Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Nucleic Acid Extraction
2.3. Screening of Hepatitis Viruses and Pegivirus
2.4. Complete Genome Sequencing
2.5. Hepacivirus RNA Titer Measurement
2.6. Sequence Analysis
3. Results
3.1. Detection of Hepatitis Viruses in Bat and Rodent Liver Samples
3.2. Screening of Rodent Serum Samples for Hepacivirus and Pegivirus
3.3. Sequence and Phylogenetic Analysis
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Appendix A
References
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Species | Tested | Positive (%) | ||
---|---|---|---|---|
Hepacivirus | HEV | HBV | ||
Bandicota indica | 38 | 0 | 1 (2.6) | 0 |
Rattus argentiventer | 275 | 2 (0.7) | 10 (3.6) | 0 |
Rattus losea | 19 | 1 (5.3) | 2 (10.5) | 0 |
Rattus norvegicus | 39 | 0 | 0 | 0 |
Rattus tanezumi | 17 | 0 | 1 (5.9) | 0 |
Rhizomys pruinosus | 82 | 35 (42.7) | 0 | 0 |
Total | 470 | 38 (8.1) | 14 (3) | 0 |
Virus | Sequence | Compared Region | Highest Nucleotide Identity (%) | Highest Amino Acid Identity (%) | Closest Match |
---|---|---|---|---|---|
Rodent hepacivirus | 05VZ-14-103 | Complete cds | 59.7 | 63.3 | KC815310 |
05VZ-14-104 | Complete cds | 59.7 | 63.2 | KC815310 | |
05VZ-14-118 | Complete cds | 59.5 | 63.3 | KC815310 | |
05VZ-14-119 | Complete cds | 59.5 | 63.3 | KC815310 | |
Rodent HEV | 05VZ-75-65-L08-R3 | ORF1 + ORF2 | 81.5 | 93.2 | JX120573 |
Bat HBV | Bat031 | P gene | 89 | 87 | KY905324 |
S gene | 91 | 94 | KY905324 | ||
X gene | 92.4 | 86 | KY905324 | ||
C gene | 90 | 96.3 | KY905324 | ||
Bat033 | P gene | 82.5 | 80 | KY905328 | |
S gene | 87 | 84 | KY905328 | ||
X gene | 90 | 80 | KY905324 | ||
C gene | 89 | 97.2 | KY905327 | ||
Rodent pegivirus | 05VZ-14-070 | Complete cds | 65.2 | 65.5 | KJ950934 |
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Van Nguyen, D.; Van Nguyen, C.; Bonsall, D.; Ngo, T.T.; Carrique-Mas, J.; Pham, A.H.; Bryant, J.E.; Thwaites, G.; Baker, S.; Woolhouse, M.; et al. Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam. Viruses 2018, 10, 102. https://doi.org/10.3390/v10030102
Van Nguyen D, Van Nguyen C, Bonsall D, Ngo TT, Carrique-Mas J, Pham AH, Bryant JE, Thwaites G, Baker S, Woolhouse M, et al. Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam. Viruses. 2018; 10(3):102. https://doi.org/10.3390/v10030102
Chicago/Turabian StyleVan Nguyen, Dung, Cuong Van Nguyen, David Bonsall, Tue Tri Ngo, Juan Carrique-Mas, Anh Hong Pham, Juliet E. Bryant, Guy Thwaites, Stephen Baker, Mark Woolhouse, and et al. 2018. "Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam" Viruses 10, no. 3: 102. https://doi.org/10.3390/v10030102
APA StyleVan Nguyen, D., Van Nguyen, C., Bonsall, D., Ngo, T. T., Carrique-Mas, J., Pham, A. H., Bryant, J. E., Thwaites, G., Baker, S., Woolhouse, M., & Simmonds, P. (2018). Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam. Viruses, 10(3), 102. https://doi.org/10.3390/v10030102