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Vanmechelen B, Zisi Z, Gryseels S, Goüy de Bellocq J, Vrancken B, Lemey P, Maes P, Bletsa M. Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses. Viruses 2021; 13:1842. [PMID: 34578423 PMCID: PMC8473226 DOI: 10.3390/v13091842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses.
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Affiliation(s)
- Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Zafeiro Zisi
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
- OD Taxonomy and Phylogeny, Royal Institute of Natural Sciences, Vautierstreet 29, 1000 Brussels, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic;
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Prague, Czech Republic
| | - Bram Vrancken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Magda Bletsa
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
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Cai Y, Yu S, Fang Y, Bollinger L, Li Y, Lauck M, Postnikova EN, Mazur S, Johnson RF, Finch CL, Radoshitzky SR, Palacios G, Friedrich TC, Goldberg TL, O’Connor DH, Jahrling PB, Kuhn JH. Development and Characterization of a cDNA-Launch Recombinant Simian Hemorrhagic Fever Virus Expressing Enhanced Green Fluorescent Protein: ORF 2b' Is Not Required for In Vitro Virus Replication. Viruses 2021; 13:v13040632. [PMID: 33917085 PMCID: PMC8067702 DOI: 10.3390/v13040632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Simian hemorrhagic fever virus (SHFV) causes acute, lethal disease in macaques. We developed a single-plasmid cDNA-launch infectious clone of SHFV (rSHFV) and modified the clone to rescue an enhanced green fluorescent protein-expressing rSHFV-eGFP that can be used for rapid and quantitative detection of infection. SHFV has a narrow cell tropism in vitro, with only the grivet MA-104 cell line and a few other grivet cell lines being susceptible to virion entry and permissive to infection. Using rSHFV-eGFP, we demonstrate that one cricetid rodent cell line and three ape cell lines also fully support SHFV replication, whereas 55 human cell lines, 11 bat cell lines, and three rodent cells do not. Interestingly, some human and other mammalian cell lines apparently resistant to SHFV infection are permissive after transfection with the rSHFV-eGFP cDNA-launch plasmid. To further demonstrate the investigative potential of the infectious clone system, we introduced stop codons into eight viral open reading frames (ORFs). This approach suggested that at least one ORF, ORF 2b’, is dispensable for SHFV in vitro replication. Our proof-of-principle experiments indicated that rSHFV-eGFP is a useful tool for illuminating the understudied molecular biology of SHFV.
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Affiliation(s)
- Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Shuiqing Yu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Ying Fang
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (Y.F.); (Y.L.)
| | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Yanhua Li
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (Y.F.); (Y.L.)
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
| | - Elena N. Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Steven Mazur
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Reed F. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA; (S.R.R.); (G.P.)
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA; (S.R.R.); (G.P.)
| | - Thomas C. Friedrich
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI 53706, USA;
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI 53715, USA
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Correspondence: ; Tel.: +1-301-631-7245
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Di H, Morantz EK, Sadhwani H, Madden JC, Brinton MA. Insertion position as well as the inserted TRS and gene sequences differentially affect the retention of foreign gene expression by simian hemorrhagic fever virus (SHFV). Virology 2018; 525:150-160. [PMID: 30286427 DOI: 10.1016/j.virol.2018.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/26/2022]
Abstract
Recombinant SHFV infectious cDNA clones expressing a foreign gene from an additional sg mRNA were constructed. Two 3' genomic region sites, between ORF4' and ORF2b and between ORF4 and ORF5, were utilized for insertion of the myxoma M013 gene with a C-terminal V5 tag followed by one of the three inserted transcription regulatory sequences (TRS), TRS2', TRS4' or TRS7. M013 insertion at the ORF4'/ORF2b site but not the ORF4/ORF5 site generated progeny virus but only the recombinant virus with an inserted TRS2' retained the entire M013 gene through passage four. Insertion of an auto-fluorescent protein gene, iLOV, with an inserted TRS2' at the ORF4'/ORF2b site, generated viable progeny virus. iLOV expression was maintained through passage eight. Although regulation of SHFV subgenomic RNA synthesis is complex, the ORF4'/ORF2b site, which is located between the two sets of minor structural proteins, is able to tolerate foreign gene insertion.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Esther K Morantz
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Heena Sadhwani
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Joseph C Madden
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States.
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Vanmechelen B, Vergote V, Laenen L, Koundouno FR, Bore JA, Wada J, Kuhn JH, Carroll MW, Maes P. Expanding the Arterivirus Host Spectrum: Olivier's Shrew Virus 1, A Novel Arterivirus Discovered in African Giant Shrews. Sci Rep 2018; 8:11171. [PMID: 30042503 PMCID: PMC6057926 DOI: 10.1038/s41598-018-29560-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
The family Arteriviridae harbors a rapidly expanding group of viruses known to infect a divergent group of mammals, including horses, pigs, possums, primates, and rodents. Hosts infected with arteriviruses present with a wide variety of (sub) clinical symptoms, depending on the virus causing the infection and the host being infected. In this study, we determined the complete genome sequences of three variants of a previously unknown virus found in Olivier's shrews (Crocidura olivieri guineensis) sampled in Guinea. On the nucleotide level, the three genomes of this new virus, named Olivier's shrew virus 1 (OSV-1), are 88-89% similar. The genome organization of OSV-1 is characteristic of all known arteriviruses, yet phylogenetic analysis groups OSV-1 separately from all currently established arterivirus lineages. Therefore, we postulate that OSV-1 represents a member of a novel arterivirus genus. The virus described here represents the first discovery of an arterivirus in members of the order Eulipotyphla, thereby greatly expanding the known host spectrum of arteriviruses.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | - Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | | | | | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, Maryland, 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, Maryland, 21702, USA
| | - Miles W Carroll
- Research & Development Institute, National Infections Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium.
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5
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Zhang M, Veit M. Differences in signal peptide processing between GP3 glycoproteins of Arteriviridae. Virology 2018; 517:69-76. [DOI: 10.1016/j.virol.2017.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 11/15/2022]
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Di H, McIntyre AA, Brinton MA. New insights about the regulation of Nidovirus subgenomic mRNA synthesis. Virology 2018; 517:38-43. [PMID: 29475599 PMCID: PMC5987246 DOI: 10.1016/j.virol.2018.01.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 01/19/2023]
Abstract
The members of the Order Nidovirales share a similar genome organization with two overlapping nonstructural polyproteins encoded in the 5' two-thirds and the structural proteins encoded in the 3' third. They also express their 3' region proteins from a nested set of 3' co-terminal subgenomic messenger RNAs (sg mRNAs). Some but not all of the Nidovirus sg mRNAs also have a common 5' leader sequence that is acquired by a discontinuous RNA synthesis mechanism regulated by multiple 3' body transcription regulating sequences (TRSs) and the 5' leader TRS. Initial studies detected a single major body TRS for each 3' sg mRNA with a few alternative functional TRSs reported. The recent application of advanced techniques, such as next generation sequencing and ribosomal profiling, in studies of arteriviruses and coronaviruses has revealed an expanded sg mRNA transcriptome and coding capacity.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Ayisha A McIntyre
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA.
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Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus. Proc Natl Acad Sci U S A 2017; 114:E8895-E8904. [PMID: 29073030 DOI: 10.1073/pnas.1706696114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the order Nidovirales express their structural protein ORFs from a nested set of 3' subgenomic mRNAs (sg mRNAs), and for most of these ORFs, a single genomic transcription regulatory sequence (TRS) was identified. Nine TRSs were previously reported for the arterivirus Simian hemorrhagic fever virus (SHFV). In the present study, which was facilitated by next-generation sequencing, 96 SHFV body TRSs were identified that were functional in both infected MA104 cells and macaque macrophages. The abundance of sg mRNAs produced from individual TRSs was consistent over time in the two different cell types. Most of the TRSs are located in the genomic 3' region, but some are in the 5' ORF1a/1b region and provide alternative sources of nonstructural proteins. Multiple functional TRSs were identified for the majority of the SHFV 3' ORFs, and four previously identified TRSs were found not to be the predominant ones used. A third of the TRSs generated sg mRNAs with variant leader-body junction sequences. Sg mRNAs encoding E', GP2, or ORF5a as their 5' ORF as well as sg mRNAs encoding six previously unreported alternative frame ORFs or 14 previously unreported C-terminal ORFs of known proteins were also identified. Mutation of the start codon of two C-terminal ORFs in an infectious clone reduced virus yield. Mass spectrometry detected one previously unreported protein and suggested translation of some of the C-terminal ORFs. The results reveal the complexity of the transcriptional regulatory mechanism and expanded coding capacity for SHFV, which may also be characteristic of other nidoviruses.
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Moncla LH, Weiler AM, Barry G, Weinfurter JT, Dinis JM, Charlier O, Lauck M, Bailey AL, Wahl-Jensen V, Nelson CW, Johnson JC, Caì Y, Goldberg TL, O'Connor DH, Jahrling PB, Kuhn JH, Friedrich TC. Within-Host Evolution of Simian Arteriviruses in Crab-Eating Macaques. J Virol 2017; 91:e02231-16. [PMID: 27974564 PMCID: PMC5286893 DOI: 10.1128/jvi.02231-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/03/2016] [Indexed: 02/06/2023] Open
Abstract
Simian arteriviruses are a diverse clade of viruses infecting captive and wild nonhuman primates. We recently reported that Kibale red colobus virus 1 (KRCV-1) causes a mild and self-limiting disease in experimentally infected crab-eating macaques, while simian hemorrhagic fever virus (SHFV) causes lethal viral hemorrhagic fever. Here we characterize how these viruses evolved during replication in cell culture and in experimentally infected macaques. During passage in cell culture, 68 substitutions that were localized in open reading frames (ORFs) likely associated with host cell entry and exit became fixed in the KRCV-1 genome. However, we did not detect any strong signatures of selection during replication in macaques. We uncovered patterns of evolution that were distinct from those observed in surveys of wild red colobus monkeys, suggesting that these species may exert different adaptive challenges for KRCV-1. During SHFV infection, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome. Overall, our data suggest that patterns of evolution differ markedly among simian arteriviruses and among host species. IMPORTANCE Certain RNA viruses can cross species barriers and cause disease in new hosts. Simian arteriviruses are a diverse group of related viruses that infect captive and wild nonhuman primates, with associated disease severity ranging from apparently asymptomatic infections to severe, viral hemorrhagic fevers. We infected nonhuman primate cell cultures and then crab-eating macaques with either simian hemorrhagic fever virus (SHFV) or Kibale red colobus virus 1 (KRCV-1) and assessed within-host viral evolution. We found that KRCV-1 quickly acquired a large number of substitutions in its genome during replication in cell culture but that evolution in macaques was limited. In contrast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins. These patterns suggest that in addition to diverse pathogenic phenotypes, these viruses may also exhibit distinct patterns of within-host evolution both in vitro and in vivo.
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Affiliation(s)
- Louise H Moncla
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Gabrielle Barry
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | | | - Jorge M Dinis
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Olivia Charlier
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Michael Lauck
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Adam L Bailey
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Victoria Wahl-Jensen
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
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9
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Yú S, Caì Y, Lyons C, Johnson RF, Postnikova E, Mazur S, Johnson JC, Radoshitzky SR, Bailey AL, Lauck M, Goldberg TL, O’Connor DH, Jahrling PB, Friedrich TC, Kuhn JH. Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization. PLoS One 2016; 11:e0151313. [PMID: 26963736 PMCID: PMC4786270 DOI: 10.1371/journal.pone.0151313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/26/2016] [Indexed: 12/19/2022] Open
Abstract
Simian hemorrhagic fever (SHF) is an often lethal disease of Asian macaques. Simian hemorrhagic fever virus (SHFV) is one of at least three distinct simian arteriviruses that can cause SHF, but pathogenesis studies using modern methods have been scarce. Even seemingly straightforward studies, such as examining viral tissue and cell tropism in vivo, have been difficult to conduct due to the absence of standardized SHFV-specific reagents. Here we report the establishment of an in situ hybridization assay for the detection of SHFV and distantly related Kibale red colobus virus 1 (KRCV-1) RNA in cell culture. In addition, we detected SHFV RNA in formalin-fixed, paraffin-embedded tissues from an infected rhesus monkey (Macaca mulatta). The assay is easily performed and can clearly distinguish between SHFV and KRCV-1. Thus, if further developed, this assay may be useful during future studies evaluating the mechanisms by which a simian arterivirus with a restricted cell tropism can cause a lethal nonhuman primate disease similar in clinical presentation to human viral hemorrhagic fevers.
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Affiliation(s)
- Shuǐqìng Yú
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Cassandra Lyons
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Reed F. Johnson
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Elena Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Steven Mazur
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Joshua C. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America
| | - Adam L. Bailey
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Lauck
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tony L. Goldberg
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Thomas C. Friedrich
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
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10
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Lauck M, Alkhovsky SV, Bào Y, Bailey AL, Shevtsova ZV, Shchetinin AM, Vishnevskaya TV, Lackemeyer MG, Postnikova E, Mazur S, Wada J, Radoshitzky SR, Friedrich TC, Lapin BA, Deriabin PG, Jahrling PB, Goldberg TL, O'Connor DH, Kuhn JH. Historical Outbreaks of Simian Hemorrhagic Fever in Captive Macaques Were Caused by Distinct Arteriviruses. J Virol 2015; 89:8082-7. [PMID: 25972539 PMCID: PMC4505640 DOI: 10.1128/jvi.01046-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/07/2015] [Indexed: 02/04/2023] Open
Abstract
Simian hemorrhagic fever (SHF) is lethal for macaques. Based on clinical presentation and serological diagnosis, all reported SHF outbreaks were thought to be caused by different strains of the same virus, simian hemorrhagic fever virus (SHFV; Arteriviridae). Here we show that the SHF outbreaks in Sukhumi in 1964 and in Alamogordo in 1989 were caused not by SHFV but by two novel divergent arteriviruses. Our results indicate that multiple divergent simian arteriviruses can cause SHF.
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Affiliation(s)
- Michael Lauck
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sergey V Alkhovsky
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Adam L Bailey
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zinaida V Shevtsova
- Scientific-Research Institute of Experimental Pathology and Therapy, Abkhazian Academy of Sciences, Sukhumi, Georgia
| | - Alexey M Shchetinin
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatyana V Vishnevskaya
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Matthew G Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Elena Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Steven Mazur
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | | | - Boris A Lapin
- Scientific-Research Institute of Medical Primatology, Russian Academy of Medical Sciences, Sochi, Russia
| | - Petr G Deriabin
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
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11
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Brinton MA, Di H, Vatter HA. Simian hemorrhagic fever virus: Recent advances. Virus Res 2014; 202:112-9. [PMID: 25455336 PMCID: PMC4449332 DOI: 10.1016/j.virusres.2014.11.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 11/28/2022]
Abstract
SHFV induces hemorrhagic fever in macaques but not in African nonhuman primates. SHFV infection of macaque but not baboon cells induces proinflammatory cytokines. Unique N- and C-terminal genes encoded by SHFV were functionally analyzed. PLP1γ can cleave at upstream sites as well as at the expected downstream site. Eight minor structural proteins are required for infectious virus production.
The simian hemorrhagic fever virus (SHFV) genome differs from those of other members of the family Arteriviridae in encoding three papain-like one proteases (PLP1α, PLP1β and PLP1γ) at the 5′ end and two adjacent sets of four minor structural proteins at the 3′ end. The catalytic Cys and His residues and cleavage sites for each of the SHFV PLP1s were predicted and their functionality was tested in in vitro transcription/translation reactions done with wildtype or mutant polyprotein constructs. Mass spectrometry analyses of selected autoproteolytic products confirmed cleavage site locations. The catalytic Cys of PLP1α is unusual in being adjacent to an Ala instead of a Typ. PLP1γ cleaves at both downstream and upstream sites. Intermediate precursor and alternative cleavage products were detected in the in vitro transcription/translation reactions but only the three mature nsp1 proteins were detected in SHFV-infected MA104 cell lysates with SHFV nsp1 protein-specific antibodies. The duplicated sets of SHFV minor structural proteins were predicted to be functionally redundant. A stable, full-length, infectious SHFV-LVR cDNA clone was constructed and a set of mutant infectious clones was generated each with the start codon of one of the minor structural proteins mutated. All eight of the minor structural proteins were found to be required for production of infectious extracellular virus. SHFV causes a fatal hemorrhagic fever in macaques but asymptomatic, persistent infections in natural hosts such as baboons. SHFV infections were compared in macrophages and myeloid dendritic cells from baboons and macaques. Virus yields were higher from macaque cells than from baboon cells. Macrophage cultures from the two types of animals differed dramatically in the percentage of cells infected. In contrast, similar percentages of myeloid dendritic cells were infected but virus replication was efficient in the macaque cells but inefficient in the baboon cells. SHFV infection induced the production of pro-inflammatory cytokines, including IL-1β, IL-6, IL-12/23(p40), TNF-α and MIP-1α, in macaque cells but not baboon cells.
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Affiliation(s)
| | - Han Di
- Georgia State University, Atlanta, GA, USA
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12
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Vatter HA, Donaldson EF, Huynh J, Rawlings S, Manoharan M, Legasse A, Planer S, Dickerson MF, Lewis AD, Colgin LMA, Axthelm MK, Pecotte JK, Baric RS, Wong SW, Brinton MA. A simian hemorrhagic fever virus isolate from persistently infected baboons efficiently induces hemorrhagic fever disease in Japanese macaques. Virology 2014; 474:186-98. [PMID: 25463617 PMCID: PMC4304765 DOI: 10.1016/j.virol.2014.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 11/10/2022]
Abstract
Simian hemorrhagic fever virus is an arterivirus that naturally infects species of African nonhuman primates causing acute or persistent asymptomatic infections. Although it was previously estimated that 1% of baboons are SHFV-positive, more than 10% of wild-caught and captive-bred baboons tested were SHFV positive and the infections persisted for more than 10 years with detectable virus in the blood (100–1000 genomes/ml). The sequences of two baboon SHFV isolates that were amplified by a single passage in primary macaque macrophages had a high degree of identity to each other as well as to the genome of SHFV-LVR, a laboratory strain isolated in the 1960s. Infection of Japanese macaques with 100 PFU of a baboon isolate consistently produced high level viremia, pro-inflammatory cytokines, elevated tissue factor levels and clinical signs indicating coagulation defects. The baboon virus isolate provides a reliable BSL2 model of viral hemorrhagic fever disease in macaques. More than 10% of wild-caught and captive-bred baboons tested are SHFV positive. Baboons remain persistently infected for longer than 10 years. The sequences of baboon SHFV isolates were similar to each other and to SHFV LVR. A baboon SHFV (100 PFU) consistently induced hemorrhagic fever disease in macaques. A reliable BSL2 macaque model of viral hemorrhagic fever disease was developed.
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Affiliation(s)
- Heather A Vatter
- Department of Biology, Georgia State University, Atlanta, GA 30302, United States
| | - Eric F Donaldson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jeremy Huynh
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Stephanie Rawlings
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, United States
| | - Minsha Manoharan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, United States
| | - Alfred Legasse
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Shannon Planer
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Mary F Dickerson
- Division of Comparative Medicine, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Anne D Lewis
- Division of Comparative Medicine, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Lois M A Colgin
- Division of Comparative Medicine, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, United States; Division of Pathobiology and Immunology, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Jerilyn K Pecotte
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, United States
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Scott W Wong
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, United States; Division of Pathobiology and Immunology, Oregon National Primate Research Center, Beaverton, OR 97006, United States
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA 30302, United States.
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13
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Lauck M, Palacios G, Wiley MR, L Y, Fāng Y, Lackemeyer MG, Caì Y, Bailey AL, Postnikova E, Radoshitzky SR, Johnson RF, Alkhovsky SV, Deriabin PG, Friedrich TC, Goldberg TL, Jahrling PB, O'Connor DH, Kuhn JH. Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (Arteriviridae: Arterivirus). GENOME ANNOUNCEMENTS 2014; 2:e00978-14. [PMID: 25301647 PMCID: PMC4192379 DOI: 10.1128/genomea.00978-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 09/02/2014] [Indexed: 11/20/2022]
Abstract
Simian hemorrhagic fever virus (SHFV) variant NIH LVR42-0/M6941 is the only remaining SHFV in culture, and only a single genome sequence record exists in GenBank/RefSeq. We compared the genomic sequence of NIH LVR42-0/M6941 acquired from the ATCC in 2011 to NIH LVR42-0/M6941 genomes sequenced directly from nonhuman primates experimentally infected in 1989.
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Affiliation(s)
- Michael Lauck
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Michael R Wiley
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Yànhuá L
- Kansas State University, Manhattan, Kansas, USA
| | - Yīng Fāng
- Kansas State University, Manhattan, Kansas, USA
| | - Matthew G Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Adam L Bailey
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elena Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Reed F Johnson
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | | | | | | | | | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
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