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Kuhn JH, Sibley SD, Chapman CA, Knowles NJ, Lauck M, Johnson JC, Lawson CC, Lackemeyer MG, Valenta K, Omeja P, Jahrling PB, O’Connor DH, Goldberg TL. Discovery of Lanama Virus, a Distinct Member of Species Kunsagivirus C ( Picornavirales: Picornaviridae), in Wild Vervet Monkeys ( Chlorocebus pygerythrus). Viruses 2020; 12:v12121436. [PMID: 33327396 PMCID: PMC7764893 DOI: 10.3390/v12121436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/16/2022] Open
Abstract
We report the discovery and sequence-based molecular characterization of a novel virus, lanama virus (LNMV), in blood samples obtained from two wild vervet monkeys (Chlorocebus pygerythrus), sampled near Lake Nabugabo, Masaka District, Uganda. Sequencing of the complete viral genomes and subsequent phylogenetic analysis identified LNMV as a distinct member of species Kunsagivirus C, in the undercharacterized picornavirid genus Kunsagivirus.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
- Correspondence: (J.H.K.); (T.L.G.); Tel.: +1-301-631-7245 (J.H.K.); +1-608-890-2618 (T.L.G.)
| | - Samuel D. Sibley
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Colin A. Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA;
- School of Life Sciences, Pietermaritzburg Campus, University of KwaZulu-Natal, Scottsville 3209, South Africa
- Shaanxi Key Laboratory for Animal Conservation, School of Life Sciences, Northwest University, Xi’an 710069, China
- Makerere University Biological Field Station, P.O. Box 409, Fort Portal, Uganda;
| | - Nick J. Knowles
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, UK;
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (M.L.); (D.H.O.)
| | - Joshua C. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Matthew G. Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Kim Valenta
- Department of Anthropology, University of Florida, Gainesville, FL 32603, USA;
| | - Patrick Omeja
- Makerere University Biological Field Station, P.O. Box 409, Fort Portal, Uganda;
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (M.L.); (D.H.O.)
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence: (J.H.K.); (T.L.G.); Tel.: +1-301-631-7245 (J.H.K.); +1-608-890-2618 (T.L.G.)
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Shankar A, Sibley SD, Goldberg TL, Switzer WM. Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes. Viruses 2019; 11:E605. [PMID: 31277268 PMCID: PMC6669568 DOI: 10.3390/v11070605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.
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Affiliation(s)
- Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
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Goldberg TL, Clyde VL, Gendron-Fitzpatrick A, Sibley SD, Wallace R. Severe neurologic disease and chick mortality in crested screamers (Chauna torquata) infected with a novel Gyrovirus. Virology 2018; 520:111-115. [DOI: 10.1016/j.virol.2018.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/17/2018] [Accepted: 05/20/2018] [Indexed: 12/19/2022]
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4
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Bennett AJ, Sibley SD, Lauck M, Weny G, Hyeroba D, Tumukunde A, Friedrich TC, O'Connor DH, Johnson CA, Rothman JM, Goldberg TL. Naturally Circulating Hepatitis A Virus in Olive Baboons, Uganda. Emerg Infect Dis 2018; 22:1308-10. [PMID: 27315373 PMCID: PMC4918173 DOI: 10.3201/eid2207.151837] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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5
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Nelson CW, Sibley SD, Kolokotronis SO, Hamer GL, Newman CM, Anderson TK, Walker ED, Kitron UD, Brawn JD, Ruiz MO, Goldberg TL. Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors. Virus Evol 2018; 4:vey013. [PMID: 29942654 PMCID: PMC6007309 DOI: 10.1093/ve/vey013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a 'hot spot' of virus transmission in Chicago, IL, USA. We generated full coding WNV genome sequences from spatiotemporally matched bird and mosquito samples using high-throughput sequencing, allowing a molecular evolutionary assessment with deep coverage. Mean FST among samples was 0.66 (±0.02 SE) and was bimodal, with mean nucleotide diversity being higher between samples (interhost πN = 0.001; πS = 0.024) than within them (intrahost πN < 0.0001; πS < 0.001). Eight genomic sites with FST > 1.01 (in the PrM, NS2a, NS3, NS4b, and 5'-noncoding genomic regions) showed bird versus mosquito variant frequency differences of >30 per cent and/or polymorphisms fixed in ≥5 host or vector individuals, suggesting host tropism for these variants. However, phylogenetic analyses demonstrated a lack of grouping by bird or mosquito, most inter-sample differences were synonymous (mean interhost πN/πS = 0.04), and there was no significant difference between hosts and vectors in either their nucleotide diversities or levels of purifying selection (mean intrahost πN/πS = 0.28 in birds and πN/πS = 0.21 in mosquitoes). This finding contrasts with the 'trade-off' and 'selective sieve' hypotheses that have been proposed and tested in the laboratory, which predict strong host versus vector effects on WNV genetic variation, with heightened selective constraint in birds alternating with heightened viral diversity in mosquitoes. Overall, our data show WNV to be highly selectively constrained within and between both hosts and vectors but still able to vary at a limited number of sites across the genome. Such site-specific plasticity in the face of overall selective constraint may offer a mechanism whereby highly constrained viruses such as WNV and its relatives can still adapt and emerge.
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Affiliation(s)
- Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Medical Center, Brooklyn, NY 11203-2098, USA
| | - Gabriel L Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843-2475, USA
| | - Christina M Newman
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tavis K Anderson
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edward D Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, Lansing, MI 48824-4320, USA
| | - Uriel D Kitron
- Department of Environmental Studies, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey D Brawn
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Marilyn O Ruiz
- Department of Pathobiology, University of Illinois, Urbana, IL 61802, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- Global Health Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
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Toohey-Kurth K, Sibley SD, Goldberg TL. Metagenomic assessment of adventitious viruses in commercial bovine sera. Biologicals 2017; 47:64-68. [PMID: 28366627 DOI: 10.1016/j.biologicals.2016.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/29/2022] Open
Abstract
Animal serum is an essential supplement for cell culture media. Contamination of animal serum with adventitious viruses has led to major regulatory action and product recalls. We used metagenomic methods to detect and characterize viral contaminants in 26 bovine serum samples from 12 manufacturers. Across samples, we detected sequences with homology to 20 viruses at depths of up to 50,000 viral reads per million. The viruses detected represented nine viral families plus four taxonomically unassigned viruses and had both RNA genomes and DNA genomes. Sequences ranged from 28% to 96% similar at the amino acid level to viruses in the GenBank database. The number of viruses varied from zero to 11 among samples and from one to 11 among suppliers, with only one product from one supplier being entirely "clean." For one common adventitious virus, bovine viral diarrhea virus (BVDV), abundance estimates calculated from metagenomic data (viral reads per million) closely corresponded to Ct values from quantitative real-time reverse transcription polymerase chain reaction (rtq-PCR), with metagenomics being approximately as sensitive as rtq-PCR. Metagenomics is useful for detecting taxonomically and genetically diverse adventitious viruses in commercial serum products, and it provides sensitive and quantitative information.
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Affiliation(s)
- Kathy Toohey-Kurth
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; Wisconsin Veterinary Diagnostic Laboratory, 445 Easterday Lane, Madison, WI 53706, USA
| | - Samuel D Sibley
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA
| | - Tony L Goldberg
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; University of Wisconsin-Madison Global Health Institute, 1300 University Avenue, Madison, WI 53706, USA.
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7
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Moreira ASD, Raabis SM, Graham ME, Dreyfus JM, Sibley SD, Godhardt-Cooper JA, Toohey-Kurth KL, Goldberg TL, Peek SF. Identification by next-generation sequencing of Aichivirus B in a calf with enterocolitis and neurologic signs. J Vet Diagn Invest 2017; 29:208-211. [PMID: 28176615 DOI: 10.1177/1040638716685597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 11-d-old Holstein bull calf was presented to the Veterinary Medical Teaching Hospital at the University of Wisconsin-Madison because of a 4-d history of diarrhea and persistent low-grade fever. Initial diagnosis was enteritis caused by Cryptosporidium and rotavirus. During hospitalization, the calf became stuporous and was only responsive to noxious stimuli, with hypotonia of all 4 limbs, tail, head, and neck. A cerebrospinal fluid analysis revealed xanthochromia, with marked lymphocytic pleocytosis, which was suggestive of viral meningitis and/or encephalitis. Aichivirus B, which belongs to the Kobuvirus genus, was tentatively identified in spinal fluid by next-generation DNA sequencing. This virus can affect a multitude of species, including humans and cattle, and has been isolated from both healthy and diarrheic individuals. However, to date, a possible connection with neurologic disease has not been described, to our knowledge.
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Affiliation(s)
- Ana S D Moreira
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Sarah M Raabis
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Melissa E Graham
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer M Dreyfus
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Samuel D Sibley
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer A Godhardt-Cooper
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Kathy L Toohey-Kurth
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Tony L Goldberg
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Simon F Peek
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
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Lee LM, Wallace RS, Clyde VL, Gendron-Fitzpatrick A, Sibley SD, Stuchin M, Lauck M, O'Connor DH, Nakao M, Lavikainen A, Hoberg EP, Goldberg TL. Definitive Hosts of Versteria Tapeworms (Cestoda: Taeniidae) Causing Fatal Infection in North America. Emerg Infect Dis 2016; 22:707-10. [PMID: 26983004 PMCID: PMC4806962 DOI: 10.3201/eid2204.151446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We previously reported fatal infection of a captive Bornean orangutan with metacestodes of a novel taeniid tapeworm, Versteria sp. New data implicate mustelids as definitive hosts of these tapeworms in North America. At least 2 parasite genetic lineages circulate in North America, representing separate introductions from Eurasia.
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Sibley SD, Finley MA, Baker BB, Puzach C, Armién AG, Giehtbrock D, Goldberg TL. Novel reovirus associated with epidemic mortality in wild largemouth bass (Micropterus salmoides). J Gen Virol 2016; 97:2482-2487. [DOI: 10.1099/jgv.0.000568] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Samuel D. Sibley
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | - Megan A. Finley
- Wisconsin Department of Natural Resources, Bureau of Fisheries Management, Madison, WI, USA
| | - Bridget B. Baker
- Wisconsin Department of Natural Resources, Bureau of Fisheries Management, Madison, WI, USA
| | - Corey Puzach
- United States Fish and Wildlife Service, La Crosse Fish Health Center, Onalaska, WI, USA
| | - Aníbal G. Armién
- Minnesota Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - David Giehtbrock
- Wisconsin Department of Natural Resources, Bureau of Fisheries Management, Madison, WI, USA
| | - Tony L. Goldberg
- Global Health Institute, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, USA
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10
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Ladner JT, Wiley MR, Beitzel B, Auguste AJ, Dupuis AP, Lindquist ME, Sibley SD, Kota KP, Fetterer D, Eastwood G, Kimmel D, Prieto K, Guzman H, Aliota MT, Reyes D, Brueggemann EE, St John L, Hyeroba D, Lauck M, Friedrich TC, O'Connor DH, Gestole MC, Cazares LH, Popov VL, Castro-Llanos F, Kochel TJ, Kenny T, White B, Ward MD, Loaiza JR, Goldberg TL, Weaver SC, Kramer LD, Tesh RB, Palacios G. A Multicomponent Animal Virus Isolated from Mosquitoes. Cell Host Microbe 2016; 20:357-367. [PMID: 27569558 DOI: 10.1016/j.chom.2016.07.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/09/2016] [Accepted: 07/26/2016] [Indexed: 11/24/2022]
Abstract
RNA viruses exhibit a variety of genome organization strategies, including multicomponent genomes in which each segment is packaged separately. Although multicomponent genomes are common among viruses infecting plants and fungi, their prevalence among those infecting animals remains unclear. We characterize a multicomponent RNA virus isolated from mosquitoes, designated Guaico Culex virus (GCXV). GCXV belongs to a diverse clade of segmented viruses (Jingmenvirus) related to the prototypically unsegmented Flaviviridae. The GCXV genome comprises five segments, each of which appears to be separately packaged. The smallest segment is not required for replication, and its presence is variable in natural infections. We also describe a variant of Jingmen tick virus, another Jingmenvirus, sequenced from a Ugandan red colobus monkey, thus expanding the host range of this segmented and likely multicomponent virus group. Collectively, this study provides evidence for the existence of multicomponent animal viruses and their potential relevance for animal and human health.
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Affiliation(s)
- Jason T Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Michael R Wiley
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Brett Beitzel
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alan P Dupuis
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - Michael E Lindquist
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Krishna P Kota
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - David Fetterer
- Research Support Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Gillian Eastwood
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - David Kimmel
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Karla Prieto
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Hilda Guzman
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Matthew T Aliota
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - Daniel Reyes
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Ernst E Brueggemann
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Lena St John
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Michael Lauck
- Wisconsin National Primate Research Center, Madison, WI 53715, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Marie C Gestole
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Lisa H Cazares
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; Henry M. Jackson Foundation, Bethesda, MD 20817, USA; DoD Biotechnology High Performance Computing Software Applications Institute, Frederick, MD 21702, USA; Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Vsevolod L Popov
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | - Tara Kenny
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Bailey White
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Michael D Ward
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad de Panamá, Panamá
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Makerere University, Kampala, Uganda; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Laura D Kramer
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA; School of Public Health, State University of New York at Albany, One University Place Rensselaer, East Greenbush, NY 12144, USA
| | - Robert B Tesh
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
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11
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Bailey AL, Lauck M, Mohns M, Peterson EJ, Beheler K, Brunner KG, Crosno K, Mejia A, Mutschler J, Gehrke M, Greene J, Ericsen AJ, Weiler A, Lehrer-Brey G, Friedrich TC, Sibley SD, Kallas EG, Capuano S, Rogers J, Goldberg TL, Simmons HA, O'Connor DH. Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection. Sci Transl Med 2016; 7:305ra144. [PMID: 26378244 DOI: 10.1126/scitranslmed.aab3467] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human pegivirus (HPgV)-formerly known as GB virus C and hepatitis G virus-is a poorly characterized RNA virus that infects about one-sixth of the global human population and is transmitted frequently in the blood supply. We create an animal model of HPgV infection by infecting macaque monkeys with a new simian pegivirus (SPgV) discovered in wild baboons. Using this model, we provide a high-resolution, longitudinal picture of SPgV viremia where the dose, route, and timing of infection are known. We detail the highly variable acute phase of SPgV infection, showing that the viral load trajectory early in infection is dependent on the infecting dose, whereas the chronic-phase viremic set point is not. We also show that SPgV has an extremely low propensity for accumulating sequence variation, with no consensus-level variants detected during the acute phase of infection and an average of only 1.5 variants generated per 100 infection-days. Finally, we show that SPgV RNA is highly concentrated in only two tissues: spleen and bone marrow, with bone marrow likely producing most of the virus detected in plasma. Together, these results reconcile several paradoxical observations from cross-sectional analyses of HPgV in humans and provide an animal model for studying pegivirus biology.
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Affiliation(s)
- Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Mariel Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Eric J Peterson
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Kerry Beheler
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Kevin G Brunner
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Kristin Crosno
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Andres Mejia
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - James Mutschler
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Matthew Gehrke
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Justin Greene
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Adam J Ericsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Andrea Weiler
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Gabrielle Lehrer-Brey
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Samuel D Sibley
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Esper G Kallas
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo 01310-911, Brazil
| | - Saverio Capuano
- Wisconsin National Primate Research Center, Madison, WI 53711, USA
| | - Jeffrey Rogers
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tony L Goldberg
- Wisconsin National Primate Research Center, Madison, WI 53711, USA. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA. Wisconsin National Primate Research Center, Madison, WI 53711, USA.
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12
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Lauck M, Switzer WM, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Shankar A, Greene JM, Ericsen AJ, Zheng H, Ting N, Chapman CA, Friedrich TC, Goldberg TL, O'Connor DH. Discovery and full genome characterization of a new SIV lineage infecting red-tailed guenons (Cercopithecus ascanius schmidti) in Kibale National Park, Uganda. Retrovirology 2014; 11:55. [PMID: 24996566 PMCID: PMC4226943 DOI: 10.1186/1742-4690-11-55] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/24/2014] [Indexed: 11/10/2022] Open
Abstract
Background Human immunodeficiency virus (HIV) type 1 and 2, the causative agents of acquired immunodeficiency syndrome (AIDS), emerged from African non-human primates (NHPs) through zoonotic transmission of simian immunodeficiency viruses (SIV). Among African NHPs, the Cercopithecus genus contains the largest number of species known to harbor SIV. However, our understanding of the diversity and evolution of SIVs infecting this genus is limited by incomplete taxonomic and geographic sampling, particularly in East Africa. In this study, we screened blood specimens from red-tailed guenons (Cercopithecus ascanius schmidti) from Kibale National Park, Uganda, for the presence of novel SIVs using unbiased deep-sequencing. Findings We describe and characterize the first full-length SIV genomes from wild red-tailed guenons in Kibale National Park, Uganda. This new virus, tentatively named SIVrtg_Kib, was detected in five out of twelve animals and is highly divergent from other Cercopithecus SIVs as well as from previously identified SIVs infecting red-tailed guenons, thus forming a new SIV lineage. Conclusions Our results show that the genetic diversity of SIVs infecting red-tailed guenons is greater than previously appreciated. This diversity could be the result of cross-species transmission between different guenon species or limited gene flow due to geographic separation among guenon populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - David H O'Connor
- Wisconsin National Primate Research Center, 555 Science Dr, 53705 Madison, WI, USA.
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13
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Sibley SD, Lauck M, Bailey AL, Hyeroba D, Tumukunde A, Weny G, Chapman CA, O’Connor DH, Goldberg TL, Friedrich TC. Discovery and characterization of distinct simian pegiviruses in three wild African Old World monkey species. PLoS One 2014; 9:e98569. [PMID: 24918769 PMCID: PMC4053331 DOI: 10.1371/journal.pone.0098569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/05/2014] [Indexed: 01/08/2023] Open
Abstract
Within the Flaviviridae, the recently designated genus Pegivirus has expanded greatly due to new discoveries in bats, horses, and rodents. Here we report the discovery and characterization of three simian pegiviruses (SPgV) that resemble human pegivirus (HPgV) and infect red colobus monkeys (Procolobus tephrosceles), red-tailed guenons (Cercopithecus ascanius) and an olive baboon (Papio anubis). We have designated these viruses SPgVkrc, SPgVkrtg and SPgVkbab, reflecting their host species' common names, which include reference to their location of origin in Kibale National Park, Uganda. SPgVkrc and SPgVkrtg were detected in 47% (28/60) of red colobus and 42% (5/12) red-tailed guenons, respectively, while SPgVkbab infection was observed in 1 of 23 olive baboons tested. Infections were not associated with any apparent disease, despite the generally high viral loads observed for each variant. These viruses were monophyletic and equally divergent from HPgV and pegiviruses previously identified in chimpanzees (SPgVcpz). Overall, the high degree of conservation of genetic features among the novel SPgVs, HPgV and SPgVcpz suggests conservation of function among these closely related viruses. Our study describes the first primate pegiviruses detected in Old World monkeys, expanding the known genetic diversity and host range of pegiviruses and providing insight into the natural history of this genus.
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Affiliation(s)
- Samuel D. Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Adam L. Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | | | | | - Colin A. Chapman
- Makerere University, Kampala, Uganda
- Department of Anthropology and McGill School of Environment, Montreal, Quebec, Canada
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Makerere University, Kampala, Uganda
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
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14
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Bailey AL, Lauck M, Weiler A, Sibley SD, Dinis JM, Bergman Z, Nelson CW, Correll M, Gleicher M, Hyeroba D, Tumukunde A, Weny G, Chapman C, Kuhn JH, Hughes AL, Friedrich TC, Goldberg TL, O'Connor DH. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population. PLoS One 2014; 9:e90714. [PMID: 24651479 PMCID: PMC3961216 DOI: 10.1371/journal.pone.0090714] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/03/2014] [Indexed: 12/20/2022] Open
Abstract
Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV)-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 106–107 RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF) 5 (SHFV-krc2 only) and 7 (SHFV-krc1 and SHFV-krc2). Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses.
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Affiliation(s)
- Adam L. Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Andrea Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Samuel D. Sibley
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jorge M. Dinis
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Zachary Bergman
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Chase W. Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Michael Correll
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael Gleicher
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | | | | | | | - Colin Chapman
- Makerere University, Kampala, Uganda
- Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, Canada
| | - 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
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Tony L. Goldberg
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- * E-mail:
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15
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Lauck M, Switzer WM, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Taylor B, Shankar A, Ting N, Chapman CA, Friedrich TC, Goldberg TL, O'Connor DH. Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Retrovirology 2013; 10:107. [PMID: 24139306 PMCID: PMC4016034 DOI: 10.1186/1742-4690-10-107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/03/2013] [Indexed: 01/06/2023] Open
Abstract
Background African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and “unbiased” deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses. Results We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more. Conclusions Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of “unbiased” deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.
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16
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Ghai RR, Sibley SD, Lauck M, Dinis JM, Bailey AL, Chapman CA, Omeja P, Friedrich TC, O'Connor DH, Goldberg TL. Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients. J Gen Virol 2013; 94:2670-2678. [PMID: 24077364 DOI: 10.1099/vir.0.055509-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Human pegivirus (HPgV), formerly 'GB virus C' or 'hepatitis G virus', is a member of the genus Flavivirus (Flaviviridae) that has garnered significant attention due to its inhibition of HIV, including slowing disease progression and prolonging survival in HIV-infected patients. Currently, there are six proposed HPgV genotypes that have roughly distinct geographical distributions. Genotypes 2 and 3 are the most comprehensively characterized, whereas those genotypes occurring on the African continent, where HPgV prevalence is highest, are less well studied. Using deep sequencing methods, we identified complete coding HPgV sequences in four of 28 patients (14.3%) in rural Uganda, east Africa. One of these sequences corresponds to genotype 1 and is the first complete genome of this genotype from east Africa. The remaining three sequences correspond to genotype 5, a genotype that was previously considered exclusively South African. All four positive samples were collected within a geographical area of less than 25 km(2), showing that multiple HPgV genotypes co-circulate in this area. Analysis of intra-host viral genetic diversity revealed that total single-nucleotide polymorphism frequency was approximately tenfold lower in HPgV than in hepatitis C virus. Finally, one patient was co-infected with HPgV and HIV, which, in combination with the high prevalence of HIV, suggests that this region would be a useful locale to study the interactions and co-evolution of these viruses.
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Affiliation(s)
- Ria R Ghai
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Samuel D Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Jorge M Dinis
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin A Chapman
- Department of Anthropology and McGill School of Environment, Montreal, QC, Canada, and Wildlife Conservation Society, NY, USA
| | - Patrick Omeja
- Makerere University Biological Field Station, Fort Portal, Uganda
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, Madison, WI, USA
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Tony L Goldberg
- Wisconsin National Primate Research Center, Madison, WI, USA
- Makerere University Biological Field Station, Fort Portal, Uganda
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
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17
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Lauck M, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Chapman CA, Ting N, Switzer WM, Kuhn JH, Friedrich TC, O'Connor DH, Goldberg TL. Exceptional simian hemorrhagic fever virus diversity in a wild African primate community. J Virol 2013; 87:688-91. [PMID: 23077302 PMCID: PMC3536393 DOI: 10.1128/jvi.02433-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/10/2012] [Indexed: 11/20/2022] Open
Abstract
Simian hemorrhagic fever virus (SHFV) is an arterivirus that causes severe disease in captive macaques. We describe two new SHFV variants subclinically infecting wild African red-tailed guenons (Cercopithecus ascanius). Both variants are highly divergent from the prototype virus and variants infecting sympatric red colobus (Procolobus rufomitratus). All known SHFV variants are monophyletic and share three open reading frames not present in other arteriviruses. Our data suggest a need to modify the current arterivirus classification.
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Affiliation(s)
- Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Samuel D. Sibley
- Department of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | | | - Colin A. Chapman
- Makerere University, Kampala, Uganda
- Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William M. Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, 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, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Makerere University, Kampala, Uganda
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
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Abstract
The association of the cationic macrolide antimicrobial clarithromycin (CLA) with dissolved Elliot soil humic acid (ESHA) was investigated as a function of solution chemistry. CLA-ESHA association was strongly pH-dependent, reaching a maximum near pH 6.5, and was modeled successfully using FITEQL as a 1:1 complexation reaction between CLA+ and discreet deprotonated acidic functional groups with pKa values of 4 and 6. Approximate order of magnitude increases in ionic strength produced approximately 10-fold decreases in CLA+ -ESHA association. Coefficients for CLA+ -ESHA association were significantly smaller in the presence of K+ vs Na+. Sorption data were well-fit by the Freundlich model; the Freundlich exponent was <1, suggesting CLA+ interacted with sites having a range of binding energies. Sorption appeared largely reversible; little sorption-desorption hysteresis was observed. The affinities of erythromycin and CLA+ for ESHA association sites were indistinguishable, suggesting interaction with specific sorption sites. Comparison of experimentally determined CLA-ESHA association coefficients with those predicted from single-parameter linear free energy relationships based on log Kow suggested limited contribution of hydrophobic interactions to CLA-ESHA association at environmentally relevant pH values. CLA-ESHA association constants were similar in magnitude (10(3.9)-10(4.6) to those of many nonpolar organic contaminants, and macroscopic binding data were consistent with cation exchange dominating CLA+ -ESHA association.
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Affiliation(s)
- Samuel D Sibley
- Environmental Chemistry and Technology Program, and Department of Soil Science, University of Wisconsin, Madison, Wisconsin 53706, USA
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Gu C, Karthikeyan KG, Sibley SD, Pedersen JA. Complexation of the antibiotic tetracycline with humic acid. Chemosphere 2007; 66:1494-501. [PMID: 17084433 DOI: 10.1016/j.chemosphere.2006.08.028] [Citation(s) in RCA: 224] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 08/15/2006] [Accepted: 08/18/2006] [Indexed: 05/11/2023]
Abstract
The effect of solution chemistry and sorbate-to-sorbent ratio on the interaction of the antibiotic tetracycline with Elliott soil humic acid (ESHA) was investigated using equilibrium dialysis and FITEQL modeling. Tetracycline speciation strongly influenced its sorption to ESHA. Sorption was strongly pH-dependent with a maximum around pH 4.3, and competition with H+ and electrolyte cation (Na+) was evident. The pH-dependent trend was consistent with complexation between the cationic/zwitterionic tetracycline species and deprotonated sites in ESHA (mainly carboxylic functional groups). Modification of ESHA by Ca2+ addition increased tetracycline sorption suggesting that ternary complex formation (ESHA-metal-tetracycline) may be important at higher concentrations of multivalent metal cations. The macroscopic data (pH-envelope and sorption isotherms) were successfully modeled using a discrete logK function with the FITEQL 4.0 chemical equilibrium program indicating that ESHA-tetracycline interaction could be reasonably represented as complex formation of a monoacid with discrete sites in humic acid. Sorption-desorption hysteresis was observed; both sorption and desorption isotherms were well described by the Freundlich equation.
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Affiliation(s)
- Cheng Gu
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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20
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Sibley SD, Hokanson JE, Steffes MW, Purnell JQ, Marcovina SM, Cleary PA, Brunzell JD. Increased small dense LDL and intermediate-density lipoprotein with albuminuria in type 1 diabetes. Diabetes Care 1999; 22:1165-70. [PMID: 10388983 PMCID: PMC2635089 DOI: 10.2337/diacare.22.7.1165] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE This population study examines the relationship between LDL density and persistent albuminuria in subjects with type 1 diabetes at the end of the Diabetes Control and Complications Trial (DCCT). RESEARCH DESIGN AND METHODS Subjects were classified as persistently normoalbuminuric (albumin excretion rate [AER] < 30 mg/d, n = 1,056), microalbuminuric (AER > or = 30-299 mg/day, n = 80), and macroalbuminuric (AER = 300 mg/day, n = 24) based on the last two AER measures. RESULTS Triglyceride (P < 0.01) and LDL cholesterol (P < 0.01) levels were higher in macroalbuminuric subjects compared with normoalbuminuric subjects. Cholesterol distribution by density-gradient ultracentrifugation showed an increase in intermediate-density lipoprotein (IDL) and a shift in peak LDL from buoyant toward more dense particles with progressive albuminuria. In the entire group, there was a significant negative correlation between the peak buoyancy of LDL particles and albuminuria (r = -0.238, P < 0.001, n = 1,160). This correlation persisted in the normoalbuminuric DCCT group (r = -0.138, P < 0.001, n = 1,056). CONCLUSIONS As albuminuria increases in subjects with type 1 diabetes, dyslipidemia occurs with an increase in IDL and dense LDL that may lead to increased cardiovascular disease.
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Affiliation(s)
- S D Sibley
- Division of Metabolism, Endocrinology, and Nutrition, University of Washington, Seattle 98195, USA.
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Solomon SS, Sibley SD, Dismukes JR. Growth hormone-enhanced lipolysis in the spontaneously diabetic BB rat. J Lab Clin Med 1991; 118:99-105. [PMID: 2066650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Responsiveness to lipolytic agents and glycerol output from rat adipocytes is altered by the diabetic process. We have confirmed reports that preincubation is required for growth hormone-induced lipolysis in isolated fat cells. Isolated fat cells were prepared from the epididymal fat pads of normal and spontaneously diabetic BB Wistar rats (weight, 250-400 gm) and their nondiabetic littermates by collagenase digestion. Lipolysis was measured by glycerol release after sequential perifusion with buffer alone, bovine growth hormone 1 microgram/ml, buffer alone, and epinephrine, 0.5 mumol/L. In each case isolated fat cells from control, nondiabetic, and spontaneously diabetic rats were perifused under two conditions, with and without preincubation with bovine growth hormone. Isolated fat cells from control and nondiabetic rats did not respond to bovine growth hormone without preincubation. When preincubation with bovine growth hormone, response in control rats increased from nonpreincubated glycerol values of 4.9 to 13.5 nmol glycerol released/10(6) cells/min. In contrast to controls, non-preincubated isolated fat cells from spontaneously diabetic rats that were stimulated with 1 microgram/ml bovine growth hormone went from 18.0 to 42.6 nmol of glycerol released/10(6) cells/min. No preincubation was necessary in spontaneously diabetic rats. In addition, in all situations in which preincubation or the diabetic state enhanced lipolysis with growth hormone, similar enhancement was seen with epinephrine. For nondiabetic rats both preincubated and nonpreincubated isolated fat cells respond minimally to bovine growth hormone. In conclusion, preincubation with bovine growth hormone is not required to elicit lipolysis in perifused isolated fat cells from spontaneously diabetic BB rats.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S S Solomon
- Department of Medicine, Veterans Affairs Medical Center, Memphis, TN 38104
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Abstract
Using an isolated fat cells (IFC) perifusion system and bovine growth hormone (bGH), we demonstrate that the lipolytic response in normal rat IFC is markedly enhanced after preincubation with bGH. In contrast, when IFC are prepared from diabetic animals or in the spontaneous diabetic BB rat (SDR-BB), no such preincubation is necessary. These IFC respond immediately to bGH with maximal release of glycerol. Using a binding assay established for rat growth hormone (rGH) receptors, we measured the number of GH receptors in IFC from these rats. We demonstrate a 75% increase in GH receptors after preincubation with GH in normal rat IFC, and a 125% increase in GH receptors in diabetic IFC, without preincubation. These data support the concept that enhanced sensitivity to GH is an important feature of diabetes in rats and that this sensitivity is at least in part controlled by up-regulation of GH receptors.
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Affiliation(s)
- S S Solomon
- Research and Medical Services, VAMC, Memphis, TN
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