Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China
Background Deformed wing virus (DWV) is one of many viruses that infect honeybees and has been extensively studied because of its close association with honeybee colony collapse that is induced by Varroa destructor. However, virus genotypes, sequence characteristics, and genetic variations of DWV re...
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PeerJ Inc.
2019-06-01
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| author | Dongliang Fei Yaxi Guo Qiong Fan Haoqi Wang Jiadi Wu Ming Li Mingxiao Ma |
| author_facet | Dongliang Fei Yaxi Guo Qiong Fan Haoqi Wang Jiadi Wu Ming Li Mingxiao Ma |
| author_sort | Dongliang Fei |
| collection | DOAJ |
| description | Background Deformed wing virus (DWV) is one of many viruses that infect honeybees and has been extensively studied because of its close association with honeybee colony collapse that is induced by Varroa destructor. However, virus genotypes, sequence characteristics, and genetic variations of DWV remain unknown in China. Methods Two DWV strains were isolated from Jinzhou and Qinhuangdao cities in China, and were named China1-2017 (accession number: MF770715) and China2-2018 (accession number: MH165180), respectively, and their complete genome sequences were analyzed. To investigate the phylogenetic relationships of the DWV isolates, a phylogenetic tree of the complete open reading frame (ORF), structural protein VP1, and non-structural protein 3C+RdRp of the DWV sequences was constructed using the MEGA 5.0 software program. Then, the similarity and recombinant events of the DWV isolated strains were analyzed using recombination detection program (RDP4) software and genetic algorithm for recombination detection (GARD). Results The complete genomic analysis showed that the genomes of the China1-2017 and China2-2018 DWV strains consisted of 10,141 base pairs (bp) and 10,105 bp, respectively, and contained a single, large ORF (China1-2017: 1,146–9,827 bp; China2-2018: 1,351–9,816 bp) that encoded 2,894 amino acids. The sequences were compared with 20 previously reported DWV sequences from different countries and with sequences of two closely related viruses, Kakugo virus (KV) and V. destructor virus-1. Multiple sequence comparisons revealed a nucleotide identity of 84.3–96.7%, and identity of 94.7–98.6% in amino acids between the two isolate strains and 20 reference strains. The two novel isolates showed 96.7% nucleotide identity and 98.1% amino acid identity. The phylogenetic analyses showed that the two isolates belonged to DWV Type A and were closely related to the KV-2001 strain from Japan. Based on the RDP4 and GARD analyses, the recombination of the China2-2018 strain was located at the 4,266–7,507 nt region, with Korea I-2012 as an infer unknown parent and China-2017 as a minor parent, which spanned the entire helicase ORF. To the best of our knowledge, this is the first study to the complete sequence of DWV isolated from Apis cerana and the possible DWV recombination events in China. Our findings are important for further research of the phylogenetic relationship of DWVs in China with DWV strains from other countries and also contribute to the understanding of virological properties of these complex DWV recombinants. |
| first_indexed | 2024-03-09T06:53:01Z |
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| spelling | doaj.art-471c106fff61409db686a4d20717cfed2023-12-03T10:16:33ZengPeerJ Inc.PeerJ2167-83592019-06-017e721410.7717/peerj.7214Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in ChinaDongliang Fei0Yaxi Guo1Qiong Fan2Haoqi Wang3Jiadi Wu4Ming Li5Mingxiao Ma6Institute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaInstitute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaJinzhou Animal Disease Prevention and Control Center, Jinzhou, Liaoning, ChinaInstitute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaInstitute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaInstitute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaInstitute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, ChinaBackground Deformed wing virus (DWV) is one of many viruses that infect honeybees and has been extensively studied because of its close association with honeybee colony collapse that is induced by Varroa destructor. However, virus genotypes, sequence characteristics, and genetic variations of DWV remain unknown in China. Methods Two DWV strains were isolated from Jinzhou and Qinhuangdao cities in China, and were named China1-2017 (accession number: MF770715) and China2-2018 (accession number: MH165180), respectively, and their complete genome sequences were analyzed. To investigate the phylogenetic relationships of the DWV isolates, a phylogenetic tree of the complete open reading frame (ORF), structural protein VP1, and non-structural protein 3C+RdRp of the DWV sequences was constructed using the MEGA 5.0 software program. Then, the similarity and recombinant events of the DWV isolated strains were analyzed using recombination detection program (RDP4) software and genetic algorithm for recombination detection (GARD). Results The complete genomic analysis showed that the genomes of the China1-2017 and China2-2018 DWV strains consisted of 10,141 base pairs (bp) and 10,105 bp, respectively, and contained a single, large ORF (China1-2017: 1,146–9,827 bp; China2-2018: 1,351–9,816 bp) that encoded 2,894 amino acids. The sequences were compared with 20 previously reported DWV sequences from different countries and with sequences of two closely related viruses, Kakugo virus (KV) and V. destructor virus-1. Multiple sequence comparisons revealed a nucleotide identity of 84.3–96.7%, and identity of 94.7–98.6% in amino acids between the two isolate strains and 20 reference strains. The two novel isolates showed 96.7% nucleotide identity and 98.1% amino acid identity. The phylogenetic analyses showed that the two isolates belonged to DWV Type A and were closely related to the KV-2001 strain from Japan. Based on the RDP4 and GARD analyses, the recombination of the China2-2018 strain was located at the 4,266–7,507 nt region, with Korea I-2012 as an infer unknown parent and China-2017 as a minor parent, which spanned the entire helicase ORF. To the best of our knowledge, this is the first study to the complete sequence of DWV isolated from Apis cerana and the possible DWV recombination events in China. Our findings are important for further research of the phylogenetic relationship of DWVs in China with DWV strains from other countries and also contribute to the understanding of virological properties of these complex DWV recombinants.https://peerj.com/articles/7214.pdfDWVIsolationPhylogenetic analysisRecombinationChina |
| spellingShingle | Dongliang Fei Yaxi Guo Qiong Fan Haoqi Wang Jiadi Wu Ming Li Mingxiao Ma Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China PeerJ DWV Isolation Phylogenetic analysis Recombination China |
| title | Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China |
| title_full | Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China |
| title_fullStr | Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China |
| title_full_unstemmed | Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China |
| title_short | Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China |
| title_sort | phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in china |
| topic | DWV Isolation Phylogenetic analysis Recombination China |
| url | https://peerj.com/articles/7214.pdf |
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