Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania

Donath Damian; Modester Damas; Jonas Johansson Wensman; Mikael Berg

doi:doi:10.11648/j.ajbio.20200806.12

| Peer-Reviewed

Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania

Donath Damian, Modester Damas, Jonas Johansson Wensman, Mikael Berg

Published in American Journal of BioScience (Volume 8, Issue 6)

Received: 3 December 2020 Accepted: 16 December 2020 Published: 28 December 2020

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Many of the recent emerging infectious diseases have occurred due to the transmission of the viruses that have wildlife reservoirs. Arthropods, such as ticks, are known to be important vectors for spreading viruses and other pathogens from wildlife to domestic animals and humans. In the present study, we explored the diversity of viruses in hard ticks (Ixodidae) from select areas of a wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using a metagenomic approach. cDNA and DNA were amplified with random amplification and Illumina high-throughput sequencing was performed. The high-throughput sequenced data was imported to the CLC genomic workbench and trimmed based on quality (Q = 20) and length (≥ 50). The trimmed reads were assembled and annotated through Blastx using Diamond against the National Center for Biotechnology Information non-redundant database and its viral database. The MEGAN Community was used to analyze and to compare the taxonomy of the viral community. The obtained contigs and singletons were further subjected to alignment and mapping against reference sequences. The viral sequences identified were classified into bacteria, vertebrates, and invertebrates, plants, and protozoans viruses. Sequences related to known viral families; Retroviridae, Flaviviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Phenuiviridae, Totiviridae, Rhabdoviridae, Parvoviridae, Caulimoviridae, Mimiviridae and several Phages were reported. This result indicates that there are many viruses present in the study region, which we are not aware of and do not know the role they have or if they have the potential to spread to other species and cause diseases. Therefore, further studies are required to delineate the viral community present in the region over a large scale.

Published in	American Journal of BioScience (Volume 8, Issue 6)
DOI	10.11648/j.ajbio.20200806.12
Page(s)	150-157
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2020. Published by Science Publishing Group

Keywords

Ticks, Viral Metagenomics, Virus, Mikumi National Park

References

[1]	Weaver, S. C.; Reisen, W. K. Present and future arboviral threats. Antivir. Res. 2010, 85, 328–345.
[2]	Olival, K. J.; Hosseini, P. R.; Zambrana-Torrelio, C.; Ross, N.; Bogich, T. L.; Daszak, P. Host and viral traits predict zoonotic spillover from mammals. Nature 2017, 546, 646–650.
[3]	Valarcher, J. F.; Hagglund, S.; Juremalm, M.; Blomqvist, G.; Renstrom, L.; Zohari, S.; Leijon, M.; Chirico, J. Tick-borne encephalitis. Rev. Sci. Tech. 2015, 34, 453–466.
[4]	Guglielmone, A. A.; Venzal, J. M.; Battesti, D.; Onofrio, V. C.; Trajano, E.; Firminho, J. V. L. Ticks (Acari: Ixodida) of the Neotropical Zoogeographic Region; Consortium on Ticks and Tick-borne Diseases (ICTTD-2): Houten, The Netherlands, 2003; p. 173.
[5]	Estrada-Pena A and de la Fuente J. The ecology of ticks and epidemiologyof tick-borne viral diseases. Antiviral Res. 2014; 108: 104–128.
[6]	Labuda M, Nuttall PA. Tick-borne viruses. Parasitology. 2004; 129 (Suppl): S221–S45.
[7]	Damian D, Maghembe R, Damas M, Wensman JJ, Berg M. Application of viral metagenomics for study of emerging and reemerging tick-borne viruses. Vector-borne and zoonotic diseases. 2020; 20 (8), 557-565.
[8]	Blomstrom A, Ye X, Fossum C and Berg M. Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs. Viruses 2018; 10: 38.
[9]	BlomstromAL, Fossum C, Wallgren P, Berg, M. Viral Metagenomics Analysis Displays the Co- Infection Situation in Healthy and PMWS Affected Pigs. PLoS ONE 2016; 11: 11.
[10]	Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011 Mar 15; 27 (6): 863–864.
[11]	Buchfink, B.; Xie, C.; Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 2015, 12, 59–60.
[12]	Huson, D. H.; Beier, S.; Flade, I.; Gorska, A.; El-Hadidi, M.; Mitra, S.; Ruscheweyh, H. J.; Tappu, R. MEGAN Community Edition—Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoSComput. Biol. 2016, 12, e1004957.
[13]	Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 2016, 33, 1870–1874.
[14]	Vandegrift, K. J.; Kapoor, A. The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health. Viruses 2019, 11, 529.
[15]	Shi, M.; Lin, X. D.; Tian, J. H.; Chen, L. J.; Chen, X.; Li, C. X.; Qin, X. C.; Li, J.; Cao, J. P.; Eden, J. S.; et al. Redefining the invertebrate RNA virosphere. Nature 2016, 540, 539–543.
[16]	Dietzgen, R. G.; Kondo, H.; Goodin, M. M.; Kurath, G.; Vasilakis, N. The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins. Virus Res. 2017, 227, 158–170.
[17]	Xia, H.; Hu, C.; Zhang, D.; Tang, S.; Zhang, Z.; Kou, Z.; Fan, Z.; Bente, D.; Zeng, C.; Li, T. Metagenomic profile of the viral communities in Rhipicephalus spp. ticks from Yunnan, China. PLoS ONE 2015, 10, e0121609.
[18]	Souza, W. M.; Fumagalli, M. J.; Torres Carrasco, A. O.; Romeiro, M. F.; Modha, S.; Seki, M. C.; Gheller, J. M.; Daffre, S.; Nunes, M. R. T.; Murcia, P. R.; et al. Viral diversity of Rhipicephalusmicroplus parasitizing cattle in southern Brazil. Sci. Rep. 2018, 8, 16315.
[19]	Sakamoto JM, Ng TFF, Suzuki Y, et al. Bunyaviruses are common in male and female Ixodesscapularis ticks in central Pennsylvania. PeerJ. 2016; 4: e2324.
[20]	McMullan LK, Folk SM, Kelly AJ, MacNeil A et al. A new phlebovirus associated with severe febrile illness in Missouri. N. Engl. J. Med. 2012; 367, 834–841.
[21]	Sameroff S, Tokarz R, Charles R, Jain K, Oleynik A, Che X, Georges K, Carrington C. Viral Diversity of tick species parasitizing Cattle and Dogs in Trinidad and Tobago. Scientific reports. 2019; 9: 10421.
[22]	Cholleti H, Hayer J, Berg M, Blomström AL et al. Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique. Infection ecology & epidemiology 2018; 8: 1.
[23]	Francois S, Filloux D, Roumagnac P, et al. Discovery of parvovirus-related sequences in an unexpected broad range of animals. Sci Rep. 2016 Sep 07; (6): 30880.
[24]	Liu H, Fu Y, Xie J, et al. Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J Virol. 2011 Oct; 85 (19): 9863–9876.

Cite This Article

Plain Text BibTeX RIS

APA Style

Donath Damian, Modester Damas, Jonas Johansson Wensman, Mikael Berg. (2020). Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. American Journal of BioScience, 8(6), 150-157. https://doi.org/10.11648/j.ajbio.20200806.12

Copy | Download

ACS Style

Donath Damian; Modester Damas; Jonas Johansson Wensman; Mikael Berg. Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. Am. J. BioScience 2020, 8(6), 150-157. doi: 10.11648/j.ajbio.20200806.12

Copy | Download

AMA Style

Donath Damian, Modester Damas, Jonas Johansson Wensman, Mikael Berg. Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. Am J BioScience. 2020;8(6):150-157. doi: 10.11648/j.ajbio.20200806.12

Copy | Download

@article{10.11648/j.ajbio.20200806.12,
  author = {Donath Damian and Modester Damas and Jonas Johansson Wensman and Mikael Berg},
  title = {Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania},
  journal = {American Journal of BioScience},
  volume = {8},
  number = {6},
  pages = {150-157},
  doi = {10.11648/j.ajbio.20200806.12},
  url = {https://doi.org/10.11648/j.ajbio.20200806.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajbio.20200806.12},
  abstract = {Many of the recent emerging infectious diseases have occurred due to the transmission of the viruses that have wildlife reservoirs. Arthropods, such as ticks, are known to be important vectors for spreading viruses and other pathogens from wildlife to domestic animals and humans. In the present study, we explored the diversity of viruses in hard ticks (Ixodidae) from select areas of a wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using a metagenomic approach. cDNA and DNA were amplified with random amplification and Illumina high-throughput sequencing was performed. The high-throughput sequenced data was imported to the CLC genomic workbench and trimmed based on quality (Q = 20) and length (≥ 50). The trimmed reads were assembled and annotated through Blastx using Diamond against the National Center for Biotechnology Information non-redundant database and its viral database. The MEGAN Community was used to analyze and to compare the taxonomy of the viral community. The obtained contigs and singletons were further subjected to alignment and mapping against reference sequences. The viral sequences identified were classified into bacteria, vertebrates, and invertebrates, plants, and protozoans viruses. Sequences related to known viral families; Retroviridae, Flaviviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Phenuiviridae, Totiviridae, Rhabdoviridae, Parvoviridae, Caulimoviridae, Mimiviridae and several Phages were reported. This result indicates that there are many viruses present in the study region, which we are not aware of and do not know the role they have or if they have the potential to spread to other species and cause diseases. Therefore, further studies are required to delineate the viral community present in the region over a large scale.},
 year = {2020}
}

Copy | Download

TY  - JOUR
T1  - Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania
AU  - Donath Damian
AU  - Modester Damas
AU  - Jonas Johansson Wensman
AU  - Mikael Berg
Y1  - 2020/12/28
PY  - 2020
N1  - https://doi.org/10.11648/j.ajbio.20200806.12
DO  - 10.11648/j.ajbio.20200806.12
T2  - American Journal of BioScience
JF  - American Journal of BioScience
JO  - American Journal of BioScience
SP  - 150
EP  - 157
PB  - Science Publishing Group
SN  - 2330-0167
UR  - https://doi.org/10.11648/j.ajbio.20200806.12
AB  - Many of the recent emerging infectious diseases have occurred due to the transmission of the viruses that have wildlife reservoirs. Arthropods, such as ticks, are known to be important vectors for spreading viruses and other pathogens from wildlife to domestic animals and humans. In the present study, we explored the diversity of viruses in hard ticks (Ixodidae) from select areas of a wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using a metagenomic approach. cDNA and DNA were amplified with random amplification and Illumina high-throughput sequencing was performed. The high-throughput sequenced data was imported to the CLC genomic workbench and trimmed based on quality (Q = 20) and length (≥ 50). The trimmed reads were assembled and annotated through Blastx using Diamond against the National Center for Biotechnology Information non-redundant database and its viral database. The MEGAN Community was used to analyze and to compare the taxonomy of the viral community. The obtained contigs and singletons were further subjected to alignment and mapping against reference sequences. The viral sequences identified were classified into bacteria, vertebrates, and invertebrates, plants, and protozoans viruses. Sequences related to known viral families; Retroviridae, Flaviviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Phenuiviridae, Totiviridae, Rhabdoviridae, Parvoviridae, Caulimoviridae, Mimiviridae and several Phages were reported. This result indicates that there are many viruses present in the study region, which we are not aware of and do not know the role they have or if they have the potential to spread to other species and cause diseases. Therefore, further studies are required to delineate the viral community present in the region over a large scale.
VL  - 8
IS  - 6
ER  -

Copy | Download

Author Information

Donath Damian

Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
Modester Damas

Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
Jonas Johansson Wensman

Section of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
Mikael Berg

Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Donath Damian, Modester Damas, Jonas Johansson Wensman, Mikael Berg. (2020). Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. American Journal of BioScience, 8(6), 150-157. https://doi.org/10.11648/j.ajbio.20200806.12

Copy | Download

ACS Style

Donath Damian; Modester Damas; Jonas Johansson Wensman; Mikael Berg. Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. Am. J. BioScience 2020, 8(6), 150-157. doi: 10.11648/j.ajbio.20200806.12

Copy | Download

AMA Style

Donath Damian, Modester Damas, Jonas Johansson Wensman, Mikael Berg. Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania. Am J BioScience. 2020;8(6):150-157. doi: 10.11648/j.ajbio.20200806.12

Copy | Download

@article{10.11648/j.ajbio.20200806.12,
  author = {Donath Damian and Modester Damas and Jonas Johansson Wensman and Mikael Berg},
  title = {Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania},
  journal = {American Journal of BioScience},
  volume = {8},
  number = {6},
  pages = {150-157},
  doi = {10.11648/j.ajbio.20200806.12},
  url = {https://doi.org/10.11648/j.ajbio.20200806.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajbio.20200806.12},
  abstract = {Many of the recent emerging infectious diseases have occurred due to the transmission of the viruses that have wildlife reservoirs. Arthropods, such as ticks, are known to be important vectors for spreading viruses and other pathogens from wildlife to domestic animals and humans. In the present study, we explored the diversity of viruses in hard ticks (Ixodidae) from select areas of a wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using a metagenomic approach. cDNA and DNA were amplified with random amplification and Illumina high-throughput sequencing was performed. The high-throughput sequenced data was imported to the CLC genomic workbench and trimmed based on quality (Q = 20) and length (≥ 50). The trimmed reads were assembled and annotated through Blastx using Diamond against the National Center for Biotechnology Information non-redundant database and its viral database. The MEGAN Community was used to analyze and to compare the taxonomy of the viral community. The obtained contigs and singletons were further subjected to alignment and mapping against reference sequences. The viral sequences identified were classified into bacteria, vertebrates, and invertebrates, plants, and protozoans viruses. Sequences related to known viral families; Retroviridae, Flaviviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Phenuiviridae, Totiviridae, Rhabdoviridae, Parvoviridae, Caulimoviridae, Mimiviridae and several Phages were reported. This result indicates that there are many viruses present in the study region, which we are not aware of and do not know the role they have or if they have the potential to spread to other species and cause diseases. Therefore, further studies are required to delineate the viral community present in the region over a large scale.},
 year = {2020}
}

Copy | Download

TY  - JOUR
T1  - Diversity of Viruses in Hard Ticks (Ixodidae) from Select Areas of a Wildlife-livestock Interface Ecosystem at Mikumi National Park, Tanzania
AU  - Donath Damian
AU  - Modester Damas
AU  - Jonas Johansson Wensman
AU  - Mikael Berg
Y1  - 2020/12/28
PY  - 2020
N1  - https://doi.org/10.11648/j.ajbio.20200806.12
DO  - 10.11648/j.ajbio.20200806.12
T2  - American Journal of BioScience
JF  - American Journal of BioScience
JO  - American Journal of BioScience
SP  - 150
EP  - 157
PB  - Science Publishing Group
SN  - 2330-0167
UR  - https://doi.org/10.11648/j.ajbio.20200806.12
AB  - Many of the recent emerging infectious diseases have occurred due to the transmission of the viruses that have wildlife reservoirs. Arthropods, such as ticks, are known to be important vectors for spreading viruses and other pathogens from wildlife to domestic animals and humans. In the present study, we explored the diversity of viruses in hard ticks (Ixodidae) from select areas of a wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using a metagenomic approach. cDNA and DNA were amplified with random amplification and Illumina high-throughput sequencing was performed. The high-throughput sequenced data was imported to the CLC genomic workbench and trimmed based on quality (Q = 20) and length (≥ 50). The trimmed reads were assembled and annotated through Blastx using Diamond against the National Center for Biotechnology Information non-redundant database and its viral database. The MEGAN Community was used to analyze and to compare the taxonomy of the viral community. The obtained contigs and singletons were further subjected to alignment and mapping against reference sequences. The viral sequences identified were classified into bacteria, vertebrates, and invertebrates, plants, and protozoans viruses. Sequences related to known viral families; Retroviridae, Flaviviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Phenuiviridae, Totiviridae, Rhabdoviridae, Parvoviridae, Caulimoviridae, Mimiviridae and several Phages were reported. This result indicates that there are many viruses present in the study region, which we are not aware of and do not know the role they have or if they have the potential to spread to other species and cause diseases. Therefore, further studies are required to delineate the viral community present in the region over a large scale.
VL  - 8
IS  - 6
ER  -

Copy | Download