Identification and complete genomic sequence of a novel sadwavirus discovered in pineapple (Ananas comosus)

Authors: LARREA-SARMIENTO, ADRIANA - University Of Hawaii; OLMEDO-VELARDE, ALEJANDRO - University Of Hawaii; GREEN, JAMES - University Of Hawaii; AL RWAHNIH, MAHER - University Of California, Davis; WANG, XUPENG - University Of Hawaii; LI, YUN-HE - Chinese Academy Of Tropical Agricultural Sciences; WU, WEIHUAI - Chinese Academy Of Tropical Agricultural Sciences; ZHANG, JINGXIN - Guangdong Academy Of Agricultural Sciences; Matsumoto Brower, Tracie; Suzuki, Jon; Wall, Marisa; MELZER, MICHAEL - University Of Hawaii; HU, JOHN - University Of Hawaii

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2020
Publication Date: 3/29/2020
Citation: Larrea-Sarmiento, A., Olmedo-Velarde, A., Green, J.C., Al Rwahnih, M., Wang, X., Li, Y., Wu, W., Zhang, J., Matsumoto Brower, T.K., Suzuki, J.Y., Wall, M.M., Melzer, M.J., Hu, J.S. 2020. Identification and complete genomic sequence of a novel sadwavirus discovered in pineapple (Ananas comosus). Archives of Virology. 165:1245-1248. https://doi.org/10.1007/s00705-020-04592-9.
DOI: https://doi.org/10.1007/s00705-020-04592-9

Interpretive Summary: Pineapple (Ananas comosus) is a monocotyledonous perennial plant originating in South America. It is now widely distributed and consumed and is the eleventh most cultivated fruit worldwide according to the Food and Agriculture Organization of the United Nations (FAO). It was introduced to Hawaii in 1813 and subsequently became an economically significant crop. Infections by plant viruses from the genus Ampelovirus have previously been found to be associated with mealybug wilt of pineapple, a disease affecting various pineapple cultivars globally. However, the situation is complicated by the fact that mealybug wilt symptoms do not always manifest, even though plants harbor the Ampelovirus-related viruses. Next generation sequencing of three asymptomatic pineapple samples from the National Clonal Germplasm Repository (NCGR) in Hilo, Hawaii did indeed reveal the presence of the Ampelovirus-related viruses, however, one of the plant samples contained in addition, sequences corresponding to a novel plant RNA virus with sequence similarity to viruses of the genus Sadwavirus of the plant virus family, Secoviridae. The proposed name for this new virus is “pineapple secovirus A” or “PSVA”. The method to enable molecular detection of PSVA in pineapple was developed in this study to enable diagnostic identification of this virus from plant samples. By this method, it was discovered that whereas 13 symptomatic pineapples in the field tested positive for one of the Ampelovirus-related viruses, 6 of the 13 pineapples in addition tested positive for PSVA. The PSVA genome sequence and development of detection methods of this new virus will aid in understanding and controlling viral-related diseases in pineapple.

Technical Abstract: The complete genomic sequence of a putative novel member of the family Secoviridae was determined by high-throughput sequencing of a pineapple accession obtained from the National Plant Germplasm Repository in Hilo, Hawaii. The predicted genome of the putative virus was composed of two RNA molecules of 6,128 and 4,161 nucleotides in length, excluding the poly-A tails. Each genome segment contained one large open reading frame (ORF) that shares homology and phylogenetic identity with members of the Secoviridae family. The presence of this new virus in pineapple was confirmed using RT-PCR and Sanger sequencing from six samples collected in Oahu, Hawaii. The name “pineapple secovirus A (PSVA)” is proposed for this putative new sadwavirus.