Viruses

Long non-coding RNAs (lncRNAs), a class of RNA molecules whose transcripts exceed 200 nucleotides in length and typically lack protein-coding capacity, were once widely regarded as “transcriptional noise.” However, recent studies have shown that lncRNAs can encode small peptides and play critical roles in biological processes, including gene expression regulation, cell differentiation, and immune response. Viral infections, as a common disease, can reshape the transcriptome of host cells, in which the differential expression of lncRNAs is a core link in host–virus interactions. This review aims to deeply analyze the multidimensional regulatory mechanisms of lncRNAs in the host antiviral innate immune response. It elaborates in detail on how lncRNAs construct the host antiviral defense by regulating pattern recognition receptor (PRR) signaling pathways, the production and signal transduction of interferons (IFNs), as well as the expression of interferon-stimulated genes (ISGs). Additionally, we conducted an in-depth analysis of the complex functions of lncRNAs in regulating programmed cell death (PCD), including key processes such as pyroptosis, autophagy, and apoptosis, and integrated specific research cases in infections caused by multiple significant viruses, including influenza A virus (IAV), human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aim to provide novel strategies for the diagnosis, treatment, and prevention of viral diseases.

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HIV-1 tropism toward the CCR5 and CXCR4 coreceptors is an important viral characteristic associated with cell entry, the potential use of specific entry inhibitors, studies of disease progression, and analyses of proviral reservoirs. The development of tools for genotypic tropism prediction also requires annotated sequence datasets with reliable phenotypic annotation. In this study, we describe a curated HIV-1 sequence dataset intended to complement, rather than replace, existing reference collections. Publications and GenBank records were searched manually using PubMed, Google Scholar, OpenAlex, cross-references, and records from the GenBank Nucleotide database. Sequences were included if a GenBank accession number could be linked to the V3 region of the HIV-1 env gene, or to a longer fragment containing this region, and to phenotypically determined tropism; records already present in LANL were removed. The final dataset comprises 1809 records associated with 32 unique PubMed-indexed publications. Subtype B predominated in the dataset; however, non-B variants accounted for 455 records (25.2%), including several Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). R5 variants accounted for 1528 records (84.5%), whereas X4 and R5/X4 variants accounted for 281 records (15.5%). The dataset includes 14 categories of phenotypic assays, geographic metadata, and sequences ranging from env gene fragments to near-complete HIV-1 genomes. This resource can be used as a complement to existing databases for the development, testing, and external validation of approaches for HIV-1 tropism prediction.