infection by a TaqMan real-time PCR assay.

          Results

          A total of 4498 sand flies (1158 males and 3340 females) were caught by trapping in six provinces in four regions of Thailand. The sand flies were morphologically classified into eight species belonging to three genera ( Sergentomyia, Phlebotomus and Idiophlebotomus). Sergentomyia iyengari was found at all collection sites and was the dominant species at most of these, followed in frequency by Sergentomyia barraudi and Phlebotomus stantoni, respectively. DNA barcodes generated from 68 sand flies allowed sorting into 14 distinct species with 25 operational taxonomic units, indicating a higher diversity (by 75%) than that based on morphological identification. Twelve barcoding sequences could not be assigned to any species for which cytochrome c oxidase subunit I sequences are available. All tested sand flies were negative for Leishmania DNA.

          Conclusions

          Our results confirm the presence of several sand fly species in different provinces of Thailand, highlighting the importance of using DNA barcoding as a tool to study sand fly species diversity. While all female sand flies tested in this study were negative for Leishmania, the circulation of Leishmania spp. in the investigated areas cannot be ruled out.

          Graphical abstract

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13071-021-04856-6.

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          Most cited references41

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

            Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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              Biological identifications through DNA barcodes.

              Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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                Author and article information

                Contributors
                poom.adi@mahidol.edu
                alongkotp.fsn@afrims.org
                Journal
                Parasit Vectors
                Parasit Vectors
                Parasites & Vectors
                BioMed Central (London )
                1756-3305
                3 July 2021
                3 July 2021
                2021
                : 14
                : 352
                Affiliations
                [1 ]GRID grid.10223.32, ISNI 0000 0004 1937 0490, Department of Helminthology, Faculty of Tropical Medicine, , Mahidol University, ; Bangkok, 10400 Thailand
                [2 ]GRID grid.413910.e, ISNI 0000 0004 0419 1772, Vector Biology and Control Section, Department of Entomology, , Armed Forces Research Institute of Medical Sciences (AFRIMS), ; Bangkok, 10400 Thailand
                Author information
                http://orcid.org/0000-0002-0313-9900
                Article
                4856
                10.1186/s13071-021-04856-6
                8254935
                34217359
                7e6f7621-f9b0-499c-a6ee-dd9c3099ae96
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 27 February 2021
                : 20 June 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100014035, Armed Forces Health Surveillance Branch;
                Award ID: ProMIS ID: P0108_19_AF_05, Funding Year: 2019
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2021

                Parasitology
                sand fly,phlebotomine,dna barcoding,coi,leishmania detection
                Parasitology
                sand fly, phlebotomine, dna barcoding, coi, leishmania detection

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