Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Virus Discovery
2.3. Screening and Sequencing
2.4. Sequence and Phylogenetic Analyses
2.5. Codon Usage and Nucleotide Frequency Analyses
2.6. Statistical Analyses
3. Results
3.1. Positivity Rates
3.2. Molecular Features of the Novel Chaphamaparvoviruses
3.2.1. Genome Organization
3.2.2. Phylogenetic Analyses
3.3. Molecular Features of the Novel Ambidensoviruses
3.3.1. Genome Organization
3.3.2. Phylogenetic Analysis
3.4. Codon Usage and Nucleotide Frequency Bias Analyses
4. Discussion
4.1. Duck-Associated Chapparvovirus (DAC) and Duck-Associated Ambidensovirus (DAAD) Are Novel Viral Species
4.2. Potential Hosts and Epidemiology of DAC and DAAD
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Host | DAC 1 | DAAD 1 | |
---|---|---|---|
Ducks | Total, n = 123 | 7 (5.7%) | 26 (21.1%) |
American black duck, n = 109 | 6 (27.3%) | 22 (20.2%) | |
Mallard, n = 9 | 1 (11.1%) | 2 (22.2%) | |
Northern pintail, n = 1 | 0 (0%) | 1 (100%) | |
Hybrids, n = 4 | 0 (0%) | 1 (25%) | |
Gulls | Total, n = 21 | 0 (0%) | 0 (0%) |
Herring gull, n = 8 | 0 (0%) | 0 (0%) | |
Iceland gull, n = 4 | 0 (0%) | 0 (0%) | |
Ring-billed gull, n = 9 | 0 (0%) | 0 (0%) |
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Canuti, M.; Verhoeven, J.T.P.; Munro, H.J.; Roul, S.; Ojkic, D.; Robertson, G.J.; Whitney, H.G.; Dufour, S.C.; Lang, A.S. Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis. Viruses 2021, 13, 193. https://doi.org/10.3390/v13020193
Canuti M, Verhoeven JTP, Munro HJ, Roul S, Ojkic D, Robertson GJ, Whitney HG, Dufour SC, Lang AS. Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis. Viruses. 2021; 13(2):193. https://doi.org/10.3390/v13020193
Chicago/Turabian StyleCanuti, Marta, Joost T. P. Verhoeven, Hannah J. Munro, Sheena Roul, Davor Ojkic, Gregory J. Robertson, Hugh G. Whitney, Suzanne C. Dufour, and Andrew S. Lang. 2021. "Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis" Viruses 13, no. 2: 193. https://doi.org/10.3390/v13020193