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      Genotypic Characterization of Emerging Avian Reovirus Genetic Variants in California

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          Abstract

          This study focuses on virus isolation of avian reoviruses from a tenosynovitis outbreak between September 2015 and June 2018, the molecular characterization of selected isolates based on partial S1 gene sequences, and the full genome characterization of seven isolates. A total of 265 reoviruses were detected and isolated, 83.3% from tendons and joints, 12.3% from the heart and 3.7% from intestines. Eighty five out of the 150 (56.6%) selected viruses for sequencing and characterization were successfully detected, amplified and sequenced. The characterized reoviruses grouped in six distinct genotypic clusters (GC1 to GC6). The most represented clusters were GC1 (51.8%) and GC6 (24.7%), followed by GC2 (12.9%) and GC4 (7.2%), and less frequent GC5 (2.4%) and GC3 (1.2%). A shift on cluster representation throughout time occurred. A reduction of GC1 and an increase of GC6 classified strains was noticed. The highest homologies to S1133 reovirus strain were detected in GC1 (~77%) while GC2 to GC6 homologies ranged between 58.5 and 54.1%. Over time these homologies have been maintained. Seven selected isolates were full genome sequenced. Results indicated that the L3, S1 and M2 genes, coding for proteins located in the virus capsid accounted for most of the variability of these viruses. The information generated in the present study helps the understanding of the epidemiology of reoviruses in California. In addition, provides insights on how other genes that are not commonly studied add variability to the reovirus genome.

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          Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages.

          Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The sigma C-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the sigma C-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the sigma C-encoding gene and sigma C protein was higher than for the other S-class genes and other family of viruses. With the exception of the sigma C-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses.
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            Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011–2014

            Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates.
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              The history of avian reovirus.

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                Author and article information

                Contributors
                ragallardo@ucdavis.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                27 June 2019
                27 June 2019
                2019
                : 9
                : 9351
                Affiliations
                [1 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, University of California, Davis, School of Veterinary Medicine, ; Davis, 95616 CA United States
                [2 ]ISNI 0000 0001 2297 8753, GRID grid.252546.2, Auburn University Department of Pathobiology and Department of Poultry Science, ; Auburn, 36832 AL USA
                [3 ]ISNI 0000 0001 0049 1282, GRID grid.266096.d, University of California, Davis, California Animal Health & Food Safety Laboratory System, ; 95380 CA Turlock, USA
                [4 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, University of California, Davis, California Animal Health & Food Safety Laboratory System, ; 93274 CA Tulare, USA
                [5 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, University of California, Davis, California Animal Health & Food Safety Laboratory System, ; 95616 CA Davis, USA
                [6 ]Foster Farms, Livingston, 95334 CA USA
                [7 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, University of California, Davis, School of Agriculture, ; Davis, 95616 CA United States
                Author information
                http://orcid.org/0000-0002-2468-2507
                Article
                45494
                10.1038/s41598-019-45494-4
                6597705
                31249323
                ddaf558e-20a3-4f8c-9c85-a1055252abb1
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 31 December 2018
                : 7 June 2019
                Funding
                Funded by: US Poultry and Egg Association F079 Center for food animal health UC Davis CA-V-PHR-4068-RR
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                viral epidemiology,nutrition disorders
                Uncategorized
                viral epidemiology, nutrition disorders

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