Viruses

17 pages, 315 KiB

Open AccessReview

Virus Shedding and Diarrhea: A Review of Human Norovirus Genogroup II Infection in Gnotobiotic Pigs

by Charlotte Nyblade and Lijuan Yuan

Viruses 2024, 16(9), 1432; https://doi.org/10.3390/v16091432 (registering DOI) - 7 Sep 2024

For nearly twenty years, gnotobiotic (Gn) pigs have been used as a model of human norovirus (HuNoV) infection and disease. Unique in their ability to develop diarrhea and shed virus post oral challenge, Gn pigs have since been used to evaluate the infectivity [...] Read more.

For nearly twenty years, gnotobiotic (Gn) pigs have been used as a model of human norovirus (HuNoV) infection and disease. Unique in their ability to develop diarrhea and shed virus post oral challenge, Gn pigs have since been used to evaluate the infectivity of several genogroup II HuNoV strains. Nearly all major pandemic GII.4 variants have been tested in Gn pigs, with varying rates of infectivity. Some induce an asymptomatic state despite being shed in large quantities in stool, and others induce high incidence of both diarrhea and virus shedding. Non-GII.4 strains, including GII.12 and GII.6, have also been evaluated in Gn pigs. Again, rates of diarrhea and virus shedding tend to vary between studies. Several factors may influence these findings, including age, dosage, biological host factors, or bacterial presence. The impact of these factors is nuanced and requires further evaluation to elucidate the exact mechanisms behind increases or decreases in infection rates. Regardless, the value of Gn pig models in HuNoV research cannot be understated, and the model will surely continue to contribute to the field in years to come. Full article

(This article belongs to the Special Issue Human Norovirus 2024)

10 pages, 7169 KiB

Open AccessArticle

Retrospective Analyses of Porcine Circovirus Type 3 (PCV-3) in Switzerland

by Giuliana Rosato, Grace Makanaka Makoni, Àlex Cobos, Marina Sibila, Joaquim Segalés, Hanna Marti, Barbara Prähauser and Frauke Seehusen

Viruses 2024, 16(9), 1431; https://doi.org/10.3390/v16091431 (registering DOI) - 7 Sep 2024

Abstract

Porcine circovirus 3 (PCV-3) has emerged as a significant pathogen affecting global swine populations, yet its epidemiology and clinical implications remain incompletely understood. This retrospective study aimed to investigate the prevalence and histopathological features of PCV-3 infection in pigs from Switzerland, focusing on [...] Read more.

Porcine circovirus 3 (PCV-3) has emerged as a significant pathogen affecting global swine populations, yet its epidemiology and clinical implications remain incompletely understood. This retrospective study aimed to investigate the prevalence and histopathological features of PCV-3 infection in pigs from Switzerland, focusing on archival cases of suckling and weaner piglets presenting with suggestive lesions. An in-house qPCR assay was developed for detecting PCV-3 in frozen and formalin-fixed paraffin-embedded tissues, enhancing the national diagnostic capabilities. Histopathological reassessment identified PCV-3 systemic disease (PCV-3-SD) compatible lesions in 19 (6%) of archival cases, with 47% testing positive by qPCR across various organs. Notably, vascular lesions predominated, particularly in mesenteric arteries, heart, and kidneys. The study confirms the presence of PCV-3 in Switzerland since at least 2020, marking the first documented cases within the Swiss swine population. Despite challenges in in situ hybridization validation due to prolonged formalin fixation, the findings indicate viral systemic dissemination. These results contribute to the understanding of PCV-3 epidemiology in Swiss pigs, emphasizing the need for continued surveillance and further research on its clinical implications and interaction with host factors. Our study underscores the utility and limitations of molecular techniques in confirming PCV-3 infections. Full article

(This article belongs to the Section Animal Viruses)

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16 pages, 5616 KiB

Open AccessArticle

Evaluation of Different Formulations on the Viability of Phages for Use in Agriculture

by Marcela León, Jorge Araya, Mauricio Nuñez, Manuel Arce, Fanny Guzmán, Carolina Yáñez, Ximena Besoain and Roberto Bastías

Viruses 2024, 16(9), 1430; https://doi.org/10.3390/v16091430 (registering DOI) - 7 Sep 2024

Abstract

Bacteriophages have been proposed as biological controllers to protect plants against different bacterial pathogens. In this scenario, one of the main challenges is the low viability of phages in plants and under adverse environmental conditions. This work explores the use of 12 compounds [...] Read more.

Bacteriophages have been proposed as biological controllers to protect plants against different bacterial pathogens. In this scenario, one of the main challenges is the low viability of phages in plants and under adverse environmental conditions. This work explores the use of 12 compounds and 14 different formulations to increase the viability of a phage mixture that demonstrated biocontrol capacity against Pseudomonas syringae pv. actinidiae (Psa) in kiwi plants. The results showed that the viability of the phage mixture decreases at 44 °C, at a pH lower than 4, and under UV radiation. However, using excipients such as skim milk, casein, and glutamic acid can prevent the viability loss of the phages under these conditions. Likewise, it was demonstrated that the use of these compounds prolongs the presence of phages in kiwi plants from 48 h to at least 96 h. In addition, it was observed that phages remained stable for seven weeks when stored in powder with skim milk, casein, or sucrose after lyophilization and at 4 °C. Finally, the phages with glutamic acid, sucrose, or skim milk maintained their antimicrobial activity against Psa on kiwi leaves and persisted within kiwi plants when added through roots. This study contributes to overcoming the challenges associated with the use of phages as biological controllers in agriculture. Full article

(This article belongs to the Special Issue Bacteriophage-Based Biocontrol in Agriculture, 2nd Edition)

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20 pages, 2115 KiB

Open AccessArticle

Evaluation of Commercial RNA Extraction Protocols for Avian Influenza Virus Using Nanopore Metagenomic Sequencing

by Maria Chaves, Amro Hashish, Onyekachukwu Osemeke, Yuko Sato, David L. Suarez and Mohamed El-Gazzar

Viruses 2024, 16(9), 1429; https://doi.org/10.3390/v16091429 (registering DOI) - 7 Sep 2024

Abstract

Avian influenza virus (AIV) is a significant threat to the poultry industry, necessitating rapid and accurate diagnosis. The current AIV diagnostic process relies on virus identification via real-time reverse transcription–polymerase chain reaction (rRT-PCR). Subsequently, the virus is further characterized using genome sequencing. This [...] Read more.

Avian influenza virus (AIV) is a significant threat to the poultry industry, necessitating rapid and accurate diagnosis. The current AIV diagnostic process relies on virus identification via real-time reverse transcription–polymerase chain reaction (rRT-PCR). Subsequently, the virus is further characterized using genome sequencing. This two-step diagnostic process takes days to weeks, but it can be expedited by using novel sequencing technologies. We aim to optimize and validate nucleic acid extraction as the first step to establishing Oxford Nanopore Technologies (ONT) as a rapid diagnostic tool for identifying and characterizing AIV from clinical samples. This study compared four commercially available RNA extraction protocols using AIV-known-positive clinical samples. The extracted RNA was evaluated using total RNA concentration, viral copies as measured by rRT-PCR, and purity as measured by a 260/280 absorbance ratio. After NGS testing, the number of total and influenza-specific reads and quality scores of the generated sequences were assessed. The results showed that no protocol outperformed the others on all parameters measured; however, the magnetic particle-based method was the most consistent regarding C_T value, purity, total yield, and AIV reads, and it was less error-prone. This study highlights how different RNA extraction protocols influence ONT sequencing performance. Full article

(This article belongs to the Special Issue Recent Advances of Avian Viruses Research)

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17 pages, 12790 KiB

Open AccessArticle

Vesicular Stomatitis Virus Detected in Biting Midges and Black Flies during the 2023 Outbreak in Southern California

by Stacey L. P. Scroggs, Dustin A. Swanson, Taylor D. Steele, Amy R. Hudson, Lindsey M. Reister-Hendricks, Jessica Gutierrez, Phillip Shults, Bethany L. McGregor, Caitlin E. Taylor, Travis M. Davis, Nadine Lamberski, Kristen A. Phair, Lauren L. Howard, Nathan E. McConnell, Nikos Gurfield, Barbara S. Drolet, Angela M. Pelzel-McCluskey and Lee W. Cohnstaedt

Viruses 2024, 16(9), 1428; https://doi.org/10.3390/v16091428 (registering DOI) - 7 Sep 2024

Abstract

Vesicular stomatitis (VS) is a viral disease that affects horses, cattle, and swine that is transmitted by direct contact and hematophagous insects. In 2023, a multi-state outbreak of vesicular stomatitis New Jersey virus (VSNJV) occurred in California, Nevada, and Texas, infecting horses, cattle, [...] Read more.

Vesicular stomatitis (VS) is a viral disease that affects horses, cattle, and swine that is transmitted by direct contact and hematophagous insects. In 2023, a multi-state outbreak of vesicular stomatitis New Jersey virus (VSNJV) occurred in California, Nevada, and Texas, infecting horses, cattle, and rhinoceros. To identify possible insect vectors, we conducted insect surveillance at various locations in San Diego County, CA, including at a wildlife park. CO₂ baited traps set from mid-May to mid-August 2023 collected 2357 Culicoides biting midges and 1215 Simulium black flies, which are insect genera implicated in VSNJV transmission. Insects were pooled by species, location, and date, then tested for viral RNA. Nine RNA-positive pools of Culicoides spp. and sixteen RNA-positive pools of Simulium spp were detected. Infectious virus was detected by cytopathic effect in 96% of the RNA-positive pools. This is the first report of VSNJV in wild-caught C. bergi, C. freeborni, C. occidentalis, S. argus, S. hippovorum, and S. tescorum. The vector competency of these species for VSNJV has yet to be determined but warrants examination. Active vector surveillance and testing during disease outbreaks increases our understanding of the ecology and epidemiology of VS and informs vector control efforts. Full article

(This article belongs to the Special Issue Vesicular Stomatitis Virus (VSV))

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15 pages, 1103 KiB

Open AccessReview

Cytomegalovirus Retinitis: Clinical Manifestations, Diagnosis and Treatment

by Jing Zhang, Koju Kamoi, Yuan Zong, Mingming Yang, Yaru Zou, Miki Miyagaki and Kyoko Ohno-Matsui

Viruses 2024, 16(9), 1427; https://doi.org/10.3390/v16091427 (registering DOI) - 7 Sep 2024

Abstract

Cytomegalovirus (CMV) retinitis is the most common eye disease associated with CMV infection in immunocompromised individuals. The CMVR may initially be asymptomatic; however, relatively mild vitreous inflammation at the onset may be an important differential point from other diseases in HIV patients. Fundus [...] Read more.

Cytomegalovirus (CMV) retinitis is the most common eye disease associated with CMV infection in immunocompromised individuals. The CMVR may initially be asymptomatic; however, relatively mild vitreous inflammation at the onset may be an important differential point from other diseases in HIV patients. Fundus photography, CD4 T-cell count, and telemedicine could be used to screen and monitor the high-risk population, particularly in resource-limited regions. Retinitis generally starts in the peripheral retina and advances toward the posterior pole, which could develop to the characteristic “pizza pie” appearance marked by central retinal necrosis and intraretinal hemorrhage. CMVR causes vision loss if left untreated, and early antiviral therapy significantly reduces the risk of vision loss. Alongside traditional antiviral treatments, immunotherapies including CMV-specific adoptive T-cell therapy and CMV immunoglobulin (CMVIG) are emerging as promising treatment options due to their favorable tolerability and reduced mortality. This review comprehensively examines CMV retinitis, encompassing the clinical features, differential diagnosis, laboratory tests, and updated treatment strategies to inform clinical management. Full article

(This article belongs to the Special Issue Ocular Diseases in Viral Infection)

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8 pages, 500 KiB

Open AccessBrief Report

ddPCR for the Detection and Absolute Quantification of Oropouche Virus

by Elena Pomari, Andrea Matucci, Silvia Accordini, Rebeca Passarelli Mantovani, Natasha Gianesini, Antonio Mori and Concetta Castilletti

Viruses 2024, 16(9), 1426; https://doi.org/10.3390/v16091426 (registering DOI) - 7 Sep 2024

Abstract

Background: Oropouche virus (OROV) is a segmented RNA virus belonging to the genus Orthobunyavirus in the family Peribunyaviridae. Herein, an in-house droplet digital PCR (ddPCR) assay was used for the detection and quantification of OROV. Methods: The ddPCR reaction was assessed as [...] Read more.

Background: Oropouche virus (OROV) is a segmented RNA virus belonging to the genus Orthobunyavirus in the family Peribunyaviridae. Herein, an in-house droplet digital PCR (ddPCR) assay was used for the detection and quantification of OROV. Methods: The ddPCR reaction was assessed as duplex assay using the human housekeeping gene RPP30. Limit of detection (LoD) analysis was performed in whole blood, serum, and urine. The assay was executed on a total of 28 clinical samples (whole blood n = 9, serum n = 11, and urine n = 8), of which 16 specimens were tested positive at the routine molecular diagnostics (endpoint and real-time PCRs). Results: The LoD of the ddPCR performed using 10-fold serial dilution of OROV detected up to 1 cp/µL in all the biological matrices. Compared to the routine molecular diagnostics, the ddPCR assay showed 100% sensitivity for whole blood and serum and 75% for urine, highlighting higher positive rate of ddPCR. Conclusion: We have established a quantitative RNA detection method of OROV with high sensitivity and specificity based on ddPCR. This test is capable of quantitatively monitoring the viral load of OROV and can contribute, in addition to laboratory diagnosis, to shed light on the pathogenesis, filling in the knowledge gaps of this neglected disease and to the vector control programs. Full article

(This article belongs to the Special Issue Zoonotic and Vector-Borne Viral Diseases)

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26 pages, 1818 KiB

Open AccessReview

Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research

by Federico Vello, Francesco Filippini and Irene Righetto

Viruses 2024, 16(9), 1425; https://doi.org/10.3390/v16091425 - 6 Sep 2024

Abstract

Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of “big data”, which has also affected the [...] Read more.

Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of “big data”, which has also affected the field of virology. The collaboration between the communities of bioinformaticians and virologists already started a few decades ago and it was strongly enhanced by the recent SARS-CoV-2 pandemics. In this article, which is the first in a series on how bioinformatics can enhance virus research, we show that highly useful information is retrievable from selected general and dedicated databases. Indeed, an enormous amount of information—both in terms of nucleotide/protein sequences and their annotation—is deposited in the general databases of international organisations participating in the International Nucleotide Sequence Database Collaboration (INSDC). However, more and more virus-specific databases have been established and are progressively enriched with the contents and features reported in this article. Since viruses are intracellular obligate parasites, a special focus is given to host-pathogen protein-protein interaction databases. Finally, we illustrate several phylogenetic and phylodynamic tools, combining information on algorithms and features with practical information on how to use them and case studies that validate their usefulness. Databases and tools for functional inference will be covered in the next article of this series: Bioinformatics goes viral: II. Sequence-based and structure-based functional analyses for boosting virus research. Full article

(This article belongs to the Section General Virology)

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12 pages, 2934 KiB

Open AccessArticle

Coat Proteins of the Novel Victoriviruses FaVV1 and FaVV2 Suppress Sexual Reproduction and Virulence in the Pathogen of Fusarium Head Blight

by Shulin Cao, Xiaoyue Yang, Lele Xia, Xing Zhang, Haiyan Sun, Yuanyu Deng, Yan Shu, Aixiang Zhang, Huaigu Chen and Wei Li

Viruses 2024, 16(9), 1424; https://doi.org/10.3390/v16091424 - 6 Sep 2024

Abstract

Fusarium head blight (FHB), a disease inflicted by Fusarium graminearum and F. asiaticum, poses a growing threat to wheat in China, particularly in the face of climate change and evolving agricultural practices. This study unveiled the discovery of the victorivirus FgVV2 from [...] Read more.

Fusarium head blight (FHB), a disease inflicted by Fusarium graminearum and F. asiaticum, poses a growing threat to wheat in China, particularly in the face of climate change and evolving agricultural practices. This study unveiled the discovery of the victorivirus FgVV2 from the F. asiaticum strain F16176 and comprehensively characterized the function of the two victoriviruses FaVV1 and FaVV2 in virulence. Through comparative analysis with a virus-free strain, we established that these mycoviruses markedly repress the sexual reproduction and pathogenicity of their fungal hosts. Furthermore, we synthesized the coat protein (CP) genes CP1 from FaVV1 and CP2 from FaVV2, which were fused with the green fluorescent protein (GFP) gene and successfully expressed in Fusarium strains in wild-type isolates of F. asiaticum and F. graminearum. Similar to virus-infected strains, the transformed strains expressing CPs showed a significant decrease in perithecia formation and pathogenicity. Notably, CP2 exhibited a stronger inhibitory effect than CP1, yet the suppression of sexual reproduction in F. graminearum was less pronounced than that in F. asiaticum. Additionally, the pathogenicity of the F. asiaticum and F. graminearum strains expressing CP1 or CP2 was substantially diminished against wheat heads. The GFP-tagged CP1 and CP2 revealed distinct cellular localization patterns, suggesting various mechanisms of interaction with the host. The findings of this study provide a significant research foundation for the study of the interaction mechanisms between FaVV1 and FaVV2 with their hosts, as well as for the exploration and utilization of fungal viral resources. Full article

(This article belongs to the Collection Mycoviruses)

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30 pages, 5716 KiB

Open AccessReview

Exploring HIV-1 Maturation: A New Frontier in Antiviral Development

by Aidan McGraw, Grace Hillmer, Stefania M. Medehincu, Yuta Hikichi, Sophia Gagliardi, Kedhar Narayan, Hasset Tibebe, Dacia Marquez, Lilia Mei Bose, Adleigh Keeting, Coco Izumi, Kevin Peese, Samit Joshi, Mark Krystal, Kathleen L. DeCicco-Skinner, Eric O. Freed, Luca Sardo and Taisuke Izumi

Viruses 2024, 16(9), 1423; https://doi.org/10.3390/v16091423 - 6 Sep 2024

Abstract

HIV-1 virion maturation is an essential step in the viral replication cycle to produce infectious virus particles. Gag and Gag-Pol polyproteins are assembled at the plasma membrane of the virus-producer cells and bud from it to the extracellular compartment. The newly released progeny [...] Read more.

HIV-1 virion maturation is an essential step in the viral replication cycle to produce infectious virus particles. Gag and Gag-Pol polyproteins are assembled at the plasma membrane of the virus-producer cells and bud from it to the extracellular compartment. The newly released progeny virions are initially immature and noninfectious. However, once the Gag polyprotein is cleaved by the viral protease in progeny virions, the mature capsid proteins assemble to form the fullerene core. This core, harboring two copies of viral genomic RNA, transforms the virion morphology into infectious virus particles. This morphological transformation is referred to as maturation. Virion maturation influences the distribution of the Env glycoprotein on the virion surface and induces conformational changes necessary for the subsequent interaction with the CD4 receptor. Several host factors, including proteins like cyclophilin A, metabolites such as IP6, and lipid rafts containing sphingomyelins, have been demonstrated to have an influence on virion maturation. This review article delves into the processes of virus maturation and Env glycoprotein recruitment, with an emphasis on the role of host cell factors and environmental conditions. Additionally, we discuss microscopic technologies for assessing virion maturation and the development of current antivirals specifically targeting this critical step in viral replication, offering long-acting therapeutic options. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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14 pages, 4458 KiB

Open AccessArticle

Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy

by Daniele Armenia, Luca Carioti, Valeria Micheli, Isabella Bon, Tiziano Allice, Celestino Bonura, Bianca Bruzzone, Fiorenza Bracchitta, Francesco Cerutti, Giovanni Maurizio Giammanco, Federica Stefanelli, Maria Addolorata Bonifacio, Ada Bertoli, Marialinda Vatteroni, Gabriele Ibba, Federica Novazzi, Maria Rosaria Lipsi, Nunzia Cuomo, Ilaria Vicenti, Francesca Ceccherini-Silberstein, Barbara Rossetti, Antonia Bezenchek, Francesco Saladini, Maurizio Zazzi and Maria Mercedes Santoro Show full author list Hide full author list

Viruses 2024, 16(9), 1422; https://doi.org/10.3390/v16091422 - 6 Sep 2024

Abstract

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting. Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories [...] Read more.

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting. Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories with the AD4SEQ HIV-1 Solution v2 commercial kit. NGS results were interpreted by the SmartVir system provided by the kit and by two online tools (HyDRA Web and Stanford HIVdb). NGS-GRT was considered valid when the coverage was >100 reads (100×) at each PR/RT/IN resistance-associated position listed in the HIVdb 9.5.1 algorithm. Results: Among 629 NGS-GRT, 75.2%, 74.2%, and 70.9% were valid according to SmartVir, HyDRA Web, and HIVdb. Considering at least two interpretation tools, 463 (73.6%) NGS-GRT had a valid coverage for resistance analyses. The proportion of valid samples was affected by viremia <10,000–1000 copies/mL and non-B subtypes. Mutations at an NGS frequency >10% showed fair concordance among different interpretation tools. Conclusion: This Italian survey on NGS resistance testing suggests that viremia levels and HIV subtype affect NGS-GRT coverage. Within the current routine method for NGS-GRT, only mutations with frequency >10% seem reliably detected across different interpretation tools. Full article

(This article belongs to the Special Issue Antiviral Resistance Mutations)

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15 pages, 4323 KiB

Open AccessArticle

Topical Protease Inhibitor Increases Tumor-Free and Overall Survival in CD4-Depleted Mouse Model of Anal Cancer

by Evan Yao, Laura Gunder, Tyra Moyer, Kristina A. Matkowskyj, Kathryn Fox, Yun Zhou, Sakura Haggerty, Hillary Johnson, Nathan Sherer and Evie Carchman

Viruses 2024, 16(9), 1421; https://doi.org/10.3390/v16091421 - 5 Sep 2024

Abstract

Patients with immunodeficiencies and older age are at an increased risk of anal cancer. Transgenic K14E6/E7 mice with established high-grade anal dysplasia were treated topically at the anus with the protease inhibitor saquinavir (SQV) in the setting of CD4+ T-cell depletion to mimic [...] Read more.

Patients with immunodeficiencies and older age are at an increased risk of anal cancer. Transgenic K14E6/E7 mice with established high-grade anal dysplasia were treated topically at the anus with the protease inhibitor saquinavir (SQV) in the setting of CD4+ T-cell depletion to mimic immunodeficiency. To ensure tumor development, specific groups were treated with a topical carcinogen (7,12-Dimethylbenz[a]anthracene (DMBA)). The treatment groups included the vehicle (control), DMBA only, topical SQV, and topical SQV with DMBA, as well as the same four groups with CD4 depletion. The mice were monitored weekly for tumor development. Upon reaching 20 weeks of treatment, the mice were sacrificed, and their anal tissue was harvested for histological analysis. None of the mice in the SQV or control groups developed overt anal tumors, except three mice that were CD4-depleted. The CD4-depleted mice treated with DMBA had significantly increased tumor-free survival and overall survival as well as decreased tumor-volume growth over time when treated with SQV. These data suggest that topical SQV, in the setting of CD4 depletion and high-grade anal dysplasia, can increase tumor-free and overall survival; thus, it may represent a viable topical therapy to decrease the risk of progression of anal dysplasia to anal cancer. Full article

(This article belongs to the Special Issue Viral Proteases: Modulation of Immune Responses and Antiviral Therapies)

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14 pages, 1343 KiB

Open AccessArticle

Demonstration of Insect Vector-Mediated Transfer of a Betasatellite between Two Helper Viruses

by Noun Fouad, Martine Granier, Stéphane Blanc, Gaël Thébaud and Cica Urbino

Viruses 2024, 16(9), 1420; https://doi.org/10.3390/v16091420 - 5 Sep 2024

Abstract

Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread [...] Read more.

Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread and association of these molecules with helper viruses in host plants are thus matters of concern. Here, we focus on the propagation of betasatellites and, more specifically, on their transfer between different helper viruses and hosts through vector transmission. Our results show that the cotton leaf curl Gezira betasatellite (CLCuGeB), initially acquired with its helper virus cotton leaf curl Gezira virus (CLCuGeV) from an okra plant, can be transmitted and assisted by a different helper virus, tomato yellow leaf curl virus (TYLCV), in a different host plant (tomato plant). The new association can be formed whether TYLCV and CLCuGeB encounter each other in a host plant previously infected with TYLCV or in whiteflies having acquired the different components separately. Our findings reveal two pathways by which betasatellites can be transferred between helper viruses and host plants and highlight the ability of betasatellites to spread in begomovirus-infected environments. Full article

(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)

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17 pages, 9841 KiB

Open AccessArticle

Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance

by Vincent N. Azzolino, Ala M. Shaqra, Akbar Ali, Nese Kurt Yilmaz and Celia A. Schiffer

Viruses 2024, 16(9), 1419; https://doi.org/10.3390/v16091419 - 5 Sep 2024

Abstract

Enterovirus-D68 (EV68) has emerged as a global health concern over the last decade with severe symptomatic infections resulting in long-lasting neurological deficits and death. Unfortunately, there are currently no FDA-approved antiviral drugs for EV68 or any other non-polio enterovirus. One particularly attractive class [...] Read more.

Enterovirus-D68 (EV68) has emerged as a global health concern over the last decade with severe symptomatic infections resulting in long-lasting neurological deficits and death. Unfortunately, there are currently no FDA-approved antiviral drugs for EV68 or any other non-polio enterovirus. One particularly attractive class of potential drugs are small molecules inhibitors, which can target the conserved active site of EV68-3C protease. For other viral proteases, we have demonstrated that the emergence of drug resistance can be minimized by designing inhibitors that leverage the evolutionary constraints of substrate specificity. However, the structural characterization of EV68-3C protease bound to its substrates has been lacking. Here, we have determined the substrate specificity of EV68-3C protease through molecular modeling, molecular dynamics (MD) simulations, and co-crystal structures. Molecular models enabled us to successfully characterize the conserved hydrogen-bond networks between EV68-3C protease and the peptides corresponding to the viral cleavage sites. In addition, co-crystal structures we determined have revealed substrate-induced conformational changes of the protease which involved new interactions, primarily surrounding the S1 pocket. We calculated the substrate envelope, the three-dimensional consensus volume occupied by the substrates within the active site. With the elucidation of the EV68-3C protease substrate envelope, we evaluated how 3C protease inhibitors, AG7088 and SG-85, fit within the active site to predict potential resistance mutations. Full article

(This article belongs to the Special Issue Structure-Guided Antiviral Discovery: From Target Validation to Drug Design to Candidate Selection)

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18 pages, 4190 KiB

Open AccessArticle

KSHV ORF20 Promotes Coordinated Lytic Reactivation for Increased Infectious Particle Production

by Odelia Orbaum-Harel, Anna Sloutskin, Inna Kalt and Ronit Sarid

Viruses 2024, 16(9), 1418; https://doi.org/10.3390/v16091418 - 5 Sep 2024

Abstract

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a cancer-causing virus that establishes life-long infection. KSHV is implicated in the etiology of Kaposi’s sarcoma, and a number of rare hematopoietic malignancies. The present study focuses on the KSHV open reading frame 20 (ORF20), a member of [...] Read more.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a cancer-causing virus that establishes life-long infection. KSHV is implicated in the etiology of Kaposi’s sarcoma, and a number of rare hematopoietic malignancies. The present study focuses on the KSHV open reading frame 20 (ORF20), a member of the conserved herpesvirus UL24 protein family containing five conserved homology domains and a conserved PD-(D/E)XK putative endonuclease motif, whose nuclease function has not been established to date. ORF20 encodes three co-linear protein isoforms, full length, intermediate, and short, though their differential functions are unknown. In an effort to determine the role of ORF20 during KSHV infection, we generated a recombinant ORF20-Null KSHV genome, which fails to express all three ORF20 isoforms. This genome was reconstituted in iSLK cells to establish a latent infection, which resulted in an accelerated transcription of viral mRNAs, an earlier accumulation of viral lytic proteins, an increase in the quantity of viral DNA copies, and a significant decrease in viral yield upon lytic reactivation. This was accompanied by early cell death of cells infected with the ORF20-Null virus. Functional complementation of the ORF20-Null mutant with the short ORF20 isoform rescued KSHV production, whereas its endonuclease mutant form failed to enhance lytic reactivation. Complementation with the short isoform further revealed a decrease in cell death as compared with ORF20-Null virus. Finally, expression of IL6 and CXCL8, previously shown to be affected by the hCMV UL24 homolog, was relatively low upon reactivation of cells infected with the ORF20-Null virus. These findings suggest that ORF20 protein, with its putative endonuclease motif, promotes coordinated lytic reactivation for increased infectious particle production. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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14 pages, 1878 KiB

Open AccessArticle

Characterization of Avian Influenza Viruses Detected in Kenyan Live Bird Markets and Wild Bird Habitats Reveal Genetically Diverse Subtypes and High Proportion of A(H9N2), 2018–2020

by Peninah Munyua, Eric Osoro, Joyce Jones, George Njogu, Genyan Yang, Elizabeth Hunsperger, Christine M. Szablewski, Ruth Njoroge, Doris Marwanga, Harry Oyas, Ben Andagalu, Romona Ndanyi, Nancy Otieno, Vincent Obanda, Carolyne Nasimiyu, Obadiah Njagi, Juliana DaSilva, Yunho Jang, John Barnes, Gideon O. Emukule, Clayton O. Onyango and C. Todd Davis Show full author list Hide full author list

Viruses 2024, 16(9), 1417; https://doi.org/10.3390/v16091417 - 5 Sep 2024

Abstract

Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and [...] Read more.

Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and poultry workers in live bird markets and among wild migratory birds in various lakes that are resting sites during migration to assess introduction and circulation of avian influenza viruses in these populations. We tested 7464 specimens (oropharyngeal (OP) and cloacal specimens) from poultry and 6531 fresh fecal specimens from wild birds for influenza A viruses by real-time RT-PCR. Influenza was detected in 3.9% (n = 292) of specimens collected from poultry and 0.2% (n = 10) of fecal specimens from wild birds. On hemagglutinin subtyping, most of the influenza A positives from poultry (274/292, 93.8%) were H9. Of 34 H9 specimens randomly selected for further subtyping, all were H9N2. On phylogenetic analysis, these viruses were genetically similar to other H9 viruses detected in East Africa. Only two of the ten influenza A-positive specimens from the wild bird fecal specimens were successfully subtyped; sequencing analysis of one specimen collected in 2018 was identified as a low-pathogenicity avian influenza H5N2 virus of the Eurasian lineage, and the second specimen, collected in 2020, was subtyped as H11. A total of 18 OP and nasal specimens from poultry workers with acute respiratory illness (12%) were collected; none were positive for influenza A virus. We observed significant circulation of H9N2 influenza viruses in poultry in live bird markets in Kenya. During the same period, low-pathogenic H5N2 virus was detected in a fecal specimen collected in a site hosting a variety of migratory and resident birds. Although HPAI H5N8 was not detected in this survey, these results highlight the potential for the introduction and establishment of highly pathogenic avian influenza viruses in poultry populations and the associated risk of spillover to human populations. Full article

(This article belongs to the Section Animal Viruses)

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7 pages, 631 KiB

Open AccessBrief Report

Hazardous Alcohol Use and Its Effect on Direct-Acting Antiviral Therapy Initiation among People with Active Injection Drug Use and Current Hepatitis C Infection

by Hamidreza Karimi-Sari, Gregory M. Lucas, Katie Zook, Brian Weir, Miles Landry, Susan G. Sherman, Kathleen R. Page and Oluwaseun Falade-Nwulia

Viruses 2024, 16(9), 1416; https://doi.org/10.3390/v16091416 - 5 Sep 2024

Abstract

Background: Hepatitis C virus (HCV) infection and hazardous alcohol use are both preventable causes of morbidity and mortality among people who inject drugs (PWID). In the general population, hazardous alcohol is associated with a reduced likelihood of HCV treatment initiation. Less is known [...] Read more.

Background: Hepatitis C virus (HCV) infection and hazardous alcohol use are both preventable causes of morbidity and mortality among people who inject drugs (PWID). In the general population, hazardous alcohol is associated with a reduced likelihood of HCV treatment initiation. Less is known about the prevalence and impact of hazardous alcohol use on direct-acting antiviral (DAA) therapy initiation among PWID with active injection drug use. Methods: PWID were recruited via street outreach in Baltimore, Maryland, between 2018 and 2019 and were enrolled in a study cohort. Participants completed a study survey and underwent HCV testing. Self-reported DAA therapy initiation was evaluated at follow-up visits every six months. Hazardous alcohol use was determined based on an AUDIT-C score of ≥4 for men or ≥3 for women. Data were analyzed using multivariable logistic regression with generalized estimating equations. Results: Of the 720 PWID recruited, 291 had detectable HCV RNA, and only 134 were aware of their HCV infection. The mean (±standard deviation) age of those that were aware of their infection was 48.7 (±10.3) years, with a slight majority (53.0%) being male and predominantly African American (64.9%). The majority (80/134, 59.7%) met criteria for hazardous alcohol use. Only 16 (11.9%) PWID reported DAA therapy initiation within six months, and 20 (14.9%) reported it within 12 months of follow-up. Hazardous alcohol use (aOR = 1.23, 95% CI = 0.43–3.53) was not associated with DAA treatment initiation. Conclusions: There was a high prevalence of hazardous alcohol use, low rates of oral DAA therapy initiation, and no association between self-reported hazardous alcohol use and initiation of oral DAA therapy in our sample of PWID that were aware of their chronic HCV infection. Strategies to increase HCV treatment uptake in PWID with active drug use are urgently needed and should integrate alcohol and drug use evaluation and care. Full article

(This article belongs to the Special Issue Hepatitis Viral Infections, Pathogenesis and Therapeutics)

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9 pages, 2663 KiB

Open AccessCase Report

Case Report of Two Independent Moroccan Families with Syndromic Epidermodysplasia Verruciformis and STK4 Deficiency

by Assiya El Kettani, Hind Ouair, Farida Marnissi, Jalila El Bakkouri, Rémi Chevalier, Lazaro Lorenzo, Halima Kholaiq, Vivien Béziat, Emmanuelle Jouanguy, Jean-Laurent Casanova and Ahmed Aziz Bousfiha

Viruses 2024, 16(9), 1415; https://doi.org/10.3390/v16091415 - 5 Sep 2024

Abstract

Epidermodysplasia verruciformis (EV) is a rare genodermatosis caused by β-human papillomaviruses (HPV) in immunodeficient patients. EV is characterized by flat warts and pityriasis-like lesions and might be isolated or syndromic, associated with some other infectious manifestations. We report here three patients from two [...] Read more.

Epidermodysplasia verruciformis (EV) is a rare genodermatosis caused by β-human papillomaviruses (HPV) in immunodeficient patients. EV is characterized by flat warts and pityriasis-like lesions and might be isolated or syndromic, associated with some other infectious manifestations. We report here three patients from two independent families, with syndromic EV for both of them. By whole exome sequencing, we found that the patients carry new homozygous variants in STK4, both leading to a premature stop codon. STK4 deficiency causes a combined immunodeficiency characterized by a broad infectious susceptibility to bacteria, viruses, and fungi. Auto-immune manifestations were also reported. Deep immunophenotyping revealed multiple cytopenia in the three affected patients, in particular deep CD4⁺ T cells deficiency. We report here the fourth and the fifth cases of the syndromic EV due to STK4 deficiency. Full article

(This article belongs to the Special Issue Human and Animal Papillomavirus: Infections, Genetics, and Vaccines)

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16 pages, 1603 KiB

Open AccessArticle

Genomic Diversity and Evolutionary Insights of Avian Paramyxovirus-1 in Avian Populations in Pakistan

by Muhammad Zubair Shabbir, Sahar Mahmood, Aziz Ul-Rahman, Ashley C. Banyard and Craig S. Ross

Viruses 2024, 16(9), 1414; https://doi.org/10.3390/v16091414 - 5 Sep 2024

Abstract

The virulent form of Avian paramyxovirus-1 (APMV-1), commonly known as Newcastle Disease Virus (NDV), is a pathogen with global implications for avian health, affecting both wild and domestic bird populations. In Pakistan, recurrent Newcastle Disease (caused by NDV) outbreaks have posed significant challenges [...] Read more.

The virulent form of Avian paramyxovirus-1 (APMV-1), commonly known as Newcastle Disease Virus (NDV), is a pathogen with global implications for avian health, affecting both wild and domestic bird populations. In Pakistan, recurrent Newcastle Disease (caused by NDV) outbreaks have posed significant challenges to the poultry industry. Extensive surveillance in Pakistan over 20 years has demonstrated a dynamic genetic diversity among circulating APMV-1 strains, emphasizing the potential necessity for customized vaccination strategies and continuous surveillance. In this study, 13 APMV-1-positive isolates harboring four different APMV-1 genotypes circulating throughout Pakistan were identified. These included the highly virulent genotypes VII and XIII, genotype XXI, commonly associated with Columbiformes, and genotype II, hypothesized to have been detected following vaccination. These findings underscore the intricate interplay of mutational events and host-immune interactions shaping the evolving NDV landscape. This study advances our understanding of the evolutionary dynamics of APMV-1 in Pakistan, highlighting the need for tailored vaccination strategies and continuous surveillance to enable effective APMV-1 management in avian populations, further emphasizing the importance of globally coordinated strategies to tackle APMV-1, given its profound impact on wild and domestic birds. Full article

(This article belongs to the Special Issue Newcastle Disease and Other Avian Orthoavulaviruses 1)

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