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Megawati D, Stroup JN, Park C, Clarkson T, Tazi L, Brennan G, Rothenburg S. Tanapox Virus and Yaba Monkey Tumor Virus K3 Orthologs Inhibit Primate Protein Kinase R in a Species-Specific Fashion. Viruses 2024; 16:1095. [PMID: 39066257 PMCID: PMC11281682 DOI: 10.3390/v16071095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Yaba monkey tumor virus (YMTV) and Tanapox virus (TPV) are members of the Yatapoxvirus genus and can infect humans and other primates. Despite the threat posed by yatapoxviruses, the factors determining their host range are poorly understood. In this study, we analyzed the ability of YMTV and TPV orthologs of vaccinia virus K3 (called 012 in YMTV and TPV), which share 75% amino acid identity with one another, to inhibit PKR from 15 different primate species. We first used a luciferase-based reporter, and found that YMTV and TPV K3 orthologs inhibited PKR in a species-specific manner and showed distinct PKR inhibition profiles. TPV 012 inhibited PKR from 11 primates, including humans, substantially better than YMTV 012. In contrast, both K3 orthologs inhibited the other four primate PKRs comparably well. Using YMTV 012 and TPV 012 hybrids, we mapped the region responsible for the differential PKR inhibition to the C- terminus of the K3 orthologs. Next, we generated chimeric vaccinia virus strains to investigate whether TPV K3 and YMTV K3 orthologs could rescue the replication of a vaccinia virus strain that lacks PKR inhibitors K3L and E3L. Virus replication in primate-derived cells generally correlated with the patterns observed in the luciferase-based assay. Together, these observations demonstrate that yatapoxvirus K3 orthologs have distinct PKR inhibition profiles and inhibit PKR in a species-specific manner, which may contribute to the differential susceptibility of primate species to yatapoxvirus infections.
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Affiliation(s)
- Dewi Megawati
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar 80239, Bali, Indonesia
| | - Jeannine N. Stroup
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Taylor Clarkson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Loubna Tazi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
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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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Hewel C, Schmidt H, Runkel S, Kohnen W, Schweiger-Seemann S, Michel A, Bikar SE, Lieb B, Plachter B, Hankeln T, Linke M, Gerber S. Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case. J Med Virol 2024; 96:e29610. [PMID: 38654702 DOI: 10.1002/jmv.29610] [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: 11/06/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.
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Affiliation(s)
- Charlotte Hewel
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hanno Schmidt
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Runkel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Transfusion Unit & Test Center, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Wolfgang Kohnen
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hygiene and Infection Prevention, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susann Schweiger-Seemann
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - André Michel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Medical Management Department, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sven-Ernö Bikar
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- StarSEQ GmbH, Mainz, Germany
| | | | - Bodo Plachter
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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Diaz-Cánova D, Moens U, Brinkmann A, Nitsche A, Okeke MI. Whole genome sequencing of recombinant viruses obtained from co-infection and superinfection of Vero cells with modified vaccinia virus ankara vectored influenza vaccine and a naturally occurring cowpox virus. Front Immunol 2024; 15:1277447. [PMID: 38633245 PMCID: PMC11021749 DOI: 10.3389/fimmu.2024.1277447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Modified vaccinia virus Ankara (MVA) has been widely tested in clinical trials as recombinant vector vaccine against infectious diseases and cancers in humans and animals. However, one biosafety concern about the use of MVA vectored vaccine is the potential for MVA to recombine with naturally occurring orthopoxviruses in cells and hosts in which it multiplies poorly and, therefore, producing viruses with mosaic genomes with altered genetic and phenotypic properties. We previously conducted co-infection and superinfection experiments with MVA vectored influenza vaccine (MVA-HANP) and a feline Cowpox virus (CPXV-No-F1) in Vero cells (that were semi-permissive to MVA infection) and showed that recombination occurred in both co-infected and superinfected cells. In this study, we selected the putative recombinant viruses and performed genomic characterization of these viruses. Some putative recombinant viruses displayed plaque morphology distinct of that of the parental viruses. Our analysis demonstrated that they had mosaic genomes of different lengths. The recombinant viruses, with a genome more similar to MVA-HANP (>50%), rescued deleted and/or fragmented genes in MVA and gained new host ranges genes. Our analysis also revealed that some MVA-HANP contained a partially deleted transgene expression cassette and one recombinant virus contained part of the transgene expression cassette similar to that incomplete MVA-HANP. The recombination in co-infected and superinfected Vero cells resulted in recombinant viruses with unpredictable biological and genetic properties as well as recovery of delete/fragmented genes in MVA and transfer of the transgene into replication competent CPXV. These results are relevant to hazard characterization and risk assessment of MVA vectored biologicals.
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Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Malachy Ifeanyi Okeke
- Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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5
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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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6
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Atasoy MO, Naggar RFE, Rohaim MA, Munir M. Zoonotic and Zooanthroponotic Potential of Monkeypox. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:75-90. [PMID: 38801572 DOI: 10.1007/978-3-031-57165-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The current multicounty outbreak of monkeypox virus (MPXV) posed an emerging and continued challenge to already strained public healthcare sector, around the globe. Since its first identification, monkeypox disease (mpox) remained enzootic in Central and West African countries where reports of human cases are sporadically described. Recent trends in mpox spread outside the Africa have highlighted increased incidence of spillover of the MPXV from animal to humans. While nature of established animal reservoirs remained undefined, several small mammals including rodents, carnivores, lagomorphs, insectivores, non-human primates, domestic/farm animals, and several species of wildlife are proposed to be carrier of the MPXV infection. There are established records of animal-to-human (zoonotic) spread of MPXV through close interaction of humans with animals by eating bushmeat, contracting bodily fluids or trading possibly infected animals. In contrast, there are reports and increasing possibilities of human-to-animal (zooanthroponotic) spread of the MPXV through petting and close interaction with pet owners and animal care workers. We describe here the rationales and molecular factors which predispose the spread of MPXV not only amongst humans but also from animals to humans. A range of continuing opportunities for the spread and evolution of MPXV are discussed to consider risks beyond the currently identified groups. With the possibility of MPXV establishing itself in animal reservoirs, continued and broad surveillance, investigation into unconventional transmissions, and exploration of spillover events are warranted.
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Affiliation(s)
- Mustafa O Atasoy
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Furness College, Lancaster University, Tower Ave, Bailrigg, LA1 4YG, UK
| | - Rania F El Naggar
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Furness College, Lancaster University, Tower Ave, Bailrigg, LA1 4YG, UK
| | - Mohammed A Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Furness College, Lancaster University, Tower Ave, Bailrigg, LA1 4YG, UK
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Furness College, Lancaster University, Tower Ave, Bailrigg, LA1 4YG, UK.
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Kumar A, Gupta N, Fayaz A, Mageswary R, Bano R, ChandraSekar S, Muthuchelvan D, Dhama K, Pandey AB, Ramakrishnan MA. Molecular epidemiology of swinepox viruses circulating in India. Vet Q 2023; 43:1-10. [PMID: 36408854 PMCID: PMC9828724 DOI: 10.1080/01652176.2022.2150791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Swinepox is a sporadic virus disease of domestic and wild pigs that mainly occurs during the rainy season. Though the disease is known for a century, research on swinepox especially genetic characterization is scanty. Self-limiting nature of the disease, the non-availability of specific diagnostics as well as the resemblance of clinical signs with other pathogens are some of the issues in the slow progress in swinepox-related research. Recent whole genome sequencing data from the USA, India, and Germany enhanced our understanding of the biology of swinepox virus (SWPV). The objective of the present study is to investigate the molecular epidemiology of two swinepox outbreaks that occurred in 2015 and 2016 one each in Uttar Pradesh, and the Haryana states of India. The appearance of clinical signs in different swine breeds was recorded. The scab samples from infected pigs were collected, DNA extracted, host range genes of SWPV were PCR amplified, sequenced and analyzed for genetic and phylogenetic characterization. Desi (nondescript breed), Yorkshire White pigs, and Landrace cross were found to be infected with SWPV. Host range genes of SWPV analyzed from clinical samples showed very high nucleotide identity with each other. Phylogenetic analyses revealed that SWPVs circulating in India are distinct (Indian lineage) from the SWPV of the USA, Germany, and Russia (European-North American lineage). Our study affirms the existence of two distinct lineages of SWPV globally with differences in clinical lesions between breeds.
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Affiliation(s)
- Ashok Kumar
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Nikunj Gupta
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Arfa Fayaz
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Rajangam Mageswary
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Rukhsana Bano
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Shanmugam ChandraSekar
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Dhanavelu Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Awadh B. Pandey
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India
| | - Muthannan Andavar Ramakrishnan
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand, India,CONTACT Muthannan Andavar Ramakrishnan Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttarakhand263 138, India
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8
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Lucena-Neto FD, Falcão LFM, Vieira-Junior AS, Moraes ECS, David JPF, Silva CC, Sousa JR, Duarte MIS, Vasconcelos PFC, Quaresma JAS. Monkeypox Virus Immune Evasion and Eye Manifestation: Beyond Eyelid Implications. Viruses 2023; 15:2301. [PMID: 38140542 PMCID: PMC10747317 DOI: 10.3390/v15122301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Monkeypox virus (MPXV), belonging to the Poxviridae family and Orthopoxvirus genus, is closely related to the smallpox virus. Initial prodromal symptoms typically include headache, fever, and lymphadenopathy. This review aims to detail various ocular manifestations and immune evasion associated with the monkeypox viral infection and its complications, making it appropriate as a narrative review. Common external ocular manifestations of MPXV typically involve a generalized pustular rash, keratitis, discharges, and dried secretions related to conjunctival pustules, photophobia, and lacrimation. Orthopoxviruses can evade host immune responses by secreting proteins that antagonize the functions of host IFNγ, CC and CXC chemokines, IL-1β, and the complement system. One of the most important transcription factors downstream of pattern recognition receptors binding is IRF3, which controls the expression of the crucial antiviral molecules IFNα and IFNβ. We strongly recommend that ophthalmologists include MPXV as part of their differential diagnosis when they encounter similar cases presenting with ophthalmic manifestations such as conjunctivitis, blepharitis, or corneal lesions. Furthermore, because non-vaccinated individuals are more likely to exhibit these symptoms, it is recommended that healthcare administrators prioritize smallpox vaccination for at-risk groups, including very young children, pregnant women, older adults, and immunocompromised individuals, especially those in close contact with MPXV cases.
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Affiliation(s)
- Francisco D. Lucena-Neto
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Luiz F. M. Falcão
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Adolfo S. Vieira-Junior
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Evelly C. S. Moraes
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Joacy P. F. David
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Camilla C. Silva
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Jorge R. Sousa
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Maria I. S. Duarte
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
| | - Pedro F. C. Vasconcelos
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Juarez A. S. Quaresma
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
- Virology Section, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
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9
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Gao Z, He X, Chen G, Fang Y, Meng Z, Tian H, Zhang H, Jing Z. The Viral Protein Poly(A) Polymerase Catalytic Subunit Interacts with Guanylate-Binding Proteins 2 to Antagonize the Antiviral Ability of Targeting Ectromelia Virus. Int J Mol Sci 2023; 24:15750. [PMID: 37958732 PMCID: PMC10648259 DOI: 10.3390/ijms242115750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The recent spread of the monkeypox virus among humans has heightened concerns regarding orthopoxvirus infections. Consequently, conducting a comprehensive study on the immunobiology of the monkeypox virus is imperative for the development of effective therapeutics. Ectromelia virus (ECTV) closely resembles the genetic and disease characteristics of monkeypox virus, making it a valuable research tool for studying orthopoxvirus-host interactions. Guanylate-binding proteins (GBPs), highly expressed interferon-stimulated genes (ISGs), have antagonistic effects against various intracellular pathogenic microorganisms. Our previous research has shown that GBP2 has a mild but statistically significant inhibitory effect on ECTV infection. The presence of a significant number of molecules in the poxvirus genome that encode the host immune response raises questions about whether it also includes proteins that counteract the antiviral activity of GBP2. Using IP/MS and co-IP technology, we discovered that the poly(A) polymerase catalytic subunit (PAPL) protein of ECTV is a viral regulatory molecule that interacts with GBP2. Further studies have shown that PAPL antagonizes the antiviral activity of GBP2 by reducing its protein levels. Knocking out the PAPL gene of ECTV with the CRISPR/Cas9 system significantly diminishes the replication ability of the virus, indicating the indispensable role of PAPL in the replication process of ECTV. In conclusion, our study presents preliminary evidence supporting the significance of PAPL as a virulence factor that can interact with GBP2.
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Affiliation(s)
- Zhenzhen Gao
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Xiaobing He
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Guohua Chen
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Yongxiang Fang
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Zejing Meng
- School of Public Health, Lanzhou University, Lanzhou 730000, China;
| | - Huihui Tian
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Hui Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
| | - Zhizhong Jing
- State Key Laboratory for Animal Disease Control and Prevention, Ministry of Agriculture Key Laboratory of Veterinary Public Health, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Z.G.); (X.H.); (G.C.); (Y.F.); (H.T.); (H.Z.)
- School of Public Health, Lanzhou University, Lanzhou 730000, China;
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10
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Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC. Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity. Cell Rep 2023; 42:112878. [PMID: 37494187 DOI: 10.1016/j.celrep.2023.112878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Viruses acquire host genes via horizontal transfer and can express them to manipulate host biology during infections. Some homologs retain sequence identity, but evolutionary divergence can obscure host origins. We use structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identify vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirms this homology, and cell-based assays reveal that A47 interferes with caspase function. We also identify vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2-related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting differential modulation during infections. Our findings demonstrate the increasing power of structural homology screens to reveal proteins with unique combinations of domains that viruses capture from host genes and combine in unique ways.
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Affiliation(s)
- Ian N Boys
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Meghan R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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11
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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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12
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Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC. Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.529821. [PMID: 36909515 PMCID: PMC10002665 DOI: 10.1101/2023.02.26.529821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.
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Affiliation(s)
- Ian N. Boys
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Alex G. Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Meghan Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
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13
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First Report of Swinepox in a Wild Boar in Italy: Pathologic and Molecular Findings. Pathogens 2023; 12:pathogens12030472. [PMID: 36986394 PMCID: PMC10056785 DOI: 10.3390/pathogens12030472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Swinepox virus (SWPV) is responsible for sporadic acute poxvirus infections in swine worldwide, causing a pathognomonic eruptive proliferative dermatitis. Beside direct and congenital transmission, the pig louse Haematopinus suis acts as a mechanical vector and favors virus infection through skin lesions. Infections are generally described in domestic pigs, while only a few cases have been reported in wild boars, in Austria and Germany. In September 2022, SWPV infection was suspected at post-mortem examination of a wild boar piglet with characteristic lesions in Liguria, Northwest Italy. The piglet was heavily parasitized by swine lice (H. suis). SWPV was then confirmed by histological and molecular analyses. Possible viral co-infections were also investigated (African swine fever virus, classical swine fever virus, parvovirus, circovirus, Aujeszky’s disease virus and hepatitis E virus). This article describes gross and histopathologic features of SWPV infection, differential diagnosis, and potential vector-borne transmission to domestic pigs, presenting a brief review of the literature on the topic. SWPV infection is reported in wild boars in Italy for the first time. The finding of SWPV in a wild boar in an area with a very limited pig population may suggest the existence of a “wildlife cycle” in the area. Further investigations are needed to understand the real risk of transmission of SWPV to domestic pigs as well as the role of other arthropod vectors.
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14
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Guan H, Gul I, Xiao C, Ma S, Liang Y, Yu D, Liu Y, Liu H, Zhang CY, Li J, Qin P. Emergence, phylogeography, and adaptive evolution of mpox virus. New Microbes New Infect 2023; 52:101102. [PMID: 36815201 PMCID: PMC9937731 DOI: 10.1016/j.nmni.2023.101102] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Mpox (Monkeypox) is a zoonotic disease caused by mpox virus (MPXV). A multi-country MPXV outbreak in non-endemic demographics was identified in May 2022. A systematic evaluation of MPXV evolutionary trajectory and genetic diversity could be a timely addition to the MPXV diagnostics and prophylaxis. Herein, we integrated a systematic evolution analysis including phylogenomic and phylogeographic, followed by an in-depth analysis of the adaptive evolution and amino acid variations in type I interferon binding protein (IFNα/βBP). Mutations in IFNα/βBP protein may impair its binding capacity, affecting the MPXV immune evasion strategy. Based on the equilibrated data, we found an evolutionary rate of 7.75 × 10 - 5 substitutions/site/year, and an earlier original time (2021.25) of the clade IIb. We further discovered significant genetic variations in MPXV genomes from different regions and obtained six plausible spread trajectories from its intricate viral flow network, implying that North America might have acted as a bridge for the spread of MPXV from Africa to other continents. We identified two amino acids under positive selection in the Rifampicin resistance protein and extracellular enveloped virus (EEV) type-I membrane glycoprotein, indicating a role in adaptive evolution. Our research sheds light on the emergence, dispersal, and adaptive evolution of MPXV, providing theoretical support for mitigating and containing its expansion.
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Affiliation(s)
- Haifei Guan
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Ijaz Gul
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Chufan Xiao
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Shuyue Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yingshan Liang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Dongmei Yu
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong, 264209, China
| | - Ying Liu
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, 518060, China
| | - Hong Liu
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, 518060, China
| | - Can Yang Zhang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Juan Li
- Advanced Research Institute for Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
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15
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Brennan G, Stoian AMM, Yu H, Rahman MJ, Banerjee S, Stroup JN, Park C, Tazi L, Rothenburg S. Molecular Mechanisms of Poxvirus Evolution. mBio 2023; 14:e0152622. [PMID: 36515529 PMCID: PMC9973261 DOI: 10.1128/mbio.01526-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.
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Affiliation(s)
- Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Ana M. M. Stoian
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Huibin Yu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - M. Julhasur Rahman
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Shefali Banerjee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Jeannine N. Stroup
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Loubna Tazi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
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16
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Cowpox Viruses: A Zoo Full of Viral Diversity and Lurking Threats. Biomolecules 2023; 13:biom13020325. [PMID: 36830694 PMCID: PMC9953750 DOI: 10.3390/biom13020325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Cowpox viruses (CPXVs) exhibit the broadest known host range among the Poxviridae family and have caused lethal outbreaks in various zoo animals and pets across 12 Eurasian countries, as well as an increasing number of human cases. Herein, we review the history of how the cowpox name has evolved since the 1700s up to modern times. Despite early documentation of the different properties of CPXV isolates, only modern genetic analyses and phylogenies have revealed the existence of multiple Orthopoxvirus species that are currently constrained under the CPXV designation. We further chronicle modern outbreaks in zoos, domesticated animals, and humans, and describe animal models of experimental CPXV infections and how these can help shaping CPXV species distinctions. We also describe the pathogenesis of modern CPXV infections in animals and humans, the geographic range of CPXVs, and discuss CPXV-host interactions at the molecular level and their effects on pathogenicity and host range. Finally, we discuss the potential threat of these viruses and the future of CPXV research to provide a comprehensive review of CPXVs.
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17
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Ghabeshi S, Ghasemi S, Mousavizadeh L. The effective factors in human-specific tropism and viral pathogenicity in orthopoxviruses. Cell Biol Int 2023; 47:341-351. [PMID: 36317465 DOI: 10.1002/cbin.11941] [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: 08/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022]
Abstract
The orthopoxvirus (OPV) genus includes several species that infect humans, including variola, monkeypox, vaccinia, and cowpox. Variola and monkeypox are often life-threatening diseases, while vaccinia and cowpox are usually associated with local lesions. The epidemic potential for OPVs may be lower than respiratory-borne viruses or RNA viruses. However, OPVs are notable for their spread and distribution in different environments and among different hosts. The emergence or re-emergence of OPVs in the human population can also occur in wild or domestic animals as intermediate hosts. More effective and safer vaccines for poxvirus can be developed by understanding how immunity is regulated in poxvirus and vaccines for DNA viruses. Downstream events in cells affected by the virus are regulated functionally by a series of characteristics that are affected by host cell interactions and responses of cells against viral infections, including the interferon pathway and apoptosis. Furthermore, infection outcome is greatly influenced by the distinct selection of host-range and immune-modulatory genes that confer the potential for pathogenesis and host-to-host transmission and the distinct host-range properties of each immune-modulatory gene. The present study reviewed the effective factors in human-restricted tropism and virus pathogenicity in OPVs.
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Affiliation(s)
- Soad Ghabeshi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Health Policy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sorayya Ghasemi
- Cancer Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Leila Mousavizadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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18
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Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M. Evolution of the orthopoxvirus core genome. Virus Res 2023; 323:198975. [PMID: 36280003 PMCID: PMC9586335 DOI: 10.1016/j.virusres.2022.198975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses. We show that, despite their strong constraint, some genes involved in viral morphogenesis and transcription/replication were targets of pervasive positive selection, which was relatively uncommon in immunomodulatory genes. However at least three of the positively selected genes, E3L, A24R, and H3L, might have evolved in response to immune selection. Episodic positive selection was particularly common on the internal branches of the orthopox phylogeny and on the monkeypox virus lineage. The latter showed evidence of episodic positive selection at the D14L gene, which encodes a modulator of complement activation (MOPICE). Notably, two genes (B1R and A33R) targeted by episodic selection on more than one branch are involved in forms of intra-genomic conflict. Finally, we found that, in orthopoxvirus proteomes, intrinsically disordered regions (IDRs) tend to be less constrained and are common targets of positive selection. Extension of our analysis to all poxviruses showed no evidence that the IDR fraction differs with host range. Conversely, we found a strong effect of base composition, which was however not sufficient to explain IDR fraction. We thus suggest that, in poxviruses, the IDR fraction is maintained by modulating GC content to accommodate disorder-promoting codons. Overall, our data provide novel insight in orthopoxvirus evolution and provide a list of genes and sites that are expected to modulate viral phenotypes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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19
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Shafaati M, Zandi M. Human monkeypox (hMPXV) re-emergence: Host immunity status and current vaccines landscape. J Med Virol 2023; 95:e28251. [PMID: 36271768 DOI: 10.1002/jmv.28251] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/19/2022] [Indexed: 01/11/2023]
Abstract
Monkeypox virus is a member of the Orthopoxvirus genus and the Poxviridae family. Orthopoxviruses are among the most intricate animal viruses. The pathogenicity of human monkeypox infection has been emphasized in response to its recent emergence in non-endemic countries and the threat of bioterrorism. It is always necessary to take appropriate precautions in exposure to emerging or re-emerging infections. Here, we focus on the current state of the human monkeypox infection outbreak, research & development of immune responses, and clinical interventions to prevent and treat the human monkeypox virus and other human poxviruses.
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Affiliation(s)
- Maryam Shafaati
- Department of Microbiology, Faculty of Science, Jahrom Branch, Islamic Azad University, Jahrom, Iran
- Occupational Sleep Research, Baharloo Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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20
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Xiang Y, White A. Monkeypox virus emerges from the shadow of its more infamous cousin: family biology matters. Emerg Microbes Infect 2022; 11:1768-1777. [PMID: 35751396 PMCID: PMC9278444 DOI: 10.1080/22221751.2022.2095309] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Monkeypox virus (MPXV) is closely related to the infamous variola (smallpox) virus, causing a febrile rash illness in humans similar to but milder than smallpox. In the twentieth century, human monkeypox had been mostly a rare zoonotic disease confined to forested areas in West and Central Africa. However, the case number and geographic range have increased significantly in this century, coincided with the waning of the smallpox vaccine-induced immunity in the global population. The outbreak of human monkeypox in multiple countries since May 2022 has been unusual in its large case number and the absence of direct links to endemic countries, raising concerns for a possible change in monkeypox transmission pattern that could pose a greater global threat. Here, we review aspects of MPXV biology that are relevant for risk assessment and preparedness for a monkeypox epidemic, with an emphasis on recent progress in understanding of the virus host range, evolutionary potential, and neutralization targets.
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Affiliation(s)
- Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Addison White
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, USA
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21
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Ophinni Y, Frediansyah A, Sirinam S, Megawati D, Stoian AM, Enitan SS, Akele RY, Sah R, Pongpirul K, Abdeen Z, Aghayeva S, Ikram A, Kebede Y, Wollina U, Subbaram K, Koyanagi A, Al Serouri A, Blaise Nguendo-Yongsi H, Edwards J, Sallam DE, Khader Y, Viveiros-Rosa SG, Memish ZA, Amir-Behghadami M, Vento S, Rademaker M, Sallam M. Monkeypox: Immune response, vaccination and preventive efforts. NARRA J 2022; 2:e90. [PMID: 38449905 PMCID: PMC10914130 DOI: 10.52225/narra.v2i3.90] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/20/2022] [Indexed: 02/05/2023]
Abstract
Infectious threats to humans are continuously emerging. The 2022 worldwide monkeypox outbreak is the latest of these threats with the virus rapidly spreading to 106 countries by the end of September 2022. The burden of the ongoing monkeypox outbreak is manifested by 68,000 cumulative confirmed cases and 26 deaths. Although monkeypox is usually a self-limited disease, patients can suffer from extremely painful skin lesions and complications can occur with reported mortalities. The antigenic similarity between the smallpox virus (variola virus) and monkeypox virus can be utilized to prevent monkeypox using smallpox vaccines; treatment is also based on antivirals initially designed to treat smallpox. However, further studies are needed to fully decipher the immune response to monkeypox virus and the immune evasion mechanisms. In this review we provide an up-to-date discussion of the current state of knowledge regarding monkeypox virus with a special focus on innate immune response, immune evasion mechanisms and vaccination against the virus.
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Affiliation(s)
- Youdiil Ophinni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Andri Frediansyah
- PRTPP-National Research and Innovation Agency (BRIN), Yogyakarta, Indonesia
| | - Salin Sirinam
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Dewi Megawati
- Department of Veterinary Pathobiology, School of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Department of Microbiology and Parasitology, School of Medicine, Universitas Warmadewa, Bali, Indonesia
| | - Ana M. Stoian
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, CA, United States
| | - Seyi S. Enitan
- Department of Medical Laboratory Science, Babcock University, Ilishan-Remo, Nigeria
| | - Richard Y. Akele
- Department of Biomedical Science, School of Applied Science, University of Brighton, London, United Kingdom
| | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - Krit Pongpirul
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Bumrungrad International Hospital, Bangkok, Thailand
| | - Ziad Abdeen
- Department of Community Health, Faculty of Medicine, Al-Quds University, Jerusalem
| | - Sevda Aghayeva
- Department of Gastroenterology, Baku Medical Plaza Hospital, Baku, Azerbaijan
| | - Aamer Ikram
- National Institute of Heath, Islamabad, Pakistan
| | - Yohannes Kebede
- Department of Health, Behavior and Society, Faculty of Public Health, Jimma University, Jimma, Ethiopia
| | - Uwe Wollina
- Department of Dermatology and Allergology, Städtisches Klinikum Dresden, Dresden, Germany
| | - Kannan Subbaram
- School of Medicine, The Maldives National University, Maldives
| | - Ai Koyanagi
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, CIBERSAM, ISCIII, Barcelona, Spain
| | | | - H. Blaise Nguendo-Yongsi
- Department of Epidemiology, School of Health Sciences, Catholic University of Central Africa, Yaoundé, Cameroon
| | - Jeffrey Edwards
- Medical Research Foundation of Trinidad and Tobago, Port of Spain, Trinidad
| | - Dina E. Sallam
- Department of Pediatrics and Pediatric Nephrology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yousef Khader
- The Center of Excellence for Applied Epidemiology, The Eastern Mediterranean Public Health Network (EMPHNET), Amman, Jordan
| | | | - Ziad A. Memish
- Research & Innovation Centre, King Saud Medical City, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
- College of Medicine, AlFaisal University, Riyadh, Kingdom of Saudi Arabia
| | - Mehrdad Amir-Behghadami
- Iranian Center of Excellence in Health Management, Department of Health Service Management, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sandro Vento
- Faculty of Medicine, University of Puthisastra, Phnom Penh, Cambodia
| | - Marius Rademaker
- Clinical Trial New Zealand, Waikato Hospital Campus, Hamilton, New Zealand
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
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22
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Rahman MM, McFadden G. Role of cytokines in poxvirus host tropism and adaptation. Curr Opin Virol 2022; 57:101286. [PMID: 36427482 PMCID: PMC9704024 DOI: 10.1016/j.coviro.2022.101286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022]
Abstract
Poxviruses are a diverse family of double-stranded DNA viruses that cause mild-to-severe disease in selective hosts, including humans. Although most poxviruses are restricted to their hosts, some members can leap host species and cause zoonotic diseases and, therefore, are genuine threats to human and animal health. The recent global spread of monkeypox in humans suggests that zoonotic poxviruses can adapt to a new host, spread rapidly in the new host, and evolve to better evade host innate barriers. Unlike many other viruses, poxviruses express an extensive repertoire of self-defense proteins that play a vital role in the evasion of host innate and adaptive immune responses in their newest host species. The function of these viral immune modulators and host-specific cytokine responses can result in different host tropism and poxvirus disease progression. Here, we review the role of different cytokines that control poxvirus host tropism and adaptation.
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23
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Sofyantoro F, Kusuma HI, Vento S, Rademaker M, Frediansyah A. Global research profile on monkeypox-related literature (1962-2022): A bibliometric analysis. NARRA J 2022; 2:e96. [PMID: 38449907 PMCID: PMC10914125 DOI: 10.52225/narra.v2i3.96] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/12/2022] [Indexed: 09/22/2023]
Abstract
The recent monkeypox or mpox outbreak has been a global concern. The present study evaluated the global research outputs, research trends, and topics of published research on monkeypox using a bibliometric approach. The Scopus database was searched for terms associated with "monkeypox" or "monkey pox" up until 19 November 2022. Maps and bibliometric indicators of the retrieved documents were shown and analyzed. A total of 1,422 documents were obtained from Scopus. Other than monkeypox, the most commonly used terms included epidemic, disease outbreaks, smallpox vaccine, and orthopoxvirus. In total, 90.3% of the documents were published between 2002 and 2022. The United States, the United Kingdom, and India were the top three countries in terms of productivity. Most of the institutions were from the United States. The International Journal of Surgery, the Journal of Medical Virology, and the Travel Medicine and Infectious Disease are some of the top journals currently publishing research on monkeypox. Tecovirimat, coronavirus disease 2019 (COVID-19), homosexuality, and pandemic are emerging topics related to monkeypox.
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Affiliation(s)
- Fajar Sofyantoro
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendrix I. Kusuma
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh, Indonesia
- Department of Biology Education, Faculty of Tarbiyah and Teacher Training, Universitas Islam Negeri Ar-Raniry, Banda Aceh, Indonesia
| | - Sandro Vento
- Faculty of Medicine, University of Puthisastra, Phnom Penh, Cambodia
| | - Marius Rademaker
- Clinical Trial New Zealand, Waikato Hospital Campus, Hamilton, New Zealand
| | - Andri Frediansyah
- PRTPP, National Research and Innovation Agency (BRIN), Yogyakarta, Indonesia
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24
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Conrad SJ, Raza T, Peterson EA, Liem J, Connor R, Nounamo B, Cannon M, Liu J. Myxoma virus lacking the host range determinant M062 stimulates cGAS-dependent type 1 interferon response and unique transcriptomic changes in human monocytes/macrophages. PLoS Pathog 2022; 18:e1010316. [PMID: 36103568 PMCID: PMC9473615 DOI: 10.1371/journal.ppat.1010316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
The evolutionarily successful poxviruses possess effective and diverse strategies to circumvent or overcome host defense mechanisms. Poxviruses encode many immunoregulatory proteins to evade host immunity to establish a productive infection and have unique means of inhibiting DNA sensing-dependent type 1 interferon (IFN-I) responses, a necessity given their dsDNA genome and exclusively cytoplasmic life cycle. We found that the key DNA sensing inhibition by poxvirus infection was dominant during the early stage of poxvirus infection before DNA replication. In an effort to identify the poxvirus gene products which subdue the antiviral proinflammatory responses (e.g., IFN-I response), we investigated the function of one early gene that is the known host range determinant from the highly conserved poxvirus host range C7L superfamily, myxoma virus (MYXV) M062. Host range factors are unique features of poxviruses that determine the species and cell type tropism. Almost all sequenced mammalian poxviruses retain at least one homologue of the poxvirus host range C7L superfamily. In MYXV, a rabbit-specific poxvirus, the dominant and broad-spectrum host range determinant of the C7L superfamily is the M062R gene. The M062R gene product is essential for MYXV infection in almost all cells tested from different mammalian species and specifically inhibits the function of host Sterile αMotif Domain-containing 9 (SAMD9), as M062R-null (ΔM062R) MYXV causes abortive infection in a SAMD9-dependent manner. In this study we investigated the immunostimulatory property of the ΔM062R. We found that the replication-defective ΔM062R activated host DNA sensing pathway during infection in a cGAS-dependent fashion and that knocking down SAMD9 expression attenuated proinflammatory responses. Moreover, transcriptomic analyses showed a unique feature of the host gene expression landscape that is different from the dsDNA alone-stimulated inflammatory state. This study establishes a link between the anti-neoplastic function of SAMD9 and the regulation of innate immune responses. Poxviruses encode a group of genes called host range determinants to maintain or expand their host tropism. The mechanism by which many viral host range factors function remains elusive. Some host range factors possess immunoregulatory functions responsible for evading or subduing host immune defense mechanisms. Most known immunoregulatory proteins encoded by poxviruses are dispensable for viral replication in vitro. The uniqueness of MYXV M062R is that it is essential for viral infection in vitro and belongs to one of the most conserved poxvirus host range families, the C7L superfamily. There is one known host target of the MYXV M062 protein, SAMD9. SAMD9 is constitutively expressed in mammalian cells and exclusively present in the cytoplasm with an anti-neoplastic function. Humans with deleterious mutations in SAMD9 present disease that ranges from lethality at a young age to a predisposition to myelodysplastic syndromes (MDS) that often require bone marrow transplantation. More importantly, SAMD9 serves as an important antiviral intrinsic molecule to many viruses. The cellular function of SAMD9 remains unclear mostly due to the difficulty of studying this protein, i.e., its large size, long half-life, and its constitutive expression in most cells. In this study we used M062R-null MYXV as a tool to study SAMD9 function and report a functional link between SAMD9 and the regulation of the proinflammatory responses triggered by cGAS-dependent DNA sensing.
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Affiliation(s)
- Steven J. Conrad
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Tahseen Raza
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Jason Liem
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Richard Connor
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Bernice Nounamo
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Martin Cannon
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
- Center of Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, United States of America
- * E-mail:
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25
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Fixsen SM, Cone KR, Goldstein SA, Sasani TA, Quinlan AR, Rothenburg S, Elde NC. Poxviruses capture host genes by LINE-1 retrotransposition. eLife 2022; 11:63332. [PMID: 36069526 PMCID: PMC9578705 DOI: 10.7554/elife.63332] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.
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Affiliation(s)
- Sarah M Fixsen
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Kelsey R Cone
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, United States
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, United States
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26
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Rahman MJ, Haller SL, Stoian AMM, Li J, Brennan G, Rothenburg S. LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses. eLife 2022; 11:63327. [PMID: 36069678 PMCID: PMC9578709 DOI: 10.7554/elife.63327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/06/2022] [Indexed: 11/27/2022] Open
Abstract
There is ample phylogenetic evidence that many critical virus functions, like immune evasion, evolved by the acquisition of genes from their hosts through horizontal gene transfer (HGT). However, the lack of an experimental system has prevented a mechanistic understanding of this process. We developed a model to elucidate the mechanisms of HGT into vaccinia virus, the prototypic poxvirus. All identified gene capture events showed signatures of long interspersed nuclear element-1 (LINE-1)-mediated retrotransposition, including spliced-out introns, polyadenylated tails, and target site duplications. In one case, the acquired gene integrated together with a polyadenylated host U2 small nuclear RNA. Integrations occurred across the genome, in some cases knocking out essential viral genes. These essential gene knockouts were rescued through a process of complementation by the parent virus followed by nonhomologous recombination during serial passaging to generate a single, replication-competent virus. This work links multiple evolutionary mechanisms into one adaptive cascade and identifies host retrotransposons as major drivers for virus evolution.
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Affiliation(s)
- M Julhasur Rahman
- Department of Medial Microbiology and Immunology, University of California, Davis, Davis, United States
| | - Sherry L Haller
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch at Galveston, Galveston, United States
| | - Ana M M Stoian
- Department of Medial Microbiology and Immunology, University of California, Davis, Davis, United States
| | - Jie Li
- Genome Center, University of California, Davis, Davis, United States
| | - Greg Brennan
- Department of Medial Microbiology and Immunology, University of California, Davis, Davis, United States
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, United States
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27
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MacNeill AL. Comparative Pathology of Zoonotic Orthopoxviruses. Pathogens 2022; 11:pathogens11080892. [PMID: 36015017 PMCID: PMC9412692 DOI: 10.3390/pathogens11080892] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
This review provides a brief history of the impacts that a human-specific Orthopoxvirus (OPXV), Variola virus, had on mankind, recalls how critical vaccination was for the eradication of this disease, and discusses the consequences of discontinuing vaccination against OPXV. One of these consequences is the emergence of zoonotic OPXV diseases, including Monkeypox virus (MPXV). The focus of this manuscript is to compare pathology associated with zoonotic OPXV infection in veterinary species and in humans. Efficient recognition of poxvirus lesions and other, more subtle signs of disease in multiple species is critical to prevent further spread of poxvirus infections. Additionally included are a synopsis of the pathology observed in animal models of MPXV infection, the recent spread of MPXV among humans, and a discussion of the potential for this virus to persist in Europe and the Americas.
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Affiliation(s)
- Amy L MacNeill
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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28
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Poxviral ANKR/F-box Proteins: Substrate Adapters for Ubiquitylation and More. Pathogens 2022; 11:pathogens11080875. [PMID: 36014996 PMCID: PMC9414399 DOI: 10.3390/pathogens11080875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
Poxviruses are double-stranded DNA viruses that infect insects and a variety of vertebrate species. The large genomes of poxviruses contain numerous genes that allow these viruses to successfully establish infection, including those that help evade the host immune response and prevent cell death. Ankyrin-repeat (ANKR)/F-box proteins are almost exclusively found in poxviruses, and they function as substrate adapters for Skp1-Cullin-1-F-box protein (SCF) multi-subunit E3 ubiquitin (Ub)-ligases. In this regard, they use their C-terminal F-box domain to bind Skp1, Cullin-1, and Roc1 to recruit cellular E2 enzymes to facilitate the ubiquitylation, and subsequent proteasomal degradation, of proteins bound to their N-terminal ANKRs. However, these proteins do not just function as substrate adapters as they also have Ub-independent activities. In this review, we examine both Ub-dependent and -independent activities of ANKR/F-box proteins and discuss how poxviruses use these proteins to counteract the host innate immune response, uncoat their genome, replicate, block cell death, and influence transcription. Finally, we consider important outstanding questions that need to be answered in order to better understand the function of this versatile protein family.
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29
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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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30
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Abstract
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015 Paris, France.
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31
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Hood AJM, Sumner RP, Maluquer de Motes C. Disruption of the cGAS/STING axis does not impair sensing of MVA in BHK21 cells. J Gen Virol 2022; 103. [PMID: 35584007 DOI: 10.1099/jgv.0.001755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modified vaccinia Ankara (MVA) is an attenuated strain of vaccinia virus (VACV), a dsDNA virus that replicates its genome in the cytoplasm and as a result is canonically sensed by the cyclic GMP-AMP synthase (cGAS) and its downstream stimulator of interferon genes (STING). MVA has a highly restricted host range due to major deletions in its genome including inactivation of immunomodulatory genes, only being able to grow in avian cells and the hamster cell line BHK21. Here we studied the interplay between MVA and the cGAS/STING DNA in this permissive cell line and determined whether manipulation of this axis could impact MVA replication and cell responses. We demonstrate that BHK21 cells retain a functional cGAS/STING axis that responds to canonical DNA sensing agonists, upregulating interferon stimulated genes (ISGs). BHK21 cells also respond to MVA, but with a distinct ISG profile. This profile remains unaltered after CRISPR/Cas9 knock-out editing of STING and ablation of cytosolic DNA responses, indicating that MVA responses are independent of the cGAS/STING axis. Furthermore, infection by MVA diminishes the ability of BHK21 cells to respond to exogenous DNA suggesting that MVA still encodes uncharacterised inhibitors of DNA sensing. This suggests that using attenuated strains in permissive cell lines may assist in identification of novel host-virus interactions that may be of relevance to disease or the therapeutic applications of poxviruses.
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Affiliation(s)
- Alasdair J M Hood
- Department of Microbial Sciences, University of Surrey, Guildford, UK
| | - Rebecca P Sumner
- Department of Microbial Sciences, University of Surrey, Guildford, UK
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32
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Senkevich TG, Yutin N, Wolf YI, Koonin EV, Moss B. Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes. mBio 2021; 12:e0149521. [PMID: 34253028 PMCID: PMC8406176 DOI: 10.1128/mbio.01495-21] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 01/27/2023] Open
Abstract
The survival of viruses depends on their ability to resist host defenses and, of all animal virus families, the poxviruses have the most antidefense genes. Orthopoxviruses (ORPV), a genus within the subfamily Chordopoxvirinae, infect diverse mammals and include one of the most devastating human pathogens, the now eradicated smallpox virus. ORPV encode ∼200 genes, of which roughly half are directly involved in virus genome replication and expression as well as virion morphogenesis. The remaining ∼100 "accessory" genes are responsible for virus-host interactions, particularly counter-defense of innate immunity. Complete sequences are currently available for several hundred ORPV genomes isolated from a variety of mammalian hosts, providing a rich resource for comparative genomics and reconstruction of ORPV evolution. To identify the provenance and evolutionary trends of the ORPV accessory genes, we constructed clusters including the orthologs of these genes from all chordopoxviruses. Most of the accessory genes were captured in three major waves early in chordopoxvirus evolution, prior to the divergence of ORPV and the sister genus Centapoxvirus from their common ancestor. The capture of these genes from the host was followed by extensive gene duplication, yielding several paralogous gene families. In addition, nine genes were gained during the evolution of ORPV themselves. In contrast, nearly every accessory gene was lost, some on multiple, independent occasions in numerous lineages of ORPV, so that no ORPV retains them all. A variety of functional interactions could be inferred from examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently. IMPORTANCE Orthopoxviruses (ORPV) include smallpox (variola) virus, one of the most devastating human pathogens, and vaccinia virus, comprising the vaccine used for smallpox eradication. Among roughly 200 ORPV genes, about half are essential for genome replication and expression as well as virion morphogenesis, whereas the remaining half consists of accessory genes counteracting the host immune response. We reannotated the accessory genes of ORPV, predicting the functions of uncharacterized genes, and reconstructed the history of their gain and loss during the evolution of ORPV. Most of the accessory genes were acquired in three major waves antedating the origin of ORPV from chordopoxviruses. The evolution of ORPV themselves was dominated by gene loss, with numerous genes lost at the base of each major group of ORPV. Examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently during ORPV evolution allows prediction of different types of functional interactions.
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Affiliation(s)
- Tatiana G. Senkevich
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Instutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Instutes of Health, Bethesda, Maryland, USA
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33
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Palmer S, Chappidi S, Pinkham C, Hancks DC. Evolutionary profile for (host and viral) MLKL indicates its activities as a battlefront for extensive counteradaptation. Mol Biol Evol 2021; 38:5405-5422. [PMID: 34436583 PMCID: PMC8662602 DOI: 10.1093/molbev/msab256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pathogen infection triggers host innate defenses which may result in the activation of regulated cell death (RCD) pathways such as apoptosis. Given a vital role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptosis. Yet, it is unclear whether components of this emerging RCD pathway display signatures associated with pathogen conflict that are rare in combination but common to key host defense factors, namely, rapid evolution, viral homolog (virolog), and cytokine induction. We leveraged evolutionary sequence analysis that examines rates of amino acid replacement, which revealed: 1) strong and recurrent signatures of positive selection for primate and bat RIPK3 and MLKL, and 2) elevated rates of amino acid substitution on multiple RIPK3/MLKL surfaces suggestive of past antagonism with multiple, distinct pathogen-encoded inhibitors. Furthermore, our phylogenomics analysis across poxvirus genomes illuminated volatile patterns of evolution for a recently described MLKL viral homolog. Specifically, poxviral MLKLs have undergone numerous gene replacements mediated by duplication and deletion events. In addition, MLKL protein expression is stimulated by interferons in human and mouse cells. Thus, MLKL displays all three hallmarks of pivotal immune factors of which only a handful of factors like OAS1 exhibit. These data support the hypothesis that over evolutionary time MLKL functions—which may include execution of necroptosis—have served as a major determinant of infection outcomes despite gene loss in some host genomes.
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Affiliation(s)
- Suzette Palmer
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sruthi Chappidi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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34
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Bourquain D, Schrick L, Tischer BK, Osterrieder K, Schaade L, Nitsche A. Replication of cowpox virus in macrophages is dependent on the host range factor p28/N1R. Virol J 2021; 18:173. [PMID: 34425838 PMCID: PMC8381512 DOI: 10.1186/s12985-021-01640-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/10/2021] [Indexed: 11/23/2022] Open
Abstract
Zoonotic orthopoxvirus infections continue to represent a threat to human health. The disease caused by distinct orthopoxviruses differs in terms of symptoms and severity, which may be explained by the unique repertoire of virus factors that modulate the host’s immune response and cellular machinery. We report here on the construction of recombinant cowpox viruses (CPXV) which either lack the host range factor p28 completely or express truncated variants of p28. We show that p28 is essential for CPXV replication in macrophages of human or mouse origin and that the C-terminal RING finger domain of p28 is necessary to allow CPXV replication in macrophages.
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Affiliation(s)
- Daniel Bourquain
- Centre for Biological Threats and Special Pathogens 1, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Livia Schrick
- Centre for Biological Threats and Special Pathogens 1, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Bernd Karsten Tischer
- Institute of Virology, Department of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Klaus Osterrieder
- Institute of Virology, Department of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens 1, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens 1, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
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35
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Lant S, Maluquer de Motes C. Poxvirus Interactions with the Host Ubiquitin System. Pathogens 2021; 10:pathogens10081034. [PMID: 34451498 PMCID: PMC8399815 DOI: 10.3390/pathogens10081034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
The ubiquitin system has emerged as a master regulator of many, if not all, cellular functions. With its large repertoire of conjugating and ligating enzymes, the ubiquitin system holds a unique mechanism to provide selectivity and specificity in manipulating protein function. As intracellular parasites viruses have evolved to modulate the cellular environment to facilitate replication and subvert antiviral responses. Poxviruses are a large family of dsDNA viruses with large coding capacity that is used to synthetise proteins and enzymes needed for replication and morphogenesis as well as suppression of host responses. This review summarises our current knowledge on how poxvirus functions rely on the cellular ubiquitin system, and how poxviruses exploit this system to their own advantage, either facilitating uncoating and genome release and replication or rewiring ubiquitin ligases to downregulate critical antiviral factors. Whilst much remains to be known about the intricate interactions established between poxviruses and the host ubiquitin system, our knowledge has revealed crucial viral processes and important restriction factors that open novel avenues for antiviral treatment and provide fundamental insights on the biology of poxviruses and other virus families.
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36
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Yu H, Bruneau RC, Brennan G, Rothenburg S. Battle Royale: Innate Recognition of Poxviruses and Viral Immune Evasion. Biomedicines 2021; 9:biomedicines9070765. [PMID: 34356829 PMCID: PMC8301327 DOI: 10.3390/biomedicines9070765] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/17/2022] Open
Abstract
Host pattern recognition receptors (PRRs) sense pathogen-associated molecular patterns (PAMPs), which are molecular signatures shared by different pathogens. Recognition of PAMPs by PRRs initiate innate immune responses via diverse signaling pathways. Over recent decades, advances in our knowledge of innate immune sensing have enhanced our understanding of the host immune response to poxviruses. Multiple PRR families have been implicated in poxvirus detection, mediating the initiation of signaling cascades, activation of transcription factors, and, ultimately, the expression of antiviral effectors. To counteract the host immune defense, poxviruses have evolved a variety of immunomodulators that have diverse strategies to disrupt or circumvent host antiviral responses triggered by PRRs. These interactions influence the outcomes of poxvirus infections. This review focuses on our current knowledge of the roles of PRRs in the recognition of poxviruses, their elicited antiviral effector functions, and how poxviral immunomodulators antagonize PRR-mediated host immune responses.
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37
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Park C, Peng C, Rahman MJ, Haller SL, Tazi L, Brennan G, Rothenburg S. Orthopoxvirus K3 orthologs show virus- and host-specific inhibition of the antiviral protein kinase PKR. PLoS Pathog 2021; 17:e1009183. [PMID: 33444388 PMCID: PMC7840043 DOI: 10.1371/journal.ppat.1009183] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/27/2021] [Accepted: 11/25/2020] [Indexed: 01/06/2023] Open
Abstract
The antiviral protein kinase R (PKR) is an important host restriction factor, which poxviruses must overcome to productively infect host cells. To inhibit PKR, many poxviruses encode a pseudosubstrate mimic of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), designated K3 in vaccinia virus. Although the interaction between PKR and eIF2α is highly conserved, some K3 orthologs from host-restricted poxviruses were previously shown to inhibit PKR in a species-specific manner. To better define this host range function, we compared the sensitivity of PKR from 17 mammals to inhibition by K3 orthologs from closely related orthopoxviruses, a genus with a generally broader host range. The K3 orthologs showed species-specific inhibition of PKR and exhibited three distinct inhibition profiles. In some cases, PKR from closely related species showed dramatic differences in their sensitivity to K3 orthologs. Vaccinia virus expressing the camelpox virus K3 ortholog replicated more than three orders of magnitude better in human and sheep cells than a virus expressing vaccinia virus K3, but both viruses replicated comparably well in cow cells. Strikingly, in site-directed mutagenesis experiments between the variola virus and camelpox virus K3 orthologs, we found that different amino acid combinations were necessary to mediate improved or diminished inhibition of PKR derived from different host species. Because there is likely a limited number of possible variations in PKR that affect K3-interactions but still maintain PKR/eIF2α interactions, it is possible that by chance PKR from some potential new hosts may be susceptible to K3-mediated inhibition from a virus it has never previously encountered. We conclude that neither the sensitivity of host proteins to virus inhibition nor the effectiveness of viral immune antagonists can be inferred from their phylogenetic relatedness but must be experimentally determined. Most virus families are composed of large numbers of virus species. However, in general, only a few prototypic viruses are experimentally studied in-depth, and it is often assumed that the obtained results are representative of other viruses in the same family. In order to test this assumption, we compared the sensitivity of the antiviral protein kinase PKR from various mammals to inhibition by multiple orthologs of K3, a PKR inhibitor expressed by several closely related orthopoxviruses. We found strong differences in PKR inhibition by the K3 orthologs, demonstrating that sensitivity to a specific inhibitor was not indicative of broad sensitivity to orthologs of these inhibitors from closely related viruses. We also show that PKR from even closely related species displayed markedly different sensitivities to these poxvirus inhibitors. Furthermore, we identified amino acid residues in these K3 orthologs that are critical for enhanced or decreased PKR inhibition and found that distinct amino acid combinations affected PKRs from various species differently. Our study shows that even closely related inhibitors of an antiviral protein can vary dramatically in their inhibitory potential, and cautions that results from host-virus interaction studies of a prototypic virus genus member cannot necessarily be extrapolated to other viruses in the same genus without experimental verification.
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Affiliation(s)
- Chorong Park
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Chen Peng
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Laboratory of Viral Diseases, Bethesda, Maryland, United States of America
| | - M. Julhasur Rahman
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Sherry L. Haller
- University of Texas Medical Branch at Galveston, Department of Microbiology and Immunology, Galveston, Texas, United States of America
| | - Loubna Tazi
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Greg Brennan
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Stefan Rothenburg
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
- * E-mail:
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38
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Liu Z, Nailwal H, Rector J, Rahman MM, Sam R, McFadden G, Chan FKM. A class of viral inducer of degradation of the necroptosis adaptor RIPK3 regulates virus-induced inflammation. Immunity 2021; 54:247-258.e7. [PMID: 33444549 DOI: 10.1016/j.immuni.2020.11.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022]
Abstract
The vaccine strain against smallpox, vaccinia virus (VACV), is highly immunogenic yet causes relatively benign disease. These attributes are believed to be caused by gene loss in VACV. Using a targeted small interfering RNA (siRNA) screen, we identified a viral inhibitor found in cowpox virus (CPXV) and other orthopoxviruses that bound to the host SKP1-Cullin1-F-box (SCF) machinery and the essential necroptosis kinase receptor interacting protein kinase 3 (RIPK3). This "viral inducer of RIPK3 degradation" (vIRD) triggered ubiquitination and proteasome-mediated degradation of RIPK3 and inhibited necroptosis. In contrast to orthopoxviruses, the distantly related leporipoxvirus myxoma virus (MYXV), which infects RIPK3-deficient hosts, lacks a functional vIRD. Introduction of vIRD into VACV, which encodes a truncated and defective vIRD, enhanced viral replication in mice. Deletion of vIRD reduced CPXV-induced inflammation, viral replication, and mortality, which were reversed in RIPK3- and MLKL-deficient mice. Hence, vIRD-RIPK3 drives pathogen-host evolution and regulates virus-induced inflammation and pathogenesis.
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Affiliation(s)
- Zhijun Liu
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA
| | - Himani Nailwal
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jonah Rector
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA
| | - Masmudur M Rahman
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Richard Sam
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Grant McFadden
- Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Francis Ka-Ming Chan
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA; Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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39
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Zhang X, Tong J, Milikaimu T, He C, Wang W, Li Y. Construction and purification of ANK gene deleted recombinant goatpox virus. Virusdisease 2021; 31:526-533. [PMID: 33381625 DOI: 10.1007/s13337-020-00620-z] [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: 04/15/2020] [Accepted: 07/30/2020] [Indexed: 11/26/2022] Open
Abstract
Sheeppox virus (SPPV) and goatpox virus (GTPV) are two pathogens of host specificity. Previous studies have hypothesized that ankyrin (ANK) family may play an important role in determining host range of SPPV and GTPV. In order to verify the function of ANK proteins, it is critical to generate and purify the ANK gene deleted GTPV. In this study, the GFP gene as a reporter gene was connected with two homologous arms of ANK gene by fusion PCR. The ANK gene deleted transfer vectors were generated by inserting the PCR products into PET42b, and were transfected into testicular primary cells which were infected by GTPV. The rGTPV were identified as green fluorescence positive and properly purified. The results showed that GFP gene and two homologous arms of ANK gene were connected. The sequence was inserted in PET42b to form ANK deleted transfer vector. ANK deleted rGTPV was generated successfully by transferring vector and GTPV in cells. The ANK deleted rGTPV was purified and identified in this study. The study successfully generated the ANK deleted rGTPV. It overcomes the technical barrier for future studies about the function of ANK genes.
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Affiliation(s)
- Xueping Zhang
- Construction Corps Key Laboratory of Livestock Technology in Tarim, Alar, 843300 Xinjiang China
- College of Life Science, Tarim University, Alar, 843300 Xinjiang China
| | - Jianjun Tong
- Construction Corps Key Laboratory of Livestock Technology in Tarim, Alar, 843300 Xinjiang China
- College of Animal Science, Tarim University, Alar, 843300 Xinjiang China
| | - Tuohetiniyazi Milikaimu
- Construction Corps Key Laboratory of Livestock Technology in Tarim, Alar, 843300 Xinjiang China
- College of Animal Science, Tarim University, Alar, 843300 Xinjiang China
| | - Chuanchuan He
- Construction Corps Key Laboratory of Livestock Technology in Tarim, Alar, 843300 Xinjiang China
- College of Animal Science, Tarim University, Alar, 843300 Xinjiang China
| | - Wei Wang
- College of Animal Science, Tarim University, Alar, 843300 Xinjiang China
| | - Youwen Li
- Construction Corps Key Laboratory of Livestock Technology in Tarim, Alar, 843300 Xinjiang China
- College of Animal Science, Tarim University, Alar, 843300 Xinjiang China
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40
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Mühlemann B, Vinner L, Margaryan A, Wilhelmson H, de la Fuente Castro C, Allentoft ME, de Barros Damgaard P, Hansen AJ, Holtsmark Nielsen S, Strand LM, Bill J, Buzhilova A, Pushkina T, Falys C, Khartanovich V, Moiseyev V, Jørkov MLS, Østergaard Sørensen P, Magnusson Y, Gustin I, Schroeder H, Sutter G, Smith GL, Drosten C, Fouchier RAM, Smith DJ, Willerslev E, Jones TC, Sikora M. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science 2020; 369:369/6502/eaaw8977. [PMID: 32703849 DOI: 10.1126/science.aaw8977] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
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Affiliation(s)
- Barbara Mühlemann
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Ashot Margaryan
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences of Armenia, 0014 Yerevan, Armenia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden.,Sydsvensk Arkeologi AB, 291 22 Kristianstad, Sweden
| | | | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, 6102 Perth, WA, Australia
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Anders Johannes Hansen
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Sofie Holtsmark Nielsen
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Lisa Mariann Strand
- Department of Archaeology and Cultural History, Norwegian University of Science and Technology University Museum, 7491 Trondheim, Norway
| | - Jan Bill
- Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Alexandra Buzhilova
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow 125009, Russian Federation
| | - Tamara Pushkina
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow 119992, Russian Federation
| | - Ceri Falys
- Thames Valley Archaeological Services, Reading RG1 5NR, UK
| | - Valeri Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russian Federation
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russian Federation
| | - Marie Louise Schjellerup Jørkov
- Laboratory of Biological Anthropology, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | | | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Hannes Schroeder
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, LMU University of Munich, 80539 Munich, Germany.,German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Centre, 3015 CN Rotterdam, Netherlands
| | - Derek J Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark. .,Lundbeck Foundation GeoGenetics Center, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Terry C Jones
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. .,Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.
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41
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Vipat S, Brennan G, Park C, Haller SL, Rothenburg S. Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection. J Vis Exp 2020. [PMID: 32510495 DOI: 10.3791/61049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Vaccinia virus (VACV) was instrumental in eradicating variola virus (VARV), the causative agent of smallpox, from nature. Since its first use as a vaccine, VACV has been developed as a vector for therapeutic vaccines and as an oncolytic virus. These applications take advantage of VACV's easily manipulated genome and broad host range as an outstanding platform to generate recombinant viruses with a variety of therapeutic applications. Several methods have been developed to generate recombinant VACV, including marker selection methods and transient dominant selection. Here, we present a refinement of a host range selection method coupled with visual identification of recombinant viruses. Our method takes advantage of selective pressure generated by the host antiviral protein kinase R (PKR) coupled with a fluorescent fusion gene expressing mCherry-tagged E3L, one of two VACV PKR antagonists. The cassette, including the gene of interest and the mCherry-E3L fusion is flanked by sequences derived from the VACV genome. Between the gene of interest and mCherry-E3L is a smaller region that is identical to the first ~150 nucleotides of the 3' arm, to promote homologous recombination and loss of the mCherry-E3L gene after selection. We demonstrate that this method permits efficient, seamless generation of rVACV in a variety of cell types without requiring drug selection or extensive screening for mutant viruses.
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Affiliation(s)
- Sameera Vipat
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis
| | - Greg Brennan
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis
| | - Chorong Park
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis
| | - Sherry L Haller
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | - Stefan Rothenburg
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis;
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Rodrigues TCS, Subramaniam K, Varsani A, McFadden G, Schaefer AM, Bossart GD, Romero CH, Waltzek TB. Genome characterization of cetaceanpox virus from a managed Indo-Pacific bottlenose dolphin (Tursiops aduncus). Virus Res 2020; 278:197861. [PMID: 31923559 DOI: 10.1016/j.virusres.2020.197861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
Cetaceanpox viruses (CePVs) are associated with a cutaneous disease in cetaceans often referred to as "tattoo" lesions. To date, only partial genomic data are available for CePVs, and thus, they remain unclassified members of the subfamily Chordopoxvirinae within the family Poxviridae. Herein, we describe the first complete CePV genome sequenced from the tattoo lesion of a managed Indo-Pacific bottlenose dolphin (Tursiops aduncus), using next-generation sequencing. The T. aduncus CePV genome (CePV-TA) was determined to encode 120 proteins, including eight genes unique to the CePV-TA and five genes predicted to function as immune-evasion genes. The results of CePV-TA genetic analyses supported the creation of a new chordopoxvirus genus for CePVs. The complete sequencing of a CePV represents an important first step in unraveling the evolutionary relationship and taxonomy of CePVs, and significantly increases our understanding of the genomic characteristics of these chordopoxviruses.
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Affiliation(s)
- Thaís C S Rodrigues
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2187 Mowry Road, 32611 Gainesville, Florida, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2187 Mowry Road, 32611 Gainesville, Florida, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, 85287 Tempe, Arizona, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, Western Cape 7701, South Africa
| | - Grant McFadden
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, 85287 Tempe, Arizona, USA
| | - Adam M Schaefer
- Harbor Branch Oceanographic Institute at Florida Atlantic University, 5600 US 1, North, 34946 Fort Pierce, Florida, USA
| | - Gregory D Bossart
- Georgia Aquarium, 225 Baker Street, 30313 Atlanta, Georgia, USA; University of Miami, PO Box 016960 (R-46), 33101 Miami, Florida, USA
| | - Carlos H Romero
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2187 Mowry Road, 32611 Gainesville, Florida, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2187 Mowry Road, 32611 Gainesville, Florida, USA.
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What a Difference a Gene Makes: Identification of Virulence Factors of Cowpox Virus. J Virol 2020; 94:JVI.01625-19. [PMID: 31645446 DOI: 10.1128/jvi.01625-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 12/25/2022] Open
Abstract
Cowpox virus (CPXV) is a zoonotic orthopoxvirus (OPV) that causes spillover infections from its animal hosts to humans. In 2009, several human CPXV cases occurred through transmission from pet rats. An isolate from a diseased rat, RatPox09, exhibited significantly increased virulence in Wistar rats and caused high mortality compared to that caused by the mildly virulent laboratory strain Brighton Red (BR). The RatPox09 genome encodes four genes which are absent in the BR genome. We hypothesized that their gene products could be major factors influencing the high virulence of RatPox09. To address this hypothesis, we employed several BR-RatPox09 chimeric viruses. Using Red-mediated mutagenesis, we generated BR-based knock-in mutants with single or multiple insertions of the respective RatPox09 genes. High-throughput sequencing was used to verify the genomic integrity of all recombinant viruses, and transcriptomic analyses confirmed that the expression profiles of the genes that were adjacent to the modified ones were unaltered. While the in vitro growth kinetics were comparable to those of BR and RatPox09, we discovered that a knock-in BR mutant containing the four RatPox09-specific genes was as virulent as the RatPox09 isolate, causing death in over 75% of infected Wistar rats. Unexpectedly, the insertion of gCPXV0030 (g7tGP) alone into the BR genome resulted in significantly higher clinical scores and lower survival rates matching the rate for rats infected with RatPox09. The insertion of gCPXV0284, encoding the BTB (broad-complex, tramtrack, and bric-à-brac) domain protein D7L, also increased the virulence of BR, while the other two open reading frames failed to rescue virulence independently. In summary, our results confirmed our hypothesis that a relatively small set of four genes can contribute significantly to CPXV virulence in the natural rat animal model.IMPORTANCE With the cessation of vaccination against smallpox and its assumed cross-protectivity against other OPV infections, waning immunity could open up new niches for related poxviruses. Therefore, the identification of virulence mechanisms in CPXV is of general interest. Here, we aimed to identify virulence markers in an experimental rodent CPXV infection model using bacterial artificial chromosome (BAC)-based virus recombineering. We focused our work on the recent zoonotic CPXV isolate RatPox09, which is highly pathogenic in Wistar rats, unlike the avirulent BR reference strain. In several animal studies, we were able to identify a novel set of CPXV virulence genes. Two of the identified virulence genes, encoding a putative BTB/POZ protein (CPXVD7L) and a B22R-family protein (CPXV7tGP), respectively, have not yet been described to be involved in CPXV virulence. Our results also show that single genes can significantly affect virulence, thus facilitating adaptation to other hosts.
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Jeske K, Weber S, Pfaff F, Imholt C, Jacob J, Beer M, Ulrich RG, Hoffmann D. Molecular Detection and Characterization of the First Cowpox Virus Isolate Derived from a Bank Vole. Viruses 2019; 11:v11111075. [PMID: 31752129 PMCID: PMC6893522 DOI: 10.3390/v11111075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Cowpox virus (CPXV) is a zoonotic orthopoxvirus (OPV) that infects a wide range of mammals. CPXV-specific DNA and antibodies were detected in different vole species, such as common voles (Microtus arvalis) and bank voles (Myodes glareolus). Therefore, voles are the putative main reservoir host of CPXV. However, CPXV was up to now only isolated from common voles. Here we report the detection and isolation of a bank vole-derived CPXV strain (GerMygEK 938/17) resulting from a large-scale screening of bank voles collected in Thuringia, Germany, during 2017 and 2018. Phylogenetic analysis using the complete viral genome sequence indicated a high similarity of the novel strain to CPXV clade 3 and to OPV “Abatino” but also to Ectromeliavirus (ECTV) strains. Phenotypic characterization of CPXV GerMygEK 938/17 using inoculation of embryonated chicken eggs displayed hemorrhagic pock lesions on the chorioallantoic membrane that are typical for CPXV but not for ECTV. CPXV GerMygEK 938/17 replicated in vole-derived kidney cell lines but at lower level than on Vero76 cell line. In conclusion, the first bank vole-derived CPXV isolate provides new insights into the genetic variability of CPXV in the putative reservoir host and is a valuable tool for further studies about CPXV-host interaction and molecular evolution of OPV.
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Affiliation(s)
- Kathrin Jeske
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Saskia Weber
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Christian Imholt
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute, Toppheideweg 88, 48161 Münster, Germany
| | - Jens Jacob
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute, Toppheideweg 88, 48161 Münster, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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45
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Biswas S, Noyce RS, Babiuk LA, Lung O, Bulach DM, Bowden TR, Boyle DB, Babiuk S, Evans DH. Extended sequencing of vaccine and wild-type capripoxvirus isolates provides insights into genes modulating virulence and host range. Transbound Emerg Dis 2019; 67:80-97. [PMID: 31379093 DOI: 10.1111/tbed.13322] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/22/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022]
Abstract
The genus Capripoxvirus in the subfamily Chordopoxvirinae, family Poxviridae, comprises sheeppox virus (SPPV), goatpox virus (GTPV) and lumpy skin disease virus (LSDV), which cause the eponymous diseases across parts of Africa, the Middle East and Asia. These diseases cause significant economic losses and can have a devastating impact on the livelihoods and food security of small farm holders. So far, only live classically attenuated SPPV, GTPV and LSDV vaccines are commercially available and the history, safety and efficacy of many have not been well established. Here, we report 13 new capripoxvirus genome sequences, including the hairpin telomeres, from both pathogenic field isolates and vaccine strains. We have also updated the genome annotations to incorporate recent advances in our understanding of poxvirus biology. These new genomes and genes grouped phenetically with other previously sequenced capripoxvirus strains, and these new alignments collectively identified several recurring alterations in genes thought to modulate virulence and host range. In particular, some of the many large capripoxvirus ankyrin and kelch-like proteins are commonly mutated in vaccine strains, while the variola virus B22R-like gene homolog has also been disrupted in many vaccine isolates. Among these vaccine isolates, frameshift mutations are especially common and clearly present a risk of reversion to wild type in vaccines bearing these mutations. A consistent pattern of gene inactivation from LSDV to GTPV and then SPPV is also observed, much like the pattern of gene loss in orthopoxviruses, but, rather surprisingly, the overall genome size of ~150 kbp remains relatively constant. These data provide new insights into the evolution of capripoxviruses and the determinants of pathogenicity and host range. They will find application in the development of new vaccines with better safety, efficacy and trade profiles.
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Affiliation(s)
- Siddhartha Biswas
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Ryan S Noyce
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Lorne A Babiuk
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease (NCFAD), Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Dieter M Bulach
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - Timothy R Bowden
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - David B Boyle
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease (NCFAD), Canadian Food Inspection Agency, Winnipeg, MB, Canada.,Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - David H Evans
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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46
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Gigante CM, Gao J, Tang S, McCollum AM, Wilkins K, Reynolds MG, Davidson W, McLaughlin J, Olson VA, Li Y. Genome of Alaskapox Virus, A Novel Orthopoxvirus Isolated from Alaska. Viruses 2019; 11:E708. [PMID: 31375015 PMCID: PMC6723315 DOI: 10.3390/v11080708] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 01/10/2023] Open
Abstract
Since the eradication of smallpox, there have been increases in poxvirus infections and the emergence of several novel poxviruses that can infect humans and domestic animals. In 2015, a novel poxvirus was isolated from a resident of Alaska. Diagnostic testing and limited sequence analysis suggested this isolate was a member of the Orthopoxvirus (OPXV) genus but was highly diverged from currently known species, including Akhmeta virus. Here, we present the complete 210,797 bp genome sequence of the Alaska poxvirus isolate, containing 206 predicted open reading frames. Phylogenetic analysis of the conserved central region of the genome suggested the Alaska isolate shares a common ancestor with Old World OPXVs and is diverged from New World OPXVs. We propose this isolate as a member of a new OPXV species, Alaskapox virus (AKPV). The AKPV genome contained host range and virulence genes typical of OPXVs but lacked homologs of C4L and B7R, and the hemagglutinin gene contained a unique 120 amino acid insertion. Seven predicted AKPV proteins were most similar to proteins in non-OPXV Murmansk or NY_014 poxviruses. Genomic analysis revealed evidence suggestive of recombination with Ectromelia virus in two putative regions that contain seven predicted coding sequences, including the A-type inclusion protein.
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Affiliation(s)
- Crystal M Gigante
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jinxin Gao
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Shiyuyun Tang
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Andrea M McCollum
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kimberly Wilkins
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Mary G Reynolds
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Whitni Davidson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph McLaughlin
- Alaska Division of Public Health, Section of Epidemiology, Anchorage, AK 99503, USA
| | - Victoria A Olson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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Merchlinsky M, Albright A, Olson V, Schiltz H, Merkeley T, Hughes C, Petersen B, Challberg M. The development and approval of tecoviromat (TPOXX ®), the first antiviral against smallpox. Antiviral Res 2019; 168:168-174. [PMID: 31181284 DOI: 10.1016/j.antiviral.2019.06.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022]
Abstract
The classification of smallpox by the U.S. Centers for Disease Control and Prevention (CDC) as a Category A Bioterrorism threat agent has resulted in the U.S. Government investing significant funds to develop and stockpile a suite of medical countermeasures to ameliorate the consequences of a smallpox epidemic. This stockpile includes both vaccines for prophylaxis and antivirals to treat symptomatic patients. In this manuscript, we describe the path to approval for the first therapeutic against smallpox, identified during its development as ST-246, now known as tecovirimat and TPOXX®, a small-molecule antiviral compound sponsored by SIGA Technologies to treat symptomatic smallpox. Because the disease is no longer endemic, the development and approval of TPOXX® was only possible under the U.S. Food and Drug and Administration Animal Rule (FDA 2002). In this article, we describe the combination of animal model studies and clinical trials that were used to satisfy the FDA requirements for the approval of TPOXX ® under the Animal Rule.
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Affiliation(s)
- Michael Merchlinsky
- Biomedical Advanced Research and Development Authority, 300 C Street SW, Washington DC, 20201, USA.
| | - Andrew Albright
- Biomedical Advanced Research and Development Authority, 300 C Street SW, Washington DC, 20201, USA
| | - Victoria Olson
- National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Mail Stop G-06, 1600 Clifton Road, NE, Atlanta, 30333, Georgia
| | - Helen Schiltz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, MSC 9825, 5601 Fishers Lane, Rockville, MD, 20851, USA
| | - Tyler Merkeley
- Biomedical Advanced Research and Development Authority, 300 C Street SW, Washington DC, 20201, USA
| | - Claiborne Hughes
- Biomedical Advanced Research and Development Authority, 300 C Street SW, Washington DC, 20201, USA
| | - Brett Petersen
- National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Mail Stop G-06, 1600 Clifton Road, NE, Atlanta, 30333, Georgia
| | - Mark Challberg
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, MSC 9825, 5601 Fishers Lane, Rockville, MD, 20851, USA
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Karki M, Kumar A, Arya S, Ramakrishnan MA, Venkatesan G. Poxviral E3L ortholog (Viral Interferon resistance gene) of orf viruses of sheep and goats indicates species-specific clustering with heterogeneity among parapoxviruses. Cytokine 2019; 120:15-21. [PMID: 30991229 DOI: 10.1016/j.cyto.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 11/15/2022]
Abstract
Orf is a contagious disease posing a serious threat to animal and human health. E3L is one of the evolutionarily acquired immunomodulatory proteins present in orf virus (ORFV) and is responsible for conferring resistance to interferons among poxviruses. Genetic analysis of ORFV isolates of different geographical regions including Indian subcontinent targeting viral interferon resistance (VIR) gene (a homolog of vaccinia virus E3L gene) revealed a high percentage of identity among themselves and other ORFV isolates at both nt and aa levels as compared to low identity among parapoxviruses (PPVs). Phylogenetic analysis showed species-specific clustering among PPVs along with sub-clusters based on host species of origin among ORFVs infecting sheep and goats. Conserved amino acids in N-terminal Z-DNA binding domain and C-terminal ds RNA binding domain of VIR proteins of PPVs corresponding to ORFV VIR positions namely N37, Y41, P57, and W59 (necessary for Z-DNA binding) and E116, F127, F141, and K160 (necessary for dsRNA binding) were found. Further, the predicted protein characteristics and homology model of VIR protein of ORFV showed high structural conservation among poxviruses. This study on E3L genetic analysis of ORFV isolates may provide a better understanding of the molecular epidemiology of circulating strains in India and neighboring countries. Also, E3L deleted or mutated ORFV may be an as vaccine candidate and/or compounds blocking E3L may prove as an effective method for treating broad spectrum poxviral infections, suggesting a wider application in control of poxvirus infections.
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Affiliation(s)
- Monu Karki
- Division of Virology, ICAR-IVRI, Mukteswar 263 138, Nainital, Uttarakhand, India
| | - Amit Kumar
- Division of Virology, ICAR-IVRI, Mukteswar 263 138, Nainital, Uttarakhand, India
| | - Sargam Arya
- Division of Virology, ICAR-IVRI, Mukteswar 263 138, Nainital, Uttarakhand, India
| | - M A Ramakrishnan
- Division of Virology, ICAR-IVRI, Mukteswar 263 138, Nainital, Uttarakhand, India
| | - G Venkatesan
- Division of Virology, ICAR-IVRI, Mukteswar 263 138, Nainital, Uttarakhand, India.
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49
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Park C, Peng C, Brennan G, Rothenburg S. Species-specific inhibition of antiviral protein kinase R by capripoxviruses and vaccinia virus. Ann N Y Acad Sci 2019; 1438:18-29. [PMID: 30644558 DOI: 10.1111/nyas.14000] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
Abstract
Double-stranded RNA-activated protein kinase R (PKR) is an important and rapidly evolving antiviral kinase. Most poxviruses contain two distinct PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), the prototypic orthopoxvirus. E3 prevents PKR homodimerization by binding double-stranded RNA, while K3 acts as a pseudosubstrate inhibitor by binding directly to activated PKR and thereby inhibiting interaction with its substrate eIF2α. In our study here, we analyzed E3 and K3 orthologs from the phylogenetically distinct capripoxviruses (CaPVs), which include lumpy skin disease virus, sheeppox virus, and goatpox virus. Whereas the sheeppox virus E3 ortholog did not substantially inhibit PKR, all three CaPV K3 orthologs showed species-specific inhibition of PKR, with strong inhibition of sheep, goat, and human PKR but only weak inhibition of cow and mouse PKR. In contrast, VACV K3 strongly inhibited cow and mouse PKR but not sheep, goat, or human PKR. Infection of cell lines from the respective species with engineered VACV strains that contained different K3 orthologs showed a good correlation of PKR inhibition with virus replication and eIF2α phosphorylation. Our results show that K3 orthologs can have dramatically different effects on PKR of different species and indicate that effective PKR inhibition by K3 orthologs is crucial for virus replication.
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Affiliation(s)
- Chorong Park
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
| | - Chen Peng
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Greg Brennan
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
| | - Stefan Rothenburg
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
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50
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Conrad SJ, Liu J. Poxviruses as Gene Therapy Vectors: Generating Poxviral Vectors Expressing Therapeutic Transgenes. Methods Mol Biol 2019; 1937:189-209. [PMID: 30706397 DOI: 10.1007/978-1-4939-9065-8_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Treatments with poxvirus vectors can have long-lasting immunological impact in the host, and thus they have been extensively studied to treat diseases and for vaccine development. More importantly, the oncolytic properties of poxviruses have led to their development as cancer therapeutics. Two poxviruses, vaccinia virus (VACV) and myxoma virus (MYXV), have been extensively studied as virotherapeutics with promising results. Vaccinia virus vectors have advanced to the clinic and have been tested as oncolytic therapeutics for several cancer types with successes in phase I/II clinical trials. In addition to oncolytic applications, MYXV has been explored for additional applications including immunotherapeutics, purging of cancer progenitor cells, and treatments for graft-versus-host diseases. These novel therapeutic applications have encouraged its advancement into clinical trials. To meet the demands of different treatment needs, VACV and MYXV can be genetically engineered to express therapeutic transgenes. The engineering process used in poxvirus vectors can be very different from that of other DNA virus vectors (e.g., the herpesviruses). This chapter is intended to serve as a guide to those wishing to engineer poxvirus vectors for therapeutic transgene expression and to produce viral preparations for preclinical studies.
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Affiliation(s)
- Steven J Conrad
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA. .,The Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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