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Fedurek P, Asiimwe C, Rice GK, Akankwasa WJ, Reynolds V, Hobaiter C, Kityo R, Muhanguzi G, Zuberbühler K, Crockford C, Cer RZ, Bennett AJ, Rothman JM, Bishop-Lilly KA, Goldberg TL. Selective deforestation and exposure of African wildlife to bat-borne viruses. Commun Biol 2024; 7:470. [PMID: 38649441 PMCID: PMC11035629 DOI: 10.1038/s42003-024-06139-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017-2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how "upstream" drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk.
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Affiliation(s)
- Pawel Fedurek
- Division of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
| | | | - Gregory K Rice
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | | | - Vernon Reynolds
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Anthropology, University of Oxford, 51/53 Banbury Road, Oxford, OX2 6PE, UK
| | - Catherine Hobaiter
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
| | - Robert Kityo
- Department of Zoology, Entomology & Fisheries Sciences, Makerere University, PO Box 7062, Kampala, Uganda
| | | | - Klaus Zuberbühler
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Institut des Sciences Cognitives, 67 Bd Pinel, 69500, Bron, France
| | - Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Andrew J Bennett
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Tony L Goldberg
- School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison, 1656 Linden Drive, Madison, WI, USA.
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2
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Paskey AC, Schully KL, Voegtly LJ, Arnold CE, Cer RZ, Frey KG, Blair PW, Clark DV, Ge H, Richards AL, Farris CM, Bishop-Lilly KA. A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens. Front Microbiol 2024; 15:1387208. [PMID: 38659991 PMCID: PMC11039911 DOI: 10.3389/fmicb.2024.1387208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Paul W. Blair
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Danielle V. Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Allen L. Richards
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Christina M. Farris
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
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3
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Aslam S, Roach D, Nikolich MP, Biswas B, Schooley RT, Lilly-Bishop KA, Rice GK, Cer RZ, Hamilton T, Henry M, Luong T, Salabarria AC, Sisk-Hackworth L, Filippov AA, Lebreton F, Hall L, Nir-Paz R, Onallah H, Livni G, Shostak E, Wieder-Finesod A, Yahav D, Yerushalmy O, Alkalay-Oren S, Braunstein R, Khalifa L, Rimon A, Gelman D, Hazan R. Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases. Antimicrob Agents Chemother 2024; 68:e0172823. [PMID: 38470133 PMCID: PMC10989018 DOI: 10.1128/aac.01728-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular Pseudomonas aeruginosa LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14-51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in P. aeruginosa endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.
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Affiliation(s)
- Saima Aslam
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Dwayne Roach
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Mikeljon P. Nikolich
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Biswajit Biswas
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Robert T. Schooley
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | | | - Gregory K. Rice
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- Leidos, Inc, Reston, Virginia, USA
| | - Regina Z. Cer
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Theron Hamilton
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Matthew Henry
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- The Geneva Foundation, Tacoma, Washington, USA
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | | | - Andrey A. Filippov
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lindsey Hall
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hadil Onallah
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gilat Livni
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Eran Shostak
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Anat Wieder-Finesod
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Dafna Yahav
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Braunstein
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leron Khalifa
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Gelman
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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4
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Goguet E, Olsen CH, Meyer WA, Ansari S, Powers JH, Conner TL, Coggins SA, Wang W, Wang R, Illinik L, Sanchez Edwards M, Jackson-Thompson BM, Hollis-Perry M, Wang G, Alcorta Y, Wong MA, Saunders D, Mohammed R, Balogun B, Kobi P, Kosh L, Bishop-Lilly K, Cer RZ, Arnold CE, Voegtly LJ, Fitzpatrick M, Luquette AE, Malagon F, Ortega O, Parmelee E, Davies J, Lindrose AR, Haines-Hull H, Moser MS, Samuels EC, Rekedal MS, Graydon EK, Malloy AMW, Tribble D, Burgess TH, Campbell W, Robinson S, Broder CC, O’Connell RJ, Weiss CD, Pollett S, Laing E, Mitre E. Immune and behavioral correlates of protection against symptomatic post-vaccination SARS-CoV-2 infection. Front Immunol 2024; 15:1287504. [PMID: 38566991 PMCID: PMC10985347 DOI: 10.3389/fimmu.2024.1287504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction We sought to determine pre-infection correlates of protection against SARS-CoV-2 post-vaccine inzfections (PVI) acquired during the first Omicron wave in the United States. Methods Serum and saliva samples from 176 vaccinated adults were collected from October to December of 2021, immediately before the Omicron wave, and assessed for SARS-CoV-2 Spike-specific IgG and IgA binding antibodies (bAb). Sera were also assessed for bAb using commercial assays, and for neutralization activity against several SARS-CoV-2 variants. PVI duration and severity, as well as risk and precautionary behaviors, were assessed by questionnaires. Results Serum anti-Spike IgG levels assessed by research assay, neutralization titers against Omicron subvariants, and low home risk scores correlated with protection against PVIs after multivariable regression analysis. Commercial assays did not perform as well as research assay, likely due to their lower dynamic range. Discussion In the 32 participants that developed PVI, anti-Spike IgG bAbs correlated with lower disease severity and shorter duration of illness.
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Affiliation(s)
- Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Cara H. Olsen
- Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | | | - Sara Ansari
- Quest Diagnostics, Secaucus, NJ, United States
| | - John H. Powers
- Clinical Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tonia L. Conner
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Si’Ana A. Coggins
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Wei Wang
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Richard Wang
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Luca Illinik
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Margaret Sanchez Edwards
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Belinda M. Jackson-Thompson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States
| | - Gregory Wang
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States
- General Dynamics Information Technology, Falls Church, VA, United States
| | - Yolanda Alcorta
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States
- General Dynamics Information Technology, Falls Church, VA, United States
| | - Mimi A. Wong
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States
- General Dynamics Information Technology, Falls Church, VA, United States
| | - David Saunders
- Translational Medicine Unit, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Roshila Mohammed
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Bolatito Balogun
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Priscilla Kobi
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Lakeesha Kosh
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kimberly Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
| | - Regina Z. Cer
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Logan J. Voegtly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Maren Fitzpatrick
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrea E. Luquette
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Orlando Ortega
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Edward Parmelee
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Julian Davies
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Alyssa R. Lindrose
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Hannah Haines-Hull
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Matthew S. Moser
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Emily C. Samuels
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Marana S. Rekedal
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Elizabeth K. Graydon
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Allison M. W. Malloy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - David R. Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Timothy H. Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Wesley Campbell
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Sara Robinson
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Robert J. O’Connell
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Carol D. Weiss
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Simon Pollett
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Eric D. Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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5
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Adhikari BN, Paskey AC, Frey KG, Bennett AJ, Long KA, Kuhn JH, Hamilton T, Glang L, Cer RZ, Goldberg TL, Bishop-Lilly KA. Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms. Virology 2024; 591:109992. [PMID: 38246037 PMCID: PMC10849055 DOI: 10.1016/j.virol.2024.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.
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Affiliation(s)
- Bishwo N Adhikari
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Adrian C Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, 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
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, 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; Department of Zoology, Makerere University, Kampala, Uganda
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA.
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6
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André MR, Ikeda P, Lee DAB, do Amaral RB, Carvalho LAL, Pinheiro DG, Torres JM, de Mello VVC, Rice GK, Cer RZ, Lourenço EC, Oliveira CE, Herrera HM, Barros-Battesti DM, Machado RZ, Bishop-Lilly KA, Dalgard CL, Dumler JS. Characterization of the bacterial microbiome of non-hematophagous bats and associated ectoparasites from Brazil. Front Microbiol 2023; 14:1261156. [PMID: 37928691 PMCID: PMC10620512 DOI: 10.3389/fmicb.2023.1261156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil. Methods Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n = 9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing. Results The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella). Discussion and conclusion Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.
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Affiliation(s)
- Marcos Rogério André
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Priscila Ikeda
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Antônio Braga Lee
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Renan Bressianini do Amaral
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Lucas Amoroso Lopes Carvalho
- Departamento de Biotecnologia Ambiental e Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Guariz Pinheiro
- Departamento de Biotecnologia Ambiental e Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Jaire Marinho Torres
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Victória Valente Califre de Mello
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Gregory K. Rice
- Leidos, Inc., Reston, VA, United States
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | - Regina Z. Cer
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | | | - Carisa Elisei Oliveira
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Heitor Miraglia Herrera
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Darci Moraes Barros-Battesti
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Rosangela Zacarias Machado
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Kimberly A. Bishop-Lilly
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | - Clifton L. Dalgard
- The American Genome Center, Center for Military Precision Health and Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - J. Stephen Dumler
- Department of Pathology, University of the Health Sciences, Bethesda, MD, United States
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7
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Troncos G, Popuche D, Adhikari BN, Long KA, Ríos J, Valerio M, Guevara C, Cer RZ, Bishop-Lilly KA, Ampuero JS, Silva M, Cruz CD. Novel Echarate Virus Variant Isolated from Patient with Febrile Illness, Chanchamayo, Peru. Emerg Infect Dis 2023; 29:1908-1912. [PMID: 37610254 PMCID: PMC10461681 DOI: 10.3201/eid2909.230374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
A new phlebovirus variant was isolated from an acute febrile patient in Chanchamayo, Peru. Genome characterization and p-distance analyses based on complete open reading frames revealed that the virus is probably a natural reassortant of the Echarate virus (large and small segments) with a yet-unidentified phlebovirus (M segment).
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8
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Huaman C, Paskey AC, Clouse C, Feasley A, Rader M, Rice GK, Luquette AE, Fitzpatrick MC, Drumm HM, Yan L, Cer RZ, Donduashvili M, Buchukuri T, Nanava A, Hulseberg CE, Washington MA, Laing ED, Malagon F, Broder CC, Bishop-Lilly KA, Schaefer BC. Genomic Surveillance of Rabies Virus in Georgian Canines. Viruses 2023; 15:1797. [PMID: 37766204 PMCID: PMC10537093 DOI: 10.3390/v15091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Rabies is a fatal zoonosis that is considered a re-emerging infectious disease. Although rabies remains endemic in canines throughout much of the world, vaccination programs have essentially eliminated dog rabies in the Americas and much of Europe. However, despite the goal of eliminating dog rabies in the European Union by 2020, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. To assess the genetic diversity of the strains recently circulating in Georgia, we sequenced seventy-eight RABV-positive samples from the brain tissues of rabid dogs and jackals using Illumina short-read sequencing of total RNA shotgun libraries. Seventy-seven RABV genomes were successfully assembled and annotated, with seventy-four of them reaching the coding-complete status. Phylogenetic analyses of the nucleoprotein (N) and attachment glycoprotein (G) genes placed all the assembled genomes into the Cosmopolitan clade, consistent with the Georgian origin of the samples. An amino acid alignment of the G glycoprotein ectodomain identified twelve different sequences for this domain among the samples. Only one of the ectodomain groups contained a residue change in an antigenic site, an R264H change in the G5 antigenic site. Three isolates were cultured, and these were found to be efficiently neutralized by the human monoclonal antibody A6. Overall, our data show that recently circulating RABV isolates from Georgian canines are predominantly closely related phylogroup I viruses of the Cosmopolitan clade. Current human rabies vaccines should offer protection against infection by Georgian canine RABVs. The genomes have been deposited in GenBank (accessions: OQ603609-OQ603685).
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Affiliation(s)
- Celeste Huaman
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Caitlyn Clouse
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Austin Feasley
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Madeline Rader
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Andrea E. Luquette
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Maren C. Fitzpatrick
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Hannah M. Drumm
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Lianying Yan
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | | | - Tamar Buchukuri
- State Laboratory of Agriculture (SLA), Tbilisi 0159, Georgia
| | - Anna Nanava
- US Army Medical Research Directorate-Georgia (USAMRD-G), Tbilisi 0198, Georgia
| | | | | | - Eric D. Laing
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | | | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Brian C. Schaefer
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
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9
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Goldberg TL, Blevins E, Leis EM, Standish IF, Richard JC, Lueder MR, Cer RZ, Bishop-Lilly KA. Plasticity, Paralogy, and Pseudogenization: Rhabdoviruses of Freshwater Mussels Elucidate Mechanisms of Viral Genome Diversification and the Evolution of the Finfish-Infecting Rhabdoviral Genera. J Virol 2023; 97:e0019623. [PMID: 37154732 PMCID: PMC10231222 DOI: 10.1128/jvi.00196-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
Viruses in the family Rhabdoviridae display remarkable genomic variation and ecological diversity. This plasticity occurs despite the fact that, as negative sense RNA viruses, rhabdoviruses rarely if ever recombine. Here, we describe nonrecombinatorial evolutionary processes leading to genomic diversification in the Rhabdoviridae inferred from two novel rhabdoviruses of freshwater mussels (Mollusca: Bivalvia: Unionida). Killamcar virus 1 (KILLV-1) from a plain pocketbook (Lampsilis cardium) is closely related phylogenetically and transcriptionally to finfish-infecting viruses in the subfamily Alpharhabdovirinae. KILLV-1 offers a novel example of glycoprotein gene duplication, differing from previous examples in that the paralogs overlap. Evolutionary analyses reveal a clear pattern of relaxed selection due to subfunctionalization in rhabdoviral glycoprotein paralogs, which has not previously been described in RNA viruses. Chemarfal virus 1 (CHMFV-1) from a western pearlshell (Margaritifera falcata) is closely related phylogenetically and transcriptionally to viruses in the genus Novirhabdovirus, the sole recognized genus in the subfamily Gammarhabdovirinae, representing the first known gammarhabdovirus of a host other than finfish. The CHMFV-1 G-L noncoding region contains a nontranscribed remnant gene of precisely the same length as the NV gene of most novirhabdoviruses, offering a compelling example of pseudogenization. The unique reproductive strategy of freshwater mussels involves an obligate parasitic stage in which larvae encyst in the tissues of finfish, offering a plausible ecological mechanism for viral host-switching. IMPORTANCE Viruses in the family Rhabdoviridae infect a variety of hosts, including vertebrates, invertebrates, plants and fungi, with important consequences for health and agriculture. This study describes two newly discovered viruses of freshwater mussels from the United States. One virus from a plain pocketbook (Lampsilis cardium) is closely related to fish-infecting viruses in the subfamily Alpharhabdovirinae. The other virus from a western pearlshell (Margaritifera falcata) is closely related to viruses in the subfamily Gammarhabdovirinae, which until now were only known to infect finfish. Genome features of both viruses provide new evidence of how rhabdoviruses evolved their extraordinary variability. Freshwater mussel larvae attach to fish and feed on tissues and blood, which may explain how rhabdoviruses originally jumped between mussels and fish. The significance of this research is that it improves our understanding of rhabdovirus ecology and evolution, shedding new light on these important viruses and the diseases they cause.
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Affiliation(s)
- Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emilie Blevins
- Xerces Society for Invertebrate Conservation, Portland, Oregon, USA
| | - Eric M. Leis
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Isaac F. Standish
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Jordan C. Richard
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- U.S. Fish and Wildlife Service, Southwestern Virginia Field Office, Abingdon, Virginia, USA
| | - Matthew R. Lueder
- Leidos, Reston, Virginia, USA
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Regina Z. Cer
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
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10
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Amaya M, Yin R, Yan L, Borisevich V, Adhikari BN, Bennett A, Malagon F, Cer RZ, Bishop-Lilly KA, Dimitrov AS, Cross RW, Geisbert TW, Broder CC. A Recombinant Chimeric Cedar Virus-Based Surrogate Neutralization Assay Platform for Pathogenic Henipaviruses. Viruses 2023; 15:v15051077. [PMID: 37243163 DOI: 10.3390/v15051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
The henipaviruses, Nipah virus (NiV), and Hendra virus (HeV) can cause fatal diseases in humans and animals, whereas Cedar virus is a nonpathogenic henipavirus. Here, using a recombinant Cedar virus (rCedV) reverse genetics platform, the fusion (F) and attachment (G) glycoprotein genes of rCedV were replaced with those of NiV-Bangladesh (NiV-B) or HeV, generating replication-competent chimeric viruses (rCedV-NiV-B and rCedV-HeV), both with and without green fluorescent protein (GFP) or luciferase protein genes. The rCedV chimeras induced a Type I interferon response and utilized only ephrin-B2 and ephrin-B3 as entry receptors compared to rCedV. The neutralizing potencies of well-characterized cross-reactive NiV/HeV F and G specific monoclonal antibodies against rCedV-NiV-B-GFP and rCedV-HeV-GFP highly correlated with measurements obtained using authentic NiV-B and HeV when tested in parallel by plaque reduction neutralization tests (PRNT). A rapid, high-throughput, and quantitative fluorescence reduction neutralization test (FRNT) using the GFP-encoding chimeras was established, and monoclonal antibody neutralization data derived by FRNT highly correlated with data derived by PRNT. The FRNT assay could also measure serum neutralization titers from henipavirus G glycoprotein immunized animals. These rCedV chimeras are an authentic henipavirus-based surrogate neutralization assay that is rapid, cost-effective, and can be utilized outside high containment.
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Affiliation(s)
- Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20814, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20814, USA
| | - Viktoriya Borisevich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bishwo N Adhikari
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Andrew Bennett
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
- Leidos, Inc., Reston, VA 20190, USA
| | - Francisco Malagon
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
- Leidos, Inc., Reston, VA 20190, USA
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Antony S Dimitrov
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20814, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
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11
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Paskey AC, Lim XF, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo R, Cer RZ, Long KA, Lueder MR, Glang L, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Anderson DE, Wang LF, Bishop-Lilly KA. Genomic Characterization of a Relative of Mumps Virus in Lesser Dawn Bats of Southeast Asia. Viruses 2023; 15:v15030659. [PMID: 36992368 PMCID: PMC10053730 DOI: 10.3390/v15030659] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The importance of genomic surveillance on emerging diseases continues to be highlighted with the ongoing SARS-CoV-2 pandemic. Here, we present an analysis of a new bat-borne mumps virus (MuV) in a captive colony of lesser dawn bats (Eonycteris spelaea). This report describes an investigation of MuV-specific data originally collected as part of a longitudinal virome study of apparently healthy, captive lesser dawn bats in Southeast Asia (BioProject ID PRJNA561193) which was the first report of a MuV-like virus, named dawn bat paramyxovirus (DbPV), in bats outside of Africa. More in-depth analysis of these original RNA sequences in the current report reveals that the new DbPV genome shares only 86% amino acid identity with the RNA-dependent RNA polymerase of its closest relative, the African bat-borne mumps virus (AbMuV). While there is no obvious immediate cause for concern, it is important to continue investigating and monitoring bat-borne MuVs to determine the risk of human infection.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Justin H. J. Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Casandra W. Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Kyle A. Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Matthew R. Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gavin J. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Correspondence:
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12
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Lizewski RA, Sealfon RSG, Park SW, Smith GR, Porter CK, Gonzalez-Reiche AS, Ge Y, Miller CM, Goforth CW, Pincas H, Termini MS, Ramos I, Nair VD, Lizewski SE, Alshammary H, Cer RZ, Chen HW, George MC, Arnold CE, Glang LA, Long KA, Malagon F, Marayag JJ, Nunez E, Rice GK, Santa Ana E, Schilling MA, Smith DR, Sugiharto VA, Sun P, van de Guchte A, Khan Z, Dutta J, Vangeti S, Voegtly LJ, Weir DL, Metcalf CJE, Troyanskaya OG, Bishop-Lilly KA, Grenfell BT, van Bakel H, Letizia AG, Sealfon SC. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology 2022; 33:797-807. [PMID: 35944149 PMCID: PMC9531985 DOI: 10.1097/ede.0000000000001523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/20/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised, 2-week, pre-entry quarantine. We characterize SARS-CoV-2 transmission in this cohort. METHODS Between May and November 2020, we monitored 2,469 unvaccinated, mostly male, Marine recruits prospectively during basic training. If participants tested negative for SARS-CoV-2 by quantitative polymerase chain reaction (qPCR) at the end of quarantine, they were transferred to the training site in segregated companies and underwent biweekly testing for 6 weeks. We assessed the effects of coronavirus disease 2019 (COVID-19) prevention measures on other respiratory infections with passive surveillance data, performed phylogenetic analysis, and modeled transmission dynamics and testing regimens. RESULTS Preventive measures were associated with drastically lower rates of other respiratory illnesses. However, among the trainees, 1,107 (44.8%) tested SARS-CoV-2-positive, with either mild or no symptoms. Phylogenetic analysis of viral genomes from 580 participants revealed that all cases but one were linked to five independent introductions, each characterized by accumulation of mutations across and within companies, and similar viral isolates in individuals from the same company. Variation in company transmission rates (mean reproduction number R 0 ; 5.5 [95% confidence interval [CI], 5.0, 6.1]) could be accounted for by multiple initial cases within a company and superspreader events. Simulations indicate that frequent rapid-report testing with case isolation may minimize outbreaks. CONCLUSIONS Transmission of wild-type SARS-CoV-2 among Marine recruits was approximately twice that seen in the community. Insights from SARS-CoV-2 outbreak dynamics and mutations spread in a remote, congregate setting may inform effective mitigation strategies.
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Affiliation(s)
| | - Rachel S. G. Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY
| | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Regina Z. Cer
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Hua Wei Chen
- Naval Medical Research Center, Silver Spring, MD
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
| | | | - Catherine E. Arnold
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Defense Threat Reduction Agency, Fort Belvoir, VA
| | - Lindsay A. Glang
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Kyle A. Long
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Francisco Malagon
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | | | - Edgar Nunez
- Naval Medical Research Center, Silver Spring, MD
| | - Gregory K. Rice
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | | | | | - Darci R. Smith
- Immunodiagnostics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Victor A. Sugiharto
- Naval Medical Research Center, Silver Spring, MD
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
| | - Peifang Sun
- Naval Medical Research Center, Silver Spring, MD
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Logan J. Voegtly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
- Leidos, Reston, VA
| | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD
| | | | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY
- Department of Computer Science, Princeton University, Princeton, NJ
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Kimberly A. Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
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13
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Cer RZ, Voegtly LJ, Adhikari BN, Pike BL, Lueder MR, Glang LA, Malagon F, Ana ES, Regeimbal JM, Potts-Szoke MF, Schully KL, Smith DR, Bishop-Lilly KA. Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters. Front Microbiol 2022; 13:960932. [PMID: 36033872 PMCID: PMC9399806 DOI: 10.3389/fmicb.2022.960932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Early in the pandemic, in March of 2020, an outbreak of COVID-19 occurred aboard the aircraft carrier USS Theodore Roosevelt (CVN-71), during deployment in the Western Pacific. Out of the crew of 4,779 personnel, 1,331 service members were suspected or confirmed to be infected with SARS-CoV-2. The demographic, epidemiologic, and laboratory findings of service members from subsequent investigations have characterized the outbreak as widespread transmission of virus with relatively mild symptoms and asymptomatic infection among mostly young healthy adults. At the time, there was no available vaccination against COVID-19 and there was very limited knowledge regarding SARS-CoV-2 mutation, dispersal, and transmission patterns among service members in a shipboard environment. Since that time, other shipboard outbreaks from which data can be extracted have occurred, but these later shipboard outbreaks have occurred largely in settings where the majority of the crew were vaccinated, thereby limiting spread of the virus, shortening duration of the outbreaks, and minimizing evolution of the virus within those close quarters settings. On the other hand, since the outbreak on the CVN-71 occurred prior to widespread vaccination, it continued over the course of roughly two months, infecting more than 25% of the crew. In order to better understand genetic variability and potential transmission dynamics of COVID-19 in a shipboard environment of immunologically naïve, healthy individuals, we performed whole-genome sequencing and virus culture from eighteen COVID-19-positive swabs collected over the course of one week. Using the unique variants identified in those genomes, we detected seven discrete groups of individuals within the population aboard CVN-71 infected with viruses of distinct genomic signature. This is in stark contrast to a recent outbreak aboard another U.S. Navy ship with >98% vaccinated crew after a port visit in Reykjavik, Iceland, where the outbreak lasted only approximately 2 weeks and the virus was clonal. Taken together, these results demonstrate the utility of sequencing from complex clinical samples for molecular epidemiology and they also suggest that a high rate of vaccination among a population in close communities may greatly reduce spread, thereby restricting evolution of the virus.
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Affiliation(s)
- Regina Z. Cer
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Logan J. Voegtly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Bishwo N. Adhikari
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Ft. Belvoir, VA, United States
| | - Brian L. Pike
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay A. Glang
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Ernesto Santa Ana
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - James M. Regeimbal
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Maria F. Potts-Szoke
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kevin L. Schully
- The Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Darci R. Smith
- Department of Microbiology and Immunology, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- *Correspondence: Kimberly A. Bishop-Lilly,
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14
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Goguet E, Powers JH, Olsen CH, Tribble DR, Davies J, Illinik L, Jackson-Thompson BM, Hollis-Perry M, Maiolatesi SE, Pollett S, Duplessis CA, Wang G, Ramsey KF, Reyes AE, Alcorta Y, Wong MA, Ortega O, Parmelee E, Lindrose AR, Moser M, Samuels EC, Coggins SA, Graydon E, Robinson S, Campbell W, Malloy AMW, Voegtly LJ, Arnold CE, Cer RZ, Malagon F, Bishop-Lilly KA, Burgess TH, Broder CC, Laing ED, Mitre E. Prospective Assessment of Symptoms to Evaluate Asymptomatic SARS-CoV-2 Infections in a Cohort of Health Care Workers. Open Forum Infect Dis 2022; 9:ofac030. [PMID: 35198647 PMCID: PMC8860153 DOI: 10.1093/ofid/ofac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 12/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The frequency of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unclear and may be influenced by how symptoms are evaluated. In this study, we sought to determine the frequency of asymptomatic SARS-CoV-2 infections in a prospective cohort of health care workers (HCWs). METHODS A prospective cohort of HCWs, confirmed negative for SARS-CoV-2 exposure upon enrollment, were evaluated for SARS-CoV-2 infection by monthly analysis of SARS-CoV-2 antibodies as well as referral for polymerase chain reaction testing whenever they exhibited symptoms of coronavirus disease 2019 (COVID-19). Participants completed the standardized and validated FLU-PRO Plus symptom questionnaire scoring viral respiratory disease symptom intensity and frequency at least twice monthly during baseline periods of health and each day they had any symptoms that were different from their baseline. RESULTS Two hundred sixty-three participants were enrolled between August 25 and December 31, 2020. Through February 28, 2021, 12 participants were diagnosed with SARS-CoV-2 infection. Symptom analysis demonstrated that all 12 had at least mild symptoms of COVID-19, compared with baseline health, near or at time of infection. CONCLUSIONS These results suggest that asymptomatic SARS-CoV-2 infection in unvaccinated, immunocompetent adults is less common than previously reported. While infectious inoculum doses and patient factors may have played a role in the clinical manifestations of SARS-CoV-2 infections in this cohort, we suspect that the high rate of symptomatic disease was due primarily to participant attentiveness to symptoms and collection of symptoms in a standardized, prospective fashion. These results have implications for studies that estimate SARS-CoV-2 infection prevalence and for public health measures to control the spread of this virus.
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Affiliation(s)
- Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - John H Powers
- Clinical Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Cara H Olsen
- Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Julian Davies
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Luca Illinik
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Belinda M Jackson-Thompson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Santina E Maiolatesi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Simon Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Christopher A Duplessis
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Gregory Wang
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Kathleen F Ramsey
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Anatalio E Reyes
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Yolanda Alcorta
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Mimi A Wong
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Orlando Ortega
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Parmelee
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Alyssa R Lindrose
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Matthew Moser
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Emily C Samuels
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Si’Ana A Coggins
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Elizabeth Graydon
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sara Robinson
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Wesley Campbell
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Allison M W Malloy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Logan J Voegtly
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Catherine E Arnold
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
| | - Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
| | - Francisco Malagon
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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15
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Servies TE, Larsen EC, Lindsay RC, Jones JS, Cer RZ, Voegtly LJ, Lueder MR, Malagon F, Bishop-Lilly KA, Riegodedios AJ. Notes from the Field: Outbreak of COVID-19 Among a Highly Vaccinated Population Aboard a U.S. Navy Ship After a Port Visit - Reykjavik, Iceland, July 2021. MMWR Morb Mortal Wkly Rep 2022; 71:279-281. [PMID: 35176006 PMCID: PMC8853479 DOI: 10.15585/mmwr.mm7107a5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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16
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Smith DR, Singh C, Green J, Lueder MR, Arnold CE, Voegtly LJ, Long KA, Rice GK, Luquette AE, Miner HL, Glang L, Bennett AJ, Miller RH, Malagon F, Cer RZ, Bishop-Lilly KA. Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel. Front Med (Lausanne) 2022; 8:836658. [PMID: 35155489 PMCID: PMC8829001 DOI: 10.3389/fmed.2021.836658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.
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Affiliation(s)
- Darci R. Smith
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Christopher Singh
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
- Parsons, Centreville, VA, United States
| | - Jennetta Green
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Logan J. Voegtly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Kyle A. Long
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Gregory K. Rice
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrea E. Luquette
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Haven L. Miner
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay Glang
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrew J. Bennett
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Robin H. Miller
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Regina Z. Cer
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
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17
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Letizia AG, Arnold CE, Adhikari BN, Voegtly LJ, Glang L, Rice GK, Goforth CW, Schilling MA, Weir DL, Malagon F, Ramos I, Vangeti S, Gonzalez-Reiche AS, Cer RZ, Sealfon SC, van Bakel H, Bishop-Lilly KA. Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit. Pathogens 2021; 10:pathogens10121589. [PMID: 34959544 PMCID: PMC8709254 DOI: 10.3390/pathogens10121589] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
We used epidemiologic and viral genetic information to identify a case of likely reinfection in an otherwise healthy, young Marine recruit enrolled in the prospective, longitudinal COVID-19 Health Action Response for Marines (CHARM) study, and we paired these findings with serological studies. This participant had a positive RT-PCR to SARS-CoV-2 upon routine sampling on study day 7, although he was asymptomatic at that time. He cleared the infection within seven days. On study day 46, he had developed symptoms consistent with COVID-19 and tested positive by RT-PCR for SARS-CoV-2 again. Viral whole genome sequencing was conducted from nares swabs at multiple time points. The day 7 sample was determined to be lineage B.1.340, whereas both the day 46 and day 49 samples were B.1.1. The first positive result for anti-SARS-CoV-2 IgM serology was collected on day 49 and for IgG on day 91. This case appears most consistent with a reinfection event. Our investigation into this case is unique in that we compared sequence data from more than just paired specimens, and we also assayed for immune response after both the initial infection and the later reinfection. These data demonstrate that individuals who have experienced an infection with SARS-CoV-2 may fail to generate effective or long-lasting immunity, similar to endemic human beta coronaviruses.
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Affiliation(s)
- Andrew G. Letizia
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Catherine E. Arnold
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Bishwo N. Adhikari
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Carl W. Goforth
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Megan A. Schilling
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Dawn L. Weir
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Correspondence:
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18
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Maljkovic Berry I, Rutvisuttinunt W, Voegtly LJ, Prieto K, Pollett S, Cer RZ, Kugelman JR, Bishop-Lilly KA, Morton L, Waitumbi J, Jarman RG. A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya. Front Genet 2020; 11:577563. [PMID: 33101395 PMCID: PMC7546821 DOI: 10.3389/fgene.2020.577563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of the United States Government and the Department of Defense (DoD). Next generation sequencing (NGS) and Bioinformatics (BI) enhances traditional biosurveillance by providing additional data to understand transmission, identify resistance and virulence factors, make predictions, and update risk assessments. As more and more laboratories adopt NGS and BI technologies they encounter challenges in building local capacity. In addition to choosing the right sequencing platform and approach, considerations must also be made for the complexity of bioinformatics analyses, data storage, as well as personnel and computational requirements. To address these needs, a comprehensive training program was developed covering wet lab and bioinformatics approaches to NGS. The program is meant to be modular and adaptive to meet both common and individualized needs of medical research and public health laboratories across the DoD. The training program was first deployed internationally to the Basic Science Laboratory of the US Army Medical Research Directorate-Africa in Kisumu, Kenya, which is an overseas Lab of the Walter Reed Army Institute of Research (WRAIR). A week-long workshop with intensive focus on targeted sequencing and the bioinformatics of genome assembly (n = 24 participants) was held. Post-workshop self-assessment (completed by 21 participants) noted significant median gains in knowledge domains related to NGS targeted sequencing, bioinformatics for genome assembly, and sequence quality assessment. The participants also reported that the information on study design, sample preparation, sequencing quality control, data quality assessment, reporting, and basic and advanced bioinformatics analysis were the most useful information presented in the training. While longer-term evaluations are planned, the training resulted in significant short-term improvement of a laboratory’s self-reported wet lab and bioinformatics capabilities. This framework can be used for future DoD laboratory development in the area of NGS and BI for infectious disease surveillance, ultimately enhancing this global DoD capability.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Office of Genomics and Advanced Technologies National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Logan J Voegtly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Karla Prieto
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States.,Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Regina Z Cer
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Jeffrey R Kugelman
- Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Kimberly A Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, MD, United States
| | - John Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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19
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Larson D, Brodniak SL, Voegtly LJ, Cer RZ, Glang LA, Malagon FJ, Long KA, Potocki R, Smith DR, Lanteri C, Burgess T, Bishop-Lilly KA. A Case of Early Re-infection with SARS-CoV-2. Clin Infect Dis 2020; 73:e2827-e2828. [PMID: 32949240 PMCID: PMC7543357 DOI: 10.1093/cid/ciaa1436] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Derek Larson
- Division of Infectious Disease, Fort Belvoir Community Hospital, Fort Belvoir, VA, United States of America
| | - Sterling L Brodniak
- Department of Family Medicine, Fort Belvoir Community Hospital, Fort Belvoir, VA, United States of America
| | - Logan J Voegtly
- Leidos, VA, United States of America.,Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Regina Z Cer
- Leidos, VA, United States of America.,Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Lindsay A Glang
- Leidos, VA, United States of America.,Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Francisco J Malagon
- Leidos, VA, United States of America.,Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Kyle A Long
- Leidos, VA, United States of America.,Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Ronald Potocki
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Darci R Smith
- Immunodiagnostics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
| | - Charlotte Lanteri
- Infectious Disease Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University, Bethesda, MD, United States of America
| | - Timothy Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University, Bethesda, MD, United States of America
| | - Kimberly A Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, MD, United States of America
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20
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Rozo M, Schully KL, Philipson C, Fitkariwala A, Nhim D, Som T, Sieng D, Huot B, Dul S, Gregory MJ, Heang V, Vaughn A, Vantha T, Prouty AM, Chao CC, Zhang Z, Belinskaya T, Voegtly LJ, Cer RZ, Bishop-Lilly KA, Duplessis C, Lawler JV, Clark DV. An Observational Study of Sepsis in Takeo Province Cambodia: An in-depth examination of pathogens causing severe infections. PLoS Negl Trop Dis 2020; 14:e0008381. [PMID: 32804954 PMCID: PMC7430706 DOI: 10.1371/journal.pntd.0008381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/16/2019] [Accepted: 05/11/2020] [Indexed: 01/20/2023] Open
Abstract
The world's most consequential pathogens occur in regions with the fewest diagnostic resources, leaving the true burden of these diseases largely under-represented. During a prospective observational study of sepsis in Takeo Province Cambodia, we enrolled 200 patients over an 18-month period. By coupling traditional diagnostic methods such as culture, serology, and PCR to Next Generation Sequencing (NGS) and advanced statistical analyses, we successfully identified a pathogenic cause in 46.5% of our cohort. In all, we detected 25 infectious agents in 93 patients, including severe threat pathogens such as Burkholderia pseudomallei and viral pathogens such as Dengue virus. Approximately half of our cohort remained undiagnosed; however, an independent panel of clinical adjudicators determined that 81% of those patients had infectious causes of their hospitalization, further underscoring the difficulty of diagnosing severe infections in resource-limited settings. We garnered greater insight as to the clinical features of severe infection in Cambodia through analysis of a robust set of clinical data.
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Affiliation(s)
- Michelle Rozo
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, Maryland, United States of America
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kevin L. Schully
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, Maryland, United States of America
| | - Casandra Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America
- Defense Threat Reduction Agency, Fort Belvoir, Virginia, United States of America
| | | | | | - Tin Som
- Chenda Polyclinic, Phnom Penh, Cambodia
| | - Darith Sieng
- Lucerent Clinical Solutions, Phnom Penh, Cambodia
| | - Bora Huot
- Chenda Polyclinic, Phnom Penh, Cambodia
| | - Sokha Dul
- Chenda Polyclinic, Phnom Penh, Cambodia
| | | | - Vireak Heang
- U.S. Naval Medical Research Unit TWO (NAMRU-2), Phnom Penh, Cambodia
| | - Andrew Vaughn
- U.S. Naval Medical Research Unit TWO (NAMRU-2), Phnom Penh, Cambodia
| | - Te Vantha
- Takeo Provincial Referral Hospital, Takeo, Cambodia
| | - Angela M. Prouty
- U.S. Naval Medical Research Unit TWO (NAMRU-2), Phnom Penh, Cambodia
| | - Chien-Chung Chao
- Viral and Rickettsial Diseases Department, Naval Medical Research Center-Silver Spring, Silver Spring, Maryland, United States of America
| | - Zhiwen Zhang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center-Silver Spring, Silver Spring, Maryland, United States of America
| | - Tatyana Belinskaya
- Viral and Rickettsial Diseases Department, Naval Medical Research Center-Silver Spring, Silver Spring, Maryland, United States of America
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America
- Leidos, Reston, Virginia, United States of America
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America
- Leidos, Reston, Virginia, United States of America
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America
| | - Chris Duplessis
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, Maryland, United States of America
| | - James V. Lawler
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, Maryland, United States of America
- Global Center for Health Security at Nebraska and Division of Infectious Disease, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Danielle V. Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, Maryland, United States of America
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
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21
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LaBreck PT, Rice GK, Paskey AC, Elassal EM, Cer RZ, Law NN, Schlett CD, Bennett JW, Millar EV, Ellis MW, Hamilton T, Bishop-Lilly KA, Merrell DS. Corrigendum: Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA. Front Microbiol 2020; 11:877. [PMID: 32477301 PMCID: PMC7241116 DOI: 10.3389/fmicb.2020.00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Patrick T LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gregory K Rice
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Emad M Elassal
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Regina Z Cer
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Natasha N Law
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Martin Army Community Hospital, Fort Benning, GA, United States
| | - Carey D Schlett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jason W Bennett
- Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Eugene V Millar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Michael W Ellis
- University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Kimberly A Bishop-Lilly
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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22
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJ, Cer RZ, Long KA, Lueder MR, Lim XF, Frey KG, Hamilton T, Anderson DE, Laing ED, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. Detection of Recombinant Rousettus Bat Coronavirus GCCDC1 in Lesser Dawn Bats ( Eonycteris spelaea) in Singapore. Viruses 2020; 12:E539. [PMID: 32422932 PMCID: PMC7291116 DOI: 10.3390/v12050539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/22/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Rousettus bat coronavirus GCCDC1 (RoBat-CoV GCCDC1) is a cross-family recombinant coronavirus that has previously only been reported in wild-caught bats in Yúnnan, China. We report the persistence of a related strain in a captive colony of lesser dawn bats captured in Singapore. Genomic evidence of the virus was detected using targeted enrichment sequencing, and further investigated using deeper, unbiased high throughput sequencing. RoBat-CoV GCCDC1 Singapore shared 96.52% similarity with RoBat-CoV GCCDC1 356 (NC_030886) at the nucleotide level, and had a high prevalence in the captive bat colony. It was detected at five out of six sampling time points across the course of 18 months. A partial segment 1 from an ancestral Pteropine orthoreovirus, p10, makes up the recombinant portion of the virus, which shares high similarity with previously reported RoBat-CoV GCCDC1 strains that were detected in Yúnnan, China. RoBat-CoV GCCDC1 is an intriguing, cross-family recombinant virus, with a geographical range that expands farther than was previously known. The discovery of RoBat-CoV GCCDC1 in Singapore indicates that this recombinant coronavirus exists in a broad geographical range, and can persist in bat colonies long-term.
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Affiliation(s)
- Adrian C. Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Justin H. J. Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Casandra W. Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060 USA
| | - Randy J.H. Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Kyle A. Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Matthew R. Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Eric D. Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Gavin J. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Kimberly A. Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
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23
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJH, Cer RZ, Long KA, Lueder MR, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. The temporal RNA virome patterns of a lesser dawn bat ( Eonycteris spelaea) colony revealed by deep sequencing. Virus Evol 2020; 6:veaa017. [PMID: 33747541 PMCID: PMC7079719 DOI: 10.1093/ve/veaa017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat-human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.
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Affiliation(s)
- Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Justin H J Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gregory K Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Casandra W Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Defense Threat Reduction Agency, 8725 John J. Kingman Rd., Fort Belvoir, VA 22060, USA
| | - Randy J H Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Matthew R Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gavin J Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
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Ko ER, Philipson CW, Burke TW, Cer RZ, Bishop-Lilly KA, Voegtly LJ, Tsalik EL, Woods CW, Clark DV, Schully KL. Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever. BMC Infect Dis 2019; 19:905. [PMID: 31660864 PMCID: PMC6819639 DOI: 10.1186/s12879-019-4462-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
Background Antibiotic resistance is rising at disturbing rates and contributes to the deaths of millions of people yearly. Antibiotic resistant infections disproportionately affect those with immunocompromising conditions, chronic colonization, and frequent antibiotic use such as transplant patients or those with cystic fibrosis. However, clinicians lack the diagnostic tools to confidently diagnose and treat infections, leading to widespread use of empiric broad spectrum antimicrobials, often for prolonged duration. Case presentation A 22 year-old Caucasian female with cystic fibrosis received a bilateral orthotopic lung transplantation 5 months prior to the index hospitalization. She underwent routine surveillance bronchoscopy and was admitted for post-procedure fever. A clear cause of infection was not identified by routine methods. Imaging and bronchoscopic lung biopsy did not identify an infectious agent or rejection. She was treated with a prolonged course of antimicrobials targeting known colonizing organisms from prior bronchoalveolar lavage cultures (Pseudomonas, Staphylococcus aureus, and Aspergillus). However, we identified Stenotrophomonas maltophilia in two independent whole blood samples using direct-pathogen sequencing, which was not identified by other methods. Conclusions This case represents a common clinical conundrum: identification of infection in a high-risk, complex patient. Here, direct-pathogen sequencing identified a pathogen that would not otherwise have been identified by common techniques. Had results been clinically available, treatment could have been customized, avoiding a prolonged course of broad spectrum antimicrobials that would only exacerbate resistance. Direct-pathogen sequencing is poised to fill a diagnostic gap for pathogen identification, allowing early identification and customization of treatment in a culture-independent, pathogen-agnostic manner.
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Affiliation(s)
- Emily R Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.,Department of Hospital Medicine, Duke Regional Hospital, Durham, NC, 27705, USA
| | - Casandra W Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA.,Defense Threat Reduction Agency, Fort Belvoir, VA, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA.,Leidos, Reston, VA, USA
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Logan J Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA.,Leidos, Reston, VA, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, 27710, USA.,Emergency Medicine Service, Durham VA Health Care System, Durham, NC, 27705, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, 27710, USA.,Medicine Service, Durham VA Health Care System, Durham, NC, 27705, USA
| | - Danielle V Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA
| | - Kevin L Schully
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, 21702, USA.
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25
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Millar EV, Rice GK, Schlett CD, Elassal EM, Cer RZ, Frey KG, Hamilton T, Ellis MW, Tribble DR, Bishop-Lilly KA, Bennett JW. Genomic epidemiology of MRSA infection and colonization isolates among military trainees with skin and soft tissue infection. Infection 2019; 47:729-737. [DOI: 10.1007/s15010-019-01282-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
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26
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LaBreck PT, Rice GK, Paskey AC, Elassal EM, Cer RZ, Law NN, Schlett CD, Bennett JW, Millar EV, Ellis MW, Hamilton T, Bishop-Lilly KA, Merrell DS. Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA. Front Microbiol 2018; 9:2664. [PMID: 30510541 PMCID: PMC6252503 DOI: 10.3389/fmicb.2018.02664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus is the leading cause of skin and soft tissue infections (SSTI). Some S. aureus strains harbor plasmids that carry genes that affect resistance to biocides. Among these genes, qacA encodes the QacA Multidrug Efflux Pump that imparts decreased susceptibility to chlorhexidine, a biocide used ubiquitously in healthcare facilities. Furthermore, chlorhexidine has been considered as a S. aureus decolonization strategy in community settings. We previously conducted a chlorhexidine-based SSTI prevention trial among Ft. Benning Army trainees. Analysis of a clinical isolate (C02) from that trial identified a novel qacA-positive plasmid, pC02. Prior characterization of qacA-containing plasmids is limited and conjugative transfer of those plasmids has not been demonstrated. Given the implications of increased biocide resistance, herein we characterized pC02. In silico analysis identified genes typically associated with conjugative plasmids. Moreover, pC02 was efficiently transferred to numerous S. aureus strains and to Staphylococcus epidermidis. We screened additional qacA-positive S. aureus clinical isolates and pC02 was present in 27% of those strains; other unique qacA-harboring plasmids were also identified. Ten strains were subjected to whole genome sequencing. Sequence analysis combined with plasmid screening studies suggest that qacA-containing strains are transmitted among military personnel at Ft. Benning and that strains carrying qacA are associated with SSTIs within this population. The identification of a novel mechanism of qacA conjugative transfer among Staphylococcal strains suggests a possible future increase in the prevalence of antiseptic tolerant bacterial strains, and an increase in the rate of infections in settings where these agents are commonly used.
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Affiliation(s)
- Patrick T LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gregory K Rice
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Emad M Elassal
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Regina Z Cer
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Natasha N Law
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Martin Army Community Hospital, Fort Benning, GA, United States
| | - Carey D Schlett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jason W Bennett
- Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Eugene V Millar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Michael W Ellis
- University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Kimberly A Bishop-Lilly
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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27
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Philipson C, Davenport K, Voegtly L, Lo CC, Li PE, Xu Y, Shakya M, Cer RZ, Bishop-Lilly KA, Hamilton T, Chain PSG. Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data. Bio Protoc 2017; 7:e2622. [PMID: 34595290 PMCID: PMC8438472 DOI: 10.21769/bioprotoc.2622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 07/31/2017] [Revised: 10/06/2017] [Accepted: 10/25/2017] [Indexed: 11/02/2022] Open
Abstract
Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming and command-line interfaces. EDGE bioinformatics was developed to offer scientists with little to no bioinformatics expertise a point-and-click platform for analyzing sequencing data in a rapid and reproducible manner. EDGE (Empowering the Development of Genomics Expertise) v1.0 released in January 2017, is an intuitive web-based bioinformatics platform engineered for the analysis of microbial and metagenomic NGS-based data ( Li et al., 2017 ). The EDGE bioinformatics suite combines vetted publicly available tools, and tracks settings to ensure reliable and reproducible analysis workflows. To execute the EDGE workflow, only raw sequencing reads and a project ID are necessary. Users can access in-house data, or run analyses on samples deposited in Sequence Read Archive. Default settings offer a robust first-glance and are often sufficient for novice users. All analyses are modular; users can easily turn workflows on/off, and modify parameters to cater to project needs. Results are compiled and available for download in a PDF-formatted report containing publication quality figures. We caution that interpreting results still requires in-depth scientific understanding, however report visuals are often informative, even to novice users.
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Affiliation(s)
- Casandra Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Logan Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, USA
- Leidos, 11955 Freedom Drive, Reston VA, USA
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Yan Xu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, USA
- Leidos, 11955 Freedom Drive, Reston VA, USA
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD, USA
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Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT. Erratum to: The somatic autosomal mutation matrix in cancer genomes. Hum Genet 2015; 134:865-7. [PMID: 26071096 PMCID: PMC4643558 DOI: 10.1007/s00439-015-1576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nuri A Temiz
- In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD, 21702, USA
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Cer RZ, Herrera-Galeano JE, Anderson JJ, Bishop-Lilly KA, Mokashi VP. miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation. Gigascience 2014; 3:20. [PMID: 25379175 PMCID: PMC4212236 DOI: 10.1186/2047-217x-3-20] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/30/2014] [Indexed: 02/04/2023] Open
Abstract
Background Understanding the biological roles of microRNAs (miRNAs) is a an active area of research that has produced a surge of publications in PubMed, particularly in cancer research. Along with this increasing interest, many open-source bioinformatics tools to identify existing and/or discover novel miRNAs in next-generation sequencing (NGS) reads become available. While miRNA identification and discovery tools are significantly improved, the development of miRNA differential expression analysis tools, especially in temporal studies, remains substantially challenging. Further, the installation of currently available software is non-trivial and steps of testing with example datasets, trying with one’s own dataset, and interpreting the results require notable expertise and time. Subsequently, there is a strong need for a tool that allows scientists to normalize raw data, perform statistical analyses, and provide intuitive results without having to invest significant efforts. Findings We have developed miRNA Temporal Analyzer (mirnaTA), a bioinformatics package to identify differentially expressed miRNAs in temporal studies. mirnaTA is written in Perl and R (Version 2.13.0 or later) and can be run across multiple platforms, such as Linux, Mac and Windows. In the current version, mirnaTA requires users to provide a simple, tab-delimited, matrix file containing miRNA name and count data from a minimum of two to a maximum of 20 time points and three replicates. To recalibrate data and remove technical variability, raw data is normalized using Normal Quantile Transformation (NQT), and linear regression model is used to locate any miRNAs which are differentially expressed in a linear pattern. Subsequently, remaining miRNAs which do not fit a linear model are further analyzed in two different non-linear methods 1) cumulative distribution function (CDF) or 2) analysis of variances (ANOVA). After both linear and non-linear analyses are completed, statistically significant miRNAs (P < 0.05) are plotted as heat maps using hierarchical cluster analysis and Euclidean distance matrix computation methods. Conclusions mirnaTA is an open-source, bioinformatics tool to aid scientists in identifying differentially expressed miRNAs which could be further mined for biological significance. It is expected to provide researchers with a means of interpreting raw data to statistical summaries in a fast and intuitive manner.
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Affiliation(s)
- Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA ; Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720-A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - J Enrique Herrera-Galeano
- Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA ; Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720-A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Joseph J Anderson
- Chem Bio Research Center of Excellence, Defense Threat Reduction Agency, 2800 Bush River Road E2800-b198, Aberdeen Proving Ground, MD 21010, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA ; Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720-A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Vishwesh P Mokashi
- Biological Defense Research Directorate, Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
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Herrera-Galeano JE, Frey KG, Cer RZ, Mateczun AJ, Bishop-Lilly KA, Mokashi VP. BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results. Source Code Biol Med 2014; 9:7. [PMID: 24685334 PMCID: PMC3974413 DOI: 10.1186/1751-0473-9-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/22/2014] [Indexed: 11/24/2022]
Abstract
Background The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how the reads that align to the same sequence are distributed. The same question applies to preparation of primers or probes for microarray experiments. Although there are several packages that allow the visualization of DNA segments in relation to a reference, in most cases they require the visualization of one reference at a time and the capture of screen shots for each segment. Such a procedure could be tedious and time consuming. The field is in need of a solution that automates the capture of coverage plots for all the segments of interest. Results We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. Conclusions BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set.
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Xu K, Rockx B, Xie Y, DeBuysscher BL, Fusco DL, Zhu Z, Chan YP, Xu Y, Luu T, Cer RZ, Feldmann H, Mokashi V, Dimitrov DS, Bishop-Lilly KA, Broder CC, Nikolov DB. Crystal structure of the Hendra virus attachment G glycoprotein bound to a potent cross-reactive neutralizing human monoclonal antibody. PLoS Pathog 2013; 9:e1003684. [PMID: 24130486 PMCID: PMC3795035 DOI: 10.1371/journal.ppat.1003684] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 06/21/2012] [Accepted: 08/20/2013] [Indexed: 12/25/2022] Open
Abstract
The henipaviruses, represented by Hendra (HeV) and Nipah (NiV) viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia, Southeast Asia, India and Bangladesh. The high morbidity and mortality rates associated with infection and lack of licensed antiviral therapies make the henipaviruses a potential biological threat to humans and livestock. Henipavirus entry is initiated by the attachment of the G envelope glycoprotein to host cell membrane receptors. Previously, henipavirus-neutralizing human monoclonal antibodies (hmAb) have been isolated using the HeV-G glycoprotein and a human naïve antibody library. One cross-reactive and receptor-blocking hmAb (m102.4) was recently demonstrated to be an effective post-exposure therapy in two animal models of NiV and HeV infection, has been used in several people on a compassionate use basis, and is currently in development for use in humans. Here, we report the crystal structure of the complex of HeV-G with m102.3, an m102.4 derivative, and describe NiV and HeV escape mutants. This structure provides detailed insight into the mechanism of HeV and NiV neutralization by m102.4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines. Since their initial emergence, henipaviruses have continued to cause spillover events in both human and livestock populations, posing significant biothreats. Currently there are no licensed or approved therapies for treatment of henipavirus infection and the human case mortality rates average >70%. We used X-ray crystallography to determine the high-resolution structures of the Hendra virus G glycoprotein in complex with a cross-reactive neutralizing human monoclonal antibody. The structures provide detailed insight into the mechanism of HeV and NiV neutralization by this potent and clinically-relevant human monoclonal antibody that is currently in development for use in humans. This monoclonal antibody was recently shown to be an effective post-exposure therapy in non-human models of lethal Hendra virus infection. Indeed, it has already been used in four people on a compassionate use request, three in Australia and one in the United States, as a therapeutic agent. Furthermore, we identified and characterized two escape mutants generated in vitro and evaluated their mechanism of escape. Our results serve as a blueprint for further optimization of this antibody and for the development of novel entry inhibitors and vaccines. This report also supports the additional pre-clinical data required for eventual licensure by detailing the antibody's mechanism of henipavirus neutralization.
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Affiliation(s)
- Kai Xu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Barry Rockx
- Sealy Center for Vaccine Development, Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yihu Xie
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Blair L. DeBuysscher
- Laboratory of Virology, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
- Division of Biological Sciences and the University of Montana, Missoula, Montana, United States of America
| | - Deborah L. Fusco
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Zhongyu Zhu
- Protein Interactions Group, CCRNP, CCR, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - Yee-Peng Chan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Yan Xu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Truong Luu
- Naval Medical Research Center, NMRC-Frederick, Fort Detrick, Maryland, United States of America
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
| | - Regina Z. Cer
- Naval Medical Research Center, NMRC-Frederick, Fort Detrick, Maryland, United States of America
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vishwesh Mokashi
- Naval Medical Research Center, NMRC-Frederick, Fort Detrick, Maryland, United States of America
| | - Dimiter S. Dimitrov
- Protein Interactions Group, CCRNP, CCR, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - Kimberly A. Bishop-Lilly
- Naval Medical Research Center, NMRC-Frederick, Fort Detrick, Maryland, United States of America
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Cer RZ, Donohue DE, Mudunuri US, Temiz NA, Loss MA, Starner NJ, Halusa GN, Volfovsky N, Yi M, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. Nucleic Acids Res 2012; 41:D94-D100. [PMID: 23125372 PMCID: PMC3531222 DOI: 10.1093/nar/gks955] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [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] [Indexed: 01/18/2023] Open
Abstract
The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.
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Affiliation(s)
- Regina Z Cer
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA
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Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, Stephens RM. Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool). ACTA ACUST UNITED AC 2012; Chapter 18:Unit 18.7.1-22. [PMID: 22470144 DOI: 10.1002/0471142905.hg1807s73] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp).
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Affiliation(s)
- R Z Cer
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc, National Cancer Institute-Frederick, Frederick, Maryland, USA
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Bacolla A, Wang G, Jain A, Chuzhanova NA, Cer RZ, Collins JR, Cooper DN, Bohr VA, Vasquez KM. Non-B DNA-forming sequences and WRN deficiency independently increase the frequency of base substitution in human cells. J Biol Chem 2011; 286:10017-26. [PMID: 21285356 DOI: 10.1074/jbc.m110.176636] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Although alternative DNA secondary structures (non-B DNA) can induce genomic rearrangements, their associated mutational spectra remain largely unknown. The helicase activity of WRN, which is absent in the human progeroid Werner syndrome, is thought to counteract this genomic instability. We determined non-B DNA-induced mutation frequencies and spectra in human U2OS osteosarcoma cells and assessed the role of WRN in isogenic knockdown (WRN-KD) cells using a supF gene mutation reporter system flanked by triplex- or Z-DNA-forming sequences. Although both non-B DNA and WRN-KD served to increase the mutation frequency, the increase afforded by WRN-KD was independent of DNA structure despite the fact that purified WRN helicase was found to resolve these structures in vitro. In U2OS cells, ∼70% of mutations comprised single-base substitutions, mostly at G·C base-pairs, with the remaining ∼30% being microdeletions. The number of mutations at G·C base-pairs in the context of NGNN/NNCN sequences correlated well with predicted free energies of base stacking and ionization potentials, suggesting a possible origin via oxidation reactions involving electron loss and subsequent electron transfer (hole migration) between neighboring bases. A set of ∼40,000 somatic mutations at G·C base pairs identified in a lung cancer genome exhibited similar correlations, implying that hole migration may also be involved. We conclude that alternative DNA conformations, WRN deficiency and lung tumorigenesis may all serve to increase the mutation rate by promoting, through diverse pathways, oxidation reactions that perturb the electron orbitals of neighboring bases. It follows that such "hole migration" is likely to play a much more widespread role in mutagenesis than previously anticipated.
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Affiliation(s)
- Albino Bacolla
- Department of Molecular Carcinogenesis, Science Park-Research Division, The University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957, USA
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Cer RZ, Bruce KH, Donohue DE, Temiz AN, Bacolla A, Mudunuri US, Yi M, Volfovsky N, Luke BT, Collins JR, Stephens RM. Introducing the non-B DNA Motif Search Tool (nBMST). Genome Biol 2011. [PMCID: PMC3439028 DOI: 10.1186/gb-2011-12-s1-p34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res 2010; 39:D383-91. [PMID: 21097885 PMCID: PMC3013731 DOI: 10.1093/nar/gkq1170] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [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] [Indexed: 12/15/2022] Open
Abstract
Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov.
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Affiliation(s)
- Regina Z Cer
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc, NCI-Frederick, Frederick, MD 21702, USA
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Abstract
Botulinum neurotoxin is a pharmaceutical treatment used for an increasing number of neurological and non-neurological indications, symptoms and diseases. Despite the wealth of clinical reports that involve the timing of the therapeutic effects of this toxin, few studies have attempted to integrate these data into unified models. Secondary reactions have also been examined including the development of adverse events, resistance to repeated applications, and nerve terminal sprouting. Our primary intent for conducting this review was to gather relevant pharmacodynamic data from suitable biomedical literature regarding botulinum neurotoxins via the use of automated data-mining techniques. We envision that mathematical models will ultimately be of value to those who are healthcare decision makers and providers, as well as clinical and basic researchers. Furthermore, we hypothesize that the combination of this computer-intensive approach with mathematical modeling will predict the percentage of patients who will favorably or adversely respond to this treatment and thus will eventually assist in developing the increasingly important area of personalized medicine.
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Affiliation(s)
- Frank J Lebeda
- Combat Casualty Care Research Program, US Army Medical Research and Materiel Command, 504 Scott Street, Ft Detrick, MD 21702-5012, USA.
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Cer RZ, Mudunuri U, Stephens R, Lebeda FJ. IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. Nucleic Acids Res 2009; 37:W441-5. [PMID: 19395593 PMCID: PMC2703898 DOI: 10.1093/nar/gkp253] [Citation(s) in RCA: 281] [Impact Index Per Article: 18.7] [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] [Indexed: 11/18/2022] Open
Abstract
A new web-server tool estimates Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules (e.g. proteins, polynucleic acids) and ligands. This converter was developed to enable end users to help gauge the quality of the underlying assumptions used in these calculations which depend on the type of mechanism of inhibitor action and the concentrations of the interacting molecular species. Additional calculations are performed for nonclassical, tightly bound inhibitors of enzyme-substrate or of macromolecule-ligand systems in which free, rather than total concentrations of the reacting species are required. Required user-defined input values include the total enzyme (or another target molecule) and substrate (or ligand) concentrations, the Km of the enzyme-substrate (or the Kd of the target-ligand) reaction, and the IC50 value. Assumptions and caveats for these calculations are discussed along with examples taken from the literature. The host database for this converter contains kinetic constants and other data for inhibitors of the proteolytic clostridial neurotoxins (http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp).
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Affiliation(s)
- R Z Cer
- Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
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Rasko DA, Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, Gill SR, Ravel J. Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1. J Bacteriol 2006; 189:52-64. [PMID: 17041058 PMCID: PMC1797222 DOI: 10.1128/jb.01313-06] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [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: 11/20/2022] Open
Abstract
The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species.
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Affiliation(s)
- David A Rasko
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J Bacteriol 2006; 188:3402-8. [PMID: 16621835 PMCID: PMC1447464 DOI: 10.1128/jb.188.9.3402-3408.2006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic relatedness of the Bacillus anthracis typing phages Gamma and Cherry was determined by nucleotide sequencing and comparative analysis. The genomes of these two phages were identical except at three variable loci, which showed heterogeneity within individual lysates and among Cherry, Wbeta, Fah, and four Gamma bacteriophage sequences.
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Affiliation(s)
- Derrick E Fouts
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, De BK, Sacchi CT, Fitzgerald C, Mayer LW, Maiden MCJ, Priest FG, Barker M, Jiang L, Cer RZ, Rilstone J, Peterson SN, Weyant RS, Galloway DR, Read TD, Popovic T, Fraser CM. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 2004; 101:8449-54. [PMID: 15155910 PMCID: PMC420414 DOI: 10.1073/pnas.0402414101] [Citation(s) in RCA: 391] [Impact Index Per Article: 19.6] [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: 12/13/2022] Open
Abstract
Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. Although homologues of the pXO2 encoded capsule genes were not found, a polysaccharide capsule cluster is encoded on a second, previously unidentified plasmid, pBC218. A/J mice challenged with B. cereus G9241 confirmed the virulence of this strain. These findings represent an example of how genomics could rapidly assist public health experts responding not only to clearly identified select agents but also to novel agents with similar pathogenic potentials. In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis.
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Affiliation(s)
- Alex R Hoffmaster
- Epidemiologic Investigations Laboratory, Meningitis and Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G34, Atlanta, GA 30333, USA
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Rasko DA, Ravel J, Økstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolstø AB, Fraser CM, Read TD. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 2004; 32:977-88. [PMID: 14960714 PMCID: PMC373394 DOI: 10.1093/nar/gkh258] [Citation(s) in RCA: 256] [Impact Index Per Article: 12.8] [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: 11/14/2022] Open
Abstract
We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.
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Affiliation(s)
- David A Rasko
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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