Journal of General Virology最新文献

Despite their great agronomic interest and widespread occurrence in germplasm resources, the quantitative resistance and tolerance of plants to their parasites have rarely been studied in terms of durability potential. Using experimental evolution under controlled conditions for 9 months, we compared the evolution of potato virus Y (PVY) (Potyvirus yituberosi) virulence, measured by the effect of viral infection on plant fresh weight, and replicative fitness, measured by systemic viral load, in five pepper (Capsicum annuum) lines contrasting in their levels of quantitative resistance and tolerance. PVY evolutionary trajectories differed between pepper lines. Three lines revealed either an increase in PVY replicative fitness or an increase or decrease in PVY virulence. Two other lines did not reveal any significant change in PVY replicative fitness or virulence. The tolerance level of three pepper lines also differed significantly when measured with initial and evolved PVY populations, often associated with changes in PVY virulence. PVY evolutionary trajectories were partly explained by parameters linked to plant resistance operating at different stages of infection (inoculation, colonization of inoculated leaves and systemic infection). This study provides information on the durability potential of quantitative resistance and tolerance to PVY in pepper.

Objective. This study aims to characterize the 20-year trends in human immunodeficiency virus 1 (HIV-1) subtypes and circulating recombinant forms (CRFs) in China, as well as patterns of transmitted drug resistance (TDR) to antiretroviral therapies commonly used in clinical practice.Methods. We analysed HIV-1 sequences from 81,563 individuals living in China between 2003 and 2024. Subtypes and CRFs were classified using COMET V2.4. Among these, pol gene sequences from 41,486 treatment-naïve individuals were used to assess TDR via the Stanford HIVdb genotypic resistance interpretation program.Results. Over the past two decades, CRF01_AE (43.9%) was the most prevalent HIV-1 strain in China, followed by CRF07_BC (19.0%), subtype B (12.3%), subtype C (8.4%) and CRF08_B (4.9%). However, subtype and CRF distributions varied considerably across provinces. CRF01_AE predominated in provinces such as Liaoning (92.4%), Guangxi (58.7%), Beijing (47.7%) and Hainan (44.8%), while CRF07_BC was dominant in Sichuan (63.6%), Chongqing (53.2%) and Xinjiang (82.7%). TDR analysis revealed elevated resistance to non-nucleoside reverse transcriptase inhibitors in certain provinces, including Yunnan (12.4%), Xinjiang (8.2%), Anhui (7.6%) and Henan (6.7%). In contrast, resistance to nucleoside reverse transcriptase inhibitors and integrase inhibitors remained low (<1%) across all regions. Notably, the TDR rate exceeded 5% for several regimens freely provided in China, including AZT+3TC+NVP (6.8%), AZT+3TC+RPV (8.0%), AZT+3TC+EFV (6.4%), TDF+3TC+NVP (6.0%), TDF+3TC+RPV (7.2%) and TDF+3TC+EFV (5.7%).Conclusion. Continued surveillance of HIV-1 genotypes and CRFs is critical, particularly in regions where routine genotypic testing is not implemented. Personalized antiretroviral regimens are urgently needed in regions with high levels of TDR.

Orthohantaviruses are emerging zoonotic pathogens that can cause life-threatening diseases in humans. Their tripartite, negative-sense RNA genome is encapsidated by the viral nucleoprotein, but the subcellular localization and dynamics of these viral RNAs and proteins remain poorly characterized. Here, we present a comprehensive microscopy-based analysis of Puumala virus, the most prevalent orthohantavirus in northern and western Europe. Using fluorescence in situ hybridization (FISH) and Multiple Sequential FISH, we mapped the distribution of viral mRNAs, viral genomic RNAs (vRNAs), nucleoproteins and associated host cell factors, quantifying their intracellular abundance, co-localization and subcellular positioning. We observed distinct clustering of vRNAs with varying degrees of nucleoprotein association, a progressive increase in nucleoprotein expression levels during infection and a concomitant rise in the abundance of P-bodies. Moreover, we report a marked spatial reorganization of actin, microtubules and P-bodies, indicating substantial structural remodelling of host cells during orthohantavirus infections. Using a novel end-specific FISH assay, we observed a preferential 5'-end degradation of vRNAs in P-bodies, shedding new light on orthohantavirus RNA turnover within host RNA-processing compartments. Finally, co-localization analyses revealed the formation of potential 'viral factories' composed of nucleoprotein, vRNAs and viral mRNAs, indicating an intricate assembly hierarchy. Collectively, these findings improve our understanding of orthohantavirus replication and highlight the dynamic interplay between virus and host cell components.

Nipah virus and Hendra virus are highly pathogenic henipaviruses for which there are no approved therapeutics for use in humans. Using recombinant Cedar virus expressing luciferase (rCedV-Luc) as a CL2 surrogate, we screened a library of 2,703 Food and Drug Administration (FDA)-approved compounds, yielding 5 promising candidates: bortezomib, harringtonine, homoharringtonine, ixazomib citrate and lanatoside C. Compounds demonstrated low half-maximal inhibitory concentration (IC₅₀) values of ≤0.45 µM and high selectivity indexes >6 in mammalian cell lines. Time-of-addition studies suggest that these compounds target a post-entry stage of henipavirus replication. This study demonstrates the utility of rCedV-Luc as a surrogate for the antiviral screening of henipaviruses and identification of promising candidates for further investigation and development as henipavirus antivirals.

Hepatitis B virus (HBV) infects human populations worldwide. HBV strains are classified into 10 genotypes, of which the HBV genotype D (HBV/D) infection is particularly prevalent in several countries. The HBV core promoter regulates viral replication and transcription, and the naturally occurring A1762T/G1764A double mutation (CP1) in the core promoter accelerates HBV replication. Previous clinical studies showed that a new core-promoter mutation, G1764T/C1766G (CP2), is frequently observed in genomes containing the G1757A substitution, which is unique to HBV/D; however, CP2 is not observed in genomes containing the 1762T/1764A double mutation. In this study, we found that the CP2 mutation dramatically increased viral replication and transcription efficiency in two cell lines; the degree of stimulation was comparable to that induced by CP1. Introduction of the 1757A substitution reduced the increase in viral replication induced by the CP1 mutation. By contrast, the addition of the 1757A substitution significantly increased the effect of the CP2 mutation. The transcriptional activity of CP1 was decreased by the 1757A substitution, due to a reduction in HNF1 binding affinity, suggesting that 1757G is an important component of the HNF1 binding consensus sequence. The HBV/D-specific CP2 mutation creates a binding site for the transcription factor HNF3, thereby increasing its transcriptional activity. HBX proteins containing substitutions reflecting the two types of core-promoter mutations did not affect the efficiency of viral replication. Therefore, we hypothesize that the introduction of the CP2 mutation represents a survival strategy for HBV/D, allowing it to escape the effect of the 1757A substitution.

There is an urgent need for alternative solutions to combat multidrug-resistant (MDR) E. coli infections. In recent years, there has been an increase in MDR strains causing urinary tract infections (UTIs), which has resulted in more challenging treatment options, increased healthcare costs and prolonged hospital stays. The utilization of bacteriophages as a prospective modality for the management of bacterial infections has garnered significant attention. The objective of this study was to isolate and describe a phage capable of infecting MDR E. coli strains isolated from the urine of patients affected with UTI. The phage EcoPhCCP1 was isolated using the plaque assay from the influent of a wastewater treatment plant. The phage was characterized by phenotypic and genomic features. Morphological characteristics such as shape and size were determined using electron microscopy, and its host range was determined against multiple MDR strains. The complete genome of the phage was subjected to whole-genome sequencing and then assembled and annotated to search for virulence or antimicrobial resistance gene (ARG). VIRIDIC was employed to compare the closest phage genomes, while VICTOR and taxMyPhage were used to construct its phylogeny. EcoPhCCP1 is a tailed phage capable of infecting and propagating in multiple MDR E. coli strains recovered from UTI. The phage genome is 44,482 bp in length, with a GC content of 50.7 mol%, and encodes 87 ORFs, 33 of which have been previously functionally annotated. Phage EcoPhCCP1 is a Kagunavirus, in the recently created Sarkviridae family. Notably, phage EcoPhCCP1 does not harbour ARGs or virulence genes, thus rendering it a promising candidate for phage therapy against clinically significant MDR E. coli strains. Moreover, phage EcoPhCCP1 possesses putative anti-CRISPR proteins.

Deltaviruses are circular, negative-sense RNA agents that replicate autonomously but depend on heterologous envelope glycoproteins for spread. Only partial sequences of deltaviruses had been reported from marsupials. By reanalysing public metatranscriptomes from the Australian fat-tailed dunnart (Sminthopsis crassicaudata), we assemble the first complete marsupial deltavirus genome and test its replication in human and animal cells. The fat-tailed dunnart deltavirus (FtDDeV) is a 1,680-nt circular RNA that folds into a canonical unbranched rod-like structure and encodes a 195-aa delta antigen (FtDDAg). Genomic and antigenomic HDV-like ribozymes are present and conserve catalytic core motifs. Phylogenetic analyses cluster FtDDAg with the Tasmanian devil sequence, and both are quite close to RDAg from the neotropical rodent species Proechimys semispinosus. A dimeric FtDDeV cDNA replicon supports time-dependent DAg accumulation in human, simian, rodent and Tasmanian devil cells, with faster kinetics in rodents and marsupial cells. FtDDAg accumulation patterns in host nuclei show characteristic viral hubs, observed with other deltaviruses. No obvious coinfecting helper viruses were detected in FtDDeV-positive libraries. Our study extends the confirmed host range of deltaviruses to marsupials and provides a replication-competent clone to investigate helper usage, host restriction and deltavirus evolution.

Coronaviruses evolve rapidly, with recombination and mutation fostering the emergence of variant strains. The avian coronavirus infectious bronchitis virus (IBV) is an important poultry pathogen and a valuable natural model for studying coronaviruses. Australian strains have evolved independently of those infecting chickens elsewhere in the world, so understanding the biology and evolution of these strains can further our understanding of factors driving the emergence of novel coronaviruses. We infected groups of specific pathogen-free Leghorn chickens with six Australian IBVs (from five distinct genotypes) isolated between 1962 and 2013. All six affected the respiratory tract, but only one was nephropathogenic (N1/62). All six induced significant lesions and actively replicated in the upper respiratory tract, but they had lower levels of replication and induced less severe lesions in the middle and lower trachea. There were significant differences between the six strains in the severity of the lesions they induced and in their tissue tropism and effect on tracheal ciliary motility. Strains N1/62 (strain T) and N1/03 caused the most severe tracheal ciliostasis and replicated to the highest levels in tissues. Strain N1/03 caused the most severe lesions at 9 days post-infection. Only strain N1/03 caused lesions in the lower trachea. Overall, strains N1/03 and N1/62 were the most virulent. This study is the first to characterize the histological changes induced by the recently isolated Australian IBVs and compare them directly with older strains. Recombination between field and vaccine strains of IBV has yielded emergent IBVs in Australia that appear to have enhanced virulence for the respiratory tract.

Previous research has demonstrated that influenza A virus (IAV) infection activates activating protein-1 (AP-1) transcription factors as part of the antiviral response. In this study, we identified cFos as the most upregulated AP-1 transcription factor during IAV infection in A549 human lung cells. Surprisingly, the knockdown of cFos resulted in impaired IAV replication. Fluorescence microscopy and functional analyses indicated that cFos is implicated in IAV infection through its nuclear function, rather than its cytoplasmic role as an activator of lipid synthesis. The investigation into the role of cFos in IAV infection revealed increased apoptosis and elevated interferon-β mRNA levels in cFos-knockdown A549 cells during IAV infection. This suggests that cFos may enhance cell survival and reduce interferon-β expression during infection, thereby facilitating IAV proliferation. Furthermore, the levels of viral NA mRNA and the expression of late viral proteins NA and M2 decreased upon cFos-knockdown. Overall, this study identifies cFos as a proviral factor for IAV, through the modulation of innate immunity and apoptosis during infection, and potentially by supporting the viral transcription.

γδ T cells are a highly abundant lymphocyte subset in chickens and play key roles in early immune responses to infection. It has been recently shown that γδ T cells restrict Marek's disease virus (MDV) pathogenesis; however, it remained elusive if they play a role in vaccine protection. In this study, we vaccinated γδ T-cell-knockout chickens with the commercial turkey herpesvirus (HVT) vaccine and challenged them with very virulent MDV. The disease incidence was significantly increased in vaccinated chickens in the absence of γδ T cells. This increase was comparable to a previous study in unvaccinated γδ T-cell-knockout chickens, suggesting that γδ T cells only play a minor role in vaccine protection. Furthermore, the viral load in the spleen was significantly increased in the absence of γδ T cells. Interestingly, viral load in the skin and in dust shed by the animals was drastically increased, suggesting that the absence of γδ T cells affects MDV shedding. In addition, we quantified various immune cell subsets to determine if these could be responsible for the observed phenotypes. Together, our data indicate that γδ T cells only play a minor role in HVT-mediated protection, but their absence drastically affects shedding of this deadly pathogen in vaccinated animals.