Zhihao Yuan’s research while affiliated with Huazhong Agricultural University and other places

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Publications (3)


(A) Amplification of the LAV2 genome by 5' and 3' RACE and RT-PCR. M, GL DNA Marker 5000. (B) The predicted secondary structures of the 5' and 3' UTRs of LAV2. (C) Schematic representation of the genome organization of LAV2.
Correction to: Molecular characterization of a novel amalgavirus infecting lilium spp. in China
  • Article
  • Publisher preview available

July 2023

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20 Reads

Archives of Virology

Zhihao Yuan

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Zhenfeng Li

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Yuexia Lu

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[...]

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Li Cai
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(A) Amplification of the LAV2 genome by 5’ and 3’ RACE and RT-PCR. M, GL DNA Marker 5000. (B) The predicted secondary structures of the 5’ and 3’ UTRs of LAV2. (C) Schematic representation of the genome organization of LAV2.
(A) Sequence alignment the RdRp motifs of LAV2 and selected members of the genus Amalgavirus. Horizontal black lines above the sequence alignment indicate the conserved motifs I to VII. Shaded areas indicate identical aa residues. LAV2 is indicated by a red star. (B) Phylogenetic analysis of LAV2 and other selected viruses based on aa sequences of ORF2 (RdRp). Sequences of ORF2 translation products were aligned using CLUSTAL X and then subjected to phylogenetic analysis using IQ-TREE. The tree is displayed as a rectangular phylogram rooted on the branch to the family Amalgaviridae, Partitiviridae, and Totiviridae members. Branch support values are shown as percentages. The scale bar indicates a genetic distance of 0.5 aa substitutions per site. LAV2 is indicated by a red star.
Molecular characterization of a novel amalgavirus infecting lilium spp. in China

June 2023

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36 Reads

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1 Citation

Archives of Virology

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.


Figure 2
Molecular characterization of a novel amalgavirus infecting Lilium spp. in China

February 2023

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19 Reads

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

Citations (1)


... The partial ORF1 and ORF2 encode an RdRp fusion protein resulting from a frameshift at the + 1 PRF motif, consisting of 1,057 amino acids with a predicted molecular mass of 118.6 kDa (Fig. 1C). An alignment of the amino acid sequence of the RdRp encoded by SGAV1 with those of 10 related amalgaviruses revealed that the SGAV1 RdRp contains all seven conserved motifs (I to VII) ( Supplementary Fig. S1A) described previously [8,9]. ...

Reference:

Complete genome sequence of a novel amalgavirus in sponge gourd, Luffa cylindrica
Molecular characterization of a novel amalgavirus infecting lilium spp. in China

Archives of Virology