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Wang X, Yu H, Zhang W, Fu L, Wang Y. Molecular Detection and Genetic Characterization of Vertically Transmitted Viruses in Ducks. Animals (Basel) 2023; 14:6. [PMID: 38200736 PMCID: PMC10777988 DOI: 10.3390/ani14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
To investigate the distribution and genetic variation in four vertically transmitted duck pathogens, including duck hepatitis B virus (DHBV), duck circovirus (DuCV), duck hepatitis A virus 3 (DHAV-3), and avian reoviruses (ARV), we conducted an epidemiology study using PCR and RT-PCR assays on a duck population. We found that DHBV was the most prevalent virus (69.74%), followed by DuCV (39.48%), and then ARV (19.92%) and DHAV-3 (8.49%). Among the 271 duck samples, two, three or four viruses were detected in the same samples, indicating that the coinfection of vertical transmission agents is common in ducks. The genetic analysis results showed that all four identified DuCV strains belonged to genotype 1, the DHAV-3 strain was closely clustered with previously identified strains from China, and the ARV stain was clustered under genotype 1. These indicate that different viral strains are circulating among the ducks. Our findings will improve the knowledge of the evolution of DuCV, DHAV-3, and ARV, and help choose suitable strains for vaccination.
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Affiliation(s)
- Xinrong Wang
- College of Veterinary Medicine, Southwest University, Chongqing 400715, China
| | - Haidong Yu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150068, China
| | - Wenli Zhang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150068, China
| | - Lizhi Fu
- Chongqing Academy of Animal Science, Chongqing 408599, China;
| | - Yue Wang
- College of Veterinary Medicine, Southwest University, Chongqing 400715, China
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Narvaez SA, Harrell TL, Oluwayinka O, Sellers HS, Khalid Z, Hauck R, Chowdhury EU, Conrad SJ. Optimizing the Conditions for Whole-Genome Sequencing of Avian Reoviruses. Viruses 2023; 15:1938. [PMID: 37766345 PMCID: PMC10536876 DOI: 10.3390/v15091938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Whole-genome sequencing (WGS) is becoming an essential tool to characterize the genomes of avian reovirus (ARV), a viral disease of economic significance to poultry producers. The current strategies and procedures used to obtain the complete genome sequences of ARV isolates are not cost-effective because most of the genetic material data resulting from next-generation sequencing belong to the host and cannot be used to assemble the viral genome. The purpose of this study was to develop a workflow to enrich the ARV genomic content in a sample before subjecting it to next-generation sequencing (NGS). Herein, we compare four different ARV purification and enrichment approaches at the virion, RNA and cDNA levels to determine which treatment or treatment combination would provide a higher proportion of ARV-specific reads after WGS. Seven ARV isolates were subjected to different combinations of virion purification via ultracentrifugation in sucrose density gradient or Capto Core 700 resin with or without a subsequent Benzonase treatment, followed by a chicken rRNA depletion step after RNA extraction and a final ARV cDNA amplification step using a single-primer amplification assay. Our results show that the combination of Capto Core 700 resin, Chicken rRNA depletion and cDNA amplification is the most cost-effective strategy to obtain ARV whole genomes after short-read sequencing.
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Affiliation(s)
- Sonsiray Alvarez Narvaez
- US Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA 30605, USA; (S.A.N.); (T.L.H.); (O.O.)
| | - Telvin L. Harrell
- US Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA 30605, USA; (S.A.N.); (T.L.H.); (O.O.)
| | - Olatunde Oluwayinka
- US Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA 30605, USA; (S.A.N.); (T.L.H.); (O.O.)
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA;
| | - Holly S. Sellers
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA;
| | - Zubair Khalid
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (Z.K.); (R.H.)
| | - Ruediger Hauck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (Z.K.); (R.H.)
- Department of Poultry Science, College of Agriculture, Auburn University, Auburn, AL 36849, USA
| | - Erfan U. Chowdhury
- Alabama Department of Agriculture and Industries, Veterinary Diagnostic Laboratory System, Auburn, AL 36832, USA;
| | - Steven J. Conrad
- US Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA 30605, USA; (S.A.N.); (T.L.H.); (O.O.)
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