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Simple Summary: Pigs are now facing an increasing number of emerging and re-emerging viral agents that can cause significant economic losses. Identifying and studying the pathogenicity of these viral agents helps to prevent and control the spread of diseases. Getah virus (GETV) is a neglected zoonotic virus that causes reproductive disorders in sows and diarrhea in newborn piglets. To date, reports on GETV in pigs have focused mainly on reproductive disorders. In this study, we found GETV was frequently detected in piglets associated with diarrhea during epidemiological surveillance in Jiangxi Province in China. Piglets infected with GETV manifested as diarrhea, which could lead to death in suckling piglets. A GETV strain was isolated and characterized. The complete genome, pathogenesis, and pathogenicity of the isolated strain was investigated. Clinical signs, gross lesions, and histological changes were observed in suckling piglets inoculated with the isolated GETV strain. The results of this study add to the knowledge of the epidemiology, viral genetics, pathogenicity, and pathogenicity of porcine GETV. Getah virus (GETV) is a mosquito-borne virus belonging to the genus Alphavirus in the family Togaviridae. Its infection poses an increasing threat to animals and public health in China. In this study, an epidemiological survey of GETV on 46 pig farms in Jiangxi Province, China, was performed; GETV isolation and characterization were carried out, including a complete sequence determination and phylogenetic analysis; and pathogenicity of the GETV was experimentally investigated by inoculating newborn piglets with the isolated GETV strain. Epidemiological studies conducted on the organs of infected pigs, aborted piglets, and the blood of aborted sows sampled from pig farms in Jiangxi Province, China, demonstrated that 44 out of the 46 pig farms were positive for GETV, which is a positivity rate of 95.65% (44/46). Of the 411 samples tested, 47.93% (197/411) were found positive for GETV. A GETV strain called GETV-JX-CHN-22 was obtained, which showed stable proliferation in Vero cells. One-step growth curve results showed that the GETV-JX-CHN-22-P7 (passage 7) isolate reached a peak titer of 108.3 TCID50/mL at 24 hpi. An analysis of the whole-genome sequencing results showed that GETV-JX-CHN-22 (prototype) and GETV-JX-CHN-22-P7 shared nucleotide sequence similarities of 95.3% to 99.6% with 73 reference strains of GETV in GenBank. Genetic evolution analysis revealed that GETV-JX-CHN-22 and GETV-JX-CHN-22-P7 belonged to the GIII group, the same group members of most strains were reported in China. Animal inoculation experiments indicated that piglets exhibited typical symptoms and pathological changes of GETV infection after 24 h inoculation, which reproduced the pathogenicity of GETV field strain infections in piglets. To our knowledge, this study is the first report on the detection and isolation of porcine GETV associated with diarrhea from pig farms in Jiangxi Province, China. It is of great importance to study the infection spectrum, transmission mechanism, and public health significance of GETV. The results provide foundations for the genomic and biological (pathogenic) characteristics of the circulating GETV in Jiangxi Province, China. [ABSTRACT FROM AUTHOR]

Significant variations have been observed in viral copies generated during SARS-CoV-2 infections. However, the factors that impact viral copies and infection dynamics are not fully understood, and may be inherently dependent upon different viral and host factors. Here, we conducted virus whole genome sequencing and measured viral copies using RT-qPCR from 9,902 SARS-CoV-2 infections over a 2-year period to examine the impact of virus genetic variation on changes in viral copies adjusted for host age and vaccination status. Using a genome-wide association study (GWAS) approach, we identified multiple single-nucleotide polymorphisms (SNPs) corresponding to amino acid changes in the SARS-CoV-2 genome associated with variations in viral copies. We further applied a marginal epistasis test to detect interactions among SNPs and identified multiple pairs of substitutions located in the spike gene that have non-linear effects on viral copies. We also analyzed the temporal patterns and found that SNPs associated with increased viral copies were predominantly observed in Delta and Omicron BA.2/BA.4/BA.5/XBB infections, whereas those associated with decreased viral copies were only observed in infections with Omicron BA.1 variants. Our work showcases how GWAS can be a useful tool for probing phenotypes related to SNPs in viral genomes that are worth further exploration. We argue that this approach can be used more broadly across pathogens to characterize emerging variants and monitor therapeutic interventions. Author summary: Our study explores why viral load (copies measured by RT-qPCR) varies during SARS-CoV-2 infections by analyzing viral mutations and measuring viral copies in 9,902 individuals over two years. We aimed to understand how genetic differences in SARS-CoV-2 influence viral copies, considering host age and vaccination status. Using a genome-wide association study (GWAS), we identified several single-nucleotide polymorphisms (SNPs) in the virus linked to variations in viral levels. Notably, interactions between certain SNPs in the spike gene had non-linear effects on viral copies. Our analysis revealed that SNPs associated with higher viral copies were common in Delta and Omicron BA.2/BA.4/BA.5/XBB variants, while those linked to lower levels were mainly found in Omicron BA.1. This research highlights GWAS as a powerful tool for exploring virus genetics and suggests it can be broadly applied to monitor new variants of COVID-19 and other infectious diseases. [ABSTRACT FROM AUTHOR]

Influenza is a highly contagious acute viral illness that affects the respiratory system, posing a significant global public health concern. Influenza B virus (IBV) causes annual seasonal epidemics. The exploration of molecular biology and reverse genetics of IBV is pivotal for understanding its replication, pathogenesis, and evolution. Reverse genetics empowers us to purposefully alter the viral genome, engineer precise genetic modifications, and unveil the secrets of virulence and resistance mechanisms. It helps us in quickly analyzing new virus strains by viral genome manipulation and the development of innovative influenza vaccines. Reverse genetics has been employed to create mutant or reassortant influenza viruses for evaluating their virulence, pathogenicity, host range, and transmissibility. Without this technique, these tasks would be difficult or impossible, making it crucial for preparing for epidemics and protecting public health. Here, we bring together the latest information on how we can manipulate the genes of the influenza B virus using reverse genetics methods, most importantly helper virus-independent techniques. [ABSTRACT FROM AUTHOR]

Rabies virus (RABV) is the causative agent of rabies, a lethal neurological disease in mammals. RABV strains can be classified into fixed strains (laboratory strains) and street strains (field/clinical strains), which have different properties including cell tropism and neuroinvasiveness. RABV Toyohashi strain is a street strain isolated in Japan from an imported case which had been bitten by rabid dog in the Philippines. In order to facilitate molecular studies of RABV, we established a reverse genetics (RG) system for the study of the Toyohashi strain. The recombinant virus was obtained from a cDNA clone of Toyohashi strain and exhibited similar growth efficiency as the original virus in cultured cell lines. Both the original and recombinant strains showed similar pathogenicity with high neuroinvasiveness in mice, and the infected mice developed a long and inconsistent incubation period, which is characteristic of street strains. We also generated a recombinant Toyohashi strain expressing viral phosphoprotein (P protein) fused with the fluorescent protein mCherry, and tracked the intracellular dynamics of the viral P protein using live-cell imaging. The presented reverse genetics system for Toyohashi strain will be a useful tool to explore the fundamental molecular mechanisms of the replication of RABV street strains. [ABSTRACT FROM AUTHOR]

Dengue viruses (DENVs), like all viruses, evolve to perpetuate transmission of their species in their hosts. However, how DENV genetics influences dengue disease outbreaks remains poorly understood. Here, we examined isolates of the South Pacific dengue virus type 2 (DENV-2) that emerged in the 1970s and caused major dengue outbreaks in islands in this region until it reached Tonga, where only a few mild cases were reported. Phylogenetically, the DENV-2 strain isolated in Tonga segregated into a clade different from those clades infecting populations in other South Pacific islands. We found that this epidemiological observation could be explained by a single histidine-to-arginine substitution in position 86 of the premembrane (prM) protein of the Tonga DENV-2 strain. This mutation attenuated viral protein translation in mammalian cells but not in midgut cells of the mosquito vector Aedes aegypti. In mammalian cells, the prM mutation resulted in reduced translation of the viral genome and subsequent reduced virus replication. In contrast, in mosquito midgut cells, the prM mutation conferred a selective infection advantage, possibly because of the positively charged arginine residue introduced by the mutation. These findings provide molecular insights into the year-long silent transmission of attenuated DENV-2 in Tonga during the 1970s dengue outbreak in the South Pacific. Editor's summary: The effects of genetic changes in dengue virus on dengue outbreaks remain unclear. Choi et al. have analyzed the 1970s dengue outbreak in the South Pacific, which began with a large number of severe dengue cases but caused only mild febrile illness once it arrived in Tonga. These investigators report that the attenuated human infection might be explained by a single histidine-to-arginine substitution in position 86 of the premembrane (prM) protein of this dengue virus strain. The authors demonstrate that this mutation conferred a selection advantage enabling the virus to more efficiently infect the midgut of the Aedes mosquito vector. These findings help to integrate dengue virus genetics into our understanding of dengue epidemiology. —Orla Smith [ABSTRACT FROM AUTHOR]

Avian infectious bronchitis is an acute respiratory disease of poultry of particular concern for global food security. Investigation of infectious bronchitis virus (IBV), the causative agent of avian infectious bronchitis, via reverse genetics enables deeper understanding of virus biology and a rapid response to emerging variants. Classic methods of reverse genetics for IBV can be time consuming, rely on recombination for the introduction of mutations, and, depending on the system, can be subject to genome instability and unreliable success rates. In this study, we have applied data-optimized Golden Gate Assembly design to create a rapidly executable, flexible, and faithful reverse genetics system for IBV. The IBV genome was divided into 12 fragments at high-fidelity fusion site breakpoints. All fragments were synthetically produced and propagated in E. coli plasmids, amenable to standard molecular biology techniques for DNA manipulation. The assembly can be carried out in a single reaction, with the products used directly in subsequent viral rescue steps. We demonstrate the use of this system for generation of point mutants and gene replacements. This Golden Gate Assembly-based reverse genetics system will enable rapid response to emerging variants of IBV, particularly important to vaccine development for controlling spread within poultry populations. [ABSTRACT FROM AUTHOR]

Recently published near full-length KSHV genomes from a Cameroon Kaposi sarcoma case-control study showed strong evidence of viral recombination and mixed infections, but no sequence variations associated with disease. Using the same methodology, an additional 102 KSHV genomes from 76 individuals with KSHV-associated diseases have been sequenced. Diagnoses comprise all KSHV-associated diseases (KAD): Kaposi sarcoma (KS), primary effusion lymphoma (PEL), KSHV-associated large cell lymphoma (KSHV-LCL), a type of multicentric Castleman disease (KSHV-MCD), and KSHV inflammatory cytokine syndrome (KICS). Participants originated from 22 different countries, providing the opportunity to obtain new near full-length sequences of a wide diversity of KSHV genomes. These include near full-length sequence of genomes with KSHV K1 subtypes A, B, C, and F as well as subtype E, for which no full sequence was previously available. High levels of recombination were observed. Fourteen individuals (18%) showed evidence of infection with multiple KSHV variants (from two to four unique genomes). Twenty-six comparisons of sequences, obtained from various sampling sites including PBMC, tissue biopsies, oral fluids, and effusions in the same participants, identified near complete genome conservation between different biological compartments. Polymorphisms were identified in coding and non-coding regions, including indels in the K3 and K15 genes and sequence inversions here reported for the first time. One such polymorphism in KSHV ORF46, specific to the KSHV K1 subtype E2, encoded a mutation in the leucine loop extension of the uracil DNA glycosylase that results in alteration of biochemical functions of this protein. This confirms that KSHV sequence variations can have functional consequences warranting further investigation. This study represents the largest and most diverse analysis of KSHV genome sequences to date among individuals with KAD and provides important new information on global KSHV genomics. Author summary: The prevalence of KSHV infection, one of eight viruses associated with human cancer, differs geographically as does the incidence of Kaposi sarcoma and other KSHV-associated diseases. Distribution of KSHV subtypes, defined solely by the sequence of the K1 gene, also differs by region. One hundred and two near full-length KSHV genomes from people with associated diseases from a wide variety of countries were sequenced, substantially increasing the number and diversity of KSHV genomes publicly available, thereby allowing the analysis of variance across geographical regions, potential contributions of viral genetics to the risk of disease, and viral evolution. Our data demonstrate that viral recombination is common, as previously published, and that infections with multiple KSHV genomes may also be frequent, which has not been widely reported. We did not find evidence of an association between viral subtypes and disease nor indications that different sampling sites from the same individual, including tumor specimens, harbored substantially different KSHV genomes. Our data significantly inform the current efforts to study epidemiology and the prevention of KSHV infection, including vaccine development, as well as the pathogenesis of associated diseases. [ABSTRACT FROM AUTHOR]

The article is a response to a comment made by Abrantes et al. on a previously published article about the genetic characteristics and phylogeographic dynamics of lagoviruses. The authors of the response address the questions raised by Abrantes et al. and defend their classification system and methodology. They argue that their classification system is not complicated and that they have used the latest tools and techniques to make it more reliable. They also explain the importance of considering recombination in virus evolution and the need to include full-length genome sequences in their analysis. The authors clarify some misunderstandings and provide additional evidence to support their findings. [Extracted from the article]

In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones. [ABSTRACT FROM AUTHOR]

We report comparisons between the complete genomic sequences of five historical Western Australian isolates of subterranean clover mottle virus (SCMoV) from 1989–2000, and an infectious clone of its 1989 isolate. Sanger Sequencing (SS) and High Throughput Sequencing (HTS), or both, were used to obtain these genomes. Four of the SCMoV isolates were sequenced by SS in 1999–2002, but re-sequenced again by HTS in 2020. The pairs of sequences obtained from these four isolates differed by only 18–59 nucleotides. This small difference resulted from the different sequencing methods, the < 1–5 years each isolate was host passaged before freeze-drying prior to HTS sequencing, or a combination of both. Since SCMoV has not been reported outside Australia, this similarity suggests the population sequenced represents the progeny of either an indigenous virus that spread from a native legume to subterranean clover after its introduction or a recent seed-borne incursion from elsewhere. The ORF1 was the most variable, and the phylogenetic tree constructed with ORF1s showed the isolates grouped according to their symptom severity in subterranean clover, indicating the probability that ORF1-encoded P1 protein is a symptom determinant. A satellite RNA was associated with all SCMoV genomes obtained by HTS but none derived by SS. [ABSTRACT FROM AUTHOR]

Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research. [ABSTRACT FROM AUTHOR]

Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology. Unsupervised machine learning methods of t-distributed stochastic neighbor embedding (t-SNE), Principal Component Analysis (PCA), and hierarchical clustering were performed to observe the DCR characteristics of the selected ORF clusters. Results: The results showed that MPXV sequences post-2022 showed an obvious linear adaptive evolution, indicating that it has become more adapted to the human host after accumulating mutations. For further accurate analysis, the ORF regions with larger variations were filtered out based on the ranking of homology difference to narrow down the key ORF clusters, which drew the same conclusion of linear adaptability. Then key differential protein structures were predicted by AlphaFold 2, which meant that difference in main domains might be one of the internal reasons for linear adaptive evolution. Discussion: Understanding the process of linear adaptation is critical in the constant evolutionary struggle between viruses and their hosts, playing a significant role in crafting effective measures to tackle viral diseases. Therefore, the present study provides valuable insights into the evolutionary patterns of the MPXV in 2022 from the perspective of genomic composition characteristics analysis through ML methods. [ABSTRACT FROM AUTHOR]

Many epidemics are caused by negative-stranded RNA viruses, leading to serious disease outbreaks that threaten human life and health. These viruses also have a significant impact on animal husbandry, resulting in substantial economic losses and jeopardizing global food security and the sustainable livelihoods of farmers. However, the pathogenic and infection mechanism of most negative-stranded RNA viruses remain unclear. Reverse genetics systems are the most powerful tools for studying viral protein function, viral gene expression regulation, viral pathogenesis, and the generation of engineered vaccines. The reverse genetics of some negative-strand viruses have been successfully constructed, while others have not. In this review, we focus on representative viruses from the Orthomyxoviridae family (IAV), the Filoviridae family (EBOV), and the Paramyxoviridae family (PPRV) to compile and summarize the existing knowledge on reverse genetics techniques for negative-strand viruses. This will provide a theoretical foundation for developing reverse genetics techniques for some negative-strand viruses. [ABSTRACT FROM AUTHOR]

Background Preexisting immunity, including memory B cells and preexisting antibodies, can modulate antibody responses to influenza in vivo to antigenically related antigens. We investigated whether preexisting hemagglutination inhibition (HAI) antibodies targeting the K163 epitope on the hemagglutinin (K163 antibodies) could affect antibody responses following vaccination with A/California/07/2009-like A(H1N1)pdm09 influenza viruses in humans. Methods Pre- and postvaccination sera collected from 300 adults (birth years, 1961–1998) in 6 seasons (2010–2016) were analyzed by HAI assays with 2 reverse genetics viruses and A(H1N1) viruses circulated from 1977 to 2018. Antibody adsorption assays were used to verify the preexisting K163 antibody–mediated suppression effect. Results Preexisting K163 antibody titers ≥80 affected HAI antibody responses following influenza vaccination containing A/California/07/2009-like antigens. At high K163 antibody concentrations (HAI antibody titers ≥160), all HAI antibody responses were suppressed. However, at moderate K163 antibody concentrations (HAI antibody titer, 80), only K163 epitope–specific antibody responses were suppressed, and novel HAI antibody responses targeting the non-K163 epitopes were induced by vaccination. Novel antibodies targeting non-K163 epitopes cross-reacted with newly emerging A(H1N1)pdm09 strains with a K163Q mutation rather than historic 1977–2007 A(H1N1) viruses. Conclusions K163 antibody–mediated suppression shapes antibody responses to A(H1N1)pdm09 vaccination. Understanding how preexisting antibodies suppress and redirect vaccine-induced antibody responses is of great importance to improve vaccine effectiveness. [ABSTRACT FROM AUTHOR]

In April 2022, a novel Goose adenovirus (GoAdV) isolated from diseased Lion head gooses exhibiting swelling and hemorrhage of liver and kidney, accumulation of fluid in pericardial, in Fujian province of China. The GoAdV was propagated in goose embryo fibroblasts (GEFs), the morphological properties of the virions were studied by electron microscopy, and the full genome sequence was determined and analyzed. The results revealed that the infected cells became round and clustered like grapes, virions accumulated and were arranged in crystal lattice formations in the nucleus of GEFs with a diameter of ∼80 nm. The new isolate (named CH-FJZZ-202201) has a viral genome size of 43,480 bp and shared 96.69% sequence identity with GoAdV-4 (P29), representing the species Goose aviadenovirus A. Phylogenetic analysis showed that CH-FJZZ-202201 was in the same genetic evolutionary branch with the viruses of Aviadenovirus and was the closest relative to GoAdV-4 P29/Hungary. This is the first report of the GoAdV-4 outside of Hungary, indicating the reemergence of new AdV strains in China. [ABSTRACT FROM AUTHOR]

Enteroviruses encode two protease active sites, in the 2A and 3C coding regions. While they target many host proteins, they first need to be excised from the viral polyprotein in which they are embedded. Polyprotein cleavage can occur either intra-molecularly (in cis) or inter-molecularly (in trans). Previous work suggested that antivirals targeting intra-molecular cleavages could generate inhibitory precursors that can suppress the outgrowth of drug-resistant variants. Therefore, we wanted to evaluate enteroviral cleavage patterns to identify such obligate intra-molecular cleavages as a method of drug target selection. Using translation extracts, we show that cis cleavage of the 2A protease N-terminal junction is conserved across three enterovirus clades, while the mechanism for the N-terminal junction of 3C varies, with enterovirus D68 3C cleavage occurring in cis and poliovirus 3C cleavage occurring in trans. Antiviral agents targeting proteases are generally identified via their ability to block the cleavage of artificial peptide substrates. Here, we show that antivirals identified for their ability to block inter-molecular cleavage can sometimes block intra-molecular cleavage of the protease from its polyprotein but with widely varying efficacy. Additionally, we demonstrate that for three enteroviral species, genomes defective in 2A protease activity suppress the growth of wild-type virus in mixed populations, supporting the hypothesis that preventing intra-molecular cleavage at the VP1·2A junction can create dominantly inhibitory precursors. These data argue that, to reduce the likelihood of drug resistance, protease-targeted antivirals should be evaluated for their ability to block intra-molecular polyprotein cleavages in addition to inter-molecular cleavage of other substrates. [ABSTRACT FROM AUTHOR]

Virus particles consist of a protein coat that protects their genetic material and delivers it to the host cell for self-replication. Understanding the interplay between virus structure and function is a requirement for understanding critical processes in the infectious cycle such as entry, uncoating, genome metabolism, capsid assembly, maturation, and propagation. Together with well-established techniques in cell and molecular biology, physical virology has emerged as a rapidly developing field, providing detailed, novel information on the basic principles of virus assembly, disassembly, and dynamics. The Spanish research community contains a good number of groups that apply their knowledge on biology, physics, or chemistry to the study of viruses. Some of these groups got together in 2010 under the umbrella of the Spanish Interdisciplinary Network on Virus Biophysics (BioFiViNet). Thirteen years later, the network remains a fertile ground for interdisciplinary collaborations geared to reveal new aspects on the physical properties of virus particles, their role in regulating the infectious cycle, and their exploitation for the development of virus-based nanotechnology tools. Here, we highlight some achievements of Spanish groups in the field of physical virology. [ABSTRACT FROM AUTHOR]

"The Age of Prediction: Algorithms, AI, and the Shifting Shadows of Risk" is a concise book that explores the role of AI in prediction and risk. Written by Igor Tulchinsky and Christopher E. Mason, the book discusses how AI operates and its benefits and dangers in various fields, such as stock dynamics, insurance markets, and predicting cancer growth. The authors highlight the importance of big data, statistical methods, and high-capacity hardware in AI modeling. They also address the potential economic consequences of AI adoption, including job displacement, and the need for regulations and ethical considerations in the development and use of AI. [Extracted from the article]

Ribonucleic acid (RNA) viruses pose heavy burdens on public-health systems. Synthetic biology holds great potential for artificially controlling their replication, a strategy that could be used to attenuate infectious viruses but is still in the exploratory stage. Herein, we used the genetic-code expansion technique to convert Enterovirus 71 (EV71), a prototypical RNA virus, into a controllable EV71 strain carrying the unnatural amino acid (UAA) Nε-2-azidoethyloxycarbonyl-L-lysine (NAEK), which we termed an EV71-NAEK virus. After NAEK supplementation, EV71-NAEK could recapitulate an authentic NAEK time- and dose-dependent infection in vitro, which could serve as a novel method to manipulate virulent viruses in conventional laboratories. We further validated the prophylactic effect of EV71-NAEK in two mouse models. In susceptible parent mice, vaccination with EV71-NAEK elicited a strong immune response and protected their neonatal offspring from lethal challenges similar to that of commercial vaccines. Meanwhile, in transgenic mice harboring a PylRS- tRNA CUA Pyl pair, substantial elements of genetic-code expansion technology, EV71-NAEK evoked an adjustable neutralizing-antibody response in a strictly external NAEK dose-dependent manner. These findings suggested that EV71-NAEK could be the basis of a feasible immunization program for populations with different levels of immunity. Moreover, we expanded the strategy to generate controllable coxsackieviruses for conceptual verification. In combination, these results could underlie a competent strategy for attenuating viruses and priming the immune system via artificial control, which might be a promising direction for the development of amenable vaccine candidates and be broadly applied to other RNA viruses. [ABSTRACT FROM AUTHOR]

Information on viral genetics, including their phylogenetic relationship, is valuable in controlling viral infection and screening for the development of virus-resistant cultivars in the future. The objectives of this study were to detect and characterize the Cymbidium mosaic virus (CymMV) from the native orchids of South Kalimantan, Indonesia, by the RT-PCR method. Also, to determine their phylogenetic relationship based on a partial genome of RdRp by the ML and PCA methods. Following RT-PCR analysis, one of 10 samples of native orchids used was positively infected by CymMV. In early detection, the RdRp region of CymMV has approximately 530 bp in size. After being sequenced and aligned with other isolates, this region has 121 polymorphic or mutation sites, a GC content of 45.21%, a transition/transversion bias value of 3.52, and nucleotide diversity (0.0415). The phylogenetic analysis revealed that CymMV from South Kalimantan, Indonesia, has closest related to similar isolates from Korea Type 2 (AF016914.1), Niigata, Japan (AB197937.1), Hawaii (EF125180.1), and Taiwan M2 (EU314803.1), with the coefficient divergence of 0.025. But, it has very distantly related to Hawaii 18-1 (EF125178.1) with a coefficient of 0.142. The results provide urgent information in supporting the native orchid's conservation and breeding efforts, locally and globally, including mitigating or controlling the viral infection and screening for the development of virus-free or resistant cultivars in the future. [ABSTRACT FROM AUTHOR]

The recent pandemic of CoVID-19 was due to severe acute respiratory syndrome 2 (SARS-CoV-2) and its various viral variants and their evolutionled to a global pandemic. SARS-CoV-2 is categorised under enveloped viruses consisting of single stranded, non-segmented, linear, positive sense strand RNA which functions as its genetic material. Further sub categorised into five important variants of concern namely, Alpha, Beta, Gamma, Delta, and Omicron. Ribovirus interacts with various receptors in human body most prominently ACE2, APN, NEU-5, results in occurrence and transmission. It is accompanied by induced hypercytokinemia, also known as a cytokine storm. Various cytokine and interlukins associated with it results in acute respiratory distress syndrome (ARDS). This review contains a summarized account of recent advancements regarding epidemiological, clinical and pathological attributes of COVID-19 along with recent progress in treatment and vaccine development. [ABSTRACT FROM AUTHOR]

Background Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. Methods Among healthy term infants we identified those with prolonged RSV infection and conducted (1) a human genome-wide association study (GWAS) to test the dependence of infection risk on host genotype, (2) a viral GWAS for association with prolonged RSV infection using RSV whole-genome sequencing, (3) an analysis of all viral public sequences, (4) an assessment of immunological responses, and (5) a summary of all major functional data. Analyses were adjusted for viral/human population structure and host factors associated with infection risk. Results We identified p.E123K/D and p.P218T/S/L in G protein that were associated with prolonged infection (P adj =.01). We found no evidence of host genetic risk for infection. The RSV variant positions approximate sequences that could bind a putative viral receptor, heparan sulfate. Conclusions Using analysis of both viral and host genetics we identified a novel RSV variant associated with prolonged infection in otherwise healthy infants and no evidence supporting host genetic susceptibility to infection. As the capacity of RSV for chronicity and its viral reservoir are not defined, these findings are important for understanding the impact of RSV on chronic disease and endemicity. [ABSTRACT FROM AUTHOR]

Avian rotaviruses (RVs) are important etiologic agents of gastroenteritis in birds. In general, avian RVs are understudied; consequently, there is a paucity of information regarding these viruses. Therefore, the characterization of these viral species is highly relevant because more robust information on genetic, epidemiologic, and evolutionary characteristics can clarify the importance of these infections, and inform efficient prevention and control measures. In this study, we describe partial genome characterizations of two avian RV species, RVF and RVG, detected in asymptomatic poultry flocks in Brazil. Complete or partial sequences of at least one of the genomic segments encoding VP1, VP2, VP4, VP6, VP7, NSP1, NSP4, NSP4, or NSP5 of 23 RVF and 3 RVG strains were obtained, and demonstrated that multiple variants of both RVF and RVG circulate among Brazilian poultry. In this study, new and important information regarding the genomic characteristics of RVF and RVG is described. In addition, the circulation of these viruses in the study region and the genetic variability of the strains detected are demonstrated. Thus, the data generated in this work should help in understanding the genetics and ecology of these viruses. Nonetheless, the availability of a greater number of sequences is necessary to advance the understanding of the evolution and zoonotic potential of these viruses. [ABSTRACT FROM AUTHOR]

Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals. [ABSTRACT FROM AUTHOR]

The detection of cucumber green mottle mosaic (CGMMV) in the Northern Territory (NT), Australia, in 2014 led to the introduction of strict quarantine measures for the importation of cucurbit seeds by the Australian federal government. Further detections in Queensland, Western Australia (WA), New South Wales and South Australia occurred in the period 2015–2020. To explore the diversity of the current Australian CGMMV population, 35 new coding sequence complete genomes for CGMMV isolates from Australian incursions and surveys were prepared for this study. In conjunction with published genomes from the NT and WA, sequence, phylogenetic, and genetic variation and variant analyses were performed, and the data were compared with those for international CGMMV isolates. Based on these analyses, it can be inferred that the Australian CGMMV population resulted from a single virus source via multiple introductions. [ABSTRACT FROM AUTHOR]

Objectives: Citrus yellow vein clearing virus (CYVCV) is an emerging disease that poses a significant threat to the citrus industry in California. In this study, the viral genomic RNA was isolated from Eureka lemon plants in the greenhouse exhibiting CYVCV symptoms. Subsequently, the corresponding DNA genome amplicon was sequenced and annotated. These efforts expand the genotype database of CYVCV, which aims to enhance detection assays, promote understanding of the virus's genetics and evolution, and support the management of this disease. Data description: In this report, we present the complete genome sequence of the CYVCV California isolate (CA1). The genome was found to be 7,530 bp in length, with a G + C content of 51.7%. The 5′ and 3′ termini were determined using 5′ and 3′ termini rapid amplification of cDNA ends (RACE) systems. Furthermore, our analysis revealed the presence of six open reading frames (ORFs) potentially encoding proteins. All sequence data and annotation have been deposited in GenBank under the accession number OR037276.1. [ABSTRACT FROM AUTHOR]

Reoviruses are used as oncolytic viruses to destroy tumor cells. The concomitant induction of anti-tumor immune responses enhances the efficacy of therapy in tumors with low amounts of immune infiltrates before treatment. The reoviruses should provoke immunogenic cell death (ICD) to stimulate a tumor cell-directed immune response. Necroptosis is considered a major form of ICD, and involves receptor-interacting protein kinase 1 (RIPK1), RIPK3 and phosphorylation of mixed-lineage kinase domain-like protein (MLKL). This leads to cell membrane disintegration and the release of damage-associated molecular patterns that can activate immune responses. Reovirus Type 3 Dearing (T3D) can induce necroptosis in mouse L929 fibroblast cells and mouse embryonic fibroblasts. Most human tumor cell lines have a defect in RIPK3 expression and consequently fail to induce necroptosis as measured by MLKL phosphorylation. We used the human colorectal adenocarcinoma HT29 cell line as a model to study necroptosis in human cells since this cell line has frequently been described in necroptosis-related studies. To stimulate MLKL phosphorylation and induce necroptosis, HT29 cells were treated with a cocktail consisting of TNFα, the SMAC mimetic BV6, and the caspase inhibitor Z-VAD-FMK. While this treatment induced necroptosis, three different reovirus T3D variants, i.e., the plasmid-based reverse genetics generated virus (T3DK), the wild-type reovirus T3D isolate R124, and the junction adhesion molecule-A-independent reovirus mutant (jin-1) failed to induce necroptosis in HT29 cells. In contrast, these viruses induced MLKL phosphorylation in murine L929 cells, albeit with varying efficiencies. Our study shows that while reoviruses efficiently induce necroptosis in L929 cells, this is not a common phenotype in human cell lines. This study emphasizes the difficulties of translating the results of ICD studies from murine cells to human cells. [ABSTRACT FROM AUTHOR]

Purpose: Immune escaping from host herd immunity has been related to changes in viral genomic sequences. The study aimed to understand the diverse immune responses to different subtypes or genotypes of human respiratory syncytial virus (RSV) in pediatric patients. Methods: The genomic sequences of different subtypes or RSV genotypes, isolated from Beijing patients, were sequenced and systematically analyzed. Specifically, the antiviral effects of Palivizumab and the cross-reactivity of human sera from RSV-positive patients to different subtypes or genotypes of RSV were determined. Then, the level of 38 cytokines and chemokines in respiratory and serum samples from RSV-positive patients was evaluated. Results: The highest nucleotide and amino acid variations and the secondary and tertiary structure diversities among different subtypes or genotypes of RSV were found in G, especially for genotype ON1 with a 72bp-insertion compared to NA1 in subtype A, while more mutations of F protein were found in the NH-2 terminal, including the antigenic site II, the target of Palivizumab, containing one change N276S. Palivizumab inhibited subtype A with higher efficiency than subtype B and had stronger inhibitory effects on the reference strains than on isolated strains. However, RSV-positive sera had stronger inhibitory effects on the strains in the same subtypes or genotypes of RSV. The level of IFN-a2, IL- 1a, and IL-1b in respiratory specimens from patients with NA1 was lower than those with ON1, while there were higher TNFa, IFNg, IL-1a, and IL-1b in the first serum samples from patients with ON1 compared to those with BA9 of subtype B. Conclusions: Diverse host immune responses were correlated with differential subtypes and genotypes of RSV in pediatric patients, demonstrating the impact of viral genetics on host immunity. [ABSTRACT FROM AUTHOR]

While hundreds of thousands of human whole genome sequences (WGS) have been collected in the effort to better understand genetic determinants of disease, these whole genome sequences have less frequently been used to study another major determinant of human health: the human virome. Using the unmapped reads from WGS of over 1000 families, we present insights into the human blood DNA virome, focusing particularly on human herpesvirus (HHV) 6A, 6B, and 7. In addition to extensively cataloguing the viruses detected in WGS of human whole blood and lymphoblastoid cell lines, we use the family structure of our dataset to show that household drives transmission of several viruses, and identify the Mendelian inheritance patterns characteristic of inherited chromsomally integrated human herpesvirus 6 (iciHHV-6). Consistent with prior studies, we find that 0.6% of our dataset's population has iciHHV, and we locate candidate integration sequences for these cases. We document genetic diversity within exogenous and integrated HHV species and within integration sites of HHV-6. Finally, in the first observation of its kind, we present evidence that suggests widespread de novo HHV-6B integration and HHV-7 integration and reactivation in lymphoblastoid cell lines. These findings show that the unmapped read space of WGS is a promising source of data for virology research. [ABSTRACT FROM AUTHOR]

Background: Canine morbillivirus (canine distemper virus, CDV) is a member of the Paramyxoviridae family. Canine distemper is a serious viral disease that affects many mammalian species, including members of the Mustelidae family. These animals have an elusive nature, which makes related virological studies extremely challenging. There is a significant knowledge gap about the evolution of their viruses and about the possible effects of these viruses to the population dynamics of the host animals. Spleen and lung tissue samples of 170 road-killed mustelids belonging to six species were collected between 1997 and 2022 throughout Hungary and tested for CDV with real-time RT-PCR. Results: Three species were positive for viral RNA, 2 out of 64 Steppe polecats (Mustela eversmanii), 1 out of 36 European polecats (Mustela putorius) and 2 out of 36 stone martens (Martes foina); all 18 pine martens (Martes martes), 10 least weasels (Mustela nivalis) and 6 stoats (Mustela erminea) tested negative. The complete CDV genome was sequenced in five samples using pan-genotype CDV-specific, amplicon-based Nanopore sequencing. Based on the phylogenetic analysis, all five viral sequences were grouped to the Europe/South America 1 lineage and the distribution of one sequence among trees indicated recombination of the Hemagglutinin gene. We verified the recombination with SimPlot analysis. Conclusions: This paper provides the first CDV genome sequences from Steppe polecats and additional complete genomes from European polecats and stone martens. The infected specimens of various species originated from distinct parts of the country over a long time, indicating a wide circulation of CDV among mustelids throughout Hungary. Considering the high virulence of CDV and the presence of the virus in these animals, we highlight the importance of conservation efforts for wild mustelids. In addition, we emphasize the importance of full genomic data acquisition and analysis to better understand the evolution of the virus. Since CDV is prone to recombination, specific genomic segment analyses may provide less representative evolutionary traits than using complete genome sequences. [ABSTRACT FROM AUTHOR]

Japanese encephalitis is a serious disease transmitted by mosquitoes. With its recent spread beyond the traditional territory of endemicity in Asia, the magnitude of global threat has increased sharply. While much of the current research are largely focused on changing epidemiology, molecular genetics of virus, and vaccination, little attention has been paid to the early history of virus isolation and phenotypic characterization of this virus. In this review, using this piece of history as an example, I review the transition of the concept and practice of virus isolation and characterization from the early period of history to modern times. The spectacular development of molecular techniques in modern times has brought many changes in practices as well as enormous amount of new knowledge. However, many aspects of virus characterization, in particular, transmission mechanism and host relationship, remain unsolved. As molecular techniques are not perfect in all respects, beneficial accommodation of molecular and biologic data is critically important in many branches of research. Accordingly, I emphasize exercising caution in applying only these modern techniques, point out unrecognized communication problems, and stress that JE research history is a rich source of interesting works still valuable even today and waiting to be discovered. [ABSTRACT FROM AUTHOR]

The genus Orthonairovirus includes highly pathogenic tick-borne viruses such as the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV). A reverse genetics system is an indispensable tool for determining the viral factors related to pathogenicity. Tofla orthonairovirus (TFLV) is a recently identified virus isolated from ticks in Japan and our research has suggested that TFLV is a useful model for studying pathogenic orthonairoviruses. In this study, we successfully established a reverse genetics system for TFLV using T7 RNA polymerase. Recombinant TFLV was generated by transfecting cloned complementary DNAs encoding the TFLV genome into BSR T7/5 cells expressing T7 RNA polymerase. We were able to rescue infectious recombinant TFLV mutant (rTFLVmt) and wild-type TFLV (rTFLVpt) viruses, which exhibited indistinguishable growth kinetics in mammalian cells and pathogenicity in A129 mice compared with the authentic virus. Our approach provides a valuable method for establishing reverse genetics system for orthonairoviruses. • T7 RNA polymerase-driven reverse genetic system of the Tofla orthonairovirus was developed. • Recombinant TFLVs showed similar virological characteristics with the parent virus. • This system provides an alternative method for reveres genetics of orthonairovirus. • TFLV recombinants harboring mutations can be generated. • This system is a useful tool for investigating viral genes responsible for pathogenicity. [ABSTRACT FROM AUTHOR]

The fast rate of viral mutations of SARS CoV-2 result in decrease in the efficacy of the vaccines that have been developed before the emergence of these mutations. Thus, it is believed that using additional measures to combat the virus is not only advisable but also beneficial. Two antiviral drugs were authorized for emergency use by the FDA, namely Pfizer's two-drug regimen sold under the brand name Paxlovid, and Merck's drug Lagevrio. Pfizer's two-drug combination consists of nirmatrelvir, a protease inhibitor that blocks coronavirus ability to multiply and another antiviral, ritonavir, that lowers the rate of drug clearance to boost the longevity and activity of the protease inhibitor. Merck's drug Lagevrio (molnupiravir) is a nucleoside analogue with a mechanism of action that aims to introduce errors into the genetic code of the virus. We believe the armament against the virus can be augmented by the addition of another class of enzyme inhibitors that are required for viral survival and its ability to replicate. Enzymes like nsp14 and nsp10/16 methyltransferases (MTases) represent another class of drug targets since they are required for viral RNA translation and evading the host immune system. In this communication, we have successfully verified that the MTase-Glo, which is universal and homogeneous MTase assay can be used to screen for inhibitors of the two pivotal enzymes nsp14 and nsp16 of SARS CoV-2. Furthermore, we have carried out extensive studies on those enzymes using different RNA substrates and tested their activity using various inhibitors and verified the utility of this assay for use in drug screening programs. We anticipate our work will be pursued further to screen for large libraries to discover new and selective inhibitors for the viral enzymes particularly that these enzymes are structurally different from their mammalian counterparts. [ABSTRACT FROM AUTHOR]

As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests that the new virus should be considered a new species for which the name alpine wild prunus virus (AWPV) is proposed. In parallel, the complete genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed that AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses. [ABSTRACT FROM AUTHOR]

The isolation of adeno-associated virus (AAV) genomes from biomaterials at the molecular level has traditionally relied on polymerase chain reaction-based and cloning-based techniques. However, when applied to samples containing multiple species, traditional techniques for isolating viral genomes can amplify artificial recombinants and introduce polymerase misincorporation errors. In this study, we describe AAV single-genome amplification (AAV-SGA): a powerful technique to isolate, amplify, and sequence single AAV genomes from mammalian genomic DNA, which can then be used to construct vectors for gene therapy. We used AAV-SGA to precisely isolate 15 novel AAV genomes belonging to AAV clades A, D, and E and the Fringe outgroup. This technique also enables investigations of AAV population dynamics and recombination events to provide insights into virus–host interactions and virus biology. Using AAV-SGA, we identified regional heterogeneity within AAV populations from different lobes of the liver of a rhesus macaque and found evidence of frequent genomic recombination between AAV populations. This study highlights the strengths of AAV-SGA and demonstrates its capability to provide valuable insights into the biology and diversity of AAVs. [ABSTRACT FROM AUTHOR]

Here, we produced nucleotide and amino acid sequences of the movement protein (MP) and the coat protein (CP) genes of apple chlorotic leaf spot virus (ACLSV) and apple stem grooving virus (ASGV) from wild apple of Xinjiang, the main progenitor of the domesticated apple. Genetic variation and phylogenetics were assessed using these and previously reported sequences. Phylogenetic analysis of ACLSV nucleotide and amino acid data sets assigned some ACLSV variants to known groups and others to novel clades. In an MP‐based phylogenetic tree, ASGV sequences downloaded from GenBank and those of wild apple isolates were assigned to separate groups. A recombinant sequence was identified in a ACLSV variant (MS‐GL‐1‐c‐3) of wild apple, and both parents of the recombinant had been isolated from the same plant (GL). Two potential recombination events of ASGV (MS‐GL‐2‐g‐3 and MS‐NF‐1‐g‐3) were identified in this study. These findings may constitute a valuable basis for future studies on variability of virus genetics and pathogenicity. [ABSTRACT FROM AUTHOR]

The study of viruses and their genetics has been an opportunity as well as a challenge for the scientific community. The recent ongoing SARSCov2 (SevereAcuteRespiratory Syndrome) pandemic proved the unpreparedness for these situations. Not only the countermeasures for the effect caused by virus need to be tackled but themutation taking place in the very genome of the virus is needed to be kept in check frequently. One major way to find out more information about such pathogens is by extracting the genetic data of such viruses. Though genetic data of viruses have been cultured and stored as well as isolated in form of their genome sequences, there is still limited methods on what new viruses can be generated in future due to mutation. This research proposes a deep learning model to predict the genome sequences of the SARS-Cov2 virus using only the previous viruses of the coronaviridae family with the help of RNN-LSTM (RecurrentNeuralNetwork-Long Short-Term Memory) and RNN-GRU (Gated Recurrent Unit) so that in the future, several counter measures can be taken by predicting possible changes in the genome with the help of existing mutations in the virus. After the process of testing the model, the F1-recall came out to be more than 0.95. The mutation detection's accuracy of both the models come out about 98.5% which shows the capability of the recurrent neural network to predict future changes in the genome of virus. [ABSTRACT FROM AUTHOR]

Background: Human papillomavirus (HPV) is the most common viral sexually transmitted infection of the reproductive tract, and cervical cancer is the most common HPV-related disease. This study estimated the prevalence, diversity of HPV genotypes, and associated risk factors in women screened for cervical cancer in northern Brazil. Methods: The cross-sectional study was conducted in Belém, Pará, in the Amazon region of Brazil, and it included 162 women who were spontaneously undergoing a Pap-smear routine. Epidemiological, sexual, and health-related information was collected by interviews, and cervical samples were collected for cytological examination and HPV-DNA detection. HPV genotypes were classified as low risk (LR) and high risk (HR) by nucleotide sequencing. Results: In total, 17.3% (28/162) of the participants had HPV-DNA, and LR-HPV was the most prevalent (71.4%). Among the 13 different types of HPV detected, HPV-11 was found most frequently (12/28; 42.9%), followed by HPV-31 (3/28; 10.7%). Of the participants with cytological alterations, HPV infection was detected in only four: two were diagnosed with low-grade squamous intraepithelial lesions (15.4%), one with atypical squamous cells of undetermined significance (7.7%), and one with atypical squamous cells, cannot exclude high-grade squamous intraepithelial lesions (7.7%). Of the 61 women who presented a normal cytology, 13 (21.3%) had positive tests for HPV infection, 4 (8.2%) of which were positive for a high-risk genotype. Conclusion: The prevalence of HPV was high in Belém, Pará, and especially in women who had normal cytology results, which suggests the need for greater screening for HPV infection in women's primary health care. [ABSTRACT FROM AUTHOR]

The article discusses the concept of quasispecies in virus evolution and presents an alternative model called the Bottleneck, Isolate, Amplify, Select (BIAS) model. The authors argue that while quasispecies theory suggests that a virus population evolves collectively, recent studies indicate that only a few genome copies have the chance to reproduce due to severe bottlenecking. This reproductive bottlenecking is enforced by virus-encoded proteins and ensures that mutations in founding copies are inherited by progeny copies, increasing their chances of expressing phenotypes and being subjected to selection. The BIAS model emphasizes natural selection as the primary driver of virus evolution. [Extracted from the article]

Drug resistance caused by mutations is a public health threat for existing and emerging viral diseases. A wealth of evidence about these mutations and their clinically associated phenotypes is scattered across the literature, but a comprehensive perspective is usually lacking. This work aimed to produce a clinically relevant view for the case of Hepatitis B virus (HBV) mutations by combining a chronic HBV clinical study with a compendium of genetic mutations systematically gathered from the scientific literature. We enriched clinical mutation data by systematically mining 2,472,725 scientific articles from PubMed Central in order to gather information about the HBV mutational landscape. By performing this analysis, we were able to identify mutational hotspots for each HBV genotype (A-E) and gene (C, X, P, S), as well as the location of disulfide bonds associated with these mutations. Through a modelling study, we also identified a mutation position common in both the clinical data and the literature that is located at the binding pocket for a known anti-HBV drug, namely entecavir. The results of this novel approach show the potential of integrated analyses to assist in the development of new drugs for viral diseases that are more robust to resistance. Such analyses should be of particular interest due to the increasing importance of viral resistance in established and emerging viruses, such as for newly developed drugs against SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The tomato chlorosis virus (ToCV), transmitted by whitefly species of the genera Bemisia and Trialeurodes in a semipersistent manner, causes significant losses in solanaceous crops including tomato (Solanum lycopersicum) and sweet pepper (Capsicum annuum). Worldwide reports of natural and experimental infection of sweet pepper plants with ToCV are contradictory, raising the question of whether the critical factor determining infection is related to the susceptibility of sweet pepper cultivars or the genetics of virus isolates. In this work, ToCV isolates obtained from different hosts and geographical origins were biologically and molecularly analysed, transmitted by B. tabaci MEAM1 and MED, and the reaction of different sweet pepper cultivars was evaluated under different environmental conditions. Brazilian ToCV isolates from tomato, potato (S. tuberosum), S. americanum, and Physalis angulata did not infect plants of five sweet pepper cultivars when transmitted by B. tabaci MEAM1. Temperatures did not affect the sweet pepper susceptibility to tomato‐ToCV isolates from São Paulo, Brazil, and Florida, USA. However, sweet pepper‐ToCV isolates from Spain and São Paulo, Brazil, were transmitted efficiently to sweet pepper plants by B. tabaci MEAM1 and MED. Although the results indicated that ToCV isolates from naturally infected sweet pepper plants seem to be better adapted to plants of C. annuum, phylogenetic analyses based on the complete nucleotide sequences of RNA1 and RNA2 as well as the p22 gene did not reveal significant nucleotide differences among them. Additional studies are needed to identify intrinsic characteristics of ToCV isolates that favour infection of sweet pepper plants. [ABSTRACT FROM AUTHOR]

Synthetic genomics is the construction of viruses, bacteria, and eukaryotic cells with synthetic genomes. It involves two basic processes: synthesis of complete genomes or chromosomes and booting up of those synthetic nucleic acids to make viruses or living cells. The first synthetic genomics efforts resulted in the construction of viruses. This led to a revolution in viral reverse genetics and improvements in vaccine design and manufacture. The first bacterium with a synthetic genome led to construction of a minimal bacterial cell and recoded Escherichia coli strains able to incorporate multiple non-standard amino acids in proteins and resistant to phage infection. Further advances led to a yeast strain with a synthetic genome and new approaches for animal and plant artificial chromosomes. On the horizon there are dramatic advances in DNA synthesis that will enable extraordinary new opportunities in medicine, industry, agriculture, and research. Synthetic genomics is a branch of synthetic biology that constructs viruses, bacteria, and eukaryotic cells with synthetic genomes. Venter and colleagues review the foundations, advances, challenges, and future prospects of synthetic genomics. [ABSTRACT FROM AUTHOR]

Rabbit haemorrhagic disease virus type 2 (RHDV2) causes a severe systemic disease with hepatic necrosis. Differently from classic RHDV, which affects only European rabbits (Oryctolagus cuniculus), RHDV2 can affect many leporid species, including hares (Lepus spp.) and cottontail rabbits (Sylvilagus spp.). RHDV2 emerged in Europe in 2010 and spread worldwide. During the last 5 years, there have been multiple outbreaks in North America since the first known event in 2016 in Quebec, Canada, including several detections in British Columbia, Canada, between 2018 and 2019, Washington State and Ohio, USA, in 2018 and 2019, and New York, USA, in 2020. However, the most widespread outbreak commenced in March 2020 in the southwestern USA and Mexico. In California, RHDV2 spread widely across several southern counties between 2020 and 2021, and the aim of this study was to report and characterize these early events of viral incursion and circulation within the state. Domestic and wild lagomorphs (n = 81) collected between August 2020 and February 2021 in California with a suspicion of RHDV2 infection were tested by reverse transcription quantitative real‐time PCR on the liver, and histology and immunohistochemistry for pan‐lagovirus were performed on liver sections. In addition, whole genome sequencing from 12 cases was performed. During this period, 33/81 lagomorphs including 24/59 domestic rabbits (O. cuniculus), 3/16 desert cottontail rabbits (Sylvilagus audubonii), and 6/6 black‐tailed jackrabbits (Lepus californicus) tested positive. All RHDV2‐positive animals had hepatic necrosis typical of pathogenic lagovirus infection, and the antigen was detected in sections from individuals of the three species. The 12 California sequences were closely related (98.9%–99.95%) to each other, and also very similar (99.0%–99.4%) to sequences obtained in other southwestern states during the 2020–2021 outbreak; however, they were less similar to strains obtained in New York in 2020 (96.7%–96.9%) and Quebec in 2016 (92.4%–92.6%), suggesting that those events could be related to different viral incursions. The California sequences were more similar (98.6%–98.7%) to a strain collected in British Columbia in 2018, which suggests that that event could have been related to the 2020 outbreak in the southwestern USA. [ABSTRACT FROM AUTHOR]

Current vaccination strategies against influenza focus on generating an antibody response against the viral haemagglutination surface protein, however there is increasing interest in neuraminidase (NA) as a target for vaccine development. A critical tool for development of vaccines that target NA or include an NA component is available validated serology assays for quantifying anti-NA antibodies. Additionally serology assays have a critical role in defining correlates of protection in vaccine development and licensure. Standardisation of these assays is important for consistent and accurate results. In this study we first validated a harmonized enzyme-linked lectin assay (ELLA)- Neuraminidase Inhibition (NI) SOP for N1 influenza antigen and demonstrated the assay was precise, linear, specific and robust within classical acceptance criteria for neutralization assays for vaccine testing. Secondly we tested this SOP with NA from influenza B viruses and showed the assay performed consistently with both influenza A and B antigens. Third, we demonstrated that recombinant NA (rNA) could be used as a source of antigen in ELLA-NI. In addition to validating a harmonized SOP we finally demonstrated a clear improvement in inter-laboratory agreement across several studies by using a calibrator. Importantly we showed that the use of a calibrator significantly improved agreement when using different sources of antigen in ELLA-NI, namely reverse genetics viruses and recombinant NA. We provide a freely available and detailed harmonized SOP for ELLA-NI. Our results add to the growing body of evidence in support of developing biological standards for influenza serology. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus (HIV) infection cannot be completely eliminated from the body because the virus integrates its genetic code into that of the host cell. The prevalence of pregnancy in women with HIV infection has increased due to the efficacy of antiretroviral therapy (ART). Placental insufficiency is associated with a reduction in blood flow and circulatory redistribution, resulting in fetal hypoxia and nutrient deprivation as a consequence of an altered placental function, and it can result in a lower birthweight. The aim of the study was to determine the combined effect of HIV infection and ART on the anthropometric parameters of infants born to HIV-positive pregnant women under ART compared to the values of these parameters in a control group of infants born to healthy mothers. There are no significant differences between the two groups in terms of gestational age at birth. We found a statistically significant lower birth weight in infants born from HIV-positive mothers under ART, with 3041 g in the control group compared to 2758 g in the group of HIV positive pregnant women (p < 0.01). There were statistically significant differences in all anthropometric parameters, these showing higher values in the control group (seronegative pregnant women). [ABSTRACT FROM AUTHOR]