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Stepien CA, Niner MD. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification. Ecol Evol 2020; 10:9740-9775. [PMID: 33005343 PMCID: PMC7520192 DOI: 10.1002/ece3.6611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 02/05/2023] Open
Abstract
Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
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Affiliation(s)
- Carol A. Stepien
- Genetics and Genomics Group (G3)NOAA Pacific Marine Environmental Laboratory (PMEL)SeattleWAUSA
| | - Megan D. Niner
- Genetics and Genomics Group (G3), Department of Environmental SciencesUniversity of ToledoToledoOHUSA
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Shityakov S, Bencurova E, Förster C, Dandekar T. Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. BMC Bioinformatics 2020; 21:132. [PMID: 32245400 PMCID: PMC7126183 DOI: 10.1186/s12859-020-3461-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/19/2020] [Indexed: 01/02/2023] Open
Abstract
Background Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of long DNA fragments, the difficulty of assembling them and the complexity of the used genomes. On the other hand, the Sanger DNA sequencing method is still considered to be the most reliable; it is a reliable choice for virtual modeling to build all possible consensus sequences from smaller DNA fragments. Results In silico and in vitro experiments were conducted: (1) to implement and test our novel sequencing algorithm, using the standard cloning vectors of different length and (2) to validate experimentally virtual shotgun sequencing using the PCR technique with the number of cycles from 1 to 9 for each reaction. Conclusions We applied a novel algorithm based on Sanger methodology to correctly predict and emphasize the performance of DNA sequencing techniques as well as in de novo DNA sequencing and its further application in synthetic biology. We demonstrate the statistical significance of our results. Graphical abstract ![]()
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Affiliation(s)
- Sergey Shityakov
- Department of Bioinformatics, University of Würzburg, 97074, Würzburg, Germany. .,Department of Psychiatry, China Medical University Hospital, 404, Taichung, Taiwan.
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, 97074, Würzburg, Germany
| | - Carola Förster
- Department of Anesthesia and Critical Care, Würzburg University Hospital, 97080, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, 97074, Würzburg, Germany.
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Gao X, Li Q, Fang L, Song H, Cui Z, Meng F, Zhang Z. The follicle promotes the evolution of variants of avian leukosis virus subgroup J in vertical transmission. Biochem Biophys Res Commun 2019; 521:1089-1094. [PMID: 31733830 DOI: 10.1016/j.bbrc.2019.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 11/17/2022]
Abstract
Avian leukosis virus (ALV) is one of the main causative agent of tumor development, which brings enormous economic losses to the poultry industry worldwide. ALV can be transmitted horizontally and vertically, and the latter often give rise to more adverse pathogenicity. However, the propagation and evolution of ALV underlying vertical transmission remain not-well understood. Herein, an animal model for the evolution of variants of ALV subgroup J (ALV-J) in the vertical transmission was built and different organs from infected hens and plasma from their ALV-positive progenies were collected, and then three segments in the hypervariable regions of ALV (gp85-A, gp85-B, LTR-C) were amplified and sequenced using conventional Sanger sequencing and MiSeq high-throughput sequencing, respectively. The results showed that the genomic diversity of ALV-J occurred in different organs from ALV-J infected hen, and that the dominant variants in different organs of parental hens, especially in follicle, changed significantly compared with original inoculum strain. Notably, the dominant variants in progenies exhibited higher homologies with variants in parental hens' follicle (88.9%-98.9%) than other organs (85.6%-91.1%), and most consistent mutations in the variants were observed between the progenies and parental hen's follicle. Furthermore, HyPhy analysis indicated that the global selection pressure value (ω) in the follicle is significantly higher than those in other organs. In summary, an animal model for vertical transmission was built and our findings revealed the evolution of variants of ALV in the process of vertical transmission, moreover, the variants were most likely to be taken to the next generation via follicle, which may be related to the higher selection pressure follicle underwent.
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Affiliation(s)
- Xintao Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Qiuchen Li
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China
| | - Lichun Fang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Haozhi Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Fanfeng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Dong X, Meng F, Hu T, Ju S, Li Y, Sun P, Wang Y, Chen W, Zhang F, Su H, Li S, Cui H, Chen J, Xu S, Fang L, Luan H, Zhang Z, Chang S, Li J, Wang L, Zhao P, Shi W, Cui Z. Dynamic Co-evolution and Interaction of Avian Leukosis Virus Genetic Variants and Host Immune Responses. Front Microbiol 2017; 8:1168. [PMID: 28694798 PMCID: PMC5483431 DOI: 10.3389/fmicb.2017.01168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/08/2017] [Indexed: 01/02/2023] Open
Abstract
Subgroup J avian leukosis virus (ALV-J), a typical retrovirus, is characterized of existence of a cloud of diverse variants and considerable genetic diversity. Previous studies describing the evolutionary dynamics of ALV-J genetic variants mainly focused on the early infection period or few randomly selected clones. Here, we inoculated 30 specific-pathogen-free chickens with the same founder ALV-J stock of known genetic background. Six (three antibody positive and three antibody negative) chickens were selected among 15 chickens with viremia. Viruses were serially isolated in 36 weeks and then sequenced using MiSeq high-throughput sequencing platform. This produced the largest ALV-J dataset to date, composed of more than three million clean reads. Our results showed that host humoral immunity could greatly enhance the genetic diversity of ALV-J genetic variants. In particular, selection pressures promoted a dynamic proportional changes in ALV-J genetic variants frequency. Cross-neutralization experiment showed that along with the change of the dominant variant, the antibody titers specific to infectious clones corresponding to the most dominant variants in weeks 12 and 28 have also changed significantly in sera collected in weeks 16 and 32. In contrast, no shift of dominant variant was observed in antibody-negative chickens. Moreover, we identified a novel hypervariable region in the gp85 gene. Our study reveals the interaction between ALV-J and the host, which could facilitate the development of vaccines and antiviral drugs.
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Affiliation(s)
- Xuan Dong
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Fanfeng Meng
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Tao Hu
- Institute of Pathogen Biology, Taishan Medical CollegeTaian, China
| | - Sidi Ju
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Yang Li
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Peng Sun
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Yixin Wang
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Wenqing Chen
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Fushou Zhang
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Hongqin Su
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Sifei Li
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - He Cui
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Junxia Chen
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Shuzhen Xu
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Lichun Fang
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Huaibiao Luan
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Zhenjie Zhang
- Institute of Pathogen Biology, Taishan Medical CollegeTaian, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Jianliang Li
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Lei Wang
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
| | - Weifeng Shi
- Institute of Pathogen Biology, Taishan Medical CollegeTaian, China
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural UniversityTaian, China
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