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Volume 7, Issue 10

Detection and genetic characterization of (, ) in hard ticks from the Colombian Caribbean Open Access

Abstract

Ticks are arthropod vectors that transmit pathogens important to human and animal health. The objective of this work was to identify in the metatranscriptome of hard ticks. Between October 2022 and June 2023, ticks were collected from rural areas of the Colombian Caribbean area of the departments of Córdoba and Cesar. High-throughput sequencing (next-generation sequencing) was performed using MGI’s DNBSEQ-G50RS. Bioinformatics analyses were performed in Galaxy, and IQ-TREE2. A total of 766 ticks were collected; 87.33% (669/766) were , 5.4% (42/766) , 4.2% (32/766) and 3.0% (23/766) . Complete and partial L and S segments of (LITV) were detected in the metatranscriptome of , and . The LITV sequences found are phylogenetically related to those detected in and A. variegatum from the French Antilles, in from Trinidad and Tobago and from Brazil. LITV was identified in and ; the first report was in . Although LITV is not considered necessary in public health, the virus belongs to the family, which includes viruses of public health importance, such as and .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): hard ticks , metatranscriptome and Uukuvirus lihanense
Funding
This study was supported by the:
  • Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) (Award BPIN 2020000100322)
    • Principal Award Recipient: NotApplicable
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-10-13
2025-11-10

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References

  1. Souza WM de, Fumagalli MJ, Torres Carrasco A de O, Romeiro MF, Modha S et al. Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil. Sci Rep 2018; 8:1–10 [View Article]
     [Google Scholar]
  2. Brackney DE, Armstrong PM. Transmission and evolution of tick-borne viruses. Curr Opin Virol 2016; 21:67–74 [View Article] [PubMed]
     [Google Scholar]
  3. Li C-X, Shi M, Tian J-H, Lin X-D, Kang Y-J et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife 2015; 4:1–26 [View Article] [PubMed]
     [Google Scholar]
  4. Yu X-J, Liang M-F, Zhang S-Y, Liu Y, Li J-D et al. Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med 2011; 364:1523–1532 [View Article] [PubMed]
     [Google Scholar]
  5. Molina-Hoyos K, Montoya-Ruíz C, Aguilar PV, Pérez-Doria A, Díaz FJ et al. Virome analyses of Amblyomma cajennense and Rhipicephalus microplus ticks collected in Colombia. Acta Trop 2024; 253:107158 [View Article] [PubMed]
     [Google Scholar]
  6. Abudurexiti A, Adkins S, Alioto D, Alkhovsky SV, Avšič-Županc T et al. Taxonomy of the order Bunyavirales: update 2019. Arch Virol 2019; 164:1949–1965 [View Article] [PubMed]
     [Google Scholar]
  7. Spiegel M, Plegge T, Pöhlmann S. The role of phlebovirus glycoproteins in viral entry, assembly and release. Viruses 2016; 8:202 [View Article] [PubMed]
     [Google Scholar]
  8. Qin X-C, Shi M, Tian J-H, Lin X-D, Gao D-Y et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc Natl Acad Sci U S A 2014; 111:6744–6749 [View Article] [PubMed]
     [Google Scholar]
  9. Matsuno K, Weisend C, Kajihara M, Matysiak C, Williamson BN et al. Comprehensive molecular detection of tick-borne phleboviruses leads to the retrospective identification of taxonomically unassigned bunyaviruses and the discovery of a novel member of the genus phlebovirus. J Virol 2015; 89:594–604 [View Article] [PubMed]
     [Google Scholar]
  10. Hubálek Z, Rudolf I. Tick-borne viruses in Europe. Parasitol Res 2012; 111:9–36 [View Article] [PubMed]
     [Google Scholar]
  11. Kosoy OI, Lambert AJ, Hawkinson DJ, Pastula DM, Goldsmith CS et al. Novel thogotovirus associated with febrile illness and death, United States, 2014. Emerg Infect Dis 2015; 21:760–764 [View Article] [PubMed]
     [Google Scholar]
  12. McMullan LK, Folk SM, Kelly AJ, MacNeil A, Goldsmith CS et al. A new phlebovirus associated with severe febrile illness in Missouri. N Engl J Med 2012; 367:834–841 [View Article] [PubMed]
     [Google Scholar]
  13. Shi M, Lin X-D, Tian J-H, Chen L-J, Chen X et al. Redefining the invertebrate RNA virosphere. Nature 2016; 540:539–543 [View Article] [PubMed]
     [Google Scholar]
  14. Dutilh BE, Reyes A, Hall RJ, Whiteson KL. Editorial: virus discovery by metagenomics: the (Im)possibilities. Front Microbiol 2017; 8:1710 [View Article] [PubMed]
     [Google Scholar]
  15. Nooij S, Schmitz D, Vennema H, Kroneman A, Koopmans MPG. Overview of virus metagenomic classification methods and their biological applications. Front Microbiol 2018; 9:749 [View Article] [PubMed]
     [Google Scholar]
  16. Gómez GF, Isaza JP, Segura JA, Alzate JF, Gutiérrez LA. Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Ticks Tick Borne Dis 2020; 11:101426 [View Article] [PubMed]
     [Google Scholar]
  17. López Y, Miranda J, Mattar S, Gonzalez M, Rovnak J. First report of lihan tick virus (Phlebovirus, Phenuiviridae) in ticks, Colombia. Virol J 2020; 17:63 [View Article] [PubMed]
     [Google Scholar]
  18. Orozco Orozco M, Gómez GF, Alzate JF, Isaza JP, Gutiérrez LA. Virome analysis of three Ixodidae ticks species from Colombia: a potential strategy for discovering and surveying tick-borne viruses. Infect Genet Evol 2021; 96:105103 [View Article] [PubMed]
     [Google Scholar]
  19. López Y, Thomas R, Muñoz-Leal S, López-Mejia Y, Galeano K et al. Hard ticks (Ixodida: Ixodidae) in the Colombian caribbean harbor the jingmen tick virus: an emerging arbovirus of public health concern. Parasit Vectors 2024; 17:268 [View Article] [PubMed]
     [Google Scholar]
  20. Asamblea Departamental de Córdoba Plan de desarrollo departamental: córdoba 2020-2023 "Ahora le toca a córdoba: oportunidades bienestary seguridad; 20201–667 https://gobcordoba.micolombiadigital.gov.co/sites/gobcordoba/content/files/000057/2828_ordenanza-0009-plan-de-desarrollo-departamental--20202023-web.pdf
  21. Kong Y, Zhang G, Jiang L, Wang P, Zhang S et al. Metatranscriptomics reveals the diversity of the tick virome in Northwest China. Microbiol Spectr 2022; 10:1–14 [View Article]
     [Google Scholar]
  22. Barros D, Arzua M, Bechara GH. Carrapatos de Importancia Medico Veterinaria Da Regiao Neotropical: Um Guia Ilustrado Para Identificação de Especies São Paulo: Vox/ICTTD-3/Butantan; 2006
     [Google Scholar]
  23. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article]
     [Google Scholar]
  24. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article]
     [Google Scholar]
  25. Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article] [PubMed]
     [Google Scholar]
  26. Bağcı C, Patz S, Huson DH. DIAMOND+MEGAN: fast and easy taxonomic and functional analysis of short and long microbiome sequences. Curr Protoc 2021; 1:e59 [View Article] [PubMed]
     [Google Scholar]
  27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  28. Broom BM, Ryan MC, Brown RE, Ikeda F, Stucky M et al. A galaxy implementation of next-generation clustered heatmaps for interactive exploration of molecular profiling data. Cancer Res 2017; 77:e23–e26 [View Article] [PubMed]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  30. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res 2004; 32:D23–6 [View Article] [PubMed]
     [Google Scholar]
  31. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
     [Google Scholar]
  32. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  33. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
     [Google Scholar]
  34. Yuan S, Chan HCS, Filipek S, Vogel H. PyMOL and inkscape bridge the data and the data visualization. Structure 2016; 24:2041–2042 [View Article] [PubMed]
     [Google Scholar]
  35. Sameroff S, Tokarz R, Charles RA, Jain K, Oleynik A et al. Viral diversity of tick species parasitizing cattle and dogs in trinidad and tobago. Sci Rep 2019; 9:10421 [View Article] [PubMed]
     [Google Scholar]
  36. Gondard M, Temmam S, Devillers E, Pinarello V, Bigot T et al. RNA viruses of Amblyomma variegatum and Rhipicephalus microplus and cattle susceptibility in the French antilles. Viruses 2020; 12:1–23 [View Article] [PubMed]
     [Google Scholar]
  37. Palacios G, Savji N, Travassos da Rosa A, Guzman H, Yu X et al. Characterization of the uukuniemi virus group (Phlebovirus: Bunyaviridae): evidence for seven distinct species. J Virol 2013; 87:3187–3195 [View Article] [PubMed]
     [Google Scholar]
  38. Guo L, Ma J, Lin J, Chen M, Liu W et al. Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China. Front Microbiol 2022; 13:1–9 [View Article]
     [Google Scholar]
  39. Parry R, James ME, Asgari S. Uncovering the worldwide diversity and evolution of the virome of the mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms 2021; 9:1–28 [View Article] [PubMed]
     [Google Scholar]
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Detection and genetic characterization of Uukuvirus lihanense (Uukuvirus, Phenuiviridae) in hard ticks from the Colombian Caribbean
Access Microbiology 7, 000941.v3 (2025); https://doi.org/10.1099/acmi.0.000941.v3
/content/journal/acmi/10.1099/acmi.0.000941.v3
/content/journal/acmi/10.1099/acmi.0.000941.v3
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