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Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis

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Abstract

In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤ 70.80% in RdPp and ≤ 34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.

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Data availability

The complete sequences of the three genome segments of the new partitivirus characterized in the present study are openly available in the GenBank database with reference numbers MZ751043, MZ751044, and MZ751045.

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Funding

This research was supported by USDA APHIS project 20-8224-2121 IA.

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Author notes

  1. Martha Malapi-Wight

    Present address: USDA-APHIS, Biotechnology Regulatory Services, Biotechnology Risk Analysis Program, Riverdale, MD, USA

Authors and Affiliations

  1. United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA

    Larissa C. Costa, Xiaojun Hu, Martha Malapi-Wight, Mary O’Connell, Leticia M. Hendrickson, Roy S. Turner, Joseph Foster & Oscar P. Hurtado-Gonzales

  2. USDA-APHIS-PPQ, Field Operations, Raleigh, NC, USA

    Clint McFarland

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  1. Larissa C. Costa
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  2. Xiaojun Hu
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Correspondence to Oscar P. Hurtado-Gonzales.

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This article does not contain any studies with human participants performed by any of the authors.

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Handling Editor: Ioannis E. Tzanetakis.

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Costa, L.C., Hu, X., Malapi-Wight, M. et al. Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis. Arch Virol 167, 261–265 (2022). https://doi.org/10.1007/s00705-021-05294-6

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  • DOI: https://doi.org/10.1007/s00705-021-05294-6

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