The challenges in combating enteroviruses continue due to their genetic diversity and the rapid development of resistance. Combining antiviral agents offers a promising solution. Our study evaluated the combined effects of pocapavir, a potent capsid-binding inhibitor, with enterovirus-targeting compounds such as pleconaril, 2-(3,4-dichlorophenoxy)-5-nitrobenzonitrile (MDL-860), guanidine hydrochloride, oxoglaucine, and 2-α-hydroxybenzyl-benzimidazole (HBB). The combinations tested demonstrated additive to highly synergistic antiviral effects without observed combined cytotoxicity. These results suggest their potential for further research and clinical trials in combating enterovirus infections.

Long non-coding RNAs (lncRNAs) have gained prominence due to their involvement in various cellular processes, but their specific roles remain elusive. Dysregulation of lncRNAs has been implicated in the pathogenesis of several diseases. In this study, we aimed to shed light on the role of lncRNAs in individuals infected with human immunodeficiency virus type 1 (HIV-1) by examining their changes in the expression patterns related to the initiation of antiretroviral therapy (ART) during acute or chronic phases of infection, compared to healthy controls. We found 316 differentially expressed (DE) lncRNAs in patients receiving long-term ART, shedding light on their potential roles. We also observed interactions between these DE lncRNAs and specific microRNAs (miRNAs). Some of these miRNAs, such as hsa-miR-574-5p, hsa-miR-765, hsa-miR-6165, hsa-miR-1207-5p, and hsa-miR-378i, are associated with cancer progression or suppression, while others, including hsa-miR-328-5p, hsa-miR-4753-3p, and MiR-664, play roles in immune system regulation. Furthermore, our study revealed substantial enrichment in distinct Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as axon guidance, PI3K-Akt signaling, and MAPK signaling pathways. Although our results indicate possible molecular processes impacted by the discovered lncRNAs, we cannot explicitly establish causality or specific connections between lncRNAs and genes in these pathways, fostering more specific studies. Furthermore, Gene Ontology (GO) analysis highlighted terms such as cytoskeletal protein binding, ion channel function, synaptic processes, neuron projection, and the somatodendritic compartment, underscoring the relevance of lncRNAs in these cellular components within the context of HIV-1 infection and ART treatment. In conclusion, our study emphasizes the need for further exploration of lncRNAs as potential biomarkers and therapeutic targets in HIV-1-infected patients, with a particular focus on CD4+ T cells. Understanding the functions of lncRNAs in these contexts may pave the way for novel treatment strategies and improved patient outcomes, aligning with the broader goals of our research.

Humankind has witnessed increased frequency of emerging and re-emerging viral diseases in the past few decades. The major categories of pathogenic emerging and re-emerging viral infections include respiratory, arthropod-borne and bat-borne zoonotic viruses. These viral infections are notorious for causing immune dysregulation and have the potential to mount excessive immune reaction, causing immunopathology that includes tissue injury, systemic inflammation, multi-organ failure and even death. A better understanding of the emerging or re-emerging viral-mediated immunomodulation is necessary for controlling the virus, while preventing severity of the disease associated with exaggerated immune response. In this article, we review the current understanding of emerging and re-emerging respiratory, arboviral and bat-borne zoonotic viruses; and consequent immune dysregulation or immunopathology associated with these viral infections.

The incidence of reporting caliciviruses in wild birds is less common than in other animals, and the majority of cases remain unclassified. A strain of calicivirus was discovered in this study in the feces of cormorants collected at Xiamen Horticulture Expo Garden in 2021 and was named Cormcali01. The genome of Cormcali01 was 8,561 bp in length which contained characteristic motifs present in other caliciviruses. Furthermore, it demonstrated a significant deviation from all existing calicivirus nucleotide sequences, exhibiting the highest amino acid identity (47.34%) to the unclassified Ruddy turnstone calicivirus A. A pairwise comparison of the VP1 protein showed that Cormcali01 had the highest amino acid identity of 43.90% with the unassigned Ruddy turnstone calicivirus A. Phylogenetic analysis demonstrated that VP1 of Cormcali01 clustered with unassigned caliciviruses. Therefore, based on phylogenetic analysis and pairwise comparison, Cormcali01 should be affiliated with the unassigned calicivirus, which were suggested to comprise a new calicivirus genus, the Sanovirus genus. After investigating the prevalence of Cormcali01, we discovered that 22.22% of fecal samples (10/45) were tested positive. These findings expand our understanding of the genetic variation of caliciviruses and provide valuable epidemiological information regarding a potential outbreak of calicivirus disease in birds.

Influenza A viruses are enveloped viruses with a genome of eight single-stranded negative-sense RNA molecules. In virions, RNA segments are found as vRNPs associated with NP proteins. The RdRp enzyme, which catalyzes the replication/transcription of the viral genome, is carried as attached to vRNPs. In this study, it was demonstrated that the PA subunit of the viral RdRp interacts with β-actin proteins by the yeast two-hybrid assay. It was shown that the amino-terminal domains of the β-actin protein bind to the carboxy-terminal moiety of the viral PA protein in the mammalian cells. The results were supported by in silico analysis. Over-expression of the β-actin protein was found to have a negative effect on the viral RdRp activity in mini-replicon, but its mechanism of action has remained unknown. The results suggest that the interaction of β-actin and PA protein, a component of vRNPs, may have a role in the intracellular trafficking of the influenza vRNPs and/or viral transcription.

Frequent, and sometimes more dangerous, mutations in SARS-CoV-2 indicate that a stronger strategy is needed to produce an effective vaccine—a vaccine that contains a wider range of virus factors and remains effective if one or more mutations have occurred in a part of the genome. In this study, four important virus proteins were used to make a multi-epitope protein vaccine. For this purpose, antigenic determinant of 4 proteins were selected and a protein structure was designed using 4 domains containing epitopes. After examining its antigenic potential, its three-dimensional structure was designed and then docked with immune system receptors. Finally, using the dynamic molecular (MD) simulation, complexes and interactions were investigated and their interaction energies were measured. The results of the study showed that the designed structure has good relative stability and interacts well with its receptors and can be used as a vaccine candidate for further studies.

Human adenovirus-5 (hAd5) is an important gene delivery vector, which has been widely used in various fields of biomedicine, such as gene therapy, cancer therapy, and vaccine development. However, replication-competent adenovirus (RCA) generated when adenoviral vectors are prepared in HEK293 cells has remained a concern. In this study, the human adenovirus-5 was modified to shorten the length of homologous sequence between the adenovirus and HEK293 genomic DNA, thereby reducing the production of RCA. The recombinant hAd5 was amplified and serially passaged 12 times in HEK293 cells. The amounts of RCA at passage 2, 4, 6, 8, 10, and 12 were detected by quantitative real-time PCR. The results demonstrated that the modification of adenoviral vector could effectively reduce the production of RCA during serial passages in HEK293 cells.

Based on the crystal structure of the 3C-like protease/Nsp5 (PDB ID 6W63), virtual hits were screened from a natural product compounds database—containing 407270 natural products—by using the high-throughput virtual screening (HTVS) module of Discovery Studio software, and then filtering by “Lipinski’s rule of five” from the top 20 virtual hits. Two star-hits were selected by CDOCKER results and the protein-ligand interactions with the 3CLpro were analyzed. Finally, a 100 ns molecular dynamics simulation was carried out to verify the stability of the receptor-ligand complexes. We screened potent broad-spectrum non-covalent inhibitors that could bind to the SARS-CoV-2 3CLpro active binding site from the natural product compounds library through HTVS and molecular dynamics simulations methods. The LibDock scores and -CDOCKER energy value of the star-hits were higher than the original ligands (X77) bound to 3CLpro. CNP0348829 and CNP0474002, as star-hits, can bind stably to the active site of 3CLpro, which are promising candidate compounds for the treatment of SARS-CoV-2 and provide a theoretical basis for the development of antiviral drugs. The results of the present study may be useful in the prevention and therapeutic perspectives of COVID-19. However, further in vitro and in vivo validation tests are required in the future.

Rat hepatitis E virus (RHEV/HEV-C1, species Rocahepevirus ratti) is an emerging zoonotic pathogen, posing an increasing threat to public health worldwide. This study was conducted for better understanding the epidemiology and evolution of RHEV. The isolates sampled so far can be divided into two major genotypes designated a and b. According to the phylogeography, while type a has been detected in four continents, type b is restricted to East and Southeast Asia. Recombination analysis identified three chimeric isolates. Bayesian coalescent analysis suggested that RHEV began to expand around 1956 and was evolving at a high rate. Codon usage bias analysis revealed that RHEV genes are rich in G/C and have additional bias independent of compositional constraints. In codon usage, RHEV is both similar to and different from the major host Norway rat (Rattus norvegicus). Furthermore, unlike many other mammalian RNA viruses, RHEV does not mirror hosts’ marked suppression of “CG” and “TA”.

Effective control and monitoring the spread of foot-and-mouth disease (FMD) relies upon rapid and accurate laboratory detection of FMD virus (FMDV). Therefore, in this report, a multiplex TaqMan probe-based one-step RT-qPCR assay simultaneously targeting FMDV 5′UTR and 3Dpol regions, and 18S rRNA housekeeping gene (as an internal control) in a single reaction tube was developed and evaluated. The multiplex one-step RT-qPCR assay specifically detected viral genome in both FMDV-infected cell culture suspensions and clinical samples collected from known-FMD infected animals. The assay could detect FMDV RNA in the archived FMDV cell culture isolates (n = 120) collected during the last two decades in India. In addition, the new assay could also detect viral RNA in the FMD suspected clinical samples (n = 740) collected from various field outbreaks. At a cut-off Ct-value of <38, the assay could detect at least 20 and 10 copies of FMDV 3Dpol and 5′UTR genes, respectively. Further, the multiplex RT-qPCR assay proved to be robust, showing an inter-assay co-efficient of variations ranging from 1.3% to 3.03% for FMDV-3Dpol gene target, and from 1.44% to 4.69% for 5′UTR gene target. In addition, it was found that the new assay could be used to detect viral genome in a variety of samples (epithelium, saliva, OPF, milk and blood) without any significance difference in the detection limit of the assay. Hence, the multiplex one-step RT-qPCR assay could be considered a valuable tool for the detection of FMDV in India.