Journal of General Virology最新文献

The complexity and speed of evolution in viruses with RNA genomes makes predictive identification of variants with epidemic or pandemic potential challenging. In recent years, machine learning has become an increasingly capable technology for addressing this challenge, as advances in methods and computational power have dramatically improved the performance of models and led to their widespread adoption across industries and disciplines. Nascent applications of machine learning technology to virus research have now expanded, providing new tools for handling large-scale datasets and leading to a reshaping of existing workflows for phenotype prediction, phylogenetic analysis, drug discovery and more. This review explores how machine learning has been applied to and has impacted the study of viruses, before addressing the strengths and limitations of its techniques and finally highlighting the next steps that are needed for the technology to reach its full potential in this challenging and ever-relevant research area.

Boid inclusion body disease (BIBD) caused by reptarenaviruses affects captive constrictor snake collections worldwide. The disease manifests by the formation of cytoplasmic inclusion bodies in various tissues. Curiously, a snake with BIBD nearly always carries a swarm of reptarenavirus small and large segments rather than a single pair, and the composition of the swarm can vary between tissues. The role of reptarenavirus coinfections in BIBD pathogenesis remains unknown, and it is unclear whether reptarenavirus infection affects the susceptibility to superinfection or to secondary infections. For mammarenaviruses, co- and/or superinfection can occur if the infecting viruses are genetically divergent enough, and we hypothesized reptarenaviruses to behave similarly. To study this hypothesis, we employed boa constrictor kidney- and brain-derived cell cultures to perform a set of co- and superinfection experiments with one hartmanivirus and five reptarenavirus isolates. While all tested viruses replicated well in the boid kidney cells, experiments on the brain-derived cells showed differences in the replication efficacy between the viruses, suggesting that reptarenaviruses could differ in their target cell spectra. The quantification of viral RNA released from infected cells as a proxy for virus replication did not reveal overt differences between mono- and coinfections. Passaging of coinfected cell cultures revealed that one of the reptarenavirus isolates requires a coinfecting reptarena- or hartmanivirus to establish a persistent infection. Superinfection experiments on persistently reptarenavirus-infected cell lines suggested some interference between genetically similar viruses. We hypothesized that such interference would be mediated by the viral Z protein (ZP) specifically locking the genetically similar viral polymerase in a catalytically inactive state. Curiously, experiments on ZP-expressing cell lines indicated ZP overexpression not to significantly affect the amount of released viral RNA. Our experiments showed very little co- or superinfection interference between genetically dissimilar reptarenaviruses, reflecting the naturally occurring reptarenavirus coinfections in snakes with BIBD.

Respiratory syncytial virus (RSV) is a leading cause of respiratory infection, hospitalization and death in infants worldwide. No fully effective RSV therapy using direct antivirals is marketed. Since clinical efficacy data from naturally infected patients for such antivirals are not available yet, animal studies are indispensable to predict therapeutic intervention. Here, we report the impact of an RSV fusion inhibitor, JNJ-49214698, on severe RSV-associated acute lower respiratory tract infection (ALRTI) in neonatal lambs. Randomized animals were treated once daily with 25 mg/kg JNJ-49214698, starting either before RSV infection, 1 day post-infection or as late as peak lung viral load on Day 3 post-infection. Treatment efficacy was assessed by scoring clinical signs of illness, development of RSV-induced gross and microscopic lung lesions and measuring virus titres in the lungs. Treatment with JNJ-49214698 was very effective in all treatment groups. Even in animals for which treatment was delayed until peak viral load was reached, a reduced amount and severity of gross and microscopic lesions, as well as RSV titres and RNA levels, were found. These results strongly suggest that treatment with small-molecule fusion inhibitors is an effective strategy to treat patients who are diagnosed with an RSV-induced ALRTI.

In Mononegavirales, phosphoproteins (P) are essential polymerase cofactors, forming oligomers and interacting with viral components to facilitate replication. Previous studies have demonstrated that a P-derived peptide (PFr) from the respiratory syncytial virus (RSV), containing the oligomerization domain (OD) and C-terminal domain (CTD), effectively inhibits RSV replication. Here, we extend this approach to paramyxoviruses, including HPIV3, MeV and MuV. Customized PFrs exhibited potent inhibitory effects against their respective viruses, with IC₅₀ values below 100 nM, while showing minimal cytotoxicity. These findings highlight the potential of targeting P oligomerization as a broad-spectrum antiviral strategy for paramyxoviruses and other mononegaviruses.

It is important to be able to retrospectively determine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with high accuracy, both for post-coronavirus disease 2019 (COVID-19) epidemiological studies, and to distinguish between Long COVID and other multi-syndromic diseases that have overlapping symptoms. Although serum antibody levels can be measured to retrospectively diagnose SARS-CoV-2 infections, peptide stimulation of memory T cell responses is a more sensitive approach. This is because robust memory T cells are generated after SARS-CoV-2 infection and persist even after antibodies wane below detectability thresholds. In this study, we compare T cell responses using FluoroSpot-based methods and overnight stimulation of whole blood with SARS-CoV-2 peptides followed by an ELISA. Both approaches have comparable sensitivity and specificity but require different equipment and samples to be used. Furthermore, the elimination of peptides that cross-react with other coronaviruses increases the assay specificity but trades off some sensitivity. Finally, this approach can be used on archival, cryopreserved PBMCs. This work shows comparative advantages for several methods to measure SARS-CoV-2 T cell responses that could be utilized by any laboratory studying the effects of the coronavirus disease 2019 pandemic.

Enteric hepatitis, represented by the hepatitis A virus (HAV) and hepatitis E virus (HEV), remains a significant global public health concern. While much progress has been made, many aspects of the biology and pathophysiology of HAV and HEV are still not fully understood. One of the major challenges is the absence of a reliable system for virus replication. Additionally, the lack of standardized and widely accessible diagnostic tests contributes to the underestimation of the true prevalence of these viruses. Factors such as climate change, environmental shifts, globalization and increased population mobility further complicate the spread of these infections by affecting pathogen transmission, water quality and the distribution of vectors. This review approaches the emergent research challenges and trends of enteric hepatitis and focuses on developing more efficient diagnostic tools, exploring the role of zoonotic transmission and addressing the impact of environmental and climate changes on disease dynamics, underscoring the need for collaborative, interdisciplinary efforts to effectively combat enteric hepatitis in a rapidly changing world.

Lassa virus (LASV) is an Old World (OW) mammarenavirus that causes Lassa fever, a life-threatening acute febrile disease endemic in West Africa. Lymphocytic choriomeningitis virus (LCMV) is a worldwide-distributed, prototypic OW mammarenavirus of clinical significance that has been largely neglected as a human pathogen. No licensed OW mammarenavirus vaccines are available, and the current therapeutic option is limited to the off-label use of ribavirin, which offers only partial efficacy. This situation underscores the urgent need to develop novel antivirals against human pathogenic mammarenaviruses. Previously, we showed that afatinib, a pan-ErbB tyrosine kinase inhibitor, inhibited multiple steps of the life cycles of OW LASV and LCMV, as well as the New World Junín virus vaccine strain Candid#1. In the present study, we investigated the inhibitory effect of U-73122, a phospholipase C inhibitor that acts downstream of ErbB signalling, on LCMV multiplication. U-73122 inhibited WT recombinant (r) LCMV multiplication in cultured cells. Preincubation of cell-free LCMV virions with U-73122 resulted in impaired virion infectivity. U-73122 also inhibited the infection of rLCMVs expressing heterologous viral glycoproteins, including the vesicular stomatitis Indiana virus (VSIV) glycoprotein, whereas WT VSIV infection was not affected by U-73122 treatment. Our results show the novel bioactivity of U-73122 as an LCMV inhibitor and indicate the presence of a virion-associated molecule that is necessary for virion infectivity and can be exploited as a potential antiviral drug target against human pathogenic mammarenavirus infections.

The Bombyx mori nucleopolyhedrovirus (BmNPV) is a DNA virus that affects the silkworm, B. mori, causing substantial economic losses in sericulture. This study investigates the mechanisms underlying budded virus egress, focusing on the roles of the ubiquitin-proteasome pathway (UPP) machinery. BmNPV produces two virion types: budded virions (BVs) and occlusion-derived virions (ODVs), which differ in their envelope origins and functions. Recent findings suggest similarities in the budding pathways of BmNPV and Autographa californica multiple nucleopolyhedrovirus (AcMNPV), involving plasma membrane budding and multivesicular body (MVB) pathways. The study reveals that specific UPP-related proteins, including 26S proteasome non-ATPase regulatory subunit 14 (PSMD14), polyubiquitin, proteasome alpha subunit 6 (PSMA6) and proteasome zeta subunit (PSMZ), are involved in BV egress. Using recombinant viruses and UPP inhibitors, we demonstrate the necessity of these proteins for GP64 secretion and effective BV release. RNA interference and cell surface display of GP64 analyses further validate the critical role of UPP in BmNPV BV egress and protein secretion. This research enhances our understanding of the mechanisms behind BmNPV MVB budding and GP64 secretion while also identifying potential targets for controlling the virus in sericulture.

Baculovirus is one of the most complex viruses found in nature. Proteomic analysis of budded viruses (BVs) indicates that they are formed by at least 50 different structural proteins. The function of most of these structural proteins and their specific localization in individual virions remain unknown. In the present study, we have conducted single-molecule localization microscopy analysis of the spatial distribution of the nucleocapsid protein P24 and the envelope proteins GP64 and E25. Our results show that P24 and GP64 are polarized to one end of the baculovirus, while E25 distributes more homogenously along the viral envelope. This is the first study using optical microscopy to demonstrate the polarized distribution of structural proteins in individual baculoviruses.

Highly pathogenic avian influenza (HPAI) poses a substantial threat to several raptors. Between 2021 and 2023, HPAI viruses (HPAIVs) of the Goose/Guangdong lineage H5 clade 2.3.4.4b became widespread in wild birds in Norway, and H5N1 and H5N5 viruses were detected in 31 white-tailed eagles (Haliaeetus albicilla, WTEs). Post-mortem examinations of four WTEs revealed no macroscopic pathological findings. Microscopic examinations showed the presence of myocardial and splenic necroses and a few lesions in the brain. In situ hybridization revealed the presence of the virus in several organs, suggesting a multisystemic infection. The detection of HPAIV H5N5 in a WTE in February 2022 marked the first recorded occurrence of this subtype in Norway. Since then, the virus has persisted, sporadically being detected in WTEs and other wild bird species. Phylogenetic analyses reveal that at least two distinct incursions of HPAIV H5N1 Eurasian (EA) genotype C affected WTEs, likely introduced by migratory birds from Eurasia and seabirds entering from Western and Central Europe. Some WTE isolates from 2021 to 2022 clustered with those from Canada and Ireland, aligning with the transatlantic spread of H5N1. Others were related to the 2021 mass mortality of great skuas in the UK or outbreaks in seabird populations, including gannets, gulls and terns, during 2022 in the North Sea region. This suggests that the WTEs were likely preying on the affected birds. Our study highlights that WTEs can act as sentinels for some HPAIV strains, but the absence of several known circulating genotypes in WTEs suggests varying pathogenic effects on this species.