The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Mosquito Collection
2.2. Nucleic Acid Purification and High-Throughput Sequencing
2.3. PCR Screening
2.4. Phylogenetics
2.5. Accession Numbers
3. Results
3.1. Mosquito Collection
3.2. High-Throughput Sequencing
3.3. Virus Genomic Characterization
3.3.1. Positive-Sense ssRNA Viruses
Flavivirus
Nege- and Virgaviruses
Iflavirus
Luteo-Like Viruses
3.3.2. Negative-Sense ssRNA Viruses
Phenuiviruses
Qinvirus
3.3.3. Double-Stranded RNA Viruses
3.3.4. Single-Stranded DNA Virus
3.4. Virus Distribution and Prevalence
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Trap Code | Trap Location | GPS (Latitude) | GPS (Longitude) | Trap Set Date | Total Trapped Cx. annulirostris |
---|---|---|---|---|---|
B1 | Adjacent to caravan park, Broome | −17.97763161 | 122.2125935 | 9 April 2018 | 188 * |
B2 | Cemetery, Broome | −17.95775700 | 122.2244490 | 10 April 2018 | 405 * |
FC1 | Rotunda, Fitzroy Crossing | −18.10542047 | 125.7016503 | 6 April 2018 | 135 |
FC2 | Floodway, Fitzroy Crossing | −18.11554849 | 125.6773817 | 6 April 2018 | 170 |
PC1 | Jogalong Billabong, Parry’s Creek | −15.59154698 | 128.2619530 | 26 March 2018 | 1971 * |
PC2 | Mangrove, Parry’s Creek | −15.59409900 | 128.2880270 | 26 March 2018 | 17,687 * |
Agent | Target Gene | Forward Primer (5′–3′) | Reverse Primer (5′–3′) | Product Size (nt) |
---|---|---|---|---|
Jogalong virus | NS5B | CAGGTCCCTATTCTTACACGG | TCTGGTAACCGAGGTGTTGC | 337 |
Broome phasivirus 1 | RdRp | TTCAGATGGATTAAACCTGGCG | CTAGATCTTCTTGCCACTTCAGC | 269 |
Parry’s Creek phasivirus 1 | RdRp | CCAGACTGTTAGCAGCATCAATC | TCAATTCCTCTTGCCTGGAGAG | 225 |
Fitzroy Crossing tenuivirus 1 | RdRp | CTGGCATTGCCGGATTATCC | CTAGGCTTGAAATGACTCCAGG | 351 |
Parry’s Creek negev-like virus 1 | RdRp | AACTGCAGAGGGTGATATCGG | ATAGCATCGCCGCTCTTCC | 204 |
Fitzroy Crossing iflavirus 1 | Polyprotein | GTTGCAATACTACCAACGGCTC | CAAACCCACCATCGTGGTC | 240 |
Virus Name | Family | BLAST Region | BLAST Length (aa) | Most Similar Viral Sequence | Coverage (%) | BLAST Identity (%) | E-Value |
---|---|---|---|---|---|---|---|
Jogalong virus | Flaviviridae | Polyprotein | 2941 | Bald eagle hepacivirus | 91 | 40.32 | 0 |
Parry’s Creek negev-like virus 1 | Hepe-Virga * | RdRp | 2742 * | Yongsan negev-like virus 1 | 99 * | 87.71 | 0 |
Broome virga-like virus 1 | Hepe-Virga * | RdRp | 2417 | Hubei virga-like virus 18 | 100 | 81.81 | 0 |
Fitzroy Crossing iflavirus 1 | Iflaviridae | Polyprotein | 2905 | Hubei arthropod virus 1 | 96 | 47.74 | 0 |
Broome luteo-like virus 1 | Luteo-Sobemo * | RdRp | 372 | Culex mosquito virus 6 | 100 | 76.88 | 0 |
Broome phasivirus 1 | Phenuiviridae | RdRp | 2182 | Badu phasivirus | 100 | 87.53 | 0 |
Parry’s Creek phasivirus 1 | Phenuiviridae | RdRp | 2219 | Badu phasivirus | 99 | 88.27 | 0 |
Fitzroy Crossing tenui-like virus 1 | Phenuiviridae | RdRp | 2842 | Rice grassy stunt virus | 78 | 32.98 | 0 |
Fitzroy Crossing qinvirus 1 | Qinvirus * | RdRp | 1752 | Vinslov virus | 100 | 79.74 | 0 |
Broome reo-like virus 1 | Reoviridae | RdRp | 1308 | Sanxia reo-like virus 1 | 88 | 36.76 | 9 × 10−177 |
Fitzroy Crossing toti-like virus 1 | Toti-Chryso * | RdRp | 806 | Lindangsbacken virus | 100 | 79.16 | 0 |
Fitzroy Crossing toti-like virus 2 | Toti-Chryso * | Hyp. protein 2 | 758 | Hubei toti-like virus 10 | 89 | 49.93 | 0 |
Parry’s Creek toti-like virus 1 | Toti-Chryso * | RdRp | 1418 | Ahus virus | 91 | 75.48 | 0 |
Broome chryso-like virus 1 | Chrysoviridae | RdRp | 1118 | Hubei chryso-like virus 1 | 100 | 88.46 | 0 |
Broome partiti-like virus 1 | Partiti-Picobirna * | RdRp | 393 | Vespa velutina partiti-like virus 1 | 96 | 56.81 | 1 × 10−149 |
Broome densovirus 1 | Parvoviridae | NS1 | 583 | Haematobia irritans densovirus | 86 | 28.04 | 2 × 10−53 |
Site | Trap | Jogalong Virus | Parry’s Creek Negev-Like Virus 1 | Fitzroy Crossing Iflavirus 1 | Broome Phasivirus 1 | Parry’s Creek Phasivirus 1 | Fitzroy Crossing Tenui-Like Virus 1 |
---|---|---|---|---|---|---|---|
Broome | B1 | 0/50 | 0/50 | 0/50 | 35/50 (70%) | 0/50 | 0/50 |
B2 | 0/50 | 1/50 (2%) | 0/50 | 24/50 (48%) | 0/50 | 0/50 | |
Fitzroy Crossing | FC1 | 0/50 | 0/50 | 1/50 (2%) | 2/50 (4%) | 0/50 | 2/50 (4%) |
FC2 | 0/50 | 1/50 (2%) | 0/50 | 0/50 | 1/50 (2%) | 0/50 | |
Parry’s Creek | PC1 | 1/50 (2%) | 2/50 (4%) | 0/50 | 2/50 (4%) | 14/50 (28%) | 0/50 |
PC2 | 0/50 | 3/50 (6%) | 0/50 | 1/50 (2%) | 2/50 (4%) | 0/50 | |
Total | 1/300 (0.3%) | 7/300 (2.3%) | 1/300 (0.3%) | 64/300 (21.3%) | 17/300 (5.7%) | 2/300 (0.7%) |
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Williams, S.H.; Levy, A.; Yates, R.A.; Somaweera, N.; Neville, P.J.; Nicholson, J.; Lindsay, M.D.A.; Mackenzie, J.S.; Jain, K.; Imrie, A.; et al. The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia. Viruses 2020, 12, 717. https://doi.org/10.3390/v12070717
Williams SH, Levy A, Yates RA, Somaweera N, Neville PJ, Nicholson J, Lindsay MDA, Mackenzie JS, Jain K, Imrie A, et al. The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia. Viruses. 2020; 12(7):717. https://doi.org/10.3390/v12070717
Chicago/Turabian StyleWilliams, Simon H., Avram Levy, Rachel A. Yates, Nilusha Somaweera, Peter J. Neville, Jay Nicholson, Michael D. A. Lindsay, John S. Mackenzie, Komal Jain, Allison Imrie, and et al. 2020. "The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia" Viruses 12, no. 7: 717. https://doi.org/10.3390/v12070717
APA StyleWilliams, S. H., Levy, A., Yates, R. A., Somaweera, N., Neville, P. J., Nicholson, J., Lindsay, M. D. A., Mackenzie, J. S., Jain, K., Imrie, A., Smith, D. W., & Lipkin, W. I. (2020). The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia. Viruses, 12(7), 717. https://doi.org/10.3390/v12070717