Molecular characterization of a novel amalgavirus infecting lilium spp. in China

Abstract

A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing and tentatively named “lily amalgavirus 2” (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) in length and contains two open reading frames (ORFs) that putatively encode a ‘1 + 2’ fusion protein of 1053 amino acids (aa), generated by a ‘+1’ programmed ribosomal frameshift (PRF). ORF1 encodes a putative 386-aa protein of unknown function, and ORF2 overlaps ORF1 by 350 nt and encodes a putative 783-aa protein with conserved RNA-dependent RNA polymerase (RdRp) motifs. The ‘+1’ ribosomal frameshifting motif, UUU_CGN, which is highly conserved among amalgaviruses, is also found in LAV2. Sequence analysis showed that the complete genome shared 46.04%-51.59% nucleotide sequence identity with those of members of the genus Amalgavirus and had the most similarity (51.59% sequence identity) to lily amalgavirus 1 (accession no. OM782323). Phylogenetic analysis based on RdRp amino acid sequences showed that LAV2 clustered with members of the genus Amalgavirus. Overall, our data suggest that LAV2 is a new member of the genus Amalgavirus.

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ANNOTATED SEQUENCE RECORD
Archives of Virology (2023) 168:181
https://doi.org/10.1007/s00705-023-05806-6
shallot yellow stripe virus (SYSV), and arabis mosaic virus
(ArMV) have been reported to infect lily plants in China
[4–8].
The family Amalgaviridae currently has 10 members,
including blueberry latent virus (BBLV) [9], rhododendron
virus A (RHV-A) [10], southern tomato virus (STV) [11],
vicia cryptic virus M (VCV-M) [12], Allium cepa amal-
gavirus 1 (AcAV1), Allium cepa amalgavirus 2 (AcAV2)
[13], spinach amalgavirus 1 (SpAV1) [14], Zostera marina
amalgavirus 1 (ZmAV1), and Zostera marina amalgavirus
2 (ZmAV2) [15] in the genus Amalgavirus and Zygosac-
charomyces bailii virus Z (ZbV-Z) [16] in the genus Zyba-
virus. The plant amalgaviruses have small dsRNA genomes
(3316–3453 bp) and have not yet been shown to form viri-
ons. They are transmitted by seeds but cannot be transmit-
ted mechanically [13]. Their genomes contain two partially
overlapping long open reading frames (ORFs), with down-
stream ORF2 overlapping ORF1 in the ‘+1’ frame. ORF1
encodes a protein of unknown function. ORF2 encodes the
RNA-dependent RNA polymerase (RdRp), which is trans-
lated through a ‘+1’ programmed ribosomal frameshifting
Lily (Lilium spp.) is a perennial plant belonging to the genus
Lilium of the family Liliaceae, with ornamental, medici-
nal, and food value, and it has become an important eco-
nomic crop in the oricultural industry worldwide [1]. To
date, more than 20 viruses have been reported to infect lily
plants, and of these, lily mottle virus (LMoV), lily symp-
tomless virus (LSV), and cucumber mosaic virus (CMV)
are the most frequently observed, often in mixed infections
[2, 3]. Lily amalgavirus 1 (LAV1), lily yellow mosaic virus
(LYMV), prunus necrotic ringspot virus (PNRSV), CMV,
LMoV, LSV, Plantago asiatica mosaic virus (PlAMV),
Communicated by Massimo Turina
Li Cai
caili@mail.hzau.edu.cn
1 Hubei Key Laboratory of Plant Pathology, College of Plant
Science and Technology, Huazhong Agricultural University,
430070 Wuhan, China
2 National Citrus Engineering Research Center, Southwest
University, 400712 Chongqing, China
Abstract
A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput
sequencing and tentatively named “lily amalgavirus 2” (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) in
length and contains two open reading frames (ORFs) that putatively encode a ‘1 + 2’ fusion protein of 1053 amino acids
(aa), generated by a ‘+1’ programmed ribosomal frameshift (PRF). ORF1 encodes a putative 386-aa protein of unknown
function, and ORF2 overlaps ORF1 by 350 nt and encodes a putative 783-aa protein with conserved RNA-dependent RNA
polymerase (RdRp) motifs. The ‘+1’ ribosomal frameshifting motif, UUU_CGN, which is highly conserved among amal-
gaviruses, is also found in LAV2. Sequence analysis showed that the complete genome shared 46.04%-51.59% nucleotide
sequence identity with those of members of the genus Amalgavirus and had the most similarity (51.59% sequence identity)
to lily amalgavirus 1 (accession no. OM782323). Phylogenetic analysis based on RdRp amino acid sequences showed
that LAV2 clustered with members of the genus Amalgavirus. Overall, our data suggest that LAV2 is a new member of
the genus Amalgavirus.
Received: 3 February 2023 / Accepted: 26 April 2023 / Published online: 14 June 2023
© The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature 2023, corrected publication 2023
Molecular characterization of a novel amalgavirus infecting lilium spp.
in China
ZhihaoYuan1· ZhenfengLi1· YuexiaLu1· MengjiCao2· NiHong1· GuopingWang1· LiCai1
1 3
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