Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs

Virus long noncoding RNAs (vlncRNAs) play crucial roles in viral infections, yet their identification and characterization remain limited. This study identified 5,053 novel vlncRNAs across 25 viral species using third-generation sequencing, with two from Influenza A virus and Vesicular stomatitis virus validated by RT-qPCR. Most vlncRNAs originated from dsDNA viruses. Only ~1% of vlncRNAs have annotated RNA families, suggesting many novel RNA structures. Interestingly, a total of 772 vlncRNAs from 15 human viruses structurally mimicked human lncRNAs (hlncRNAs), while only seven vlncRNAs shared sequence similarities with hlncRNAs. These vlncRNA and hlncRNAs bound to similar miRNAs, potentially acting as miRNA sponges to promote essential life processes. Splicing analysis showed vlncRNAs had a prevalence of alternative first exon. Finally, we developed vlncRNAbase (http://computationalbiology.cn/vlncRNAbase/#/) to store and organize the newly identified and known vlncRNAs. Overall, the study provides a valuable resource for further investigation into vlncRNAs and deepens our understanding of the diversity, structure, and function of the molecule.