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Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization

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Abstract

Analysis of a loquat tree with leaf curl symptoms by deep sequencing revealed a novel virus with a single-stranded RNA genome, for which the name “loquat virus A” (LoVA) was proposed. The complete genome sequence comprised 7553 nucleotides (nt) and an additional poly(A) tail at the 3′ terminus. Sequence comparisons of LoVA showed moderate similarity to cherry virus A (CVA), currant virus A (CuVA), and mume virus A (MuVA), which are members of the genus Capillovirus in the family Betaflexiviridae. Phylogenetic analysis of the full-genome nt sequence and replicase-like protein supported the placement of LoVA within the genus Capillovirus. However, it has a distinct genome organization, differing from recognized capilloviruses, as it contains three open reading frames (ORFs), with the coat protein (CP) expressed separately from the replication-associated protein (RP) rather than being encoded in the same ORF. This indicates that LoVA is a novel member of the genus Capillovirus in the family Betaflexiviridae with a distinct genomic organization.

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Acknowledgements

This research was supported by the Intergovernmental International Science, Technology and Innovation (STI) Collaboration Key Project of China′s National Key R&D Program (NKP) (2017YFE0110900), Fundamental Research Funds for the Central Universities (XDJK2018AA002), Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016), Overseas Expertise Introduction Project for Discipline Innovation (111 Center) (B18044). We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript. We thank the editor and three anonymous reviewers for their constructive comments and suggestions.

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Correspondence to Mengji Cao.

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Liu, Q., Yang, L., Xuan, Z. et al. Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization. Arch Virol 165, 223–226 (2020) doi:10.1007/s00705-019-04444-1

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