Genomic sequence and host range studies reveal considerable variation within the species Arracacha virus B
Arracacha virus B type (AVB-T) and oca (AVB-O) strains from arracacha (Arracacia xanthorrhiza) and oca (Oxalis tuberosa) samples collected in 1975 and two additional isolates obtained from arracacha (AVB-PX) and potato (AVB-6A) in Peru in 1976 and 1978, respectively, were studied. In its host responses and serological properties, AVB-PX most resembled AVB-T, whereas AVB-6A most resembled AVB-O. Complete genomic sequences of the RNA-1 and RNA-2 of each isolate were obtained following high-throughput sequencing of RNA extracts from isolates preserved for 38 (AVB-PX) or 32 (the other 3 isolates) years, and compared with a genomic sequence of AVB-O obtained previously (PV-0082). RNA-2 was unexpectedly divergent compared to RNA-1, with the nucleotide (nt) sequence identity of different AVB isolates varying by up to 76% (RNA-2) and 89% (RNA-1). The coat protein amino acid sequences were the most divergent, with AVB-O and AVB-6A having only 68% identity to AVB-T and AVB-PX. Since the RNA2 sequence differences between the two isolate groupings also coincided with host range, symptom, and serological differences, AVB demonstrates considerable intraspecific divergence.
This work was supported by the UK Government’s Department of Environment, Food and Rural Affairs (Defra) under the Defra-Fera long-term services agreement and via the EUPHRESCO VirusCurate project. We thank Dr. Ray Kenten of Rothamsted Research, UK, for electron microscopy and providing both AVB-T antiserum and isolate AVB-PX, and Cesar Fribourg for propagating arracacha plants in National Agrarian University glasshouse facilities, Peru. AVB-PX symptomatology and host range were studied in International Potato Center (CIP) facilities in Lima, and CIP funded this component of the research.
Compliance with ethical standards
Conflict of interest
The authors declare no competing interests.
This article does not contain any experiments involving humans or animals that have been performed by any of the authors.
- 3.Jones RAC, Kenten RH (1980) Arracacha virus B. CMI/AAB descriptions of plant viruses, no. 270. Commonwealth Mycological Institute/Association of Applied Biologists, Wellesbourne. http://www.dpvweb.net/dpv/showdpv.php?dpvno=270
- 9.EPPO (1990) Arracacha B nepovirus, oca strain, Data Sheets on Quarantine Pests, https://gd.eppo.int/taxon/AVBO00/documents. Accessed 3 April, 2019
- 10.Jeffries CJ (1998) FAO/IPGRI technical guidelines for the safe movement of germplasm. Potato, no. 19. Food and Agriculture Organization of the United Nations, International Plant Genetic Resources Institute, Rome. https://cropgenebank.sgrp.cgiar.org/images/file/management/stogs_potato.pdf
- 11.EPPO (2019) Arracacha virus B oca strain. EPPO Global database, European and Mediterranean Plant Protection Organisation. https://gd.eppo.int/taxon/AVBO00. Accessed 3 April 2019
- 13.Fox A, Fowkes AR, Skelton A, Harju V, Buxton-Kirk A, Kelly M, Forde SMD, Pufal H, Conyers C, Ward R, Weekes R, Boonham N, Adams IP (2019) Using high-throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae). Plant Pathol 68:576–587Google Scholar
- 14.Najoshi (2011) Sickle—a windowed adaptive trimming tool for FASTQ files using quality, version 1.33. https://github.com/najoshi/sickle
- 15.Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29:644–652CrossRefGoogle Scholar
- 19.Ohshima K, Yamaguchi Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs AJ (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521CrossRefGoogle Scholar