Coxsackieviruses (CVs) belong to the genus Enterovirus and family Picornaviridae. Mutants can arise within the replication cycle of RNA viruses. The prototype CVB2 Ohio-1 (CVB2/O) strain adapted to rhabdomyosarcoma (RD) cells induced cytolytic infection and showed three-point mutations in the genome (CVB2/O/RD). The aim of this experimental study was to compare the effect of one or multiple viral mutations in viral protein 1 (VP1) or region 2C of CVB2/O on pathogenesis in two different mouse models. Male A/J and CD1 (10–12 g) mice were infected intraperitoneally with CVB2/O and its mutants or mock infected (control mice). Mice were sacrificed on days 0, 5, 7, 10, and 55 post infection. Blood, heart, and pancreas were collected for virological and histopathological analysis. The presence of viral RNA in the heart and pancreas of infected mice was studied. Different cytokines were detected in the serum. Pathological changes were absent in the hearts of infected mice. Maximum pathological changes were identified in the pancreas of infected A/J mice. Infiltration of pancreatic cells was observed depending on the mouse strain and mutants. CD1 mice were less susceptible to CVB2 infection. CVB2/O/VP1-Q164K mutant induced maximum changes in the pancreas of A/J-infected mice. We suggest that the single altered amino acid in the VP1 protein was related to the virulence factor and was associated with the pathology and presence of viral RNA in the pancreas of infected A/J mice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an enveloped, single-stranded RNA virus, is causative of coronavirus disease 2019 (COVID-19). The viral entry process is facilitated by the highly antigenic spike protein of SARS-CoV-2, which binds to the angiotensin-converting enzyme 2 (ACE2) receptor. However, research involving live SARS-CoV-2 is limited to biosafety level (BSL)-3 facilities, hindering the progress in vaccine and therapeutic development. Pseudotyped viruses have emerged as valuable tools for studying entry inhibitors, fusion inhibitors, and neutralizing assays in BSL-2 facilities. Several modifications to the spike protein have been identified to enhance the yield of pseudotyped viruses. Notably, the removal of the last 19 amino acids from the spike protein and the D614G modification have been shown to increase pseudovirus titers. In this study, we aimed to identify an effective expression vector for pseudotyping by inserting SARS-CoV-2 S Δ19 into the intron-containing pcDNA3.1 vector. The inclusion of the β-globin intron sequence led to a significant augmentation in spike protein expression and a threefold improvement in pseudotyped virus production. Furthermore, we examined whether the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE) could enhance spike protein expression by subcloning the spike protein gene into a lentiviral vector containing WPRE. Our results demonstrated that vectors containing the WPRE exhibited increased spike protein expression compared to vectors lacking the WPRE in HEK293-hACE2 cells. This study demonstrates that the inclusion of a β-globin intron and WPRE enhances the production of SARS-CoV-2 spike protein pseudotyped lentiviruses, a valuable tool for COVID-19 research.

Enterovirus 71 (EV71) is a significant causative agent of hand, foot and mouth disease (HFMD). However, the precise mechanism by which EV71 infection leads to alterations in the immune response remain elusive. To address this knowledge gap, we conducted a study where we introduced the Inner Mongolia EV71 C33λ strain into Vero cells, derived from African green monkey kidney cells. Subsequently, we performed RNA sequencing (RNA-Seq) to investigate the changes in the transcriptome of these infected Vero cells. Our primary objective was to establish a foundational understanding that could inform future research on EV71-associated immune factors. In our study, we identified a total of 942 differentially expressed genes (DEGs) in Vero cells infected with Enterovirus 71 (EV71), with 568 gene exhibiting increased expression and 374 gene showing decreased expression. To elucidate the functional implications of these DEGs, we conducted a comprehensive functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. This analysis revealed three genes that were significantly upregulated, which we subsequently validated using reverse transcription polymerase chain reaction technology (RT-qPCR). The RT-qPCR results were in strong agreement with our RNA-Seq data, confirming the reliability of our findings. This study represents the pioneering RNA-Seq analysis that delves into the cellular response of Vero cells to EV71 infection. Our results not only provide a foundational understanding of the molecular changes induced by EV71 but also offer crucial insights into the mechanisms by which EV71 modulates the host immune system. These insights are pivotal for future research endeavors aimed at developing effective therapeutic strategies against EV71 and related pathogens, as well as for understanding the broader implications of viral infections on host immunity.

The genus Potyvirus (the family Potyviridae) is the largest group of plant-infecting viruses transmitted by aphids. Through high-throughput RNA sequencing analysis of asymptomatic samples of Aconitum carmichaelii, a significant medicinal herb in Asia, we identified the genome sequences of two RNA viruses, tentatively named Aconitum potyvirus 1 (AcoPV1) and Aconitum potyvirus 2 (AcoPV2). The genomes of AcoPV1 and AcoPV2 encode polyproteins composed of 3,069 and 3,054 amino acids, respectively. Sequence comparisons and phylogenetic analyses established that AcoPV1 and AcoPV2 represent unique, novel members within the genus Potyvirus. The estimated RNA polymerase slippage rates at the GAAAAAA motif, responsible for the production of P3N-PIPO or P3N-ALT trans-frame fusion proteins, were 0.79% in AcoPV1 and 1.38% in AcoPV2. The RNA reads of AcoPV1 and AcoPV2 were predominantly found in the leaf and flower tissues, indicating potential feeding preferences of vectors for these viruses. These findings demonstrate the effectiveness of high-throughput RNA sequencing in not only uncovering novel potyviruses, but also in elucidating their genomic dynamics within host plants.

Since the last century, the spread of the genotype 2 classical swine fever virus (CSFV) has caused significant issues for the pig breeding industries. Ideal strategies for controlling CSFV include vaccination and keeping farms free of CSFV. For vaccination, several attenuated CSFV viruses originating from genotype 1 are widely used; for the latter, accurate diagnosis is required for detection of the CSFV infection. Nucleic acid testing for CSFV usually uses tonsil samples, which requires an inconvenient sampling operation that injures pigs. Commercial serological tests for CSFV antibodies or antigens are unable to distinguish the genotype for originating virus. In this study, 20 mAbs were developed from the mice hybridoma cells. Four of the mAbs were identified to have the ability to only recognize the peptides derived from sub-genotype 2.1 strain, and two of them, MM1 and MM5, were further studied to identify critical binding sites (epitopes) on the E2 protein of CSFV. A total of 353 genotype 2 collections were made worldwide in GeneBank, 90.9% of which contained MM1 or MM5 epitopes. Moreover, 95.1% of sub-genotype 2.1 isolations contained MM5 epitope. Therefore, MM1 and MM5 have the potential to be developed as a diagnostic tool for detection of genotype 2 virus antigen by indirect ELISA or antibodies by competitive ELISA.

The non-uniform usage of synonymous codons occurs in genomes of all organisms, including DNA and RNA viruses. The preferential selection of a codon at the expense of other synonymous codons within the same group is known as Codon Usage Bias. The understanding of this bias assists in unveiling the factors driving molecular evolution, as defined by the selection-mutation-drift theory. According to this model, molecular evolution is predominantly driven by mutation, natural selection, and genetic drift. Nevertheless, elements like nucleotide composition, gene length, and protein secondary structure also contribute to this process. Comprehensive genomic analyses that highlight the codon usage preference of the African Swine Fever Virus (ASFV) are infrequent. ASFV, a hemorrhagic and highly contagious viral disease, almost invariably results in 100% fatality among infected pigs and wild boars. This study, therefore, embarked on a thorough examination of codon usage patterns in ASFV’s complete genomic sequences, an endeavor of great relevance to molecular evolution studies, complex transmission models, and vaccine research. For an exhaustive evaluation of ASFV’s whole-genome codon usage, we used parameters like ENC, RSCU, and CAI. A Principal Component Analysis was carried out to reaffirm the interconnected RSCU lineages based on the continent, and their evolutionary relationships were later elucidated through phylogenetic tree construction. ASFV emerged as a low-biased codon user (ENC = 52.8) that is moderately adapted to its host. Its genome has a high AT composition (64.05%), suggesting the impact of mutational pressure on genomic evolution. However, neutrality plot analysis revealed natural selection’s slight supremacy over mutational pressure. The low codon bias (>45) implies ASFV’s diverse usage of synonymous codons within a given codon family, allowing for effective translation and subsequent successful viral replication cycles. Its moderate adaptation (CAI = 0.56) permits the virus to infect a range of hosts, including reservoirs such as warthogs and bush pigs. To the best of our knowledge, this is the pioneering report providing a comprehensive examination of ASFV’s complete genomic sequences. Consequently, research focusing on viral gene expression and regulation, gene function prediction, parasite-host interaction, immune dysfunction, and drug and vaccine design may find this report to be a valuable resource.

Cells infected with MA104 rotavirus and/or transfected with plasmids expressing NSP proteins, were analyzed for expression of cellular proteins related to NFκB and PPARγ pathways and evaluated through the ELISA, luminescence, flow cytometry and Western blot techniques. The association between cellular and viral (NSPs) proteins was examined by ELISA, epifluorescence and confocal microscopy techniques. It was observed that NSP1 protein interacts with RXR, NSP1, and NSP3 with PPARγ, NSP2 with p-IKKα/β and NSP5 with NFκB proteins. We have found that phosphorylated PPARγ is localized in cytoplasm and transcriptional activity of PPRE is diminished. These results lead to the conclusion, that RRV activates the proinflammatory pathway, increasing the expression of NFκB and possibly by PPARγ phosphorylation, its translocation to the nucleus is impeded, thus inactivating the proinflammatory pathway. Keywords: rotavirus; PPARγ; NFκB; NSPs; RRV.

Letter to the editor (No abstract) Keywords.

We have developed methods for detecting the genetic diversity of grapevine rupestris stem pitting-associated virus (GRSPaV) based on restriction fragment length polymorphism (RFLP) and single stranded conformational polymorphism (SSCP) in the 905 nt 3' sequence. The amplicons were cloned from six grapevine cultivars, and colony polymerase chain reaction (colony PCR) using recombination bacteria was subsequently analyzed by RFLP and SSCP. Four haplotypes of SSCP and six haplotypes of Sac IRFLPs were defined. The two methods had a40% discrepancy rate in showing the degree of diversity. All clones were sequenced and were used to construct aphylogenetic tree with seven previously reported GRSPaV sequences. In the tree, all the newly acquired sequences were divided into three clusters, I, II, and III, which corresponded to haplotypes I, II, and III of SSCP, respectively. Haplotype IV of SSCP was grouped into cluster II. Arecombination analysis showed that haplotype IV has undergone arecombination event. Together, these results indicate that the SSCP assay is useful for the rapid identification of genetic diversity of GRSPaV. This is the first report of an analysis of the large fragment of GRSPaV by colony PCR-SSCP. Keywords: grapevine; grapevine rupestris stem pitting-associated virus (GRSPaV); RFLP; SSCP; genetic diversity analysis.

Defensins, crucial components of the innate immune system, play avital role against infection as part of frontline immunity. Association of SARS-CoV-2 infection with defensins has not been investigated. In this study, we have investigated the expression of defensin genes in the buccal cavity from patients with COVID-19 infection along with negative control samples. Nasopharyngeal/oropharyngeal swab samples collected for screening SARS-CoV-2 infection in early 2020 from Hyderabad, India, were analyzed for the expression of major defensin genes by the quantitative real-time reverse transcription polymerase chain reaction, qRT-PCR. Forty SARS-CoV-2 infected positive and 40 negative swab samples were selected for this study. Based on the qRT-PCR analysis involving gene specific primers for defensin genes, 9 defensin genes were found to be expressed in the nasopharyngeal/oropharyngeal cavity. Four defensin genes were found to be significantly down regulated in SARS-CoV-2 infected patients in comparison with the control samples based on differential expression analysis. The significantly down regulated genes were defensin beta 4A/B, 106B, 107B, and 103A. Down regulation of human beta defensin 2, 3, 6 and 7 suggests that antiviral innate immune response provided by defensins may be compromised in SARS-CoV-2 infection resulting in progression of the disease. Correction of the down regulation process through appropriate defensin peptide-based therapy could be an attractive method of treatment. Keywords: host defense; defensins; COVID-19; gene regulation; SARS-CoV-2.