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Viruses
Volume 14
Issue 11
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Viruses, Volume 14, Issue 11 (November 2022) – 275 articles

Cover Story (view full-size image): Bacteriophages are viruses of bacteria, for which molecular mechanisms of host-hijacking remain poorly explored. In this work, we apply omics technologies—transcriptomics and proteomics—to temporally resolve transcription and protein synthesis during the T4 phage infection of E. coli on a molecular level. For E. coli, we observed degradation of its transcripts and the preservation of the proteome. For T4 phage, the correlation between the transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. Our tool, POTATO4, provides access to these first comprehensive insights into the gene expression patterns of T4 phage infection of E. coli. View this paper
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26 pages, 4539 KiB  
Review
Heterologous RNA Recombination in the Cystoviruses φ6 and φ8: A Mechanism of Viral Variation and Genome Repair
by Paul Gottlieb and Aleksandra Alimova
Viruses 2022, 14(11), 2589; https://doi.org/10.3390/v14112589 - 21 Nov 2022
Cited by 2 | Viewed by 1716
Abstract
Recombination and mutation of viral genomes represent major mechanisms for viral evolution and, in many cases, moderate pathogenicity. Segmented genome viruses frequently undergo reassortment of the genome via multiple infection of host organisms, with influenza and reoviruses being well-known examples. Specifically, major genomic [...] Read more.
Recombination and mutation of viral genomes represent major mechanisms for viral evolution and, in many cases, moderate pathogenicity. Segmented genome viruses frequently undergo reassortment of the genome via multiple infection of host organisms, with influenza and reoviruses being well-known examples. Specifically, major genomic shifts mediated by reassortment are responsible for radical changes in the influenza antigenic determinants that can result in pandemics requiring rapid preventative responses by vaccine modifications. In contrast, smaller mutational changes brought about by the error-prone viral RNA polymerases that, for the most part, lack a replication base mispairing editing function produce small mutational changes in the RNA genome during replication. Referring again to the influenza example, the accumulated mutations—known as drift—require yearly vaccine updating and rapid worldwide distribution of each new formulation. Coronaviruses with a large positive-sense RNA genome have long been known to undergo intramolecular recombination likely mediated by copy choice of the RNA template by the viral RNA polymerase in addition to the polymerase-based mutations. The current SARS-CoV-2 origin debate underscores the importance of understanding the plasticity of viral genomes, particularly the mechanisms responsible for intramolecular recombination. This review describes the use of the cystovirus bacteriophage as an experimental model for recombination studies in a controlled manner, resulting in the development of a model for intramolecular RNA genome alterations. The review relates the sequence of experimental studies from the laboratory of Leonard Mindich, PhD at the Public Health Research Institute—then in New York City—and covers a period of approximately 12 years. Hence, this is a historical scientific review of research that has the greatest relevance to current studies of emerging RNA virus pathogens. Full article
(This article belongs to the Special Issue Discovery, Classification, and Early Research on the Lipid-Containing, Double-Stranded RNA Bacteriophage φ6)
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10 pages, 1181 KiB  
Article
SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing
by Antonio Martínez-Murcia, Adrian Garcia-Sirera, Aaron Navarro and Laura Pérez
Viruses 2022, 14(11), 2588; https://doi.org/10.3390/v14112588 - 21 Nov 2022
Cited by 2 | Viewed by 1426 | Correction
Abstract
A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation [...] Read more.
A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation PCR-based protocols were not always specific, and consequently, determination of a high number of informative sites was needed for accurate lineage identification. A detailed in silico analysis of SARS-CoV-2 sequences retrieved from GISAID database revealed the S gene 921 bp-fragment, positions 22784–23705 of SARS-CoV-2 reference genome, as the most informative fragment (30 variable sites) to determine relevant SARS-CoV-2 variants. Consequently, a method consisting of the PCR-amplification of this fragment, followed by Sanger’s sequencing and a “single-click” informatic program based on a reference database, was developed and validated. PCR-fragments obtained from clinical SARS-CoV-2 samples were compared with homologous variant-sequences and the resulting phylogenetic tree allowed the identification of Alpha, Delta, Omicron, Beta, Gamma, and other variants. The data analysis procedure was automatized and simplified to the point that it did not require specific technical skills. The method is faster and cheaper than current whole-genome sequencing methods; it is available worldwide, and it may help to enhance efficient surveillance in the fight against the COVID-19 pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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14 pages, 3560 KiB  
Article
RSAD2 Is an Effective Target for High-Yield Vaccine Production in MDCK Cells
by Zilin Qiao, Yuejiao Liao, Mengyuan Pei, Zhenyu Qiu, Zhenbin Liu, Dongwu Jin, Jiayou Zhang, Zhongren Ma and Xiaoming Yang
Viruses 2022, 14(11), 2587; https://doi.org/10.3390/v14112587 - 21 Nov 2022
Cited by 2 | Viewed by 2027
Abstract
Increasingly, attention has focused on improving vaccine production in cells using gene editing technology to specifically modify key virus regulation-related genes to promote virus replication. In this study, we used DIA proteomics analysis technology to compare protein expression differences between two groups of [...] Read more.
Increasingly, attention has focused on improving vaccine production in cells using gene editing technology to specifically modify key virus regulation-related genes to promote virus replication. In this study, we used DIA proteomics analysis technology to compare protein expression differences between two groups of MDCK cells: uninfected and influenza A virus (IAV) H1N1-infected cells 16 h post infection (MOI = 0.01). Initially, 266 differentially expressed proteins were detected after infection, 157 of which were upregulated and 109 were downregulated. We screened these proteins to 23 genes related to antiviral innate immunity regulation based on functional annotation database analysis and verified the mRNA expression of these genes using qPCR. Combining our results with published literature, we focused on the proteins RSAD2, KCNN4, IDO1, and ISG20; we verified their expression using western blot, which was consistent with our proteomics results. Finally, we knocked down RSAD2 using lentiviral shRNA expression vectors and found that RSAD2 inhibition significantly increased IAV NP gene expression, effectively promoting influenza virus replication with no significant effect on cell proliferation. These results indicate that RSAD2 is potentially an effective target for establishing high-yield vaccine MDCK cell lines and will help to fully understand the interaction mechanism between host cells and influenza viruses. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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9 pages, 2231 KiB  
Case Report
Prenatal Diagnosis of Congenital Lymphocytic Choriomeningitis Virus Infection: A Case Report
by Fanny Tevaearai, Laureline Moser and Léo Pomar
Viruses 2022, 14(11), 2586; https://doi.org/10.3390/v14112586 - 21 Nov 2022
Cited by 2 | Viewed by 1699
Abstract
Lymphocytic choriomeningitis virus (LCMV) is an emerging neuroteratogen which can infect humans via contact with urine, feces, saliva, or blood of infected rodents. When the infection occurs during pregnancy, there is a risk of transplacental infection with subsequent neurological or visual impairment in [...] Read more.
Lymphocytic choriomeningitis virus (LCMV) is an emerging neuroteratogen which can infect humans via contact with urine, feces, saliva, or blood of infected rodents. When the infection occurs during pregnancy, there is a risk of transplacental infection with subsequent neurological or visual impairment in the fetus. In this article, we describe a case report of congenital LCMV infection, including fetal imaging, confirmed by positive LCMV IgM in fetal blood and cerebrospinal fluid. Full article
(This article belongs to the Special Issue Emerging Virus Infections in Adverse Pregnancy Outcomes II)
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20 pages, 5596 KiB  
Article
Dual-RNAseq Analysis Unravels Virus-Host Interactions of MetSV and Methanosarcina mazei
by Finn O. Gehlert, Till Sauerwein, Katrin Weidenbach, Urska Repnik, Daniela Hallack, Konrad U. Förstner and Ruth A. Schmitz
Viruses 2022, 14(11), 2585; https://doi.org/10.3390/v14112585 - 21 Nov 2022
Cited by 4 | Viewed by 1778
Abstract
Methanosarcina spherical virus (MetSV), infecting Methanosarcina species, encodes 22 genes, but their role in the infection process in combination with host genes has remained unknown. To study the infection process in detail, infected and uninfected M. mazei cultures were compared using dual-RNAseq, qRT-PCRs, [...] Read more.
Methanosarcina spherical virus (MetSV), infecting Methanosarcina species, encodes 22 genes, but their role in the infection process in combination with host genes has remained unknown. To study the infection process in detail, infected and uninfected M. mazei cultures were compared using dual-RNAseq, qRT-PCRs, and transmission electron microscopy (TEM). The transcriptome analysis strongly indicates a combined role of virus and host genes in replication, virus assembly, and lysis. Thereby, 285 host and virus genes were significantly regulated. Within these 285 regulated genes, a network of the viral polymerase, MetSVORF6, MetSVORF5, MetSVORF2, and the host genes encoding NrdD, NrdG, a CDC48 family protein, and a SSB protein with a role in viral replication was postulated. Ultrastructural analysis at 180 min p.i. revealed many infected cells with virus particles randomly scattered throughout the cytoplasm or attached at the cell surface, and membrane fragments indicating cell lysis. Dual-RNAseq and qRT-PCR analyses suggested a multifactorial lysis reaction in potential connection to the regulation of a cysteine proteinase, a pirin-like protein and a HicB-solo protein. Our study’s results led to the first preliminary infection model of MetSV infecting M. mazei, summarizing the key infection steps as follows: replication, assembly, and host cell lysis. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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16 pages, 10278 KiB  
Article
Characterization of Three Variants of SARS-CoV-2 In Vivo Shows Host-Dependent Pathogenicity in Hamsters, While Not in K18-hACE2 Mice
by Gabriela Toomer, Whitney Burns, Liliana Garcia, Gerelyn Henry, Anthony Biancofiori, Albert George, Ciera Duffy, Justin Chu, Morgan Sides, Melissa Muñoz, Kelly Garcia, Anya Nikolai-Yogerst, Xinjian Peng, Landon Westfall and Robert Baker
Viruses 2022, 14(11), 2584; https://doi.org/10.3390/v14112584 - 21 Nov 2022
Cited by 5 | Viewed by 2882
Abstract
Animal models are used in preclinical trials to test vaccines, antivirals, monoclonal antibodies, and immunomodulatory drug therapies against SARS-CoV-2. However, these drugs often do not produce equivalent results in human clinical trials. Here, we show how different animal models infected with some of [...] Read more.
Animal models are used in preclinical trials to test vaccines, antivirals, monoclonal antibodies, and immunomodulatory drug therapies against SARS-CoV-2. However, these drugs often do not produce equivalent results in human clinical trials. Here, we show how different animal models infected with some of the most clinically relevant SARS-CoV-2 variants, WA1/2020, B.1.617.2/Delta, B.1.1.529/Omicron, and BA5.2/Omicron, have independent outcomes. We show that in K18-hACE2 mice, B.1.617.2 is more pathogenic, followed by WA1, while B.1.1.529 showed an absence of clinical signs. Only B.1.1.529 was able to infect C57BL/6J mice, which lack the human ACE2 receptor. B.1.1.529-infected C57BL/6J mice had different T cell profiles compared to infected K18-hACE2 mice, while viral shedding profiles and viral titers in lungs were similar between the K18-hACE2 and the C57BL/6J mice. These data suggest B.1.1.529 virus adaptation to a new host and shows that asymptomatic carriers can accumulate and shed virus. Next, we show how B.1.617.2, WA1 and BA5.2/Omicron have similar viral replication kinetics, pathogenicity, and viral shedding profiles in hamsters, demonstrating that the increased pathogenicity of B.1.617.2 observed in mice is host-dependent. Overall, these findings suggest that small animal models are useful to parallel human clinical data, but the experimental design places an important role in interpreting the data. Importance: There is a need to investigate SARS-CoV-2 variant phenotypes in different animal models due to the lack of reproducible outcomes when translating experiments to the human population. Our findings highlight the correlation of clinically relevant SARS-CoV-2 variants in animal models with human infections. Experimental design and understanding of correct animal models are essential to interpreting data to develop antivirals, vaccines, and other therapeutic compounds against COVID-19. Full article
(This article belongs to the Special Issue SARS-CoV-2 and Animal Models)
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14 pages, 306 KiB  
Article
A Retrospective Study of Viral Molecular Prevalences in Cats in Southern Italy (Campania Region)
by Maria Grazia Amoroso, Francesco Serra, Gianluca Miletti, Lorena Cardillo, Claudio de Martinis, Luisa Marati, Flora Alfano, Gianmarco Ferrara, Ugo Pagnini, Esterina De Carlo, Giovanna Fusco and Serena Montagnaro
Viruses 2022, 14(11), 2583; https://doi.org/10.3390/v14112583 - 21 Nov 2022
Cited by 8 | Viewed by 1851
Abstract
From 2019 to 2021, a retrospective molecular study was conducted in the Campania region (southern Italy) to determine the prevalence of viral diseases in domestic cats. A total of 328 dead animals were analyzed by Real-Time PCR for the presence of feline panleukopenia [...] Read more.
From 2019 to 2021, a retrospective molecular study was conducted in the Campania region (southern Italy) to determine the prevalence of viral diseases in domestic cats. A total of 328 dead animals were analyzed by Real-Time PCR for the presence of feline panleukopenia virus (FPV), feline leukemia virus (FeLV), feline enteric coronavirus (FCoV), rotavirus (RVA), feline herpesvirus type 1 (FHV-1), and feline calicivirus (FCV). The possible presence of SARS-CoV-2 was also investigated by Real-Time PCR. The cats included in this study were specifically sourced and referred by local veterinarians and local authorities to the Zooprofilactic Experimental Institute of Southern Italy (IZSM) for pathological evaluation. The samples consisted of owners, catteries, and stray cats. Results revealed: 73.5% positive cats for FPV (189/257), 23.6% for FeLV (21/89), 21.5% for FCoV (56/266), 11.4% for RVA (16/140), 9.05% for FeHV-1 (21/232), and 7.04 for FCV (15/213). In contrast, SARS-CoV-2 was never detected. FPV was more prevalent in winter (p = 0.0027). FCoV FHV-1, FCV, and RVA predominated in autumn, whereas FeLV predominated in summer. As expected, viral infections were found more frequently in outdoor and shelter cats than in indoor ones, although no statistical association was found between animal lifestyle and viral presence. The study showed a high prevalence of FPV, FeLV, and FCoV and a moderate prevalence of RVA, FHV-1, and FCV. Moreover, the prevalence of these pathogens varied among the cat populations investigated. Full article
(This article belongs to the Special Issue Enteric and Respiratory Viruses in Animals 3.0)
12 pages, 2845 KiB  
Article
Effects of Klebsiella pneumoniae Bacteriophages on IRAK3 Knockdown/Knockout THP-1 Monocyte Cell Lines
by Bryce Dylan Schubert, Heng Ku, Mwila Kabwe, Trang Hong Nguyen, Helen Irving and Joseph Tucci
Viruses 2022, 14(11), 2582; https://doi.org/10.3390/v14112582 - 21 Nov 2022
Cited by 2 | Viewed by 1997
Abstract
Bacterial sepsis characterised by an immunosuppressive and cytokine storm state is a challenge to treat clinically. While conventional antibiotics have been associated with exacerbating the cytokine storm, the role that bacteriophages may play in immune modulation of sepsis remains unclear. Bacteriophages are bacterial [...] Read more.
Bacterial sepsis characterised by an immunosuppressive and cytokine storm state is a challenge to treat clinically. While conventional antibiotics have been associated with exacerbating the cytokine storm, the role that bacteriophages may play in immune modulation of sepsis remains unclear. Bacteriophages are bacterial viruses that have the capacity to lyse specific bacteria and hence provide a natural alternative to antibiotics. K. pneumoniae is known to cause sepsis in humans, and in this study we isolated two lytic bacteriophages against this pathogen, one of which was a novel jumbo bacteriophage. We employed THP-1 monocyte cell lines, with different functional phenotypes for the interleukin-1 receptor associated kinase 3 (IRAK3- a cytoplasmic homeostatic mediator and prognostic marker of inflammation), to evaluate the role of the K. pneumoniae bacteriophages in modulating the immune response in-vitro. We showed for the first time that bacteriophages did not stimulate excessive production of tumour necrosis factor alpha, or interleukin-6, in THP-1 monocyte cell lines which displayed varying levels of IRAK3 expression. Full article
(This article belongs to the Section Bacterial Viruses)
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12 pages, 760 KiB  
Article
Assessing the Pre-Vaccination Anti-SARS-CoV-2 IgG Seroprevalence among Residents and Staff in Nursing Home in Niigata, Japan, November 2020
by Keita Wagatsuma, Sayaka Yoshioka, Satoru Yamazaki, Ryosuke Sato, Wint Wint Phyu, Irina Chon, Yoshiki Takahashi, Hisami Watanabe and Reiko Saito
Viruses 2022, 14(11), 2581; https://doi.org/10.3390/v14112581 - 21 Nov 2022
Cited by 2 | Viewed by 1785
Abstract
An outbreak of coronavirus disease 2019 (COVID-19) occurred in a nursing home in Niigata, Japan, November 2020, with an attack rate of 32.0% (63/197). The present study was aimed at assessing the pre-vaccination seroprevalence almost half a year after the COVID-19 outbreak in [...] Read more.
An outbreak of coronavirus disease 2019 (COVID-19) occurred in a nursing home in Niigata, Japan, November 2020, with an attack rate of 32.0% (63/197). The present study was aimed at assessing the pre-vaccination seroprevalence almost half a year after the COVID-19 outbreak in residents and staff in the facility, along with an assessment of the performance of the enzyme-linked immunosorbent assay (ELISA) and the chemiluminescent immunoassay (CLIA), regarding test seropositivity and seronegativity in detecting immunoglobulin G (IgG) anti-severe acute respiratory syndrome 2 (SARS-CoV-2) antibodies (anti-nucleocapsid (N) and spike (S) proteins). A total of 101 people (30 reverse transcription PCR (RT-PCR)-positive and 71 RT-PCR-negative at the time of the outbreak in November 2020) were tested for anti-IgG antibody titers in April 2021, and the seroprevalence was approximately 40.0–60.0% for residents and 10.0–20.0% for staff, which was almost consistent with the RT-PCR test results that were implemented during the outbreak. The seropositivity for anti-S antibodies showed 90.0% and was almost identical to the RT-PCR positives even after approximately six months of infections, suggesting that the anti-S antibody titer test is reliable for a close assessment of the infection history. Meanwhile, seropositivity for anti-N antibodies was relatively low, at 66.7%. There was one staff member and one resident that were RT-PCR-negative but seropositive for both anti-S and anti-N antibody, indicating overlooked infections despite periodical RT-PCR testing at the time of the outbreak. Our study indicated the impact of transmission of SARS-CoV-2 in a vulnerable elderly nursing home in the pre-vaccination period and the value of a serological study to supplement RT-PCR results retrospectively. Full article
(This article belongs to the Special Issue RNA Viruses and Antibody Response)
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9 pages, 2000 KiB  
Article
Evaluation of Rapid Dot-Immunoassay for Detection Orthopoxviruses Using Laboratory-Grown Viruses and Animal’s Clinical Specimens
by Nikita Ushkalenko, Anna Ersh, Alexander Sergeev, Pavel Filatov and Alexander Poltavchenko
Viruses 2022, 14(11), 2580; https://doi.org/10.3390/v14112580 - 21 Nov 2022
Cited by 3 | Viewed by 1313
Abstract
The aim of the work was an experimental evaluation of the characteristics of the kit for the rapid immunochemical detection of orthopoxviruses (OPV). The kit is based on the method of one-stage dot-immunoassay on flat protein arrays using gold conjugates and a silver [...] Read more.
The aim of the work was an experimental evaluation of the characteristics of the kit for the rapid immunochemical detection of orthopoxviruses (OPV). The kit is based on the method of one-stage dot-immunoassay on flat protein arrays using gold conjugates and a silver developer. Rabbit polyclonal antibodies against the vaccinia virus were used as capture and detection reagents. The sensitivity of detection of OPV and the specificity of the analysis were assessed using culture crude preparations (monkeypox virus, vaccinia virus, rabbitpox virus, cowpox virus, and ectromelia virus), a suspension from a crust from a human vaccination site as well as blood and tissue suspensions of infected rabbits. It has been shown that the assay using the kit makes it possible to detect OPV within 36 min at a temperature of 18–40 °C in unpurified culture samples of the virus and clinical samples in the range of 103–104 PFU/mL. Tests of the kit did not reveal cross-reactivity with uninfected cell cultures and viral pathogens of exanthematous infections (measles, rubella and chicken pox). The kit can be used to detect or exclude the presence of a virus threat in samples and can be useful in various aspects of biosecurity. The simplicity of analysis, the possibility of visual accounting the and interpretation of the results make it possible to use the test in laboratories with a high level of biological protection and in out-of-laboratory conditions. Full article
(This article belongs to the Special Issue Diagnostics, Antiviral Therapy and Vaccination against Orthopoxvirus Infections)
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13 pages, 1477 KiB  
Article
Impact of Hepatitis B Virus Infection, Non-alcoholic Fatty Liver Disease, and Hepatitis C Virus Co-infection on Liver-Related Death among People Tested for Hepatitis B Virus in British Columbia: Results from a Large Longitudinal Population-Based Cohort Study
by Jean Damascene Makuza, Dahn Jeong, Mawuena Binka, Prince Asumadu Adu, Georgine Cua, Amanda Yu, Héctor Alexander Velásquez García, Maria Alvarez, Stanley Wong, Sofia Bartlett, Mohammad Ehsanul Karim, Eric M. Yoshida, Alnoor Ramji, Mel Krajden and Naveed Zafar Janjua
Viruses 2022, 14(11), 2579; https://doi.org/10.3390/v14112579 - 21 Nov 2022
Cited by 1 | Viewed by 3087
Abstract
Data on the contribution of hepatitis B virus (HBV) infection and related comorbidities to liver-related mortality in Canada are limited. We assessed the concurrent impact of HBV infection, non-alcoholic fatty liver disease (NAFLD), and hepatitis C virus (HCV) coinfection on liver-related deaths in [...] Read more.
Data on the contribution of hepatitis B virus (HBV) infection and related comorbidities to liver-related mortality in Canada are limited. We assessed the concurrent impact of HBV infection, non-alcoholic fatty liver disease (NAFLD), and hepatitis C virus (HCV) coinfection on liver-related deaths in British Columbia (BC), Canada. We used data from the BC Hepatitis Testers Cohort (BC-HTC). We used Fine–Gray multivariable sub-distributional hazards models to assess the effect of HBV, NAFLD, and HCV coinfection on liver-related mortality, while adjusting for confounders and competing mortality risks. The liver-related mortality rate was higher among people with HBV infection than those without (2.57 per 1000 PYs (95%CI: 2.46, 2.69) vs. 0.62 per 1000 PYs (95%CI: 0.61, 0.64), respectively). Compared with the HBV negative groups, HBV infection was associated with increased liver-related mortality risk in almost all of the subgroups: HBV mono-infection (adjusted subdistribution hazards ratio (asHR) of 3.35, 95% CI 3.16, 3.55), NAFLD with HBV infection, (asHR 12.5, 95% CI 7.08, 22.07), and HBV/HCV coinfection (asHR 8.4, 95% CI 7.62, 9.26). HBV infection is associated with a higher risk of liver-related mortality, and has a greater relative impact on people with NAFLD and those with HCV coinfection. The diagnosis and treatment of viral and fatty liver disease are required to mitigate liver-related morbidity and mortality. Full article
(This article belongs to the Special Issue Hepatitis B Virus: New Breakthroughs to Conquer an Ancient Disease)
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18 pages, 1477 KiB  
Review
Understanding the Role of HLA Class I Molecules in the Immune Response to Influenza Infection and Rational Design of a Peptide-Based Vaccine
by A. K. M. Muraduzzaman, Patricia T. Illing, Nicole A. Mifsud and Anthony W. Purcell
Viruses 2022, 14(11), 2578; https://doi.org/10.3390/v14112578 - 21 Nov 2022
Cited by 3 | Viewed by 3199
Abstract
Influenza A virus is a respiratory pathogen that is responsible for regular epidemics and occasional pandemics that result in substantial damage to life and the economy. The yearly reformulation of trivalent or quadrivalent flu vaccines encompassing surface glycoproteins derived from the current circulating [...] Read more.
Influenza A virus is a respiratory pathogen that is responsible for regular epidemics and occasional pandemics that result in substantial damage to life and the economy. The yearly reformulation of trivalent or quadrivalent flu vaccines encompassing surface glycoproteins derived from the current circulating strains of the virus does not provide sufficient cross-protection against mismatched strains. Unlike the current vaccines that elicit a predominant humoral response, vaccines that induce CD8+ T cells have demonstrated a capacity to provide cross-protection against different influenza strains, including novel influenza viruses. Immunopeptidomics, the mass spectrometric identification of human-leukocyte-antigen (HLA)-bound peptides isolated from infected cells, has recently provided key insights into viral peptides that can serve as potential T cell epitopes. The critical elements required for a strong and long-living CD8+ T cell response are related to both HLA restriction and the immunogenicity of the viral peptide. This review examines the importance of HLA and the viral immunopeptidome for the design of a universal influenza T-cell-based vaccine. Full article
(This article belongs to the Special Issue Influenza A Viruses: New Insights in 2022)
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17 pages, 1382 KiB  
Article
Novel RT-PCR Using Sugar Chain-Immobilized Gold-Nanoparticles Correlates Patients’ Symptoms: The Follow-Up Study of COVID-19 Hospitalized Patients
by Takashi Kajiya, Hayate Sawayama, Eriko Arima, Mika Okamoto, Masanori Baba, Masaaki Toyama, Kosuke Okuya, Makoto Ozawa, Nobuhiko Atsuchi, Junichiro Nishi and Yasuo Suda
Viruses 2022, 14(11), 2577; https://doi.org/10.3390/v14112577 - 21 Nov 2022
Cited by 1 | Viewed by 1574
Abstract
Background: The transmissible capacity and toxicity of SARS-CoV-2 variants are continually changing. We report here the follow-up study of hospitalized COVID-19 patients from 2020 to 2022. It is known that the PCR diagnosis for hospitalized patients sometimes causes confusion because of the incompatibility [...] Read more.
Background: The transmissible capacity and toxicity of SARS-CoV-2 variants are continually changing. We report here the follow-up study of hospitalized COVID-19 patients from 2020 to 2022. It is known that the PCR diagnosis for hospitalized patients sometimes causes confusion because of the incompatibility between their diagnosis and symptoms. We applied our sugar chain-immobilized gold-nanoparticles for the extraction and partial purification of RNA from specimens for quantitative RT-PCR assay and evaluated whether the results correlate with patients’ symptoms. Methods and Results: Saliva specimens were taken from hospitalized patients with mild or moderate symptoms every early morning. At the time of RT-PCR diagnosis, two methods for the extraction and partial purification of RNA from the specimen were performed: a commonly used Boom (Qiagen) method and our original sugar chain-immobilized gold nanoparticle (SGNP) method. For symptoms, body temperature and oxygen saturation (SpO2) of patients were monitored every 4 h. Conclusions: It was clear that patients infected with the Delta variant needed more time to recover than those with the Omicron variant, and that the SGNP method showed more realistic correlation with the symptoms of patients compared with the common Qiagen method. Full article
(This article belongs to the Special Issue Nanotechnological Applications in Virology 2023)
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13 pages, 1042 KiB  
Article
Epidemiological Aspects of Equid Herpesvirus-Associated Myeloencephalopathy (EHM) Outbreaks
by Eva Klouth, Yury Zablotski, Jessica L. Petersen, Marco de Bruijn, Gittan Gröndahl, Susanne Müller and Lutz S. Goehring
Viruses 2022, 14(11), 2576; https://doi.org/10.3390/v14112576 - 21 Nov 2022
Cited by 3 | Viewed by 1860
Abstract
Equid Herpesvirus Myeloencephalopathy (EHM) is a multifactorial disease following an EHV-1 infection in Equidae. We investigated a total of 589 horses on 13 premises in Europe in search of risk factors for the development of EHM. We found that fever (p < [...] Read more.
Equid Herpesvirus Myeloencephalopathy (EHM) is a multifactorial disease following an EHV-1 infection in Equidae. We investigated a total of 589 horses on 13 premises in Europe in search of risk factors for the development of EHM. We found that fever (p < 0.001), increasing age (p = 0.032), and female sex (p = 0.042) were risk factors for EHM in a logistic mixed model. Some breeds had a decreased risk to develop EHM compared to others (Shetland and Welsh ponies; p = 0.017; p = 0.031), and fewer EHV-1-vaccinated horses were affected by EHM compared to unvaccinated horses (p = 0.02). Data evaluation was complex due to high variability between outbreaks with regards to construction and environment; viral characteristics and the virus’s transmissibility were affected by operational management. This study confirms earlier suspected host-specific risk factors, and our data support the benefit of high vaccine coverage at high-traffic boarding facilities. Full article
(This article belongs to the Special Issue Equine Viruses in Continental Europe)
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19 pages, 18941 KiB  
Review
Immune-Mediated Pathogenesis in Dengue Virus Infection
by Arshi Khanam, Hector Gutiérrez-Barbosa, Kirsten E. Lyke and Joel V. Chua
Viruses 2022, 14(11), 2575; https://doi.org/10.3390/v14112575 - 21 Nov 2022
Cited by 9 | Viewed by 7461
Abstract
Dengue virus (DENV) infection is one of the major public health concerns around the globe, especially in the tropical regions of the world that contribute to 75% percent of dengue cases. While the majority of DENV infections are mild or asymptomatic, approximately 5% [...] Read more.
Dengue virus (DENV) infection is one of the major public health concerns around the globe, especially in the tropical regions of the world that contribute to 75% percent of dengue cases. While the majority of DENV infections are mild or asymptomatic, approximately 5% of the cases develop a severe form of the disease that is mainly attributed to sequential infection with different DENV serotypes. The severity of dengue depends on many immunopathogenic mechanisms involving both viral and host factors. Emerging evidence implicates an impaired immune response as contributing to disease progression and severity by restricting viral clearance and inducing severe inflammation, subsequently leading to dengue hemorrhagic fever and dengue shock syndrome. Moreover, the ability of DENV to infect a wide variety of immune cells, including monocytes, macrophages, dendritic cells, mast cells, and T and B cells, further dysregulates the antiviral functions of these cells, resulting in viral dissemination. Although several risk factors associated with disease progression have been proposed, gaps persist in the understanding of the disease pathogenesis and further investigations are warranted. In this review, we discuss known mechanisms of DENV-mediated immunopathogenesis and its association with disease progression and severity. Full article
(This article belongs to the Special Issue Boosting Flavivirus Research: A Pandengue Net Initiative)
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16 pages, 5382 KiB  
Article
A Characterization and an Evolutionary and a Pathogenicity Analysis of Reassortment H3N2 Avian Influenza Virus in South China in 2019–2020
by Tengfei Liu, Yuhao Huang, Shumin Xie, Lingyu Xu, Junhong Chen, Wenbao Qi, Ming Liao and Weixin Jia
Viruses 2022, 14(11), 2574; https://doi.org/10.3390/v14112574 - 21 Nov 2022
Cited by 2 | Viewed by 2396
Abstract
Seasonal H3N2 influenza virus has always been a potential threat to public health. The reassortment of the human and avian H3N2 influenza viruses has resulted in major influenza outbreaks, which have seriously damaged human life and health. To assess the possible threat of [...] Read more.
Seasonal H3N2 influenza virus has always been a potential threat to public health. The reassortment of the human and avian H3N2 influenza viruses has resulted in major influenza outbreaks, which have seriously damaged human life and health. To assess the possible threat of the H3N2 avian influenza virus to human health, we performed whole-genome sequencing and genetic evolution analyses on 10 H3N2 field strains isolated from different hosts and regions in 2019–2020 and selected representative strains for pathogenicity tests on mice. According to the results, the internal gene cassettes of nine strains had not only undergone reassortment with the H1, H2, H4, H6, and H7 subtypes, which circulate in poultry and mammals, but also with H10N8, which circulates in wild birds in the natural environment. Three reassorted strains were found to be pathogenic to mice, of these one strain harboring MP from H10N8 showed a stronger virulence in mice. This study indicates that reassorted H3N2 AIVs may cross the host barrier to infect mammals and humans, thereby, necessitating persistent surveillance of H3N2 AIVs. Full article
(This article belongs to the Section Animal Viruses)
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12 pages, 1072 KiB  
Article
Change in Nutritional and Biochemical Status in People Living with HIV-1 on Antiretroviral Therapy
by Ranilda Gama de Souza, Sandra Souza Lima, Andresa Corrêa Pinto, Jacqueline Silva Souza, Tuane Carolina Ferreira Moura, Ednelza da Silva Graça Amoras, Luiz Fernando Almeida Machado, João Farias Guerreiro, Antonio Carlos Rosário Vallinoto, Maria Alice Freitas Queiroz and Ricardo Ishak
Viruses 2022, 14(11), 2573; https://doi.org/10.3390/v14112573 - 20 Nov 2022
Cited by 2 | Viewed by 1541
Abstract
Antiretroviral therapy (ART) improves the quality of life of people living with HIV-1 (PLHIV) and reduces the mortality rate, but some individuals may develop metabolic abnormalities. This study evaluated changes in the nutritional status and biochemistry of PLHIV on antiretroviral therapy in a [...] Read more.
Antiretroviral therapy (ART) improves the quality of life of people living with HIV-1 (PLHIV) and reduces the mortality rate, but some individuals may develop metabolic abnormalities. This study evaluated changes in the nutritional status and biochemistry of PLHIV on antiretroviral therapy in a cohort that had not previously received ART and to follow up these individuals for 24 months after starting treatment. The initial cohort consisted of 110 individuals and ended with 42 people, assessed by a physical examination. A biochemical assay was performed using the colorimetric enzyme reaction technique, the proviral load was detected by qPCR and the quantification of the CD4/CD8 T lymphocytes was conducted by flow cytometry. PLHIV had increased levels of total cholesterol, LDL, triglycerides, ALT, urea and creatinine after 24 months of ART use (p < 0.05). In the assessment of the nutritional status, PLHIV had increased measures of Triciptal Skinfold, body mass index and arm circumference after the use of ART (p < 0.05). The viral load levels decreased and the CD4 levels increased after 24 months of ART use (p < 0.05). The change in the nutritional status in PLHIV on antiretroviral therapy seems to be a slow process, occurring in the long term, therefore, there is the need for a constant evaluation of these people to identify patients who need a nutritional intervention. Full article
(This article belongs to the Special Issue State-of-the-Art HIV and HTLV Research in Latin America)
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27 pages, 8463 KiB  
Article
Discovery, Genomic Sequence Characterization and Phylogenetic Analysis of Novel RNA Viruses in the Turfgrass Pathogenic Colletotrichum spp. in Japan
by Islam Hamim, Syun-ichi Urayama, Osamu Netsu, Akemi Tanaka, Tsutomu Arie, Hiromitsu Moriyama and Ken Komatsu
Viruses 2022, 14(11), 2572; https://doi.org/10.3390/v14112572 - 20 Nov 2022
Cited by 6 | Viewed by 1861
Abstract
Turfgrass used in various areas of the golf course has been found to present anthracnose disease, which is caused by Colletotrichum spp. To obtain potential biological agents, we identified four novel RNA viruses and obtained full-length viral genomes from turfgrass pathogenic Colletotrichum spp. [...] Read more.
Turfgrass used in various areas of the golf course has been found to present anthracnose disease, which is caused by Colletotrichum spp. To obtain potential biological agents, we identified four novel RNA viruses and obtained full-length viral genomes from turfgrass pathogenic Colletotrichum spp. in Japan. We characterized two novel dsRNA partitiviruses: Colletotrichum associated partitivirus 1 (CaPV1) and Colletotrichum associated partitivirus 2 (CaPV2), as well as two negative single-stranded (ss) RNA viruses: Colletotrichum associated negative-stranded RNA virus 1 (CaNSRV1) and Colletotrichum associated negative-stranded RNA virus 2 (CaNSRV2). Using specific RT-PCR assays, we confirmed the presence of CaPV1, CaPV2 and CaNSRV1 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-264, as well as CaNSRV2 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-288. This is the first time mycoviruses have been discovered in turfgrass pathogenic Colletotrichum spp. in Japan. CaPV1 and CaPV2 are new members of the newly proposed genus “Zetapartitivirus” and genus Alphapartitivirus, respectively, in the family Partitiviridae, according to genomic characterization and phylogenetic analysis. Negative sense ssRNA viruses CaNSRV1 and CaNSRV2, on the other hand, are new members of the family Phenuiviridae and the proposed family “Mycoaspirividae”, respectively. These findings reveal previously unknown RNA virus diversity and evolution in turfgrass pathogenic Colletotrichum spp. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses)
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9 pages, 1022 KiB  
Article
Comparisons of Viral Etiology and Outcomes of Hepatocellular Carcinoma Undergoing Liver Resection between Taiwan and Vietnam
by Song-Huy Nguyen-Dinh, Wei-Feng Li, Yueh-Wei Liu, Chih-Chi Wang, Yen-Hao Chen, Jing-Houng Wang and Chao-Hung Hung
Viruses 2022, 14(11), 2571; https://doi.org/10.3390/v14112571 - 20 Nov 2022
Viewed by 1554
Abstract
Epidemiologic data have suggested that etiologic variations of hepatocellular carcinoma (HCC) exist in different geographic areas, and might be associated with different outcomes. We compared the viral etiology, clinicopathological characteristics and surgical outcomes between 706 Taiwanese and 1704 Vietnamese patients with HCC undergoing [...] Read more.
Epidemiologic data have suggested that etiologic variations of hepatocellular carcinoma (HCC) exist in different geographic areas, and might be associated with different outcomes. We compared the viral etiology, clinicopathological characteristics and surgical outcomes between 706 Taiwanese and 1704 Vietnamese patients with HCC undergoing liver resection. Vietnamese patients had a significantly higher ratio of hepatitis B virus (HBV) (p < 0.001) and a lower ratio of hepatitis C virus (HCV) (p < 0.001) and non-B non-C than Taiwanese patients. Among patients with HBV or non-B non-C, the mean age was younger in Vietnam than in Taiwan (p < 0.001, p = 0.001, respectively). The HCC patients in Vietnam had significantly higher serum alpha-fetoprotein (AFP) levels (p < 0.001), larger tumors (p < 0.001), and a higher ratio of macrovascular invasion (p < 0.001) and extrahepatic metastasis (p < 0.001), compared to those in Taiwan. Patients treated in Vietnam had a higher tumor recurrent rate (p < 0.001), but no difference in overall survival was found between both groups. In subgroup analysis, the recurrent rate of HCC was the highest in patients with dual HBV/HCV, followed by HCV or HBV, and non-B non-C (p < 0.001). In conclusion, although the viral etiology and clinicopathological characteristics of HCC differed, postoperative overall survival was comparable between patients in Taiwan and Vietnam. Full article
(This article belongs to the Special Issue Hepatitis-Associated Liver Cancer)
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12 pages, 571 KiB  
Article
Recent Information on Pan-Genotypic Direct-Acting Antiviral Agents for HCV in Chronic Kidney Disease
by Fabrizio Fabrizi, Federica Tripodi, Roberta Cerutti, Luca Nardelli, Carlo M. Alfieri, Maria F. Donato and Giuseppe Castellano
Viruses 2022, 14(11), 2570; https://doi.org/10.3390/v14112570 - 20 Nov 2022
Cited by 2 | Viewed by 1612
Abstract
Background: Hepatitis C virus (HCV) is still common in patients with chronic kidney disease. It has been recently discovered that chronic HCV is a risk factor for increased incidence of CKD in the adult general population. According to a systematic review with a [...] Read more.
Background: Hepatitis C virus (HCV) is still common in patients with chronic kidney disease. It has been recently discovered that chronic HCV is a risk factor for increased incidence of CKD in the adult general population. According to a systematic review with a meta-analysis of clinical studies, pooling results of longitudinal studies (n = 2,299,134 unique patients) demonstrated an association between positive anti-HCV serologic status and increased incidence of CKD; the summary estimate for adjusted HR across the surveys was 1.54 (95% CI, 1.26; 1.87), (p < 0.0001). The introduction of direct-acting antiviral drugs (DAAs) has caused a paradigm shift in the management of HCV infection; recent guidelines recommend pan-genotypic drugs (i.e., drugs effective on all HCV genotypes) as the first-choice therapy for HCV, and these promise to be effective and safe even in the context of chronic kidney disease. Aim: The purpose of this narrative review is to show the most important data on pan-genotypic DAAs in advanced CKD (CKD stage 4/5). Methods: We recruited studies by electronic databases and grey literature. Numerous key-words (‘Hepatitis C’ AND ‘Chronic kidney disease’ AND ‘Pan-genotypic agents’, among others) were adopted. Results: The most important pan-genotypic combinations for HCV in advanced CKD are glecaprevir/pibrentasvir (GLE/PIB) and sofosbuvir/velpatasvir (SOF/VEL). Two clinical trials (EXPEDITION-4 and EXPEDITION-5) and some ‘real-world’ studies (n = 6) reported that GLE/PIB combinations in CKD stage 4/5 gave SVR12 rates ranging between 86 and 99%. We retrieved clinical trials (n = 1) and ‘real life’ studies (n = 6) showing the performance of SOF/VEL; according to our pooled analysis, the summary estimate of SVR rate was 100% in studies adopting SOF/VEL antiviral combinations. The drop-out rate (due to AEs) in patients on SOF/VEL ranged between 0 and 4.8%. Conclusions: Pan-genotypic combinations, such as GLE/PIB and SOF/VEL, appear effective and safe for HCV in advanced CKD, even if a limited number of studies with small sample sizes currently exist on this issue. Studies are under way to assess whether successful antiviral therapy with DAAs will translate into better survival in patients with advanced CKD. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation)
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12 pages, 4169 KiB  
Article
Effects of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Infection on the Surface Glycoprofiling of Porcine Pulmonary Microvascular Endothelial Cells
by Xiaoxiao Song, Yanmei Wu, Xianping Wu, Ge Hu and Tao Zhang
Viruses 2022, 14(11), 2569; https://doi.org/10.3390/v14112569 - 20 Nov 2022
Cited by 4 | Viewed by 1463
Abstract
Previously, our study has demonstrated that porcine pulmonary microvascular endothelial cells (PPMVECs) were susceptible to highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) and produced a significant non-specific immune response to it. The significance of microvascular endothelial glycocalyx is increasingly attracting attention, [...] Read more.
Previously, our study has demonstrated that porcine pulmonary microvascular endothelial cells (PPMVECs) were susceptible to highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) and produced a significant non-specific immune response to it. The significance of microvascular endothelial glycocalyx is increasingly attracting attention, and its rich carbohydrate components are not only important signaling molecules, but also remarkably influence the signaling of most proteins. Comprehending changes in the carbohydrate chains contributes to understanding cell functions. This study aimed to reveal the effects of HP-PRRSV infection on the surface carbohydrate chains of PPMVECs. PPMVECs were isolated and cultured in vitro and infected with HP-PRRSV HN and JXA1 strains. Scanning electron microscopy analysis indicated that at 48 h post-infection, some broken holes were in their cell membranes, and that the surface fibrous glycocalyx was obviously reduced or even disappeared. Lectin microarray analysis indicated that the fluorescence intensities of 8 and 7 lectin sites were significantly changed by the HP-PRRSV HN and JXA1 strains, respectively, among which there were 6 common lectin sites. The up-regulation of common lectins (RCA-I, LEL, and STL) and the down-regulation of common lectins (LCA, DSA, and PHA-E) were confirmed by lectin fluorescence staining and lectin flow cytometry, respectively. Together, the results show that the HP-PRRSV infection can induce the glycocalyx disruption of PPMVECs and their surface glycoprofiling changes, and that the poly-N-acetyllactosamine and complex N-glycan are the main up-regulated and down-regulated carbohydrate chains, respectively. Our findings may provide insights into revealing the pathogenesis of HP-PRRSV from the perspective of glycobiology. Full article
(This article belongs to the Special Issue State-of-the-Art Porcine Virus Research in China)
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7 pages, 730 KiB  
Brief Report
Features of Audio-Vestibular Deficit and 3D-FLAIR Temporal Bone MRI in Patients with Herpes Zoster Oticus
by Jiyeon Lee, Jin Woo Choi and Chang-Hee Kim
Viruses 2022, 14(11), 2568; https://doi.org/10.3390/v14112568 - 20 Nov 2022
Cited by 2 | Viewed by 1348
Abstract
Herpes zoster oticus (HZO) is characterized by otalgia and erythematous vesicles in the auricle or external auditory canal. Ramsay Hunt syndrome (RHS) can be diagnosed when facial nerve palsy is accompanied by these symptoms of HZO, and in this case, audio-vestibular symptoms such [...] Read more.
Herpes zoster oticus (HZO) is characterized by otalgia and erythematous vesicles in the auricle or external auditory canal. Ramsay Hunt syndrome (RHS) can be diagnosed when facial nerve palsy is accompanied by these symptoms of HZO, and in this case, audio-vestibular symptoms such as hearing loss or dizziness often develop. Recently, 3D-fluid-attenuated inversion recovery sequence (3D-FLAIR) magnetic resonance imaging (MRI) has been introduced in order to evaluate the inner ear structure pathology. The purpose of this study was to investigate the audio-vestibular characteristics in correlation with temporal bone MRI findings in HZO patients. From September 2018 to June 2022, 18 patients with HZO participated in the study. Thirteen patients (77%) showed high-signal intensity in the inner ear structures in 4 h post-contrast 3D-FLAIR images. In a bithermal caloric test, the lateral semicircular canal showed high signal intensity in 4 h post-contrast 3D-FLAIR images in 75% of patients with abnormal canal paresis. While the cochlea showed high signal intensity in 4 h post-contrast 3D-FLAIR images in 75% of patients with hearing loss, the vestibulo-cochlear nerve showed enhancement in post-contrast T1-weighted images in only 33% of patients with hearing loss. The present study demonstrates that audio-vestibular deficits are well-correlated with increased signal intensity of the inner ear endorgans in 4 h post contrast 3D-FLAIR MRI. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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10 pages, 1384 KiB  
Article
Longitudinal Dynamics of HPV16 Antibodies in Saliva and Serum among Pregnant Women
by Tiina Pirttilä, Stina Syrjänen, Karolina Louvanto and Vuokko Loimaranta
Viruses 2022, 14(11), 2567; https://doi.org/10.3390/v14112567 - 20 Nov 2022
Cited by 2 | Viewed by 1316
Abstract
Oral infections with high-risk (hr)HPV genotypes are associated with a subset of head and neck squamous cell carcinomas. Oral hrHPV infections may result from having oral sex, but also from horizontal infection from mouth to mouth. In such cases, saliva can serve as [...] Read more.
Oral infections with high-risk (hr)HPV genotypes are associated with a subset of head and neck squamous cell carcinomas. Oral hrHPV infections may result from having oral sex, but also from horizontal infection from mouth to mouth. In such cases, saliva can serve as a vehicle for HPV transmission. Still, the prevalence and dynamics of salivary HPV antibodies in healthy non-vaccinated individuals are poorly known and the role of the salivary antibodies in protection from oral HPV infection is unclear. We used an ELISA assay to evaluate the dynamics and correlation of oral HPV16 infection and HPV16L1 and E7 specific antibody levels in saliva and serum samples among 39 women, 13 of which had persistent oral HPV16 infection. The women were mothers-to-be, sampled before delivery and followed up for 36 months postpartum. HPV16L1 IgG and sIgA antibodies were regularly detected in saliva. Antibody levels in serum remained stable during the 36-month follow-up, while antibody levels in saliva fluctuated. There was considerable individual variation in salivary HPV16L1 antibody levels, and some women had persistent oral HPV16 infection but no salivary antibodies. No differences in salivary HPV16L1 levels were found between the women with persistent or transient oral HPV16 infection. Full article
(This article belongs to the Special Issue HPV in the Head and Neck Region 2.0)
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17 pages, 1391 KiB  
Article
Cell Type Variability in the Incorporation of Lipids in the Dengue Virus Virion
by Atitaya Hitakarun, Maia Kavanagh Williamson, Nathamon Yimpring, Wannapa Sornjai, Nitwara Wikan, Christopher J. Arthur, Julien Pompon, Andrew D. Davidson and Duncan R. Smith
Viruses 2022, 14(11), 2566; https://doi.org/10.3390/v14112566 - 19 Nov 2022
Cited by 4 | Viewed by 1915
Abstract
A lipid bilayer produced from the host membrane makes up around 20% of the weight of the dengue virus (DENV) virion and is crucial for virus entry. Despite its significance, the virion’s lipid composition is still poorly understood. In tandem with lipid profiles [...] Read more.
A lipid bilayer produced from the host membrane makes up around 20% of the weight of the dengue virus (DENV) virion and is crucial for virus entry. Despite its significance, the virion’s lipid composition is still poorly understood. In tandem with lipid profiles of the cells utilised to generate the virions, this work determined a partial lipid profile of DENV virions derived from two cell lines (C6/36 and LLC-MK2). The results showed distinctive profiles between the two cell types. In the mammalian LLC-MK2 cells, 30.8% (73/237 identified lipid species; 31 upregulated, 42 downregulated) of lipid species were altered in response to infection, whilst in insect C6/36 cells only 12.0% (25/208; 19 upregulated, 6 downregulated) of lipid species showed alterations in response to infection. For virions from LLC-MK2 cells, 14 lipids were detected specifically in virions with a further seven lipids being enriched (over mock controls). For virions from C6/36 cells, 43 lipids were detected that were not seen in mock preparations, with a further 16 being specifically enriched (over mock control). These results provide the first lipid description of DENV virions produced in mammalian and mosquito cells, as well as the lipid changes in the corresponding infected cells. Full article
(This article belongs to the Special Issue Omics of Virus-Host Interactions)
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13 pages, 293 KiB  
Conference Report
The Challenges and Opportunities of Next-Generation Rotavirus Vaccines: Summary of an Expert Meeting with Vaccine Developers
by Jessie Chen, Stephanie Grow, Miren Iturriza-Gómara, William P. Hausdorff, Alan Fix and Carl D. Kirkwood
Viruses 2022, 14(11), 2565; https://doi.org/10.3390/v14112565 - 19 Nov 2022
Cited by 4 | Viewed by 2004
Abstract
The 2nd Next Generation Rotavirus Vaccine Developers Meeting, sponsored by PATH and the Bill and Melinda Gates Foundation, was held in London, UK (7–8 June 2022), and attended by vaccine developers and researchers to discuss advancements in the development of next-generation rotavirus vaccines [...] Read more.
The 2nd Next Generation Rotavirus Vaccine Developers Meeting, sponsored by PATH and the Bill and Melinda Gates Foundation, was held in London, UK (7–8 June 2022), and attended by vaccine developers and researchers to discuss advancements in the development of next-generation rotavirus vaccines and to consider issues surrounding vaccine acceptability, introduction, and uptake. Presentations included updates on rotavirus disease burden, the impact of currently licensed oral vaccines, various platforms and approaches for next generation rotavirus vaccines, strategies for combination pediatric vaccines, and the value proposition for novel parenteral rotavirus vaccines. This report summarizes the information shared at the convening and poses various topics worthy of further exploration. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
14 pages, 4947 KiB  
Article
Identification of Three Viruses Infecting Mulberry Varieties
by Lei Chen, Zi-Long Xu, Pei-Gang Liu, Yan Zhu, Tian-Bao Lin, Tian-Yan Li, Zhi-Qiang Lv and Jia Wei
Viruses 2022, 14(11), 2564; https://doi.org/10.3390/v14112564 - 19 Nov 2022
Cited by 1 | Viewed by 1813
Abstract
Viruses-mediated genome editing in plants is a powerful strategy to develop plant cultivars with important and novel agricultural traits. Mulberry alba is an important economic tree species that has been cultivated in China for more than 5000 years. So far, only a few [...] Read more.
Viruses-mediated genome editing in plants is a powerful strategy to develop plant cultivars with important and novel agricultural traits. Mulberry alba is an important economic tree species that has been cultivated in China for more than 5000 years. So far, only a few viruses have been identified from mulberry trees, and their application potential is largely unknown. Therefore, mining more virus resources from the mulberry tree can pave the way for the establishment of useful engineering tools. In this study, eight old mulberry plants were gathered in seven geographic areas for virome analysis. Based on transcriptome analysis, we discovered three viruses associated with mulberries: Citrus leaf blotch virus isolate mulberry alba 2 (CLBV-ML2), Mulberry-associated virga-like virus (MaVLV), and Mulberry-associated narna-like virus (MaNLV). The genome of CLBV-ML2 was completely sequenced and exhibited high homology with Citriviruses, considered to be members of the genus Citrivirus, while the genomes of MaVLV and MaNLV were nearly completed lacking the 5′ and 3′ termini sequences. We tentatively consider MaVLV to be members of the family Virgaviridae and MaNLV to be members of the genus Narnavirus based on the results of phylogenetic trees. The infection experiments showed that CLBV-ML2 could be detected in the inoculated seedlings of both N. benthamiana and Morus alba, while MaVLV could only be detected in N. benthamiana. All of the infected seedlings did not show obvious symptoms. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)
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11 pages, 1995 KiB  
Article
The Impact of Urbanization and Human Mobility on Seasonal Influenza in Northern China
by Jiao Yang, Xudong Guo, Ting Zhang, Qing Wang, Xingxing Zhang, Jin Yang, Shengjie Lai, Luzhao Feng and Weizhong Yang
Viruses 2022, 14(11), 2563; https://doi.org/10.3390/v14112563 - 19 Nov 2022
Cited by 3 | Viewed by 1789
Abstract
The intensity of influenza epidemics varies significantly from year to year among regions with similar climatic conditions and populations. However, the underlying mechanisms of the temporal and spatial variations remain unclear. We investigated the impact of urbanization and public transportation size on influenza [...] Read more.
The intensity of influenza epidemics varies significantly from year to year among regions with similar climatic conditions and populations. However, the underlying mechanisms of the temporal and spatial variations remain unclear. We investigated the impact of urbanization and public transportation size on influenza activity. We used 6-year weekly provincial-level surveillance data of influenza-like disease incidence (ILI) and viral activity in northern China. We derived the transmission potential of influenza for each epidemic season using the susceptible–exposed–infectious–removed–susceptible (SEIRS) model and estimated the transmissibility in the peak period via the instantaneous reproduction number (Rt). Public transport was found to explain approximately 28% of the variance in the seasonal transmission potential. Urbanization and public transportation size explained approximately 10% and 21% of the variance in maximum Rt in the peak period, respectively. For the mean Rt during the peak period, urbanization and public transportation accounted for 9% and 16% of the variance in Rt, respectively. Our results indicated that the differences in the intensity of influenza epidemics among the northern provinces of China were partially driven by urbanization and public transport size. These findings are beneficial for predicting influenza intensity and developing preparedness strategies for the early stages of epidemics. Full article
(This article belongs to the Special Issue State-of-the-Art Influenza Virus Research in China)
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14 pages, 4105 KiB  
Article
New Insights into Avian Infectious Bronchitis Virus in Colombia from Whole-Genome Analysis
by Gloria Ramirez-Nieto, Daiana Mir, Diego Almansa-Villa, Geovanna Cordoba-Argotti, Magda Beltran-Leon, Nelida Rodriguez-Osorio, Jone Garai, Jovanny Zabaleta and Arlen P. Gomez
Viruses 2022, 14(11), 2562; https://doi.org/10.3390/v14112562 - 19 Nov 2022
Cited by 4 | Viewed by 1906
Abstract
Infectious Bronchitis (IB) is a respiratory disease caused by a highly variable Gammacoronavirus, which generates a negative impact on poultry health worldwide. GI-11 and GI-16 lineages have been identified in South America based on Infectious Bronchitis virus (IBV) partial S1 sequences. However, [...] Read more.
Infectious Bronchitis (IB) is a respiratory disease caused by a highly variable Gammacoronavirus, which generates a negative impact on poultry health worldwide. GI-11 and GI-16 lineages have been identified in South America based on Infectious Bronchitis virus (IBV) partial S1 sequences. However, full genome sequence information is limited. In this study we report, for the first time, the whole-genome sequence of IBV from Colombia. Seven IBV isolates obtained during 2012 and 2013 from farms with respiratory disease compatible with IB were selected and the complete genome sequence was obtained by NGS. According to S1 sequence phylogenetic analysis, six isolates belong to lineage GI-1 and one to lineage GVI-1. When whole genome was analyzed, five isolates were related to the vaccine strain Ma5 2016 and two showed mosaic genomes. Results from complete S1 sequence analysis provides further support for the hypothesis that GVI-1, considered a geographically confined lineage in Asia, could have originated in Colombia. Complete genome information reported in this research allow a deeper understanding of the phylogenetic evolution of variants and the recombination events between strains that are circulating worldwide, contributing to the knowledge of coronavirus in Latin America and the world. Full article
(This article belongs to the Collection Coronaviruses)
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26 pages, 4639 KiB  
Article
Isolation and Characterization of a Phapecoctavirus Infecting Multidrug-Resistant Acinetobacter baumannii in A549 Alveolar Epithelial Cells
by Phitchayapak Wintachai, Komwit Surachat, Ganyalak Chaimaha, Abdi Wira Septama and Duncan R. Smith
Viruses 2022, 14(11), 2561; https://doi.org/10.3390/v14112561 - 19 Nov 2022
Cited by 5 | Viewed by 2122
Abstract
Multidrug-resistant Acinetobacter baumannii (MDR A. baumannii) is an emerging pathogen in the ESKAPE group. The global burden of antimicrobial resistance has led to renewed interest in alternative antimicrobial treatment strategies, including phage therapy. This study isolated and characterized a phage vB_AbaM_ ABPW7 [...] Read more.
Multidrug-resistant Acinetobacter baumannii (MDR A. baumannii) is an emerging pathogen in the ESKAPE group. The global burden of antimicrobial resistance has led to renewed interest in alternative antimicrobial treatment strategies, including phage therapy. This study isolated and characterized a phage vB_AbaM_ ABPW7 (vABPW7) specific to MDR A. baumannii. Morphological analysis showed that phage vABPW7 belongs to the Myoviridae family. Genome analysis showed that the phage DNA genome consists of 148,647 bp and that the phage is a member of the Phapecoctavirus genus of the order Caudovirales. A short latent period and a large burst size indicated that phage vABPW7 was a lytic phage that could potentially be used in phage therapy. Phage vABPW7 is a high-stability phage that has high lytic activity. Phage vABPW7 could effectively reduce biofilm formation and remove preformed biofilm. The utility of phage vABPW7 was investigated in a human A549 alveolar epithelial cell culture model. Phage vABPW7 was not cytotoxic to A549 cells, and the phage could significantly reduce planktonic MDR A. baumannii and MDR A. baumannii adhesion on A549 cells without cytotoxicity. This study suggests that phage vABPW7 has the potential to be developed further as a new antimicrobial agent against MDR A. baumannii. Full article
(This article belongs to the Special Issue Viruses versus Bacteria—Novel Approaches to Phage Therapy as a Tool against Multidrug-Resistant Pathogens)
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7 pages, 263 KiB  
Perspective
Molnupiravir: From Hope to Epic Fail?
by Daniele Focosi
Viruses 2022, 14(11), 2560; https://doi.org/10.3390/v14112560 - 19 Nov 2022
Cited by 16 | Viewed by 5708
Abstract
Molnupiravir has been the first oral antiviral authorized for COVID-19 outpatients, reporting extraordinary sales and preserved in vitro efficacy against Omicron sublineages so far. However, it has recently been associated with very poor clinical efficacy, the risk of creating novel SARS-CoV-2 variants of [...] Read more.
Molnupiravir has been the first oral antiviral authorized for COVID-19 outpatients, reporting extraordinary sales and preserved in vitro efficacy against Omicron sublineages so far. However, it has recently been associated with very poor clinical efficacy, the risk of creating novel SARS-CoV-2 variants of concern, and long-term risk for mutagenicity in humans. The latter two are severe concerns, especially in the indicated population, i.e., long-replicating, immunodeficient patients. We conclude that, at this point, alternative antivirals should be preferred over molnupiravir. Full article
(This article belongs to the Special Issue SARS-CoV-2 inside and outside the Respiratory Tract: From Diagnostics to Therapies)
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