A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams ( Lutraria r
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BRIEF REPORT
A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams (Lutraria rhynchaena) Oanh T. P. Kim1 · Yuki Kagaya2 · Hoang S. Tran1 · Ryuhei Minei3 · Trang T. H. Tran1 · Ha T. T. Duong1,4 · Binh T. N. Le1 · Lua T. Dang5 · Kengo Kinoshita2 · Atsushi Ogura3 · Kei Yura4,6 Received: 17 May 2020 / Accepted: 21 August 2020 / Published online: 28 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract In this study, we present an analysis of metagenome sequences obtained from a filtrate of a siphon tissue homogenate of otter clams (Lutraria rhynchaena) with swollen-siphon disease. The viral signal was mined from the metagenomic data, and a novel circular ssDNA virus was identified. Genomic features and phylogenetic analysis showed that the virus belongs to the phylum Cressdnaviricota, which consists of viruses with circular, single-stranded DNA (ssDNA) genomes. Members of this phylum have been identified in various species and in environmental samples. The newly found virus is distantly related to the currently known members of the phylum Cressdnaviricota. Otter clam (Lutraria rhynchaena Jonas, 1844 or Lutraria philippinarum Reeve, 1854) is a bivalve species living in high-salinity waters (17-48‰) with warm temperatures (12-37°C). This species is found in Asian countries such as China, Thailand, the Philippines and Vietnam [1]. Otter clams are served as a special dish because their meat is delicious and rich in nutrients. They therefore have a significantly higher value on the market than most other bivalve mollusks. In Vietnam, this species has been successfully farmed in the northern and central parts of the country. From the northern farms (Quang Ninh Provice, Vietnam), otter clam production reached over 1,200 tons in 2011 [2]. Handling Editor: Roman Pogranichniy. * Oanh T. P. Kim [email protected] 1
Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, 100000 Ha Noi, Vietnam
2
Graduate School of Information Sciences, Tohoku University, Sendai 980‑8570, Japan
3
Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga 526‑0829, Japan
4
Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 112‑8610, Japan
5
Research Institute of Aquaculture, No. 1 Dinh Bang, Tu Son, Bac Ninh 790000, Vietnam
6
School of Advanced Science and Engineering, Waseda University, Tokyo 162‑0041, Japan
However, otter clam farming has become susceptible to new disease, which is called “swollen-siphon disease” since the end of 2011. The outbreak of this disease has resulted in a serious decline in otter clam aquaculture and in substantial economic losses in Vietnam, but the cause of the disease is still to be discovered [3, 4]. There have been several attempts to identify the causative agent of the disease. Three Vibrio bacterial species (V. alginolyticus, V. cholerae and V. splendidus) were found abundantly in infected clams from all farming areas, but a challenge (re
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