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Keywords = superinfection exclusion

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15 pages, 2270 KiB  
Article
Progress in Our Understanding of the Cross-Protection Mechanism of CTV-VT No-SY Isolates Against Homologous SY Isolates
by Grazia Licciardello, Giuseppe Scuderi, Marcella Russo, Marina Bazzano, Giuseppe Paradiso, Moshe Bar-Joseph and Antonino F. Catara
Pathogens 2025, 14(7), 701; https://doi.org/10.3390/pathogens14070701 - 16 Jul 2025
Viewed by 337
Abstract
The Citrus tristeza virus (CTV), a member of the Closterovirus genus, is considered a serious threat to citrus trees grafted onto sour orange (SO) rootstock. In the Mediterranean area, the most prevalent CTV strains are VT and T30. The VT strain includes both [...] Read more.
The Citrus tristeza virus (CTV), a member of the Closterovirus genus, is considered a serious threat to citrus trees grafted onto sour orange (SO) rootstock. In the Mediterranean area, the most prevalent CTV strains are VT and T30. The VT strain includes both mild and severe isolates, some of them associated with seedling yellows (SY) syndrome. Mild CTV-VT isolates that do not induce SY symptoms (no-SY) show minor variations in their Orf1a, p23, and p33 genes, with a single nucleotide polymorphism at position 161 of the p23 gene. These isolates can repress superinfection with homologous severe isolates. The aim of this study was to investigate the mechanism of cross-protection by means of biological indexing, real-time RT-PCR high-resolution melting (HRM), and p23 gene amplicon sequencing. Four no-SY CTV-VT isolates were inoculated onto SO seedlings and Hamlin sweet orange trees grafted on SO. These plants were later challenged with two homologous CTV-VT SY isolates and remained asymptomatic. The biological evaluation of the infection process in superinfected plants was investigated via inoculation of the bark on SO seedlings that were also asymptomatic. A parallel HRM analysis of midvein RNA extracts revealed that the melting temperature (Tm) of the no-SY isolates was statistically lower than that of the SY isolates. The Tm values of RNAs extracts from superinfected plants were not statistically different from those of the no-SY isolates. This suggests that the SY isolates failed to establish infection or replicate in plants pre-inoculated with no-SY isolates. This blockage of replication resembles superinfection exclusion, with attractive perspectives to prevent SY damage in field applications. Full article
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23 pages, 7010 KiB  
Article
Exclusion of Superinfection or Enhancement of Superinfection in Pestiviruses—APPV Infection Is Not Dependent on ADAM17
by Francesco Geranio, Sebastian Affeldt, Angelika Cechini, Sandra Barth, Carina M. Reuscher, Christiane Riedel, Till Rümenapf and Benjamin Lamp
Viruses 2024, 16(12), 1834; https://doi.org/10.3390/v16121834 - 26 Nov 2024
Viewed by 1184
Abstract
Some viruses can suppress superinfections of their host cells by related or different virus species. The phenomenon of superinfection exclusion can be caused by inhibiting virus attachment, receptor binding and entry, by replication interference, or competition for host cell resources. Blocking attachment and [...] Read more.
Some viruses can suppress superinfections of their host cells by related or different virus species. The phenomenon of superinfection exclusion can be caused by inhibiting virus attachment, receptor binding and entry, by replication interference, or competition for host cell resources. Blocking attachment and entry not only prevents unproductive double infections but also stops newly produced virions from re-entering the cell post-exocytosis. In this study, we investigated the exclusion of superinfections between the different pestivirus species. Bovine and porcine cells pre-infected with non-cytopathogenic pestivirus strains were evaluated for susceptibility to subsequent superinfection using comparative titrations. Our findings revealed significant variation in exclusion potency depending on the pre- and superinfecting virus species, as well as the host cell species. Despite this variability, all tested classical pestivirus species reduced host cell susceptibility to subsequent infections, indicating a conserved entry mechanism. Unexpectedly, pre-infection with atypical porcine pestivirus (APPV) increased host cell susceptibility to classical pestiviruses. Further analysis showed that APPV can infect SK-6 cells independently of ADAM17, a critical attachment factor for the classical pestiviruses. These results indicate that APPV uses different binding and entry mechanisms than the other pestiviruses. The observed increase in the susceptibility of cells post-APPV infection warrants further investigation and could have practical implications, such as aiding challenging pestivirus isolation from diagnostic samples. Full article
(This article belongs to the Special Issue Pestivirus 2024)
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13 pages, 4036 KiB  
Communication
Modulation of ADAM17 Levels by Pestiviruses Is Species-Specific
by Hann-Wei Chen, Marianne Zaruba, Aroosa Dawood, Stefan Düsterhöft, Benjamin Lamp, Till Ruemenapf and Christiane Riedel
Viruses 2024, 16(10), 1564; https://doi.org/10.3390/v16101564 - 2 Oct 2024
Cited by 1 | Viewed by 1208
Abstract
Upon host cell infection, viruses modulate their host cells to better suit their needs, including the downregulation of virus entry receptors. ADAM17, a cell surface sheddase, is an essential factor for infection of bovine cells with several pestiviruses. To assess the effect of [...] Read more.
Upon host cell infection, viruses modulate their host cells to better suit their needs, including the downregulation of virus entry receptors. ADAM17, a cell surface sheddase, is an essential factor for infection of bovine cells with several pestiviruses. To assess the effect of pestivirus infection on ADAM17, the amounts of cellular ADAM17 and its presence at the cell surface were determined. Mature ADAM17 levels were reduced upon infection with a cytopathic pestivirus bovis (bovine viral diarrhea virus, cpBVDV), pestivirus suis (classical swine fever virus, CSFV) or pestivirus giraffae (strain giraffe), but not negatively affected by pestivirus L (Linda virus, LindaV). A comparable reduction of ADAM17 surface levels, which represents the bioactive form, could be observed in the presence of E2 of BVDV and CSFV, but not LindaV or atypical porcine pestivirus (pestivirus scrofae) E2. Superinfection exclusion in BVDV infection is caused by at least two proteins, glycoprotein E2 and protease/helicase NS3. To evaluate whether the lowered ADAM17 levels could be involved in superinfection exclusion, persistently CSFV- or LindaV-infected cells were challenged with different pestiviruses. Persistently LindaV-infected cells were significantly more susceptible to cpBVDV infection than persistently CSFV-infected cells, whilst the other pestiviruses tested were not or only hardly able to infect the persistently infected cells. These results provide evidence of a pestivirus species-specific effect on ADAM17 levels and hints at the possibility of its involvement in superinfection exclusion. Full article
(This article belongs to the Special Issue Pestivirus 2024)
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17 pages, 1660 KiB  
Review
Unleashing Nature’s Allies: Comparing the Vertical Transmission Dynamics of Insect-Specific and Vertebrate-Infecting Flaviviruses in Mosquitoes
by Alyssa J. Peterson, Roy A. Hall, Jessica J. Harrison, Jody Hobson-Peters and Leon E. Hugo
Viruses 2024, 16(9), 1499; https://doi.org/10.3390/v16091499 - 23 Sep 2024
Cited by 3 | Viewed by 3897
Abstract
Insect-specific viruses (ISVs) include viruses that are restricted to the infection of mosquitoes and are spread mostly through transovarial transmission. Despite using a distinct mode of transmission, ISVs are often phylogenetically related to arthropod-borne viruses (arboviruses) that are responsible for human diseases and [...] Read more.
Insect-specific viruses (ISVs) include viruses that are restricted to the infection of mosquitoes and are spread mostly through transovarial transmission. Despite using a distinct mode of transmission, ISVs are often phylogenetically related to arthropod-borne viruses (arboviruses) that are responsible for human diseases and able to infect both mosquitoes and vertebrates. ISVs can also induce a phenomenon called “superinfection exclusion”, whereby a primary ISV infection in an insect inhibits subsequent viral infections of the insect. This has sparked interest in the use of ISVs for the control of pathogenic arboviruses transmitted by mosquitoes. In particular, insect-specific flaviviruses (ISFs) have been shown to inhibit infection of vertebrate-infecting flaviviruses (VIFs) both in vitro and in vivo. This has shown potential as a new and ecologically friendly biological approach to the control of arboviral disease. For this intervention to have lasting impacts for biological control, it is imperative that ISFs are maintained in mosquito populations with high rates of vertical transmission. Therefore, these strategies will need to optimise vertical transmission of ISFs in order to establish persistently infected mosquito lines for sustainable arbovirus control. This review compares recent observations of vertical transmission of arboviral and insect-specific flaviviruses and potential determinants of transovarial transmission rates to understand how the vertical transmission of ISFs may be optimised for effective arboviral control. Full article
(This article belongs to the Special Issue Insect-Specific Viruses 2.0)
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16 pages, 2557 KiB  
Review
Phage against the Machine: The SIE-ence of Superinfection Exclusion
by Michael J. Bucher and Daniel M. Czyż
Viruses 2024, 16(9), 1348; https://doi.org/10.3390/v16091348 - 23 Aug 2024
Cited by 6 | Viewed by 3840
Abstract
Prophages can alter their bacterial hosts to prevent other phages from infecting the same cell, a mechanism known as superinfection exclusion (SIE). Such alterations are facilitated by phage interactions with critical bacterial components involved in motility, adhesion, biofilm production, conjugation, antimicrobial resistance, and [...] Read more.
Prophages can alter their bacterial hosts to prevent other phages from infecting the same cell, a mechanism known as superinfection exclusion (SIE). Such alterations are facilitated by phage interactions with critical bacterial components involved in motility, adhesion, biofilm production, conjugation, antimicrobial resistance, and immune evasion. Therefore, the impact of SIE extends beyond the immediate defense against superinfection, influencing the overall fitness and virulence of the bacteria. Evaluating the interactions between phages and their bacterial targets is critical for leading phage therapy candidates like Pseudomonas aeruginosa, a Gram-negative bacterium responsible for persistent and antibiotic-resistant opportunistic infections. However, comprehensive literature on the mechanisms underlying SIE remains scarce. Here, we provide a compilation of well-characterized and potential mechanisms employed by Pseudomonas phages to establish SIE. We hypothesize that the fitness costs imposed by SIE affect bacterial virulence, highlighting the potential role of this mechanism in the management of bacterial infections. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms 2.0)
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11 pages, 805 KiB  
Perspective
Update on Effects of the Prophylactic HPV Vaccines on HPV Type Prevalence and Cervical Pathology
by Ian N. Hampson and Anthony W. Oliver
Viruses 2024, 16(8), 1245; https://doi.org/10.3390/v16081245 - 2 Aug 2024
Cited by 5 | Viewed by 3615
Abstract
Most national prophylactic HPV vaccination programs started in approximately 2008, with either the bivalent Cervarix HPV16/18 or quadrivalent Gardasil (HPV6/11/16/18) vaccines, which were then followed by introduction of the nonavalent Gardasil 9 (HPV6/11/16/18/ 31/33/45/52/58) vaccine from 2015. Since that time, these products have [...] Read more.
Most national prophylactic HPV vaccination programs started in approximately 2008, with either the bivalent Cervarix HPV16/18 or quadrivalent Gardasil (HPV6/11/16/18) vaccines, which were then followed by introduction of the nonavalent Gardasil 9 (HPV6/11/16/18/ 31/33/45/52/58) vaccine from 2015. Since that time, these products have demonstrated their ability to prevent infection with vaccine-covered HPV types and subsequent development of HPV-related cervical and genital pathologies. The data indicate that vaccination of young girls prior to sexual debut is more effective than vaccination of older HPV+ve women. Although some studies have shown a decline in the prevalence of vaccine-covered HPV types, there are national and regional differences in overall vaccine efficacy. Furthermore, several recently published studies show an increase in the prevalence of non-vaccine-covered HPV types in vaccinated populations, which is indicative of HPV type-replacement. It is also notable that vaccine-related changes in HPV type prevalence spread between vaccinated and unvaccinated women at the same geographical location—presumably via sexual transmission. In conclusion, it is not yet clear what effect dissemination of vaccine-associated changes in HPV type prevalence will have on vaccine efficacy and cervical pathology, particularly in mixed populations of vaccinated and unvaccinated women. However, it is very clear these observations do underscore the need for long-term continuation of cervical screening combined with regular reassessment of testing practices. Full article
(This article belongs to the Special Issue Human and Animal Papillomavirus: Infections, Genetics, and Vaccines)
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17 pages, 3305 KiB  
Article
Antagonism and Synergism Characterize the Interactions between Four North American Potato Virus Y Strains
by Prakash M. Niraula, Patricia Baldrich, Junaid A. Cheema, Hashir A. Cheema, Dejah S. Gaiter, Blake C. Meyers and Vincent N. Fondong
Int. J. Plant Biol. 2024, 15(2), 412-428; https://doi.org/10.3390/ijpb15020032 - 21 May 2024
Cited by 1 | Viewed by 1406
Abstract
Potato virus Y (PVY) is one of the most important constraints to potato production worldwide. There is an increasing occurrence of recombinant PVY strains PVYNTN and PVYN-Wi and a decline in the incidence of the nonrecombinant PVYO. We hypothesized [...] Read more.
Potato virus Y (PVY) is one of the most important constraints to potato production worldwide. There is an increasing occurrence of recombinant PVY strains PVYNTN and PVYN-Wi and a decline in the incidence of the nonrecombinant PVYO. We hypothesized that this may be due to the ability of these recombinant strains to antagonize and/or outcompete PVYO in mixed infections. To determine this, we investigated interactions between PVYO and three recombinant PVY strains common in North America: PVYNTN, PVYN-Wi, and PVYN:O. Overall, our study showed that these interactions are tissue-dependent. Specifically, PVYNTN, the main causal agent of potato tuber necrotic ringspot disease (PTNRD), was found to be more adaptable than PVYO, especially in potato leaves due, at least in part, to the Ny gene that confers hypersensitive resistance (HR) to PVYO. Furthermore, PVYN-Wi was found to repress PVYO in potato tubers but act synergistically in potato leaves. The PVYO-induced foliage necrosis in cultivar ‘Ranger Russet’ was observed to be more severe in plants co-infected by PVYN-Wi and PVYN:O, respectively, resulting in plant death. Strikingly, this PVYO -induced necrosis was suppressed by PVYNTN in doubly infected plants. These interactions may, at least partially, explain the decreasing incidence of PVYO in United States potato production regions, especially given that many cultivars contain the Ny gene, which likely limits PVYO enabling PVYNTN and PVYN-Wi to outcompete. We also found that replication and cell-to-cell movement of these PVY strains in tubers at 4 °C was similar to levels at ambient temperature. Full article
(This article belongs to the Topic Microbe-Induced Abiotic Stress Alleviation in Plants)
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16 pages, 3321 KiB  
Article
Partial Alleviation of Homologous Superinfection Exclusion of SeMNPV Latently Infected Cells by G1 Phase Infection and G2/M Phase Arrest
by Qi-Ming Fu, Zheng Fang, Lou Ren, Qing-Shan Wu, Jun-Bo Zhang, Qiu-Ping Liu, Lei-Tao Tan and Qing-Bei Weng
Viruses 2024, 16(5), 736; https://doi.org/10.3390/v16050736 - 6 May 2024
Cited by 3 | Viewed by 1465
Abstract
Viral infection can regulate the cell cycle, thereby promoting viral replication. Hijacking and altering the cell cycle are important for the virus to establish and maintain a latent infection. Previously, Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV)-latently infected P8-Se301-C1 cells, which grew more slowly than [...] Read more.
Viral infection can regulate the cell cycle, thereby promoting viral replication. Hijacking and altering the cell cycle are important for the virus to establish and maintain a latent infection. Previously, Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV)-latently infected P8-Se301-C1 cells, which grew more slowly than Se301 cells and interfered with homologous SeMNNPV superinfection, were established. However, the effects of latent and superinfection with baculoviruses on cell cycle progression remain unknown. In this study, the cell cycle profiles of P8-Se301-C1 cells and SeMNPV or Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-infected P8-Se301-C1 cells were characterized by flow cytometry. The results showed that replication-related genes MCM4, PCNA, and BAF were down-regulated (p < 0.05) in P8-Se301-C1 cells, and the S phase of P8-Se301-C1 cells was longer than that of Se301 cells. P8-Se301-C1 cells infected with SeMNPV did not arrest in the G2/M phase or affect the expression of Cyclin B and cyclin-dependent kinase 1 (CDK1). Furthermore, when P8-Se301-C1 cells were infected with SeMNPV after synchronized treatment with hydroxyurea and nocodazole, light microscopy and qRT-PCR analysis showed that, compared with unsynchronized cells and S and G2/M phase cells, SeMNPV-infected P8-Se301-C1 cells in G1 phase induced G2/M phase arrest, and the amount of virus adsorption and intracellular viral DNA replication were significantly increased (p < 0.05). In addition, budded virus (BV) production and occlusion body (OB)-containing cells were both increased at 120 h post-infection (p < 0.05). The expression of Cyclin B and CDK1 was significantly down-regulated at 48 h post-infection (p < 0.05). Finally, the arrest of SeMNPV-infected G1 phase cells in the G2/M phase increased BV production (p < 0.05) and the number of OB-containing cells. In conclusion, G1 phase infection and G2/M arrest are favorable to SeMNPV proliferation in P8-Se301-C1 cells, thereby alleviating the homologous superinfection exclusion. The results contribute to a better understanding of the relationship between baculoviruses and insect cell cycle progression and regulation. Full article
(This article belongs to the Special Issue Molecular Virus-Insect Interactions)
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16 pages, 2534 KiB  
Article
Minor Variants of Orf1a, p33, and p23 Genes of VT Strain Citrus Tristeza Virus Isolates Show Symptomless Reactions on Sour Orange and Prevent Superinfection of Severe VT Isolates
by Grazia Licciardello, Giuseppe Scuderi, Marcella Russo, Marina Bazzano, Moshe Bar-Joseph and Antonino F. Catara
Viruses 2023, 15(10), 2037; https://doi.org/10.3390/v15102037 - 30 Sep 2023
Cited by 5 | Viewed by 2369
Abstract
The control of tristeza quick decline (QD) of citrus is based on the use of rootstocks that are tolerant or resistant to the Citrus tristeza virus (CTV), but some of them show bio-agronomic limits. The application of cross-protection (CP) has been insufficiently explored. [...] Read more.
The control of tristeza quick decline (QD) of citrus is based on the use of rootstocks that are tolerant or resistant to the Citrus tristeza virus (CTV), but some of them show bio-agronomic limits. The application of cross-protection (CP) has been insufficiently explored. The present study examined the possibility of QD control by cross-protection (CP) following reports showing the dependence of the CP strategy on the close genetic relationships between the protective and challenging CTV isolates. Taking advantage of deep sequencing technologies, we located six naturally infected trees harboring no-seedling yellow (no-SY) and no QD decline (mild) VT isolates and used these for challenge inoculation with three QD VT isolates. Symptom monitoring showed that all six Sicilian mild no-SY isolates, based on their genomic relatedness and mild symptoms reactions, provide effective protection against the three severe local VT isolates. The differences between the six mild and three severe isolates were confined to just a few nucleotide variations conserved in eight positions of three CTV genes (p23, p33, and Orf1a). These results confirm that the superinfection exclusion (SIE mechanism) depends on close genetic relatedness between the protective and challenging severe VT strain isolates. Ten years of investigation suggest that CP could turn into an efficient strategy to contain CTV QD infections of sweet orange trees on SO rootstock. Full article
(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)
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17 pages, 3650 KiB  
Article
In Situ Hybridization (RNAscope) Detection of Bluetongue Virus Serotypes 10 and 17 in Experimentally Co-Infected Culicoides sonorensis
by Molly Carpenter, AnaMario Benavides Obon, Jennifer Kopanke, Justin Lee, Kirsten Reed, Tyler Sherman, Case Rodgers, Mark Stenglein, Emily McDermott and Christie Mayo
Pathogens 2023, 12(10), 1207; https://doi.org/10.3390/pathogens12101207 - 30 Sep 2023
Viewed by 2434
Abstract
Bluetongue virus (BTV) is a segmented, double-stranded RNA virus transmitted by Culicoides biting midges. Infection of domestic and wild ruminants with BTV can result in a devastating disease and significant economic losses. As a virus with a segmented genome, reassortment among the BTV [...] Read more.
Bluetongue virus (BTV) is a segmented, double-stranded RNA virus transmitted by Culicoides biting midges. Infection of domestic and wild ruminants with BTV can result in a devastating disease and significant economic losses. As a virus with a segmented genome, reassortment among the BTV serotypes that have co-infected a host may increase genetic diversity, which can alter BTV transmission dynamics and generate epizootic events. The objective of this study was to determine the extent of dissemination and characterize the tropism of BTV serotypes 10 and 17 in co-infected Culicoides sonorensis. Midges were exposed to both BTV serotypes via blood meal and processed for histologic slides 10 days after infection. An in situ hybridization approach was employed using the RNAscope platform to detect the nucleic acid segment 2 of both serotypes. Observations of the mosaic patterns in which serotypes did not often overlap suggest that co-infection at the cellular level may not be abundant with these two serotypes in C. sonorensis. This could be a consequence of superinfection exclusion. Understanding BTV co-infection and its biological consequences will add an important dimension to the modeling of viral evolution and emergence. Full article
(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)
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15 pages, 3164 KiB  
Article
P3 and NIa-Pro of Turnip Mosaic Virus Are Independent Elicitors of Superinfection Exclusion
by Haritha Nunna, Feng Qu and Satyanarayana Tatineni
Viruses 2023, 15(7), 1459; https://doi.org/10.3390/v15071459 - 28 Jun 2023
Cited by 6 | Viewed by 2920
Abstract
Superinfection exclusion (SIE) is an antagonistic interaction between identical or closely related viruses in host cells. Previous studies by us and others led to the hypothesis that SIE was elicited by one or more proteins encoded in the genomes of primary viruses. Here, [...] Read more.
Superinfection exclusion (SIE) is an antagonistic interaction between identical or closely related viruses in host cells. Previous studies by us and others led to the hypothesis that SIE was elicited by one or more proteins encoded in the genomes of primary viruses. Here, we tested this hypothesis using Turnip mosaic virus (TuMV), a member of the genus Potyvirus of the family Potyviridae, with significant economic consequences. To this end, individual TuMV-encoded proteins were transiently expressed in the cells of Nicotiana benthamiana leaves, followed by challenging them with a modified TuMV expressing the green fluorescent protein (TuMV-GFP). Three days after TuMV-GFP delivery, these cells were examined for the replication-dependent expression of GFP. Cells expressing TuMV P1, HC-Pro, 6K1, CI, 6K2, NIa-VPg, NIb, or CP proteins permitted an efficient expression of GFP, suggesting that these proteins failed to block the replication of a superinfecting TuMV-GFP. By contrast, N. benthamiana cells expressing TuMV P3 or NIa-Pro did not express visible GFP fluorescence, suggesting that both of them could elicit potent SIE against TuMV-GFP. The SIE elicitor activity of P3 and NIa-Pro was further confirmed by their heterologous expression from a different potyvirus, potato virus A (PVA). Plants systemically infected with PVA variants expressing TuMV P3 or NIa-Pro blocked subsequent infection by TuMV-GFP. A +1-frameshift mutation in P3 and NIa-Pro cistrons facilitated superinfection by TuMV-GFP, suggesting that the P3 and NIa-Pro proteins, but not the RNA, are involved in SIE activity. Additionally, deletion mutagenesis identified P3 amino acids 3 to 200 of 352 and NIa-Pro amino acids 3 to 40 and 181 to 242 of 242 as essential for SIE elicitation. Collectively, our study demonstrates that TuMV encodes two spatially separated proteins that act independently to exert SIE on superinfecting TuMV. These results lay the foundation for further mechanistic interrogations of SIE in this virus. Full article
(This article belongs to the Special Issue Crop Resistance to Viral Infections)
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14 pages, 496 KiB  
Systematic Review
Fungal–Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review
by Farkad Bantun
J. Fungi 2023, 9(6), 598; https://doi.org/10.3390/jof9060598 - 23 May 2023
Cited by 8 | Viewed by 3079
Abstract
This study systematically reviewed fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All [...] Read more.
This study systematically reviewed fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All articles that exclusively reported the presence of fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients were included. Seven databases produced 6937 articles as a result of the literature search. Twenty-four articles met the inclusion criteria and were included in the final analysis. The total number of samples across the studies was 10,834, with a total of 1243 (11.5%) patients admitted to the intensive care unit (ICU). Of these patients, 535 underwent mechanical ventilation (4.9%), 2386 (22.0%) were male, and 597 (5.5%) died. Furthermore, hospitalized COVID-19 patients have a somewhat high rate (23.5%) of fungal–bacterial co-infections and super-infections. Moreover, for SARS-CoV-2 patients who have a chest X-ray that suggests a bacterial infection, who require immediate ICU admission, or who have a seriously immunocompromised condition, empiric antibiotic therapy should be taken into consideration. Additionally, the prevalence of co-infections and super-infections among hospitalized COVID-19 patients may have an impact on diagnosis and treatment. It is crucial to check for fungal and bacterial co-infections and super-infections in COVID-19 patients. Full article
(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)
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24 pages, 9062 KiB  
Review
Unveil the Secret of the Bacteria and Phage Arms Race
by Yuer Wang, Huahao Fan and Yigang Tong
Int. J. Mol. Sci. 2023, 24(5), 4363; https://doi.org/10.3390/ijms24054363 - 22 Feb 2023
Cited by 24 | Viewed by 8459
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage’s nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and [...] Read more.
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage’s nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage’s resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages. Full article
(This article belongs to the Special Issue Bacteriophage Biology: From Genomics to Therapy)
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12 pages, 665 KiB  
Article
Effect of Dexamethasone on the Incidence and Outcome of COVID-19 Associated Pulmonary Aspergillosis (CAPA) in Critically Ill Patients during First- and Second Pandemic Wave—A Single Center Experience
by Simon Dubler, Ömer Can Turan, Karsten Daniel Schmidt, Peter-michael rath, Hedda-Luise Verhasselt, Sandra Maier, Annabell Skarabis, Thorsten Brenner and Frank Herbstreit
Diagnostics 2022, 12(12), 3049; https://doi.org/10.3390/diagnostics12123049 - 5 Dec 2022
Cited by 2 | Viewed by 2320
Abstract
Superinfections with Aspergillus spp. in patients with Coronavirus disease 2019 (CAPA: COVID-19-associated pulmonary aspergillosis) are increasing. Dexamethasone has shown beneficial effects in critically ill COVID-19 patients. Whether dexamethasone increases the risk of CAPA has not been studied exclusively. Moreover, this retrospective study aimed [...] Read more.
Superinfections with Aspergillus spp. in patients with Coronavirus disease 2019 (CAPA: COVID-19-associated pulmonary aspergillosis) are increasing. Dexamethasone has shown beneficial effects in critically ill COVID-19 patients. Whether dexamethasone increases the risk of CAPA has not been studied exclusively. Moreover, this retrospective study aimed to identify risk factors for a worse outcome in critically ill COVID-19 patients. Data from 231 critically ill COVID-19 patients with or without dexamethasone treatment from March 2020 and March 2021 were retrospectively analysed. Only 4/169 (6.5%) in the DEXA-group and 13/62 (7.7%) in the Non-DEXA group were diagnosed with probable CAPA (p = 0.749). Accordingly, dexamethasone was not identified as a risk factor for CAPA. Moreover, CAPA was not identified as an independent risk factor for death in multivariable analysis (p = 0.361). In contrast, elevated disease severity (as assessed by Sequential Organ Failure Assessment [SOFA]-score) and the need for organ support (kidney replacement therapy and extracorporeal membrane oxygenation [ECMO]) were significantly associated with a worse outcome. Therefore, COVID-19 treatment with dexamethasone did not increase the risk for CAPA. Moreover, adequately treated CAPA did not represent an independent risk factor for mortality. Accordingly, CAPA might reflect patients’ severe disease state instead of directly influencing outcome. Full article
(This article belongs to the Special Issue Diagnosis of Invasive Aspergillosis on ICU)
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16 pages, 6509 KiB  
Article
The Characterization of the Tobacco-Derived Wild Tomato Mosaic Virus by Employing Its Infectious DNA Clone
by Jinlong Yin, Xin Hong, Sha Luo, Jingquan Tan, Yuanming Zhang, Yanglin Qiu, Muhammad Faizan Latif, Tao Gao, Haijia Yu, Jingke Bai, Shujun Li and Kai Xu
Biology 2022, 11(10), 1467; https://doi.org/10.3390/biology11101467 - 6 Oct 2022
Cited by 6 | Viewed by 2998
Abstract
Viral diseases of cultivated crops are often caused by virus spillover from wild plants. Tobacco (N. tabacum) is an important economic crop grown globally. The viral pathogens of tobacco are traditional major subjects in virology studies and key considerations in [...] Read more.
Viral diseases of cultivated crops are often caused by virus spillover from wild plants. Tobacco (N. tabacum) is an important economic crop grown globally. The viral pathogens of tobacco are traditional major subjects in virology studies and key considerations in tobacco breeding practices. A positive-strand RNA virus, wild tomato mosaic virus (WTMV), belonging to the genus potyvirus in the family potyviridae was recently found to infect tobacco in China. In this study, diseased tobacco leaf samples were collected in the Henan Province of China during 2020–2021. Several samples from different locations were identified as WTMV positive. An infectious DNA clone was constructed based on one of the WTMV isolates. By using this clone, we found that WTMV from tobacco could establish infections on natural reservoir hosts, demonstrating a possible route of WTMV spillover and overwintering in the tobacco field. Furthermore, the WTMV infection was found to be accompanied by other tobacco viruses in the field. The co-inoculation experiments indicate the superinfection exclusion (SIE) between WTMV and other potyvirus species that infect tobacco. Overall, our work reveals novel aspects of WTMV evolution and infection in tobacco and provides an important tool for further studies of WTMV. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Plant Pathology)
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