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Complete genome organization and characterization of Hippeastrum latent virus


The complete genome sequences of two carlaviruses were determined by high-throughput sequencing of RNA extracted from ringspot and mosaic, disease symptoms on leaves of spider lily plants (Crinum asiaticum, family Amaryllidaceae) growing as landscape plants in Hawaii. One, named Nerine latent virus (NeLV)-Hawaii with a genome of 8281 nucleotide exhibited the highest nucleotide identity and amino acid similarity of 95.5% and 96.0%, respectively, to the genome sequence of an isolate of NeLV from Narcissus sp. in Australia (JQ395044). The second, named Hippeastrum latent virus (HiLV)-Hawaii with a genome of 8497 nucleotides exhibited the highest nucleotide identity and amino acid similarity, 84.3% and 88.7%, respectively, to the sequence of a previously uncharacterized HiLV isolate from a potted flowering plant, Amaryllis (Hippeastrum hybridum Hort) in Taiwan (DQ098905). The amino acid sequence similarities of replicase (Rep) and coat protein (CP) between HiLV-Hawaii and NeLV-Hawaii were 44.8% and 38.4%, respectively. Results of viral protein Rep and CP amino acid sequence comparisons from various carlaviruses provide evidence that HiLV and NeLV, previously classified as synonymous viruses are in fact unique viruses. This is the first report for the complete sequence, organization, and phylogenetic characterization of HiLV and the first detection of HiLV both in C. asiaticum and in the USA.

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Funding was provided by the National Institute of Food and Agriculture (Hatch HAW09025-H[1001478]), USDA Agricultural Research Service (58-5320-4-012), and the United States Agency for International Development (BFS-G-1100002 and EEM-G-0004-00013).

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All authors contributed to the study conception and design. Material preparation, experiments, and data collection were performed by XW. The data analysis was performed by XW and AO-V. JH supervised the study and acquired the funding. The first draft of the manuscript was written by XW and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to John Hu.

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This study did not include experiments with human or animal participants performed by any of the authors.

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Wang, X., Larrea-Sarmiento, A., Olmedo-Velarde, A. et al. Complete genome organization and characterization of Hippeastrum latent virus. Virus Genes 58, 367–371 (2022).

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  • Carlavirus
  • Spider lily
  • Hawaii
  • Hippeastrum latent virus
  • Nerine latent virus