The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.

中文翻译：

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两种常见的鳗草（Zostera marina）中的新型融合蛋白病毒的鉴定和融合蛋白+1编程的核糖体移码位点的计算机分析。

在常见的鳗草（Zostera marina）转录组数据集中鉴定了两种新型单部分RNA病毒的基因组序列。序列比较和系统发育分析表明，这两种新型病毒属于Amalgaviridae家族中的Amalgavirus属。。它们分别命名为滨海带状疱疹金合病毒1（ZmAV1）和滨海带状疱疹金合细菌2（ZmAV2）。ZmAV1和ZmAV2的基因组均包含两个重叠的开放阅读框（ORF）。ORF1编码一个假定的复制工厂基质样蛋白，而ORF2编码一个RNA依赖性RNA聚合酶（RdRp）域。ORF1和ORF2的融合蛋白（ORF1 + 2）介导RNA复制，是使用+1程序化核糖体移码（PRF）机制产生的。在ZmAV1和ZmAV2中也发现了+1个PRF基序序列UUU_CGN，在已知的汞病毒中高度保守。来自24种融合病毒的ORF1 + 2融合蛋白的多序列比对显示，+ 1 PRF仅发生在13个氨基酸长的片段内的三个不同位置，该片段在两侧均被高度保守的区域包围。这表明+1 PRF可能受到融合蛋白结构的限制。ZmAV1和ZmAV2的基因组序列是常见的鳗草中第一个被鉴定出的病毒，将作为有用的资源，用于研究合成病毒的进化和多样性。