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García-Vicente EJ, Rey-Casero I, Martín M, Pérez A, Benito-Murcia M, Risco D. Oral supplementation with postbiotics modulates the immune response produced by myxomatosis vaccination in wild rabbits. Vaccine 2024:S0264-410X(24)00585-1. [PMID: 38760270 DOI: 10.1016/j.vaccine.2024.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Rabbits (Oryctolagus cuniculus) are vitally important species in the Iberian Peninsula ecosystem. However, since 1950, there has been a significant population decline, with major repercussions. This situation is mainly due to the presence of infectious diseases, such as myxomatosis, which is expanding and is characterized by severe and fatal clinical manifestations. Current control measures, mainly those based on vaccinations, are ineffective. Therefore, new strategies need to be developed and implemented. This study aimed to evaluate whether supplementation with postbiotic products modulates the immune response in wild rabbits vaccinated against myxomatosis. For this purpose, two groups of rabbits were established: a control group fed with standard feed ad libitum from weaning (28 days) until two months of age, and a treated group, which was fed under the same conditions but supplemented with postbiotics (3 kg/Tm). All the studied rabbits were vaccinated against this disease during weaning. In addition, a blood samples were obtained from all animals immediately before vaccination and 30 days later, which allowed us to evaluate the level of antibodies against myxomatosis virus (ELISA detection) and the relative expression of gene encoding to cytokines related to the immune response (IL6, TNFα and IFNγ), at both times of the experience. Weight and length measurements were also taken at both times to calculate body index and mean daily gain (MDG). No statistically significant differences in growth parameters were observed. There were also no differences in the serological response among groups. However, a relative underexpression of gene codifying to TNFα (p-value = 0.03683) and a higher expression on IFNγ (p-value = 0.045) were observed in the treated group. This modulation in cytokines could lead to less severe lesions in wild rabbit naturally infected with myxomatosis virus.
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Affiliation(s)
- E J García-Vicente
- Department of Animal Medicine, Facultad de Veterinaria, Universidad de Extremadura, Av. de la Universidad s/n, 10003 Cáceres, Spain; Neobeitar S.L., Av. Alemania 6, 1° B, 10001, Cáceres, Spain.
| | - I Rey-Casero
- Neobeitar S.L., Av. Alemania 6, 1° B, 10001, Cáceres, Spain
| | - M Martín
- Neobeitar S.L., Av. Alemania 6, 1° B, 10001, Cáceres, Spain
| | - A Pérez
- Neobeitar S.L., Av. Alemania 6, 1° B, 10001, Cáceres, Spain
| | - M Benito-Murcia
- Neobeitar S.L., Av. Alemania 6, 1° B, 10001, Cáceres, Spain.
| | - D Risco
- Department of Animal Medicine, Facultad de Veterinaria, Universidad de Extremadura, Av. de la Universidad s/n, 10003 Cáceres, Spain.
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Haller SL, Park C, Bruneau RC, Megawati D, Zhang C, Vipat S, Peng C, Senkevich TG, Brennan G, Tazi L, Rothenburg S. Molecular basis for the host range function of the poxvirus PKR inhibitor E3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594589. [PMID: 38798513 PMCID: PMC11118487 DOI: 10.1101/2024.05.16.594589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The antiviral protein kinase R (PKR) is activated by viral double-stranded RNA and phosphorylates translation initiation factor eIF2α, thereby inhibiting translation and virus replication. Most poxviruses contain two PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), which are determinants of viral host range. The prevailing model for E3 function is that it inhibits PKR through the non-specific sequestration of double-stranded (ds) RNA. Our data revealed that Syrian hamster PKR was resistant to E3, which is at odds with the sequestration model. However, Syrian hamster PKR was still sensitive to K3 inhibition. In contrast, Armenian hamster PKR showed opposite sensitivities, being sensitive to E3 and resistant to K3 inhibition. Mutational analyses of hamster PKRs showed that sensitivity to E3 inhibition was largely determined by the region linking the dsRNA-binding domains and the kinase domain of PKR, whereas two amino acid residues in the kinase domain (helix αG) determined sensitivity to K3. Expression of PKRs in congenic cells showed that Syrian hamster PKR containing the two Armenian hamster PKR residues in helix-αG was resistant to wild type VACV infection, and that cells expressing either hamster PKR recapitulated the phenotypes observed in species-derived cell lines. The observed resistance of Syrian hamster PKR to E3 explains its host range function and challenges the paradigm that dsRNA-binding PKR inhibitors mainly act by the sequestration of dsRNA. Significance The molecular mechanisms that govern the host range of viruses are incompletely understood. A small number of poxvirus genes have been identified that influence the host range of poxviruses. We show that the host range functions of E3 and K3, two host range factors from vaccinia virus, are a result of species-specific interactions with the antiviral protein kinase R (PKR) and that PKR from closely related species displayed dramatic differences in their sensitivities to these viral inhibitors. While there is a substantial body of work demonstrating host-specific interactions with K3, the current model for E3-mediated PKR inhibition is that E3 non-specifically sequesters dsRNA to prevent PKR activation. This model does not predict species-specific sensitivity to E3; therefore, our data suggest that the current model is incomplete, and that dsRNA sequestration is not the primary mechanism for E3 activity.
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Yang CH, Song AL, Qiu Y, Ge XY. Cross-species transmission and host range genes in poxviruses. Virol Sin 2024; 39:177-193. [PMID: 38272237 PMCID: PMC11074647 DOI: 10.1016/j.virs.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The persistent epidemic of human mpox, caused by mpox virus (MPXV), raises concerns about the future spread of MPXV and other poxviruses. MPXV is a typical zoonotic virus which can infect human and cause smallpox-like symptoms. MPXV belongs to the Poxviridae family, which has a relatively broad host range from arthropods to vertebrates. Cross-species transmission of poxviruses among different hosts has been frequently reported and resulted in numerous epidemics. Poxviruses have a complex linear double-strand DNA genome that encodes hundreds of proteins. Genes related to the host range of poxvirus are called host range genes (HRGs). This review briefly introduces the taxonomy, phylogeny and hosts of poxviruses, and then comprehensively summarizes the current knowledge about the cross-species transmission of poxviruses. In particular, the HRGs of poxvirus are described and their impacts on viral host range are discussed in depth. We hope that this review will provide a comprehensive perspective about the current progress of researches on cross-species transmission and HRG variation of poxviruses, serving as a valuable reference for academic studies and disease control in the future.
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Affiliation(s)
- Chen-Hui Yang
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410012, China
| | - A-Ling Song
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410012, China
| | - Ye Qiu
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410012, China.
| | - Xing-Yi Ge
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410012, China.
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Niu X, Han J, Huang M, Wang G, Zhang Y, Zhang W, Yu H, Xu M, Li K, Gao L, Wang S, Chen Y, Cui H, Zhang Y, Liu C, Wang X, Gao Y, Qi X. Infectious bursal disease virus VP5 triggers host shutoff in a transcription-dependent manner. mBio 2024; 15:e0343323. [PMID: 38289089 PMCID: PMC10936426 DOI: 10.1128/mbio.03433-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 03/14/2024] Open
Abstract
Viruses have evolved intricate mechanisms to evade host antiviral responses and exploit cellular resources by manipulating the expression profile of host genes. During infection, viruses encode proteins with shutoff activity to globally inhibit host protein synthesis, which is an effective strategy for immune evasion. In this study, compelling evidence shows that infectious bursal disease virus (IBDV) infection triggers the suppression of host protein synthesis. Furthermore, using both in vitro and in vivo viral infection models, we have identified that IBDV specifically impedes the transcription of host genes via the shutoff activity of viral VP5, simultaneously conferring advantages to IBDV infection in these circumstances. The proposed mechanism suggests that VP5 competitively binds to RanBP1, disrupting the RanGDP/GTP gradient. This disruption interferes with cellular nucleocytoplasmic transport, impairing the nuclear import of proteins bearing nuclear localization signals. The nuclear transport of pivotal transcriptional regulatory factors, such as p65 and IFN regulatory factor 7, is also compromised, leading to the inhibition of pro-inflammatory cytokines and interferon expression. This newly discovered strategy employed by IBDV enables them to manipulate host gene expression, providing novel insights into how viruses evade host immune responses and establish infections.IMPORTANCEViruses manipulate host processes at various levels to regulate or evade both innate and adaptive immune responses, promoting self-survival and efficient transmission. The "host shutoff," a global suppression of host gene expression mediated by various viruses, is considered a critical mechanism for evading immunity. In this study, we have validated the presence of host shutoff during infectious bursal disease virus (IBDV) infection and additionally uncovered that the viral protein VP5 plays a pivotal role in inhibiting the overall synthesis of host proteins, including cytokines, through a transcription-dependent pathway. VP5 competitively binds with RanBP1, leading to disruption of the Ran protein cycle and consequently interfering with nucleocytoplasmic transport, which ultimately results in the suppression of host gene transcription. These findings unveil a novel strategy employed by IBDV to evade host innate immunity and rapidly establish infection. This study also suggests a novel supplement to understanding the pathway through which viruses inhibit host protein synthesis.
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Affiliation(s)
- Xinxin Niu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinze Han
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mengmeng Huang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guodong Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yulong Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenying Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hangbo Yu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mengmeng Xu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Kai Li
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Li Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Suyan Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Yuntong Chen
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Hongyu Cui
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Yanping Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Changjun Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaomei Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Yulong Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaole Qi
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- World Organization for Animal Health (WOAH) Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
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Rossini E, Bazzucchi M, Trocchi V, Merzoni F, Bertasio C, Knauf S, Lavazza A, Cavadini P. Identification and Characterisation of a Myxoma Virus Detected in the Italian Hare ( Lepus corsicanus). Viruses 2024; 16:437. [PMID: 38543802 PMCID: PMC10975712 DOI: 10.3390/v16030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 05/23/2024] Open
Abstract
Myxoma virus (MYXV) is a Leporipoxvirus (genus) belonging to the family Poxviridae; it is characterised by a genome of approximately 161 kb dsDNA encoding for several proteins that play an essential role in both host spectrum determination and immunomodulation. The healthy reservoir of the virus is Sylvilagus spp. At the same time, in wild and domestic European rabbits (Oryctolagus cuniculus), MYXV is the etiologic agent of myxomatosis, a disease with an extremely high mortality rate. In 2014, an interspecies jump of MYXV was reported in Lepus europaeus in the UK. In 2018, myxomatosis induced by a new recombinant strain called MYXV-To was identified during a large outbreak in Iberian hares (Lepus granatensis) in Spain. Here, we describe the case of myxomatosis in another hare species: an adult male Italian hare (Lepus corsicanus) found dead in 2018 in Sicily with lesions suggestive of myxomatosis and treponema infection. Laboratory tests, e.g., end-point PCR and negative staining electron microscopy, confirmed the presence of both pathogens. MYXV was then isolated from tissue samples in permissive cells and sequenced using NGS technology. Main genomic differences concerning known MYXV strains are discussed.
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Affiliation(s)
- Elisa Rossini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Moira Bazzucchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Valter Trocchi
- Federazione Italiana della Caccia (FIDC), Via Garigliano 57, 00198 Roma, Italy;
| | - Francesca Merzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich Loeffler Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany;
- Professorship for One Health/International Animal Health, Faculty of Veterinary Medicine, Justus Liebig University, 35392 Giessen, Germany
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
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Chambers MJ, Scobell S, Sadhu MJ. Systematic characterization of the local evolutionary space available to human PKR and vaccinia virus K3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568178. [PMID: 38076952 PMCID: PMC10705557 DOI: 10.1101/2023.11.21.568178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The interfaces between host and viral proteins can be dynamic spaces in which genetic variants are continually pursued, giving rise to evolutionary arms races. One such scenario is found between the mammalian innate immunity protein PKR (protein kinase R) and the poxvirus antagonist K3. Once activated, PKR phosphorylates the natural substrate eIF2α, which halts protein synthesis within the cell and prevents viral replication. K3 acts as a pseudosubstrate antagonist against PKR by directly antagonizing this halt in protein synthesis, enabling poxviruses to replicate in the cell. Exploring the impact of genetic variants in both PKR and K3 is necessary not only to highlight residues of evolutionary constraint and opportunity but also to elucidate the mechanism by which human PKR is able to subvert a rapidly evolving viral antagonist. To systematically explore this dynamic interface, we have generated a combinatorial library of PKR and K3 missense variants to be co-expressed and characterized in a high-throughput yeast selection assay. This assay allows us to characterize hundreds of thousands of unique PKR-K3 genetic combinations in a single pooled experiment. Our results highlight specific missense variants available to PKR that subvert the K3 antagonist. We find that improved PKR variants are readily available at sites under positive selection, with limited opportunity at sites interfacing with K3 and eIF2α. Additionally, we find many variants that improve and disable K3 antagonism, suggesting a pliable interface. We reason that this approach can be leveraged to explore the evolutionary plasticity of many other host-virus interfaces.
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Affiliation(s)
- Michael J Chambers
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Microbiology & Immunology, Georgetown University, Washington DC, USA
| | - Sophia Scobell
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meru J Sadhu
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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7
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Thijssen M, Khamisipour G, Maleki M, Devos T, Li G, Van Ranst M, Matthijnssens J, Pourkarim MR. Characterization of the Human Blood Virome in Iranian Multiple Transfused Patients. Viruses 2023; 15:1425. [PMID: 37515113 PMCID: PMC10386462 DOI: 10.3390/v15071425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool. Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.
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Affiliation(s)
- Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Gholamreza Khamisipour
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr 75146-33196, Iran
| | - Mohammad Maleki
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran 14665-1157, Iran
| | - Timothy Devos
- Laboratory of Molecular Immunology (Rega Institute), Department of Hematology, Department of Microbiology and Immunology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410083, China
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran 14665-1157, Iran
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
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8
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Jacquet S, Culbertson M, Zhang C, El Filali A, De La Myre Mory C, Pons JB, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC, Pontier D, Etienne L. Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions. SCIENCE ADVANCES 2022; 8:eadd7540. [PMID: 36417524 PMCID: PMC9683710 DOI: 10.1126/sciadv.add7540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/05/2022] [Indexed: 05/29/2023]
Abstract
Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Michelle Culbertson
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chi Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Adil El Filali
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément De La Myre Mory
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Jean-Baptiste Pons
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | | | - M. Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Barthélémy Ngoubangoye
- International Centre of Medical Research of Franceville, Primatology Centre, Franceville, Gabon
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément Verez
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Clara Dahoui
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Clayton M. Carey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Cimarelli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Lucie Etienne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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Crocodilepox Virus Protein 157 Is an Independently Evolved Inhibitor of Protein Kinase R. Viruses 2022; 14:v14071564. [PMID: 35891544 PMCID: PMC9318007 DOI: 10.3390/v14071564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/05/2023] Open
Abstract
Crocodilepox virus (CRV) belongs to the Poxviridae family and mainly infects hatchling and juvenile Nile crocodiles. Most poxviruses encode inhibitors of the host antiviral protein kinase R (PKR), which is activated by viral double-stranded (ds) RNA formed during virus replication, resulting in the phosphorylation of eIF2α and the subsequent shutdown of general mRNA translation. Because CRV lacks orthologs of known poxviral PKR inhibitors, we experimentally characterized one candidate (CRV157), which contains a predicted dsRNA-binding domain. Bioinformatic analyses indicated that CRV157 evolved independently from other poxvirus PKR inhibitors. CRV157 bound to dsRNA, co-localized with PKR in the cytosol, and inhibited PKR from various species. To analyze whether CRV157 could inhibit PKR in the context of a poxvirus infection, we constructed recombinant vaccinia virus strains that contain either CRV157, or a mutant CRV157 deficient in dsRNA binding in a strain that lacks PKR inhibitors. The presence of wild-type CRV157 rescued vaccinia virus replication, while the CRV157 mutant did not. The ability of CRV157 to inhibit PKR correlated with virus replication and eIF2α phosphorylation. The independent evolution of CRV157 demonstrates that poxvirus PKR inhibitors evolved from a diverse set of ancestral genes in an example of convergent evolution.
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Virus Infection and Systemic Inflammation: Lessons Learnt from COVID-19 and Beyond. Cells 2022; 11:cells11142198. [PMID: 35883640 PMCID: PMC9316821 DOI: 10.3390/cells11142198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
Respiratory infections with newly emerging zoonotic viruses such as SARS-CoV-2, the etiological agent of COVID-19, often lead to the perturbation of the human innate and adaptive immune responses causing severe disease with high mortality. The responsible mechanisms are commonly virus-specific and often include either over-activated or delayed local interferon responses, which facilitate efficient viral replication in the primary target organ, systemic viral spread, and rapid onset of organ-specific and harmful inflammatory responses. Despite the distinct replication strategies, human infections with SARS-CoV-2 and highly pathogenic avian influenza viruses demonstrate remarkable similarities and differences regarding the mechanisms of immune induction, disease dynamics, as well as the long-term sequelae, which will be discussed in this review. In addition, we will highlight some important lessons about the effectiveness of antiviral and immunomodulatory therapeutic strategies that this pandemic has taught us.
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