Long-range PCR and high-throughput sequencing of Ostreid herpesvirus 1 indicate high genetic diversity and complex evolution process

Type Article
Date 2019-01
Language English
Author(s) Bai Chang-MingORCID1, 2, 3, 4, Morga BenjaminORCID5, Rosani Umberto6, Shi Jie1, 2, 3, 4, Li Chen1, 2, 3, 4, Xin Lu-Sheng1, 2, 3, 4, Wang Chong-Ming1, 2, 3, 4
Affiliation(s) 1 : Chinese Acad Fishery Sci, Key Lab Maricultural Organism Dis Control, Minist Agr, Qingdao, Shandong, Peoples R China.
2 : Chinese Acad Fishery Sci, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao Natl Lab Marine Sci & Technol, Qingdao, Shandong, Peoples R China.
3 : Chinese Acad Fishery Sci, Qingdao Key Lab Mariculture Epidemiol & Biosecur, Qingdao, Shandong, Peoples R China.
4 : Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China.
5 : IFREMER, LGP, Ave Mus Loup, F-17390 La Tremblade, France.
6 : Univ Padua, Dept Biol, Padua, Italy.
Source Virology (0042-6822) (Academic Press Inc Elsevier Science), 2019-01 , Vol. 526 , P. 81-90
DOI 10.1016/j.virol.2018.09.026
WOS© Times Cited 9
Keyword(s) Long-range PCR, OsHV-1, High-throughput sequencing, Evolution, Diversity
Abstract

Ostreid herpesvirus 1 (OsHV-1) is an important pathogen associated with mass mortalities of cultivated marine mollusks worldwide. Since no cell line allows OsHV-1 replication in vitro, it is difficult to isolate enough high-purity viral DNA for High-Throughput Sequencing (HTS). We developed an efficient approach for the enrichment of OsHV-1 DNA for HTS with long-range PCR. Twenty-three primer pairs were designed to cover 99.3% of the reference genome, and their performances were examined on ten OsHV-1 infected samples. Amplicon mixtures from six successfully amplified samples were sequenced with Illumina platform, and one of them (ZK0118) was also sequenced with the PacBio platform. PacBio reads were assembled into 2 scaffolds compared to 9−68 scaffolds assembled from the Illumina reads. Genomic comparison confirmed high genetic diversity among OsHV-1 variants. Phylogenetic analysis revealed that OsHV-1 evolution was mainly impacted by its host species rather than spatial segregation.

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