Why are RNA virus mutation rates so damn high?

Whole genome sequencing and molecular detection of potato virus X in Bangladesh

Potato Virus X (PVX) is a significant viral pathogen affecting potato (Solanum tuberosum) crops globally, yet its molecular characterization in Bangladesh remains limited. This study presents the first whole genome sequence (WGS) and molecular analysis of PVX isolated from potato plants in Gazipur, Bangladesh. Initial virus detection was performed using DAS-ELISA on symptomatic potato leaves, followed by RT-PCR targeting the coat protein (CP) gene, which confirmed PVX presence in 'Patnai' and 'Challisha' potato varieties through a 562 bp amplicon. The WGS of the Patnai-PVX isolate was determined to be 6,435 nucleotides long and deposited in GenBank (accession: PQ527059). Genome analysis identified five major open reading frames encoding the RNA-dependent RNA polymerase (RdRp), triple gene block proteins (TGBp1, TGBp2, TGBp3), and CP. Basic Local Alignment Search Tool X (BLASTX) analysis revealed high sequence similarity with PVX isolates from neighboring regions, suggesting evolutionary conservation. Mutation analysis identified 265 SNPs, predominantly synonymous mutations, indicating maintained protein-coding integrity despite genetic variation. Fewer non-synonymous mutations were detected, potentially affecting viral protein functions and pathogenicity. Phylogenetic analysis based on the entire genome sequence placed the Bangladeshi isolate (PQ527059.1) in a well-supported clade (bootstrap value 99%) with isolates from Peru (MT752634.1, MT752612.1, MT752621.1), highlighting potential international transmission routes while also exhibiting unique genetic markers indicative of regional specificity. This comprehensive molecular characterization enhances understanding of PVX genetic diversity and evolution in Bangladesh, providing valuable insights for developing effective virus management strategies in potato cultivation.

Multifractal analysis and support vector machine for the classification of coronaviruses and SARS-CoV-2 variants

This study presents a novel approach for the classification of coronavirus species and variants of SARS-CoV-2 using Chaos Game Representation (CGR) and 2D Multifractal Detrended Fluctuation Analysis (2D MF-DFA). By extracting fractal parameters from CGR images, we constructed a state space that effectively distinguishes different species and variants. Our method achieved [Formula: see text] accuracy in species classification, with a notable [Formula: see text] accuracy for SARS-CoV-2 variants despite their genetic similarities. Using a Support Vector Machine (SVM) as a classifier further enhanced the performance. This approach, which requires fewer steps than most existing methods, offers an efficient and effective tool for viral classification, with implications for bioinformatics, public health, and vaccine development.

Epidemiology and evolutionary dynamics of H9N2 avian influenza virus in Bangladesh

Low pathogenicity avian influenza (LPAI) H9N2 has been enzootic in Bangladeshi poultry since 2006. H9N2 outbreaks can decrease egg production and growth and pose a risk to human health. The role of avian hosts in the persistence, evolution, and dispersion of H9N2 is poorly understood in Bangladesh. Hence, this study unveils the intricate role of major host species in virus maintenance and evolution and the temporal and seasonal patterns of H9N2 in Bangladesh from 2006 to 2023. Multinomial logistic regression analysis indicated that the circulation of H9N2 in different species and interfaces is significantly influenced by the seasons. Bayesian phylogenetic analysis of H9N2 sequences in Bangladesh revealed two distinct lineages: G1 and Eurasian. The G1 lineage split into two clusters, coexisting until 2019, at which point only one cluster persisted. Bayesian phylodynamic analysis of G1 lineage unveiled frequent bidirectional viral transitions among ducks, chickens, and quails. Chickens might be a pivotal source of H9N2 in Bangladesh, with a higher number of viral transitions from chickens to ducks and quails. Quails appear to acquire most of their viral transitions from chickens rather than ducks, suggesting that quail epizootics are primarily triggered by spillover events from chickens. Our results suggest viral circulation in commercial chickens despite vaccination. The vaccination approach should be revised, assess vaccine efficacy, and extension of vaccination to backyard chickens and quails.

Impact of an oxidative RNA lesion on in vitro replication catalyzed by SARS-CoV-2 RNA-dependent RNA polymerase

The production of reactive oxygen species in response to RNA virus infection results in the oxidation of viral genomic RNA within infected cells. These oxidative RNA lesions undergo replication catalyzed by the viral replisome. G to U transversion mutations are frequently observed in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and may be linked to the replication process catalyzed by RNA-dependent RNA polymerase (RdRp) past the oxidative RNA lesion 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG). To better understand the mechanism of viral RNA mutagenesis, it is crucial to elucidate the role of RdRp in replicating across oxidative lesions. In this study, we investigated the RNA synthesis catalyzed by the reconstituted SARS-CoV-2 RdRp past a single 8-oxo-rG. The RdRp-mediated primer extension was significantly inhibited by 8-oxo-rG on the template RNA. A steady-state multiple-turnover reaction demonstrated that the turnover rate of RdRp was significantly slow when replication was blocked by 8-oxo-rG, reflecting low bypass efficiency even with prolonged reaction time. Once RdRp was able to bypass 8-oxo-rG, it preferentially incorporated rCMP, with a lesser amount of rAMP opposite 8-oxo-rG. In contrast, RdRp demonstrated greater activity in extending from the mutagenic rA:8-oxo-rG terminus compared to the lower efficiency of extension from the rC:8-oxo-rG pair. Based on steady-state kinetic analyses for the incorporation of rNMPs opposite 8-oxo-rG and chain extension from rC:8-oxo-rG or rA:8-oxo-rG, the relative bypass frequency for rA:8-oxo-rG was found to be seven-fold higher than that for rC:8-oxo-rG. Therefore, the properties of RdRp indicated in this study may contribute to the mechanism of mutagenesis of the SARS-CoV-2 genome.

Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2

The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.

Genetic and Phenotypic Investigations of Viral Subpopulations Detected in Different Tissues of Laying Hens Following Infectious Bronchitis Virus Infection

Infectious bronchitis virus (IBV) commonly produces a range of genetic sequences during replication, particularly in the spike 1 (S1)-coding portion of the S gene, leading to distinct subpopulations within the broader viral population. It has been shown that certain microenvironments exert selective pressure on the S1-coding sequences and their encoded proteins, influencing the selection of viral subpopulations in these environments. In this study, high-throughput next-generation sequencing (NGS) was used to analyze the S1-coding sequences from tissues of the respiratory, digestive, renal, and reproductive systems of specific pathogen-free (SPF) laying hens. These tissues were collected nine days after infection with the California 1737/04 (CA1737/04) IBV strain, which is known to cause varying degrees of pathology in these tissues. Using a specific bioinformatics pipeline, 27 single nucleotide variants (SNVs) were detected in the S1-coding sequences derived from different tissues. These SNVs shaped multiple subpopulations (SP1-SP15), with SP1 being the core subpopulation present in all tissues, while others were tissue-specific. The IBV RNA loads in the tissues were negatively correlated with the number of SNVs or the Shannon entropy values, and phylogenetic analysis revealed a genetic divergence in the S1-coding sequences from certain tissues with lower viral RNA loads, particularly those from the trachea and ovary. Furthermore, the SNVs were associated with nonsynonymous mutations, primarily located in hypervariable region 2 (HVR 2) within the N-terminal domain of S1 (S1-NTD), except for those in SP7, which was exclusive to the trachea and contained changes in HVR 3 in the C-terminal domain of S1 (S1-CTD). Overall, this study adds to the existing knowledge about IBV evolution by highlighting the role of tissue-specific environments in shaping viral genetic diversity.

Ensitrelvir treatment-emergent amino acid substitutions in SARS-CoV-2 3CLpro detected in the SCORPIO-SR phase 3 trial

The impact of treatment-emergent amino acid substitutions (TEAASs) in severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) on clinical and virologic outcomes was evaluated in patients with mild-to-moderate coronavirus disease 2019 (COVID-19) who received ensitrelvir 125 mg in the SCORPIO-SR trial. Individuals were randomised to ensitrelvir or matched placebo once daily for 5 days (first dose <72 h after disease onset). 3CLpro-TEAASs were identified by sequencing nsp5 encoding 3CLpro from pre- and post-treatment nasopharyngeal swabs. Time to resolution of a composite of five characteristic COVID-19 symptoms (TTR) was compared between patients with and without the most common 3CLpro-TEAASs in the ensitrelvir arm. The ensitrelvir and placebo intention-to-treat populations comprised 345 and 341 patients, respectively. 3CLpro-TEAASs were detected in 19/204 (9.3%) ensitrelvir-treated and 3/137 (2.2%) placebo-treated patients with paired sequence data. The most common 3CLpro-TEAASs in the ensitrelvir arm were M49L (n = 12), M49I (n = 3) and S144A (n = 2). In the placebo arm, all 3CLpro-TEAASs occurred in ≤1 patient. Median (95% confidence interval) TTR was comparable between patients with and without those TEAASs (158.8 h [112.1-281.9] vs 189.7 h [151.4-234.4]). Mean viral RNA levels declined more slowly in patients with M49L/I or S144A versus those without. Reductions in viral titre were unaffected by these TEAASs. The characteristics of recombinant SARS-CoV-2 with 3CLpro mutations were explored in vitro. Recombinant viruses with some 3CLpro mutations had reduced susceptibility to ensitrelvir in vitro, with limited effects on viral and competitive fitness. Continued surveillance is warranted to monitor the spread of viruses with 3CLpro mutations.

Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence

The SARS-CoV-2 Spike glycoprotein is central to viral infectivity and immune evasion, making it a key target for vaccine and therapeutic design. This trimeric peplomer undergoes dynamic conformational changes, particularly in its Receptor Binding Domain (RBD), which transitions between closed (down) and ACE2-accessible (up) states relative to the rest of the protein, to facilitate host cell entry. Structural understanding of such critical inter-domain motions, as well as epitope exposure quantification, is essential for obtaining an effective molecular handle over this protein and, in turn, exploiting it towards improved immunogen development. Focusing on the early circulating D614G form and the later emerging Delta (B.1.617.2) variant with higher virulence, we performed large-scale molecular dynamics simulations of the soluble form of the Spike in both 'down' and 'up' conformations of the RBD. Guided by differences in overall fluctuations, we described reaction coordinates based on domain rotations and tilting to extract features that distinguish D614G versus Delta structural behavior of the N-terminal Domain (NTD) and RBD. Using reaction coordinate analysis and Principal Component Analysis (PCA), we identify allosteric coupling between the N-terminal Domain (NTD) and RBD, where NTD tilting influences RBD gating. While some of these motions are conserved across variants, Delta exhibits an optimized RBD-gating mechanism that enhances ACE2 accessibility. Additionally, glycan remodeling in Delta enhances shielding at the NTD supersite, contributing to reduced sensitivity to neutralizing antibodies. Finally, we uncover the impact of the D950N mutation in the HR1 region, which modulates downstream Spike dynamics and immune evasion. Together, our findings reveal variant-specific and conserved structural determinants of SARS-CoV-2 Spike function, providing a mechanistic basis for allosteric modulation, glycan-mediated immune evasion, and viral adaptation. These insights offer valuable guidance for rational vaccine and therapeutic design against SARS-CoV-2 and emerging variants.

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

Modes of Binding of Small Molecules Dictate the Interruption of RBD-ACE2 Complex of SARS-CoV-2

The spike protein is a vital target for therapeutic advancement to inhibit viral entrance. Given that the connection between Spike and ACE2 constitutes the initial phase of SARS-CoV-2 pathogenesis, obstructing this interaction presents a promising therapeutic approach. This work aims to find compounds from DrugBank that can modulate the stability of the spike RBD-ACE2 protein-protein complex. Employing a therapeutic repurposing strategy, we conducted molecular docking of over 9000 DrugBank compounds against the Spike RBD-ACE2 complex, on ten variants, including the wild-type. We also evaluated the intricate stability of the RBD-ACE2 proteins by molecular dynamics simulations, hydrogen bond analysis, RMSD analysis, radius of gyration analysis, and the QM-MM approach. We assessed the efficacy of the top ten candidates for each variant as an inhibitor. Our findings demonstrated for the first time that DrugBank small molecules can interact in three distinct modalities inside the extensive protein-protein interface of RBD and ACE2 complexes. The top ten analyses identified specific DrugBank candidates for each variant and molecules capable of binding to multiple variants. This comprehensive computational technique enables the screening and forecasting of hits for any big and shallow protein-protein interface drug targets.

Dual RNA-seq analyses of viral hemorrhagic septicemia virus and olive flounder (Paralichthys olivaceus) interactions at low and high water temperatures

Transcriptomic studies in fish have considerably contributed to understanding the host responses under viral hemorrhagic septicemia virus (VHSV) infection. However, changes from the perspective of the pathogen and host-pathogen interactions have been relatively underestimated. Given that VHSV genes can be poly-adenylated during replication, this study investigated the global changes from both VHSV and host perspectives using the host transcriptomic data. To achieve this, we utilized transcriptomic data from VHSV infected flounder obtained at different water temperatures (13 °C and 20 °C). We collected the sequence reads belonging to VHSV through an bioinformatic pipeline developed especially for this study. The VHSV reads were used to construct the consensus reference genome and to investigate the expression of VHSV genes and the frequency of variants under different water temperatures. In addition, both linear and logarithmic scales of VHSV transcription levels, along with host transcriptomes, were used to understand pathogen-host interaction through weighted correlation network analysis (WGCNA). The results revealed that VHSV transcription can exceed 5% of host transcriptome during the infection. Single nucleotide variants (SNVs) appeared more frequently in 13 °C groups than in 20 °C groups. While VHSV can replicate at both 13 °C and 20 °C, host transcriptomic responses were notably different, with stronger immune responses and more frequent VHSV genetic changes observed at a lower temperature. This suggests that VHSV infection at low water temperatures significantly influences both the host transcriptional changes and pathogen. Through WGCNA, numerous genes in the module that correlated with VHSV reads on a linear scale were found to be related to cytoskeleton modulation and viral activity. By contrast, the gene module (black) correlated with VHSV reads on a logarithmic scale was strongly associated with host immune responses, such as TNF signaling, necroptosis, and the NF-kappa B signaling pathway. The dual RNA-seq approaches developed in this study will immensely enhance our understanding of host-pathogen interactions across different temperatures.

(R)evolution of Viruses: Introduction to biothermodynamics of viruses

As of 26 April 2024, the International Committee on Taxonomy of Viruses has registered 14690 virus species. Of these, only several dozen have been chemically and thermodynamically characterized. Every virus species is characterized by a specific empirical formula and thermodynamic properties - enthalpy, entropy and Gibbs energy. These physical properties are used in a mechanistic model of virus-host interactions at the cell membrane and in the cytoplasm. This review article presents empirical formulas and Gibbs energies for all major variants of SARS-CoV-2. This article also reports and suggests a mechanistic model of evolutionary changes, with the example of time evolution of SARS-CoV-2 from 2019 to 2024.

Phylogenetic analysis and molecular structure of NS1 proteins of porcine parvovirus 5 isolates from Mexico

Porcine parvovirus 5 (PPV5) is an unclassified member of the family Parvoviridae with no reported pathogenicity, although it is associated with multisystemic, reproductive, and respiratory diseases. Its open reading frame 1 (ORF1) encodes non-structural protein 1 (NS1), which is predicted to have helicase activity that is essential for viral replication. This protein contains a C-motif with an invariant asparagine residue that forms the core of the enzyme's active site, in conjunction with the Walker A and B motifs. The aim of this study was the phylogenetic and molecular characterization of the NS1 of PPV5 through nested PCR and sequencing of three Mexican PPV5-positive samples. Subsequently, a phylogenetic tree, identity matrices of nucleotide and amino acid sequences, and a three-dimensional model of NS1 were constructed. The amplified sequences, which represented 96.9% of the PPV5 ORF1, occupied the same branch in the phylogenetic tree and exhibited the most nucleotide sequence similarity to the corresponding region of PPV4 and the most amino acid sequence similarity to the NS1 proteins of PPV4 and PPV6. A three-dimensional model of NS1 displayed a C-motif characteristic of superfamily 3 (SF3) helicases. The phylogenetic proximity of PPV5 to PPV4 and PPV6 suggests that it may belong to the genus Copiparvovirus. Further studies on helicases from viruses infecting domestic animals may be useful in developing antiviral drugs for both human and veterinary medicine.

Phylogeographic Characterizations of Recent (2015-2023) Senecavirus A Isolates from Canada

Senecavirus A (SVA) continues to cause vesicular lesions in swine in Canada and many regions worldwide. Since the vesicular lesions caused by SVA are similar to those caused by foot and mouth disease virus, swine vesicular disease virus and vesicular stomatitis virus, a foreign animal disease investigation must be initiated to rule out these diseases. SVA isolates from pigs displaying vesicular lesions in Canada from 2015 to 2023 were sequenced, and phylogeographic analysis was performed using the complete genome sequences. The results infer that SVA has spread between the United States and Canada several times. In addition, the results suggest that SVA spreads from different regions. SVA spread was inferred from Canada into Thailand, India and Mexico and inferred from the United States to Brazil, Columbia, Chile and China with ten separate introductions. Furthermore, recombination was observed in SVA genomes from Canada, the United States and China.

Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells

In recent years, the rapid development and employment of autonomous technology have been observed in many areas of human activity. Autonomous technology can readily adjust its function to environmental conditions and enable an efficient operation without human control. While applying the same concept to designing advanced biomolecular therapies would revolutionize nanomedicine, the design approaches to engineering biological nanocomputing agents for predefined operations within living cells remain a challenge. Autonomous nanocomputing agents made of nucleic acids and proteins are an appealing idea, and two decades of research has shown that the engineered agents act under real physical and biochemical constraints in a logical manner. Throughout all domains of life, nucleic acids and proteins perform a variety of vital functions, where the sequence-defined structures of these biopolymers either operate on their own or efficiently function together. This programmability and synergy inspire massive research efforts that utilize the versatility of nucleic and amino acids to encode functions and properties that otherwise do not exist in nature. This Perspective covers the key concepts used in the design and application of nanocomputing agents and discusses potential limitations and paths forward.

A Bibliometric Analysis on Multi-epitope Vaccine Development Against SARS-CoV-2: Current Status, Development, and Future Directions

The etiological agent for the coronavirus disease 2019 (COVID-19), the SARS-CoV-2, caused a global pandemic. Although mRNA, viral-vectored, DNA, and recombinant protein vaccine candidates were effective against the SARS-CoV-2 Wuhan strain, the emergence of SARS-CoV-2 variants of concern (VOCs) reduced the protective efficacies of these vaccines. This necessitates the need for effective and accelerated vaccine development against mutated VOCs. The development of multi-epitope vaccines against SARS-CoV-2 based on in silico identification of highly conserved and immunogenic epitopes is a promising strategy for future SARS-CoV-2 vaccine development. Considering the evolving landscape of the COVID-19 pandemic, we have conducted a bibliometric analysis to consolidate current findings and research trends in multi-epitope vaccine development to provide insights for future vaccine development strategies. Analysis of 102 publications on multi-epitope vaccine development against SARS-CoV-2 revealed significant growth and global collaboration, with India leading in the number of publications, along with an identification of the most prolific authors. Key journals included the Journal of Biomolecular Structure and Dynamics, while top collaborations involved Pakistan-China and India-USA. Keyword analysis showed a prominent focus on immunoinformatics, epitope prediction, and spike glycoprotein. Advances in immunoinformatics, including AI-driven epitope prediction, offer promising avenues for the development of safe and effective multi-epitope vaccines. Immunogenicity may be further improved through nanoparticle-based systems or the use of adjuvants along with real-time genomic surveillance to tailor vaccines against emerging variants.

Vector-Free Deep Tissue Targeting of DNA/RNA Therapeutics via Single Capacitive Discharge Conductivity-Clamped Gene Electrotransfer

Viral vector and lipid nanoparticle based gene delivery have limitations around spatiotemporal control, transgene packaging size, and vector immune reactivity, compromising translation of nucleic acid (NA) therapeutics. In the emerging field of DNA and particularly RNA-based gene therapies, vector-free delivery platforms are identified as a key unmet need. Here, this work addresses these challenges through gene electrotransfer (GET) of "naked" polyanionic DNA/mRNA using a single needle form-factor which supports "electro-lens" based compression of the local electric field, and local control of tissue conductivity, enabling single capacitive discharge minimal charge gene delivery. Proof-of-concept studies for "single capacitive discharge conductivity-clamped gene electrotransfer" (SCD-CC-GET) deep tissue delivery of naked DNA and mRNA in the mouse hindlimb skeletal muscle achieve stable (>18 month) expression of luciferase reporter synthetic DNA, and mRNA encoding the reporter yield rapid onset (<3 h) high transient expression for several weeks. Delivery of DNAs encoding secreted alkaline phosphatase and Cal/09 influenza virus hemagglutinin antigen generate high systemic circulating recombinant protein levels and antibody titres. The findings support adoption of SCD-CC-GET for vaccines and immunotherapies, and extend the utility of this technology to meet the demand for efficient vector-free, precision, deep tissue delivery of NA therapeutics.

Evolutionary dynamics of PRRS virus in Italian Pig farms: a retrospective study

Porcine Reproductive and Respiratory Syndrome (PRRS) causes huge economic losses to pig farms worldwide. Currently available vaccines do not always offer complete protection, due to the extreme variability of the virus. Therefore, good farming practices must be improved to prevent the disease from spreading across the pig production system. In this study, we inferred the dynamics of PRRSV population in Italy by applying bayesian methods on our ORF7 sequence dataset collected during a 15-years period. Random subsets from the overall dataset were built to reduce analysis runtime. Calculated evolutionary rate was consistent between subsets and with other findings on PRRSV and other RNA viruses (4-7 × 10- 3 substitution/site/year) while Time to the Most Recent Common Ancestor was less consistent (from 1980 to 1990). Despite this, in all population dynamic reconstructions, a massive increase in size calculated in early 2000s lasting until around 2010 was inferred. This spike is followed by very heterogeneous dynamics with some differences between subsets, probably due to the random sampling. Geographical origin was inferred in Emilia-Romagna region despite Lombardy being the region with the highest number of farmed animals and farm size. These findings reflect the choices regarding farm management and biosecurity taken in the last two decades, and not strictly related to PRRS. Phylogeny and phylogeography are powerful tools to better understand microorganisms population dynamics and make appropriate choices for disease control.

Viral dynamics in a high-rate algal pond reveals a burst of Phycodnaviridae diversity correlated with episodic algal mortality

This study explores virus-host dynamics in a unique environment: an industrial high-rate algal pond (HRAP). A wealth of novel DNA algal viruses are revealed, including members of Nucleocytoviricota "giant viruses" and the enigmatic Preplasmiviricota (e.g., virophages and polinton-like viruses). Several species of single-celled eukaryotic photosynthetic algae are identified (Chlorophyta) as putative hosts, with alternating dominant populations during the year of study. We specifically observe a surprising diversity of giant viruses from the family Phycodnaviridae (Nucleocytoviricota), including phylogenetically related but highly diversified genotypes appearing in the HRAP that we suggest are implicated in bloom collapse. We hypothesize that these related Phycodnaviridae lineages infect the same algal species of the genus Picochlorum that has been identified in the HRAP. This study establishes a baseline for comprehending the role viruses play in algal farming and emphasizes the necessity of controlling the viral load in future culture system development to optimize algal growth.

IMPORTANCE

The virosphere is ubiquitous, but we have yet to characterize many environments where viruses exist. In an industrial polyculture of microalgae, a wealth of viruses persist, their diversity and dynamics changing over time and consequently give evidence of their evolution and ecological strategies. Several notable infectious agents of the culture's algae appear, including giant viruses, polinton-like viruses, and a virophage. As our reliance and interest in algal compound-based cosmetics, pharmaceuticals, and bio-plastics increases, so must our understanding of these systems, including the unique viruses that appear there.

Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India

BACKGROUND

Sugarcane is host of many viral pathogens that affects its growth and productivity. High-throughput sequencing (HTS) is comprehensive diagnostic platform that permit the precise detection of viral pathogens to resolve the disease epidemiology of the crop, thus providing the phytosanitary status of plants. The current work was designed to comprehend the virome profiling of sugarcane belonging to five varieties collected from the major crop producing states in India. Additionally, a duplex OneStep RT-PCR assay was optimized for simplified detection of prevalent viruses in single reaction run along with validation and confirmation of HTS results.

RESULTS

The complete genome sequences of sugarcane streak mosaic virus (SCSMV), sugarcane yellow leaf virus (SCYLV) and sugarcane mosaic virus (SCMV) consisted of 9790, 5849 and 9600 nucleotides (nt) respectively were obtained excluding 5' UTR and 3' poly (A) tail from sugarcane samples belonging to different varieties. SCSMV and SCMV had single ORF encoding 3130 and 3063 amino acids (aa) respectively, whereas SCYLV genome comprised of six ORFs. The proteolytic cleavage sites in polyprotein region of SCSMV and SCMV revealed the unique amino acid motifs. SCSMV generated the highest number of single nucleotide variants (SNVs) 876 suggesting that it is more susceptible to mutations than other elucidated viruses in HTS. Recombination events revealed the origin of SCSMV_UP isolate from Indian and Iranian isolates as major and minor parents respectively. Further, validation assay by simplified duplex OneStep RT-PCR revealed the prevalence of SCSMV and SCYLV as mixed infection in sugarcane samples with 28 % incidence. The assay could detect the viruses up to 100 pg/µL of RNA concentration.

CONCLUSION

The first comprehensive report of sugarcane virome and use of an optimized duplex OneStep RT-PCR assay revealed the prevalence of SCSMV and SCYLV in sugarcane from India. The study also provides an insight into genetic variations in the coding region of SCSMV and SCMV and emergence of diverse variants present in a viral population. A simplified duplex OneStep RT-PCR assay for simultaneous and expeditious detection of prevalent viruses in sugarcane would be useful in certification programme for production of virus-free planting materials.

Waste management and disease spread potential: A case study of SARS-CoV-2 in garbage dumping sites in Bangkok and its vicinity

During the coronavirus disease 2019 (COVID-19) pandemic, hospitals and households have used personal protective equipment (PPE), such as masks and gloves. Some of these potentially infectious materials were discarded with other household wastes in garbage dumping sites. Thus, this study aimed to detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in contaminated wastes, environments, and mammals scavenging around these sites. From September to October 2022, we visited three garbage dumping sites located in Bangkok, Nakhon Pathom, and Nonthaburi provinces of Thailand. Oral, nasal, rectal swabs, and blood samples were collected from small mammals, stray dogs, and cats. Masks, gloves, soil, and water samples from the sites were additionally collected. Of the 582 samples collected from 238 animals, none tested positive for SARS-CoV-2 in the virus isolation, real-time reverse-transcription polymerase chain reaction, and neutralizing antibody detection. However, one sample (1.18 %; 1/85) from a rat (Rattus spp.) captured in Nonthaburi was serologically positive in the indirect enzyme-linked immunosorbent assay. The surveillance of coronaviruses in rats is strongly encouraged because rats may harbor different zoonotic pathogens, including unknown potentially zoonotic coronaviruses. Moreover, two face mask samples (4.65 %; 2/43) collected from the dumping site in Nakhon Pathom tested positive for SARS-CoV-2 by real-time RT-PCR. To reduce environmental contamination, detecting the SARS-CoV-2 viral genome in contaminated face masks highlights the critical need for proper waste management in households and communities in Thailand. Thus, to minimize exposure and prevent onward transmission, waste management personnel, including garbage dump staff and waste pickers, should be equipped with appropriate PPE and receive regular training on safe handling and disposal.

In silico prediction of pathogen's pandemic potential using the viral trait assessment for pandemics (ViTAP) model

Our world is ever evolving and interconnected, creating constant opportunities for disease outbreaks and pandemics to occur, making pandemic preparedness and pathogen management crucial for global health security. Early pathogen identification and intervention play a key role in mitigating the impacts of disease outbreaks. In this perspective, we present the Viral Trait Assessment for Pandemics (ViTAP) model to aid in the early identification of high-risk viruses that have pandemic potential, which incorporates lessons from past pandemics, including which key viral characteristics are important such as genetic makeup, transmission modes, mutation rates, and symptom severity. This model serves as the foundation for the development of powerful, quantitative tools for the early prediction of pandemic pathogens. The use of such a tool, in conjunction with other pandemic preparedness measures, can allow for early intervention and containment of the virus. This proactive approach could enable timely interventions, guiding public health responses, and resource allocation to prevent widespread outbreaks and mitigate the impact of emerging pathogens.

Shift in potential pathogenic bacteria during permafrost degradation on the Qinghai-Tibet Plateau

Permafrost acts as a potential pathogen reservoir. With accelerating climate change and intensifying permafrost degradation, the release of these pathogens poses significant threats to ecosystems and public health. However, the changes in pathogenic communities during permafrost degradation remain unclear. This study utilized quantitative PCR and Illumina high-throughput sequencing to analyze the composition and quantities of potential pathogenic bacteria in four types of permafrost soil on the northeast edge of the Qinghai-Tibet Plateau (QTP): sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP), and extremely unstable permafrost (EUP). The results showed that during permafrost degradation, the quantity of potential pathogenic bacteria decreased from 7.8 × 106 to 3.1 × 106 copies/g. Both the Richness and Shannon indices initially declined from SSP, to TP, UP, and then began to rise when permafrost degraded to EUP. A total of 216 potential pathogenic bacterial species were identified, including 166 animal pathogens, 28 zoonotic pathogens, and 22 plant pathogens. The pathogenic community intergroup differences (ANOSIM), unique taxa, and dominant pathogen analysis indicated the significant changes in pathogenic communities during permafrost degradation. The potential pathogenic community was significantly influenced by non-pathogenic bacterial communities (Procrustes analysis), with soil moisture being the primary environmental factor, followed by TDS, soil organic carbon, and total nitrogen. SourceTracker2 analysis indicated that the majority of potential pathogenic bacteria in the soil originated from external sources, only a small portion coming from the permafrost itself. These findings suggest that a large number of pathogens were released into the environment while also preserving amount from external sources. It elucidates that each stage of permafrost degradation presents unique biosecurity risks. This study highlights the release and redistribution of pathogenic bacteria associated with the potential public health risks. It provides the crucial insights into the ecological dynamics of permafrost degradation, emphasizing the need for ongoing monitoring and proactive management strategies.

A Narrative Review on the Pandemic Zoonotic RNA Virus Infections Occurred During the Last 25 Years

BACKGROUND

Pandemic zoonotic RNA virus infections have continued to threaten humans and animals worldwide. The objective of this review was to highlight the epidemiology and socioeconomic impacts of pandemic zoonotic RNA virus infections that occurred between 1997 and 2021.

METHODS

Literature search was done from Web of Science, PubMed, Google Scholar and Scopus databases, cumulative case fatalities of individual viral infection calculated, and geographic coverage of the pandemics were shown by maps.

RESULTS

Seven major pandemic zoonotic RNA virus infections occurred from 1997 to 2021 and were presented in three groups: The first group consists of highly pathogenic avian influenza (HPAI-H5N1) and swine-origin influenza (H1N1) viruses with cumulative fatality rates of 53.5% and 0.5% in humans, respectively. Moreover, HPAI-H5N1 infection caused 90-100% death in poultry and economic losses of >$10 billion worldwide. Similarly, H1N1 caused a serious infection in swine and economic losses of 0.5-1.5% of the Gross Domestic Product (GDP) of the affected countries. The second group consists of severe acute respiratory syndrome-associated coronavirus infection (SARS-CoV), Middle East Respiratory Syndrome (MERS-CoV) and Coronavirus disease 2019 (COVID-19) with case fatalities of 9.6%, 34.3% and 2.0%, respectively in humans; but this group only caused mild infections in animals. The third group consists of Ebola and Zika virus infections with case fatalities of 39.5% and 0.02%, respectively in humans but causing only mild infections in animals.

CONCLUSION

Similar infections are expected in the near future, and hence strict implementation of conventional biosecurity-based measures and development of efficacious vaccines would help minimize the impacts of the next pandemic infection.

Vaccine Strategies Against RNA Viruses: Current Advances and Future Directions

The development of vaccines against RNA viruses has undergone a rapid evolution in recent years, particularly driven by the COVID-19 pandemic. This review examines the key roles that RNA viruses, with their high mutation rates and zoonotic potential, play in fostering vaccine innovation. We also discuss both traditional and modern vaccine platforms and the impact of new technologies, such as artificial intelligence, on optimizing immunization strategies. This review evaluates various vaccine platforms, ranging from traditional approaches (inactivated and live-attenuated vaccines) to modern technologies (subunit vaccines, viral and bacterial vectors, nucleic acid vaccines such as mRNA and DNA, and phage-like particle vaccines). To illustrate these platforms' practical applications, we present case studies of vaccines developed for RNA viruses such as SARS-CoV-2, influenza, Zika, and dengue. Additionally, we assess the role of artificial intelligence in predicting viral mutations and enhancing vaccine design. The case studies underscore the successful application of RNA-based vaccines, particularly in the fight against COVID-19, which has saved millions of lives. Current clinical trials for influenza, Zika, and dengue vaccines continue to show promise, highlighting the growing efficacy and adaptability of these platforms. Furthermore, artificial intelligence is driving improvements in vaccine candidate optimization and providing predictive models for viral evolution, enhancing our ability to respond to future outbreaks. Advances in vaccine technology, such as the success of mRNA vaccines against SARS-CoV-2, highlight the potential of nucleic acid platforms in combating RNA viruses. Ongoing trials for influenza, Zika, and dengue demonstrate platform adaptability, while artificial intelligence enhances vaccine design by predicting viral mutations. Integrating these innovations with the One Health approach, which unites human, animal, and environmental health, is essential for strengthening global preparedness against future RNA virus threats.

Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression

The precise role of the highly variable coronavirus S protein in modulating innate immune responses remains unclear. In this study, we demonstrated that the mutant strain of swine coronavirus porcine enteric diarrhea virus induced significantly lower levels of double-stranded RNA (dsRNA) accumulation, inhibited protein kinase R (PKR) activation and suppressed stress granule (SG) formation compared with the classical strain. The 29th amino acid at N-terminus of S was identified as the key functional site for regulation of SG formation, and found that mutant S inhibited PKR phosphorylation and SG formation by upregulating adenosine deaminase acting on RNA 1 (ADAR1)-p150. Notably, the Zα domain of ADAR1-p150 was essential for inhibiting SG formation. Upregulation of ADAR1-p150 also reduced accumulation of dsRNA depending on its RNA editing function. Virus rescue confirmed that the mutant carrying a substitution at amino acid 29 failed to induce ADAR1-p150, leading to dsRNA accumulation, PKR activation and SG formation. Interestingly, the latest severe acute respiratory syndrome coronavirus-2 strains exhibit a novel 25PPA27 deletion at N-terminus of S that was also shown to lead to altered ADAR1-p150 expression and SG inhibition. The transcription factor TCF7L2 was identified as a player in S-mediated transcriptional enhancement of ADAR1-p150. This study is the first to clarify the crucial role of N-terminus of S in immune regulation of coronaviruses.

Rapid detection of the SARS-CoV-2 omicron variants based on high-resolution melting curve analysis

With the continuous spread of the SARS-CoV-2 globally, viral mutations have accumulated. As a result, SARS-CoV-2 became more contagious, and has a higher risk of immune escape and reinfection. To identify variants and have an awareness of the prevalence of these variants, this study selected four segments containing mutations on the S gene of the SARS-CoV-2. Then a rapid and convenient variants detection method was established using high-resolution melting(HRM) analysis combined with nested polymerase chain reaction(PCR). The total detection process takes about 5 h. Through comprehensive analysis of the results from the four reaction systems, the identification of seven important Omicron variants(BA.2, BA.2.75, BA.5.2, BF.7, BQ.1, XBB.1 and XBB.2) can be achieved, with significant differentiation in the melting curves of each variant group. The method established in this study was used to genotype positive specimens in COVID-19 nucleic acid testing, the overall concordance rate compared to whole genome sequencing results was 88.9%, and the positive concordance rate of each sublineage was greater than 80% and the negative concordance rate was greater than 94.4%. The detection of clinical specimens has demonstrated that the HRM analysis established in this study is an effective, rapid and convenient variant identification method, which can be used for monitoring SARS-CoV-2 variants and has important value in addressing public health issues caused by the ongoing mutations of the SARS-CoV-2.

Assessing the de novo assemblers: a metaviromic study of apple and first report of citrus concave gum-associated virus, apple rubbery wood virus 1 and 2 infecting apple in India

BACKGROUND

The choice of de novo assembler for high-throughput sequencing (HTS) data remains a pivotal factor in the HTS-based discovery of viral pathogens. This study assessed de novo assemblers, namely Trinity, SPAdes, and MEGAHIT for HTS datasets generated on the Illumina platform from 23 apple samples, representing 15 exotic and indigenous apple varieties and a rootstock. The assemblers were compared based on assembly quality metrics, including the largest contig, total assembly length, genome coverage, and N50.

RESULTS

MEGAHIT was most efficient assembler according to the metrics evaluated in this study. By using multiple assemblers, near-complete genome sequences of citrus concave gum-associated virus (CCGaV), apple rubbery wood virus 1 (ARWV-1), ARWV-2, apple necrotic mosaic virus (ApNMV), apple mosaic virus, apple stem pitting virus, apple stem grooving virus, apple chlorotic leaf spot virus, apple hammerhead viroid and apple scar skin viroid were reconstructed. These viruses were further confirmed through Sanger sequencing in different apple cultivars. Among them, CCGaV, ARWV-1 and ARWV-2 were recorded from apples in India for the first time. The analysis of virus richness revealed that ApNMV was dominant, followed by ARWV-1 and CCGaV. Moreover, MEGAHIT identified novel single-nucleotide variants.

CONCLUSIONS

Our analyses highlight the crucial role of assembly methods in reconstructing near-complete apple virus genomes from the Illumina reads. This study emphasizes the significance of employing multiple assemblers for de novo virus genome assembly in vegetatively propagated perennial fruit crops.

Error thresholds in the presence of epistatic interactions

Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "error threshold" leads to a loss of essential genetic information and population collapse, an effect known as the "error catastrophe." We explain how crossing this threshold, as a result of increasing mutation rates, can be understood as a second-order phase transition, even in the presence of lethal mutations. In particular, we show that, in fitness landscapes with a single peak, this collapse is equivalent to a ferroparamagnetic transition, where the back-mutation rate plays the role of the external magnetic field. We then generalize this framework to rugged fitness landscapes, like the ones that arise from epistatic interactions, and provide numerical evidence that there is a transition from a high average fitness regime to a low average fitness one, similarly to single-peaked landscapes. The onset of the transition is heralded by a sudden change in the susceptibility to variations in the mutation rate. We use insight from replica symmetry breaking mechanisms in spin glasses, in particular by considering the fluctuations of the genotype similarity distribution as the order parameter.

Advancing the field of viroporins-Structure, function and pharmacology: IUPHAR Review 39

Viroporins possess important potential as antiviral targets due to their critical roles during virus life cycles, spanning from virus entry to egress. Although the antiviral amantadine targets the M2 viroporin of influenza A virus, successful progression of other viroporin inhibitors into clinical use remains challenging. These challenges relate in varying proportions to a lack of reliable full-length 3D-structures, difficulties in functionally characterising individual viroporins, and absence of verifiable direct binding between inhibitor and viroporin. This review offers perspectives to help overcome these challenges. We provide a comprehensive overview of the viroporin family, including their structural and functional features, highlighting the moldability of their energy landscapes and actions. To advance the field, we suggest a list of best practices to aspire towards unambiguous viroporin identification and characterisation, along with considerations of potential pitfalls. Finally, we present current and future scenarios of, and prospects for, viroporin targeting drugs.

Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods

Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.

Tracking the emergence of a novel genotype of Decapod hepanhamaparvovirus in shrimp using laser microdissection and next generation sequencing

The prevalence of hepatopancreatic diseases in cultured shrimp has increased in recent years. Decapod Hepanhamaparvovirus 1 (DHPV) infection was identified by histology in samples that could not be detected by PCR-based assay for this virus. Employing Laser Microdissection (LMD), we dissected cells containing intranuclear inclusion bodies pathognomonic for DHPV infection from histological sections. Whole Genome Amplification and NGS were used to generate five complete genomes of the novel DHPV isolate that showed identities ranging from 77% to 98% to previously reported isolates. Phylogenetic analyses revealed the DHPV isolate represents a novel genotype, Genotype V. We developed PCR and in situ hybridization methods tailored for the specific detection of this genotype. Our approach of combining LMD with NGS opens avenues for rapid identification of emerging viral pathogens and retrospective studies to understand origin and evolution of viruses showcasing the transformative potential of the innovative approach used in this study.

The diversity and risk of potential pathogenic bacteria on the surface of glaciers in the southeastern Tibetan Plateau

Glaciers, which constitute the world's largest global freshwater reservoir, are also natural microbial repositories. The frequent pandemic in recent years underscored the potential biosafety risks associated with the release of microorganisms from the accelerated melting of glaciers due to global warming. However, the characteristics of pathogenic microorganisms in glaciers are not well understood. The glacier surface is the primary area where glacier melting occurs that is often the main subject of research on the dynamics of pathogenic microbial communities in efforts to assess glacier biosafety risks and devise preventive measures. In this study, high-throughput sequencing and quantitative polymerase chain reaction methods were employed in analyses of the composition and quantities of potential pathogenic bacteria on the surfaces of glaciers in the southeastern Tibetan Plateau. The study identified 441 potential pathogenic species ranging from 215 to 4.39 × 1011 copies/g, with notable seasonal and environmental variations being found in the composition and quantity of potential pathogens. The highest level of diversity was observed in April and snow, while the highest quantities were observed in October and cryoconite. Host analysis revealed that >70 % of the species were pathogens affecting animals, with the highest proportion of zoonotic pathogens being observed in April. Analysis of aerosols and glacial meltwater dispersion suggested that these microbes originated from West Asia, primarily affecting the central and southern regions of China. Null model analysis indicated that the assembly of potential pathogenic microbial communities on glacier surfaces was largely governed by deterministic processes. In conclusion, potential pathogenic bacteria on glacier surfaces mainly originated from the snow and exhibited significant temporal and spatial variation patterns. These findings can be used to enhance researchers' ability to predict potential biosafety risks associated with pathogenic bacteria in glaciers and to prevent their negative impact on populations and ecological systems.

Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay

The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.

Pioneering role of RNA in the early evolution of life

The catalytic, regulatory and structural properties of RNA, combined with their extraordinary ubiquity in cellular processes, are consistent with the proposal that this molecule played a much more conspicuous role in heredity and metabolism during the early stages of biological evolution. This review explores the pivotal role of RNA in the earliest life forms and its relevance in modern biological systems. It examines current models that study the early evolution of life, providing insights into the primordial RNA world and its legacy in contemporary biology.

Cellular dynamics shape recombination frequency in coronaviruses

Coronavirus genomes have evolutionary histories shaped extensively by recombination. Yet, how often recombination occurs at a cellular level, or the factors that regulate recombination rates, are poorly understood. Utilizing experimental co-infections with pairs of genetically distinct coronaviruses, we found that recombination is both frequent and rare during coinfection. Recombination occurred in every instance of co-infection yet resulted in relatively few recombinant RNAs. By integrating a discrete-time Susceptible-Infected-Removed (SIR) model, we found that rates of recombination are determined primarily by rates of cellular co-infection, rather than other possible barriers such as RNA compartmentalization. By staggering the order and timing of infection with each virus we also found that rates of co-infection are themselves heavily influenced by genetic and ecological mechanisms, including superinfection exclusion and the relative fitness of competing viruses. Our study highlights recombination as a potent yet regulated force: frequent enough to ensure a steady influx of genetic variation but also infrequent enough to maintain genomic integrity. As recombination is thought to be an important driver of host-switching and disease emergence, our study provides new insights into the factors that regulate coronavirus recombination and evolution more broadly.

Inhibitors of the Structural and Nonstructural Proteins of Alphaviruses

The Alphavirus genus includes viruses that cause encephalitis due to neuroinvasion and viruses that cause arthritis due to acute and chronic inflammation. There is no approved therapeutic for alphavirus infections, but significant efforts are ongoing, more so in recent years, to develop vaccines and therapeutics for alphavirus infections. This review article highlights some of the major advances made so far to identify small molecules that can selectively target the structural and the nonstructural proteins in alphaviruses with the expectation that persistent investigation of an increasingly expanding chemical space through a variety of structure-based design and high-throughput screening strategies will yield candidate drugs for clinical studies. While most of the works discussed are still in the early discovery to lead optimization stages, promising avenues remain for drug development against this family of viruses.

The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo

The COVID-19 pandemic has led to the deaths of millions of people and severe global economic impacts. Small molecule therapeutics have played an important role in the fight against SARS-CoV-2, the virus responsible for COVID-19, but their efficacy has been limited in scope and availability, with many people unable to access their benefits, and better options are needed. EDP-235 is specifically designed to inhibit the SARS-CoV-2 3CLpro, with potent nanomolar activity against all SARS-CoV-2 variants to date, as well as clinically relevant human and zoonotic coronaviruses. EDP-235 maintains potency against variants bearing mutations associated with nirmatrelvir resistance. Additionally, EDP-235 demonstrates a ≥ 500-fold selectivity index against multiple host proteases. In a male Syrian hamster model of COVID-19, EDP-235 suppresses SARS-CoV-2 replication and viral-induced hamster lung pathology. In a female ferret model, EDP-235 inhibits production of SARS-CoV-2 infectious virus and RNA at multiple anatomical sites. Furthermore, SARS-CoV-2 contact transmission does not occur when naïve ferrets are co-housed with infected, EDP-235-treated ferrets. Collectively, these results demonstrate that EDP-235 is a broad-spectrum coronavirus inhibitor with efficacy in animal models of primary infection and transmission.

A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics

Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation.

Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis

Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.

Evolutionary Invasion Analysis of Modern Epidemics Highlights the Context-Dependence of Virulence Evolution

Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict how the relationship between virulence (the harm to hosts caused by an infection) and transmission will evolve in certain virus-host contexts. In this study, we invoke evolutionary invasion analysis-a method used to identify the evolution of uninvadable strategies in dynamical systems-to examine how the virulence-transmission dichotomy can evolve in models of virus infections defined by different natural histories. We reveal peculiar patterns of virulence evolution between epidemics with different disease natural histories (SARS-CoV-2 and hepatitis C virus). We discuss the findings with regards to the public health implications of predicting virus evolution, and in broader theoretical canon involving virulence evolution in host-parasite systems.

Immunization against Medically Important Human Coronaviruses of Public Health Concern

SARS-CoV-2 is a virus that affects the human immune system. It was observed to be on the rise since the beginning of 2020 and turned into a life-threatening pandemic. Scientists have tried to develop a possible preventive and therapeutic drug against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and other related coronaviruses by assessing COVID-19-recovered persons' immunity. This study aims to review immunization against SARS-CoV-2, along with exploring the interventions that have been developed for the prevention of SARS-CoV-2. This study also highlighted the role of phototherapy in treating SARS-CoV infection. The study adopted a review approach to gathering the information available and the progress that has been made in the treatment and prevention of COVID-19. Various vaccinations, including nucleotide, subunit, and vector-based vaccines, as well as attenuated and inactivated forms that have already been shown to have prophylactic efficacy against the Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, have been summarized. Neutralizing and non-neutralizing antibodies are all associated with viral infections. Because there is no specific antiviral vaccine or therapies for coronaviruses, the main treatment strategy is supportive care, which is reinforced by combining broad-spectrum antivirals, convalescent plasma, and corticosteroids. COVID-19 has been a challenge to keep reconsidering the usual approaches to regulatory evaluation as a result of getting mixed and complicated findings on the vaccines, as well as licensing procedures. However, it is observed that medicinal herbs also play an important role in treating infection of the upper respiratory tract, the principal symptom of SARS-CoV due to their natural bioactive composite. However, some Traditional Chinese Medicines contain mutagens and nephrotoxins and the toxicological properties of the majority of Chinese herbal remedies are unknown. Therefore, to treat the COVID-19 infection along with conventional treatment, it is recommended that herb-drug interaction be examined thoroughly.

Mixed infection of two mandariviruses identified by high-throughput sequencing in Kinnow mandarin and development of their specific detection using duplex RT-PCR

In the current study, high-throughput sequencing (HTS) was used to identify viruses associated with the Kinnow mandarin (Citrus reticulata) plants exhibiting yellow vein clearing, mottling, and chlorosis symptoms at experimental farm of ICAR-Indian Agricultural Research Institute, New Delhi, India. During November 2022, leaf samples of symptomatic and asymptomatic Kinnow mandarin trees were collected, subjected to HTS and one of the representative symptomatic samples was subjected to leaf-dip electron microscopy (EM). In the EM results, flexuous virus particles typical of mandarivirus were observed. Ribosomal RNA was depleted from total RNA of pooled samples and RNA sequencing was done using NovaSeq 6000. Host unaligned reads were de novo assembled into contigs, which were annotated through BLASTn using database of plant viruses/viroids reference genomes (NCBI). Results of assembled contigs revealed near-complete genomes of two mandariviruses, i.e., citrus yellow vein clearing virus (CYVCV) and citrus yellow mottle-associated virus (CiYMaV). The values of fragments per kilo base transcript length per million fragments mapped estimation indicated the dominance of CYVCV in HTS data and it was also confirmed through krona plot distribution of viruses in the pooled samples. A rapid and reliable duplex RT-PCR assay was also developed and standardized for the simultaneous detection of both CYVCV and CiYMaV in a pooled Kinnow mandarin sample. The developed duplex RT-PCR was then validated for the presence of these viruses in individual Kinnow mandarin samples. The specificity and sensitivity results confirmed that primers were highly specific to their targets and able to detect viruses up to 10-2 dilutions of RNA in standard and duplex RT-PCR. Therefore, the developed rapid duplex RT-PCR can be used for virus indexing and production of virus-free Kinnow mandarin plants for certification programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04011-9.

Genetic Variability Among U.S.-Sentinel Cotton Plot Cotton Leafroll Dwarf Virus and Globally Available Reference Isolates Based on ORF0 Diversity

The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America, has been identified in commercial cotton plantings in the United States. Here, the CLRDV intraspecific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South American lineages. Principal component analysis (PCA) identified seven statistically supported intraspecific populations. The Bayesian phylogeny and PCA dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia and eastern Texas. The Alabama-Georgia founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central United States. Based on the geographically restricted distribution, spread of another extant Texas population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).

Exploring Variability: Inflammation Mediator Levels across Tissues and Time in Poultry Experimentally Infected by the G1a and G6 Genogroups of Infectious Bursal Disease Virus (IBDV)

Infectious bursal disease virus (IBDV) is a significant burden for poultry production and market due to both direct disease and induced immunosuppression. In the present study, the expression of different cytokines in the bursa of Fabricius and thymus was evaluated during a 28-day-long experimental infection with two strains classified in the G1a (Classical) and G6 (ITA) genogroups. Although both strains significantly affected and modulated the expression of different molecules, the G6 strain seemed to induce a delayed immune response or suppress it more promptly. A recovery in the expression of several mediators was observed in the G1a-infected group at the end of the study, but not in the G6 one, further supporting a more persistent immunosuppression. This evidence fits with the higher replication level previously reported for the G6 and with the clinical outcome, as this genotype, although subclinical, has often been considered more immunosuppressive. However, unlike other studies focused on shorter time periods after infection, the patterns observed in this paper were highly variable and complex, depending on the strain, tissue, and time point, and characterized by a non-negligible within-group variability. Besides confirming the strain/genogroup effect on immune system modulation, the present study suggests the usefulness of longer monitoring activities after experimental infection to better understand the complex patterns and interactions with the host response.

Evolutionary Profile of Mayaro Virus in the Americas: An Update into Genome Variability

The Mayaro virus (MAYV) is an arbovirus with emerging potential, though with a limited understanding of its epidemiology and evolution due to the lack of studies and surveillance. Here, we investigated 71 MAYV genome sequences from the Americas available at GenBank and characterized the phylogenetic relationship among virus strains. A phylogenetic analysis showed that sequences were grouped according to the genotypes L, D, and N. Genotype D sequences were closely related to sequences collected in adjacent years and from their respective countries, suggesting that isolates may have originated from circulating lineages. The coalescent analysis demonstrated similar results, indicating the continuous circulation of the virus between countries as well. An unidentified sequence from the USA was grouped with genotype D, suggesting the insertion of this genotype in the country. Furthermore, the recombination analysis detected homologous and three heterologous hybrids which presented an insertion into the nsP3 protein. Amino acid substitutions among sequences indicated selective pressure sites, suggesting viral adaptability. This also impacted the binding affinity between the E1-E2 protein complex and the Mxra8 receptor, associated with MAYV entry into human cells. These results provide information for a better understanding of genotypes circulating in the Americas.

Mutation prediction in the SARS-CoV-2 genome using attention-based neural machine translation

Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has been evolving rapidly after causing havoc worldwide in 2020. Since then, it has been very hard to contain the virus owing to its frequently mutating nature. Changes in its genome lead to viral evolution, rendering it more resistant to existing vaccines and drugs. Predicting viral mutations beforehand will help in gearing up against more infectious and virulent versions of the virus in turn decreasing the damage caused by them. In this paper, we have proposed different NMT (neural machine translation) architectures based on RNNs (recurrent neural networks) to predict mutations in the SARS-CoV-2-selected non-structural proteins (NSP), i.e., NSP1, NSP3, NSP5, NSP8, NSP9, NSP13, and NSP15. First, we created and pre-processed the pairs of sequences from two languages using k-means clustering and nearest neighbors for training a neural translation machine. We also provided insights for training NMTs on long biological sequences. In addition, we evaluated and benchmarked our models to demonstrate their efficiency and reliability.

Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors

After the first outbreak, SARS-CoV-2 infection continues to occur due to the emergence of new variants. There is limited information available on the comparative evaluation of evolutionary characteristics of SARS-CoV-2 among different countries over time, and its relatedness to epidemiological and socio-environmental factors within those countries. We assessed comparative Bayesian evolutionary characteristics for SARS-CoV-2 in eight countries from 2020 to 2022 using BEAST version 2.6.7. Additionally, the relatedness between virus evolution factors and both epidemiological and socio-environmental factors was analyzed using Pearson's correlation coefficient. The estimated substitution rates in the gene encoding S protein of SARS-CoV-2 exhibited a continuous increase from 2020 to 2022 and were divided into two distinct groups in 2022 (p value < 0.05). Effective population size (Ne) generally showed decreased patterns by time. Notably, the change rates of the substitution rates were negatively correlated with the cumulative vaccination rates in 2021. A strict and rapid vaccination policy in the United Arab Emirates dramatically reduced the evolution of the virus, compared to other countries. Also, the average yearly temperature in countries were negatively correlated with the substitution rates. The changes of six epitopes in SARS-CoV-2 were related to various socio-environmental factors. We figured out comparative virus evolutionary traits and the association of epidemiological and socio-environmental factors especially cumulative vaccination rates and average temperature.

Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using in silico studies

The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 Mpro. The use of AutoDock Vina for structure-based virtual screening was done first due to the importance of protein interactions in the development of drugs. Molecular docking was used in the comparative study to assess 89 different chemicals from medicinal herbs. To anticipate their effectiveness against the primary protease of SARS-CoV-2, more analysis was done on the ADMET profile, drug-likeness, and Lipinski's rule of five. The next step involved three replicas of 100 ns-long molecular dynamics simulations on the potential candidates, which were preceded by calculations of the binding free energy of MM-GBSA. The outcomes showed that Achyrodimer A, Cinchonain Ib, Symphonone F, and Lupeol acetate all performed well and had the highest 6LU7 binding affinities. Using RMSD, RMSF, and protein-ligand interactions, the stability of the protein-ligand complex was assessed. The studies indicate that bioactive substances obtained from herbal medicines may function as a COVID-19 therapeutic agent, necessitating additional wet lab research to confirm their therapeutic potential, efficacy, and pharmacological capacity against the condition.Communicated by Ramaswamy H. Sarma.

Current progress towards prevention of Nipah and Hendra disease in humans: A scoping review of vaccine and monoclonal antibody candidates being evaluated in clinical trials

OBJECTIVES

Nipah and Hendra are deadly zoonotic diseases with pandemic potential. To date, no human vaccine or monoclonal antibody (mAb) has been licensed to prevent disease caused by these pathogens. The aim of this scoping review was to identify and describe all Phase I, II, and III clinical trials of vaccine candidates or mAbs candidates designed to prevent Nipah and Hendra in humans and to compare the characteristics of the vaccine candidates to characteristics outlined in the Target Product Profile drafted by the World Health Organisation as part of the WHO Research & Development Blueprint for Action to Prevent Epidemics.

METHODS

We searched 23 clinical trial registries, the Cochrane Central Register of Clinical Trials, and grey literature up to June 2023 to identify vaccine and mAb candidates being evaluated in registered clinical trials. Vaccine candidate and trial characteristics were double-extracted for evaluation and the vaccine candidate characteristics were compared with the preferred and critical criteria of the World Health Organisation's Target Product Profile for Nipah virus vaccine.

RESULTS

Three vaccine candidates (Hendra Virus Soluble Glycoprotein Vaccine [HeV-sG-V], PHV02, and mRNA-1215) and one mAb (m102.4) had a registered human clinical trial by June 2023. All trials were phase 1, dose-ranging trials taking place in the United States of America or Australia and enrolling healthy adults. Although all vaccine candidates meet the dose regimen and route of administration criteria of the Target Product Profile, other criteria such as measures of efficacy and reactogenicity will need to be evaluated in the future as evidence becomes available.

CONCLUSION

Multiple vaccine candidates and one mAb candidate have reached the stage of human clinical trials and are reviewed here. Monitoring progress during evaluation of these candidates and candidates entering clinical trials in the future can help highlight many of the challenges that remain.