Phylogenetic and Genetic Variation Analysis of ITS1 Gene of Trypanosoma lewisi in Wild Rats Using Polymerase Chain Reaction
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Murine Trypanosomiasis is a disease caused by the blood protozoan Trypanosoma lewisi in rats, with the transmission process mediated by the flea species Xenopsylla cheopis and Nosopsyllus fasciatus. Cases of trypanosomiasis have been documented due to Trypanosoma lewisi infecting rats and humans in various countries. Diagnosis of T. lewisi is typically conducted using polymerase chain reaction (PCR), which amplifies target DNA using specific primers. One such target gene for detection is the Internal Transcribed Spacer-1 (ITS1). Subsequent sequencing of PCR products enables analysis of genetic variation employing parameters such as nucleotide composition, genetic distance, and phylogenetic analysis with MEGA software. Test results based on percent identity values indicated a 98.51% homology of blood samples with the Chinese strain of T. lewisi (FJ011094.1), demonstrating genetic variation. Phylogram reconstruction revealed that samples 18, 19, and 37 of T. lewisi exhibit very close intraspecies relationships with T. lewisi from NCBI genebank with genetic distance ranging from 0.007 to 0.01. While the closest interspecies relationship was found with T. cruzi (KT305857.1) with a genetic distance of (d = 0.61).
Anafarida, O., & Badruzsaufari, D. (2020). Genetic Analysis of Mangifera spp. Based on Gene 5.8S RRNA. Ziraa’ah, 45(2), 120–126.
Anantyarta, P. (2017). Identification of Genetic Variations in Buffalo (Bubalus bubalis) Pacitan and Tuban Based on Microsatellites. Bioeksperimen, 3(1), 11–29.
Arham, W. (2015). Utilizing 16S rRNA coding DNA sequences, identifying indigenous entomopathogenic symbiont-nematode bacteria from Bromo, East Java. [Thesis]. Biology Department. Faculty of Mathematics and Natural Sciences. University of Jember.
AVMA guidelines for the euthanasia of animals (2020). 2020 edition, pp: 60–62.
Central Statistics Agency, 2023. Regency of Malang. accessed on October 11, 2023. https://www.bps.go.id/.
Crossley, B. M., Bai, J., Glaser, A., Maes, R., Porter, E., Killian, M. L., Clement, T., & Toohey-Kurth, K. (2020). Guidelines for Sanger Sequencing and Molecular Assay Monitoring. Journal of Veterinary Diagnostic Investigation, 32(6), 767–775.
Damar P. G., & Ningrum, D. (2017). Water Conservation on Land with High Building Density in Malang City. Reka Buana Journal, 3(1), 1–9.
De Moraes Russo, C. A., & Selvatti, A. P. (2018). Bootstrap and Rogue Identification Tests for Phylogenetic Analyses. Molecular Biology and Evolution, 35(9), 2327–2333.
Desquesnes, M., Ravel, S., & Cuny, G. (2002). PCR identification of Trypanosoma lewisi, a common parasite of laboratory rats. Kinetoplastid Biology and Disease, 1, 1–6.
Dobigny, G., Poirier, P., Hima, K., Cabaret, O., Gauthier, P., Tatard, C., Jean-Marc, C., & Bretagne, S. (2011). Molecular survey of rodent-borne Trypanosoma in Niger with special emphasis on T. lewisi imported by invasive black rats. Acta Tropica, 117(3), 183–188.
Ehtisham, M., Wani, F., Wani, I., Kaur, P., & Nissar, S. (2016). Polymerase Chain Reaction (PCR): Back to Basics. Indian Journal of Contemporary Dentistry, 4(2), 30.
Fuad, A. R. M., Ita, U., & Fredy, K. (2016). Use of Commercial Agar-Agar as Gel Electrophoresis Media for Remazol Dyes: Effect of Buffer Composition, Buffer pH, and Media Concentration. Jurnal Sains dan Seni ITS, 5(2), 1–4.
Garibyan, L., & Avashia, N. (2013). Polymerase Chain Reaction. Journal of Investigative Dermatology, 133(3), 1–4.
Hoare, C. A. (1972). The trypanosomes of mammals. A Zoological Monograph. Blackwell Scientific Publications, Oxford, U.K. pp: 749.
Howie, S., Guy, M., Fleming, L., Bailey, W., Noyes, H., Faye, J. A., Pepin, J., Greenwood, B., Whittle, H., Molyneux, D., & Corrah, T. (2006). A Gambian infant with fever and an unexpected blood film. PLoS Medicine, 3(9), 1508–1512.
Jittapalapong, S., Inpankaew, T., Sarataphan, N., Herbreteau, V., Hugot, J. P., Morand, S. & Stich, R. W. (2008). Molecular detection of divergent trypanosomes among rodents of Thailand. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 8(4), 445–449.
Karki, R., Pandya, D., Elston, R. C., & Ferlini, C. (2015). Defining “Mutation” and “Polymorphism” in the Era of Personal Genomics. BMC Medical Genomics, 8(37), 1–7.
Kelley, S. T., & Didulo, D. (2018). Computational Biology: A Hypertextbook. Washington: ASM Press.
Kristina, R., & Saragih, P. (2019). Types and Density of Rats at Orphanage "X" Semarang City. Journal of Public Health, 7(1), 260–271.
Makarova, O., Contaldo, N., Paltrinieri, S., Bertaccini, A., Nyskjold, H., & Nicolaisen, M. (2013). DNA Bar-Coding for Phytoplasma Identification. Phytoplasma: Methods and Protocols. Methods in Molecular Biology, 938, 301–317.
Marc, D., Ketsarin, K., Sarawut, Y., Cristina, M., Sophie, R., Wang, M. H., Lun, Z. R., Serge, M., & Sathaporn, J. (2011). Specific Primers for PCR Amplification of the ITS1 (ribosomal DNA) of Trypanosoma lewisi. Infection, Genetics, and Evolution, 11(6), 1361–1367.
Mohd-Qawiem, F., Nur-Fazila, S. H., Ain-Fatin, R., Yong, Q. H., Nur-Mahiza, M.I ., & Yasmin, A. R. (2022) Detection of zoonotic-borne parasites in Rattus spp. in Klang Valley, Malaysia, Veterinary World, 15(4), 1006–1014.
Novita, R. (2019). Study of the Potential of Trypanosomiasis as an Emerging Zoonotic Disease in Indonesia. Journal of Disease Vectors, 13(1), 21–32.
Pumhom, P., Pognon, D., Yangtara, S., Thaprathorn, N., Milocco, C., Douangboupha, B., Herder, S., Chaval, Y., Morand, S., Jittapalapong, S., & Desquesnes, M. (2014). Molecular Prevalence of Trypanosoma spp. In Wild Rodents of Southeast Asia: Influence in Human Settlement Habitat. Epidemiol Infect, 142(6), 1221–1230.
Purnama, M. T. E., Dewi, W. K., Triana, N. M., & Ooi, H. K. (2021). Serum liver enzyme profile in Timor deer (Cervus timorensis) with fascioliasis in Indonesia. Tropical Biomedicine, 38(1), 57–61.
Qamar, W., Khan, M. R., & Arafah, A. (2017). Optimization of Conditions to Extract High-Quality DNA for PCR Analysis from Whole Blood Using SDS- proteinase K method. Saudi Journal of Biological Sciences, 24(7), 1465– 1469.
Saleky, D., & Sendy, L. M. (2021). Molekuler Filogenetik Cerithidea anticipata (Iredale, 1929) (Mollusca: Gastropoda). Scientific journals of PLATAX, 9(1), 9–17.
Shafiyyah, C. O. S., Jamaiah, I., Rohela, M., Lau, Y. L., & Aminah, F. S. (2012) Prevalence of intestinal and blood parasites among wild rats in Kuala Lumpur, Malaysia. Tropical Biomedicine, 29(4), 544–550.
Smarda, P., Bures, P., Horova, L., Leitch, I. J., Mucina, L., Pacini, E., Tichy, L., Grulich, V., & Rotreklova. (2014). Ecological and Evolutionary Significance of Genomic GC Content Diversity in Monocots. Proceedings of the National Academy of Sciences of the United States of America, 111(39), E4096–E4102.
Stuart, T. F., Isern, J., & Baron, M. H. (2010). Chapter 22 - Use of Transgenic Fluorescent Reporter Mouse Lines to Monitor Hematopoietic and Erythroid Development During Embryogenesis. Methods in Enzymology. Academic Press. 476, pp: 403–427.
Sukoco, H., Fahrodi, D. U., Said, N. S., Gading, W. T., & Mahbuba, B. (2023). Prevalence of Gastrointestinal Endoparasites of Swamp Buffaloes (Bubalus bubalis) in Polewali Mandar. Jurnal Medik Veteriner, 6(2), 173–179.
Tang, H. J., Lan, Y. G., Wen, Y. Z., Zhang, X. C., Desquesnes, M., Yang, T. B., Hide, G., & Lun, Z. R. (2012). Detection of Trypanosoma lewisi from Wild Rats in Southern China and Its Genetic Diversity Based on The ITS1 and ITS2 Sequences. Infection, Genetics and Evolution, 12(5), 1046–1051.
Taylor, M. A., Coop, R. L., & Wall, R. L. (2016). Veterinary Parasitology 4th Edition. UK: WILEY Blackwell.
Verma, A., Manchanda, S., Kumar, N., Sharma, A., Goel, M., Banerjee, P. S., Garg, R., Singh, B. P., Balharbi, F., Lejon, V., Deborggraeve, S., Rana, U. V. S., & Puliyel, J. (2011). Case Report: Trypanosoma lewisi or T. lewisi-like Infection in a 37-Day-Old Indian Infant. American Journal Tropical Medicine and Hygiene, 85(2), 221–224.
Wirdateti, E. I., & Handayani. (2016). Analysis of Mitochondrial Cytochrome Oxidase I (COI) mtDNA Sequences in Indonesian Slow Lorises (Nyticebus spp) as Markers for Developing Species Identification. Indonesian Biology Journal, 12(1), 119–128.
Wulan, Niken, D. N., & Andre P. W. (2020). East Javan Slum Settlement Management: Settlement Development and Development Strategy. Journal of Political and Social Administration, 1(2), 84–88.
Xia, W., Luo, T., Zhang, W., Mason, A. S., Huang, D., Huang, X., Tang, W., Dou, Y., Zhang, C., & Xiao, Y. (2019). Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis. Frontiers in Plant Science, 10, 130–141.
Yesica, R., Kusumarini, S., Hardian, A. B., Paramanandi, D. A., Asmara, N. W., Anggara, J. E., Atmaja, P., & Jeane G. (2022). Morphological and Morphometric Analysis of Trypanosoma lewisi and Toxoplasma gondii in Malang City, Indonesia Rats. Journal of Experimental Biology and Agricultural Sciences, 10(5), 1121–1128.
Yesica, R., Nur Holizah, Y., Pratiwi, H., Hardian, A. B., Kusumarini, S., & Wisesa, I. B. G. R. (2022). Prevalence, Spatial Mapping, Morphological,and Morphometric Analysis of Trypanosoma lewisi in Wild Rats in Malang. Acta Veterinaria Indonesiana, 10(1), 71–79.
Yuenleni. (2019). PCR Optimization Steps. Indonesian Journal of Laboratory, 1, 51–56.
Yuliadi, B., & Muhidin, S. I. (2016). Surveillance technique of Rats in Java Island. Ministry of Health Research Institute, Jakarta- Indonesia. pp: 51–71.
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