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Goethals O, Kaptein SJF, Kesteleyn B, Bonfanti JF, Van Wesenbeeck L, Bardiot D, Verschoor EJ, Verstrepen BE, Fagrouch Z, Putnak JR, Kiemel D, Ackaert O, Straetemans R, Lachau-Durand S, Geluykens P, Crabbe M, Thys K, Stoops B, Lenz O, Tambuyzer L, De Meyer S, Dallmeier K, McCracken MK, Gromowski GD, Rutvisuttinunt W, Jarman RG, Karasavvas N, Touret F, Querat G, de Lamballerie X, Chatel-Chaix L, Milligan GN, Beasley DWC, Bourne N, Barrett ADT, Marchand A, Jonckers THM, Raboisson P, Simmen K, Chaltin P, Bartenschlager R, Bogers WM, Neyts J, Van Loock M. Blocking NS3-NS4B interaction inhibits dengue virus in non-human primates. Nature 2023; 615:678-686. [PMID: 36922586 PMCID: PMC10033419 DOI: 10.1038/s41586-023-05790-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/29/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Dengue is a major health threat and the number of symptomatic infections caused by the four dengue serotypes is estimated to be 96 million1 with annually around 10,000 deaths2. However, no antiviral drugs are available for the treatment or prophylaxis of dengue. We recently described the interaction between non-structural proteins NS3 and NS4B as a promising target for the development of pan-serotype dengue virus (DENV) inhibitors3. Here we present JNJ-1802-a highly potent DENV inhibitor that blocks the NS3-NS4B interaction within the viral replication complex. JNJ-1802 exerts picomolar to low nanomolar in vitro antiviral activity, a high barrier to resistance and potent in vivo efficacy in mice against infection with any of the four DENV serotypes. Finally, we demonstrate that the small-molecule inhibitor JNJ-1802 is highly effective against viral infection with DENV-1 or DENV-2 in non-human primates. JNJ-1802 has successfully completed a phase I first-in-human clinical study in healthy volunteers and was found to be safe and well tolerated4. These findings support the further clinical development of JNJ-1802, a first-in-class antiviral agent against dengue, which is now progressing in clinical studies for the prevention and treatment of dengue.
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Affiliation(s)
- Olivia Goethals
- Janssen Global Public Health, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Suzanne J F Kaptein
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Bart Kesteleyn
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jean-François Bonfanti
- Janssen Infectious Diseases Discovery, Janssen-Cilag, Val de Reuil, France
- Galapagos, Romainville, France
| | | | | | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Babs E Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Zahra Fagrouch
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - J Robert Putnak
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Dominik Kiemel
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Oliver Ackaert
- Janssen Clinical Pharmacology and Pharmacometrics, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Roel Straetemans
- Statistics and Decision Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Peggy Geluykens
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
- Discovery, Charles River Beerse, Beerse, Belgium
| | - Marjolein Crabbe
- Statistics and Decision Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Kim Thys
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Bart Stoops
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Oliver Lenz
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Lotke Tambuyzer
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Sandra De Meyer
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Michael K McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nicos Karasavvas
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Franck Touret
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Gilles Querat
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Laurent Chatel-Chaix
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Gregg N Milligan
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - David W C Beasley
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - Nigel Bourne
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - Alan D T Barrett
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | | | - Tim H M Jonckers
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Pierre Raboisson
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
- Galapagos NV, Mechelen, Belgium
| | | | - Patrick Chaltin
- Cistim Leuven vzw, Leuven, Belgium
- Centre for Drug Design and Discovery (CD3), KU Leuven, Leuven, Belgium
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- German Centre for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
| | - Willy M Bogers
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD, USA
| | - Marnix Van Loock
- Janssen Global Public Health, Janssen Pharmaceutica NV, Beerse, Belgium.
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2
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Huang AT, Salje H, Escoto AC, Chowdhury N, Chávez C, Garcia-Carreras B, Rutvisuttinunt W, Maljkovic Berry I, Gromowski GD, Wang L, Klungthong C, Thaisomboonsuk B, Nisalak A, Trimmer-Smith LM, Rodriguez-Barraquer I, Ellison DW, Jones AR, Fernandez S, Thomas SJ, Smith DJ, Jarman R, Whitehead SS, Cummings DAT, Katzelnick LC. Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand. PLoS Pathog 2022; 18:e1010500. [PMID: 35500035 PMCID: PMC9098070 DOI: 10.1371/journal.ppat.1010500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/02/2021] [Revised: 05/12/2022] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Neutralizing antibodies are important correlates of protection against dengue. Yet, determinants of variation in neutralization across strains within the four dengue virus serotypes (DENV1-4) is imperfectly understood. Studies focus on structural DENV proteins, especially the envelope (E), the primary target of anti-DENV antibodies. Although changes in immune recognition (antigenicity) are often attributed to variation in epitope residues, viral processes influencing conformation and epitope accessibility also affect neutralizability, suggesting possible modulating roles of nonstructural proteins. We estimated effects of residue changes in all 10 DENV proteins on antigenic distances between 348 DENV collected from individuals living in Bangkok, Thailand (1994-2014). Antigenic distances were derived from response of each virus to a panel of twenty non-human primate antisera. Across 100 estimations, excluding 10% of virus pairs each time, 77 of 295 positions with residue variability in E consistently conferred antigenic effects; 52 were within ±3 sites of known binding sites of neutralizing human monoclonal antibodies, exceeding expectations from random assignments of effects to sites (p = 0.037). Effects were also identified for 16 sites on the stem/anchor of E which were only recently shown to become exposed under physiological conditions. For all proteins, except nonstructural protein 2A (NS2A), root-mean-squared-error (RMSE) in predicting distances between pairs held out in each estimation did not outperform sequences of equal length derived from all proteins or E, suggesting that antigenic signals present were likely through linkage with E. Adjusted for E, we identified 62/219 sites embedding the excess signals in NS2A. Concatenating these sites to E additionally explained 3.4% to 4.0% of observed variance in antigenic distances compared to E alone (50.5% to 50.8%); RMSE outperformed concatenating E with sites from any protein of the virus (ΔRMSE, 95%IQR: 0.01, 0.05). Our results support examining antigenic determinants beyond the DENV surface. Dengue viruses, even of the same serotype, are differentially recognized by preexisting antibodies of individuals. With antibody levels being an important indicator of infection risk and pathogenicity, understanding mechanisms underlying these differences are crucial for vaccine design and development. Investigations have primarily targeted surface regions of the envelope protein (E) where virus-antibody interactions were thought to primarily occur. However, the roles of non-surface regions of the E protein as well as nonstructural proteins has been limited. We looked at the entire virus to identify associations between specific changes in the protein sequence and differences in how viruses were recognized by antibodies. In addition to recovering known determinants on the surface, we found signals in other areas on the structural building blocks of the virus. We also identified additional signals on specific areas of a protein that does not form structures of the virus but orchestrate virus formation. Our results point towards broadening the frame of investigation to gain a more comprehensive understanding of mechanisms giving rise to antibody recognition of dengue viruses, and may aid the design and evaluation of vaccines and/or assays to characterize dengue immunity.
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Affiliation(s)
- Angkana T. Huang
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Henrik Salje
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ana Coello Escoto
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nayeem Chowdhury
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Christian Chávez
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bernardo Garcia-Carreras
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ananda Nisalak
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Luke M. Trimmer-Smith
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Isabel Rodriguez-Barraquer
- School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Damon W. Ellison
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Anthony R. Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stephen J. Thomas
- State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Derek A. T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (DATC); (LCK)
| | - Leah C. Katzelnick
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (DATC); (LCK)
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3
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Endy TP, Wang D, Polhemus ME, Jarman RG, Jasper LE, Gromowski G, Lin L, De La Barra RA, Friberg H, Currier JR, Abbott M, Ware L, Klick M, Paolino KM, Blair DC, Eckels K, Rutvisuttinunt W, Thomas SJ. A Phase 1, Open-Label Assessment of a Dengue Virus-1 Live Virus Human Challenge Strain. J Infect Dis 2021; 223:258-267. [PMID: 32572470 DOI: 10.1093/infdis/jiaa351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 05/22/2020] [Accepted: 06/18/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Dengue human infection models (DHIM) have been used as a safe means to test the viability of prophylaxis and therapeutics. METHODS A phase 1 study of 12 healthy adult volunteers using a challenge virus, DENV-1-LVHC strain 45AZ5, was performed. A dose escalating design was used to determine the safety and performance profile of the challenge virus. Subjects were evaluated extensively until 28 days and then out to 6 months. RESULTS Twelve subjects received the challenge virus: 6 with 0.5 mL of 6.5 × 103 plaque-forming units (PFU)/mL (low-dose group) and 6 with 0.5 mL of 6.5 × 104 PFU/mL (mid-dose group). All except 1 in the low-dose group developed detectable viremia. For all subjects the mean incubation period was 5.9 days (range 5-9 days) and mean time of viremia was 6.8 days (range 3-9 days). Mean peak for all subjects was 1.6 × 107 genome equivalents (GE)/mL (range 4.6 × 103 to 5 × 107 GE/mL). There were no serious adverse events or long-term safety signals noted. CONCLUSIONS We conclude that DENV-1-LVHC was well-tolerated, resulted in an uncomplicated dengue illness, and may be a suitable DHIM for therapeutic and prophylactic product testing. CLINICAL TRIALS REGISTRATION NCT02372175.
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Affiliation(s)
- Timothy P Endy
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Dongliang Wang
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Mark E Polhemus
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Louis E Jasper
- US Army Medical and Materiel Development Activity, Fort Detrick, Maryland, USA
| | - Greg Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Leyi Lin
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rafael A De La Barra
- Pilot BioProduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Heather Friberg
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mark Abbott
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Lisa Ware
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Michelle Klick
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Kristopher M Paolino
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Donald C Blair
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Kenneth Eckels
- Pilot BioProduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Stephen J Thomas
- Institute for Global Health and Translational Science, Department of Microbiology and Immunology, and Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York, USA
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4
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Andrade Justi S, Soghigian J, Pecor DB, Caicedo-Quiroga L, Rutvisuttinunt W, Li T, Stevens L, Dorn PL, Wiegmann B, Linton YM. From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae). PLoS One 2021; 16:e0247068. [PMID: 33630885 PMCID: PMC7906454 DOI: 10.1371/journal.pone.0247068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.
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Affiliation(s)
- Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
- * E-mail:
| | - John Soghigian
- Department of Entomology, North Carolina State University, Raleigh, NC, United States of America
| | - David B. Pecor
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Lori Stevens
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Patricia L. Dorn
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States of America
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC, United States of America
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
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5
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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6
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Waickman AT, Friberg H, Gromowski GD, Rutvisuttinunt W, Li T, Siegfried H, Victor K, McCracken MK, Fernandez S, Srikiatkhachorn A, Ellison D, Jarman RG, Thomas SJ, Rothman AL, Endy T, Currier JR. Temporally integrated single cell RNA sequencing analysis of PBMC from experimental and natural primary human DENV-1 infections. PLoS Pathog 2021; 17:e1009240. [PMID: 33513191 PMCID: PMC7875406 DOI: 10.1371/journal.ppat.1009240] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/26/2020] [Revised: 02/10/2021] [Accepted: 12/15/2020] [Indexed: 11/25/2022] Open
Abstract
Dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To determine the kinetic transcriptional signature associated with experimental primary DENV-1 infection and to assess how closely this profile correlates with the transcriptional signature accompanying natural primary DENV-1 infection, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both experimental and natural primary DENV-1 infection resulted in overlapping patterns of inflammatory gene upregulation, natural primary DENV-1 infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by experimental and natural primary DENV infection are similar, but that natural primary DENV-1 infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state. Dengue Human Challenge Models allow for the analysis of host/virus interactions under highly controlled experimental conditions. However, it is unclear how close the immune response generated by an attenuated challenge virus compares to that generated by a naturally acquired DENV infection. In this study, we utilized single cell RNA sequencing to assess the immune response generated by both experimental and natural primary DENV-1 infections. This analysis suggests that the immune response elicited by experiential and natural primary DENV-1 infections are similar, but that natural DENV-1 infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state.
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Affiliation(s)
- Adam T. Waickman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, New York, United States of America
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, New York, United States of America
- * E-mail:
| | - Heather Friberg
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Hayden Siegfried
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kaitlin Victor
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael K. McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, Rhode Island, United States of America
- Faculty of Medicine, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Damon Ellison
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Stephen J. Thomas
- Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Alan L. Rothman
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, Rhode Island, United States of America
| | - Timothy Endy
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Jeffrey R. Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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7
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Pollett S, Gathii K, Figueroa K, Rutvisuttinunt W, Srikanth A, Nyataya J, Mutai BK, Awinda G, Jarman RG, Berry IM, Waitumbi JN. The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications. Infect Genet Evol 2020; 90:104617. [PMID: 33161179 DOI: 10.1016/j.meegid.2020.104617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 01/17/2023]
Abstract
Kenya experiences a substantial burden of dengue, yet there are very few DENV-2 sequence data available from this country and indeed the entire continent of Africa. We therefore undertook whole genome sequencing and evolutionary analysis of fourteen dengue virus (DENV)-2 strains sampled from Malindi sub-County Hospital during the 2017 DENV-2 outbreak in the Kenyan coast. We further performed an extended East African phylogenetic analysis, which leveraged 26 complete African env genes. Maximum likelihood analysis showed that the 2017 outbreak was due to the Cosmopolitan genotype, indicating that this has been the only confirmed human DENV-2 genotype circulating in Africa to date. Phylogeographic analyses indicated transmission of DENV-2 viruses between East Africa and South/South-West Asia. Time-scaled genealogies show that DENV-2 viruses shows spatial structure at the country level in Kenya, with a time-to-most-common-recent ancestor analysis indicating that these DENV-2 strains were circulating for up to 5.38 years in Kenya before detection in the 2017 Malindi outbreak. Selection pressure analyses indicated sampled Kenyan DENV strains uniquely being under positive selection at 6 sites, predominantly across the non-structural genes, and epitope prediction analyses showed that one of these sites corresponds to a putative predicted MHC-I CD8+ DENV-2 Cosmopolitan virus epitope only evident in a sampled Kenyan virus. Taken together, our findings indicate that the 2017 Malindi DENV-2 outbreak arose from a strain which had circulated for several years in Kenya before recent detection, has experienced diversifying selection pressure, and may contain new putative immunogens relevant to vaccine design. These findings prompt further genomic epidemiology studies in this and other Kenyan locations to further elucidate the transmission dynamics of DENV in this region.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Kimita Gathii
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Abhi Srikanth
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Josphat Nyataya
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Beth K Mutai
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - George Awinda
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
| | - J N Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
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8
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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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9
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Waickman AT, Gromowski GD, Rutvisuttinunt W, Li T, Siegfried H, Victor K, Kuklis C, Gomootsukavadee M, McCracken MK, Gabriel B, Mathew A, Grinyo I Escuer A, Fouch ME, Liang J, Fernandez S, Davidson E, Doranz BJ, Srikiatkhachorn A, Endy T, Thomas SJ, Ellison D, Rothman AL, Jarman RG, Currier JR, Friberg H. Transcriptional and clonal characterization of B cell plasmablast diversity following primary and secondary natural DENV infection. EBioMedicine 2020; 54:102733. [PMID: 32315970 PMCID: PMC7170960 DOI: 10.1016/j.ebiom.2020.102733] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/19/2020] [Accepted: 03/10/2020] [Indexed: 01/06/2023] Open
Abstract
Antibody-mediated humoral immunity is thought to play a central role in mediating the immunopathogenesis of acute DENV infection, but limited data are available on the diversity, specificity, and functionality of the antibody response at the molecular level elicited by primary or secondary DENV infection. In order to close this functional gap in our understanding of DENV-specific humoral immunity, we utilized high-throughput single cell RNA sequencing to investigate B cells circulating in both primary and secondary natural DENV infections. We captured full-length paired immunoglobulin receptor sequence data from 9,027 B cells from a total of 6 subjects, including 2,717 plasmablasts. In addition to IgG and IgM class-switched cells, we unexpectedly found a high proportion of the DENV-elicited plasmablasts expressing IgA, principally in individuals with primary DENV infections. These IgA class-switched cells were extensively hypermutated even in individuals with a serologically confirmed primary DENV infection. Utilizing a combination of conventional biochemical assays and high-throughput shotgun mutagenesis, we determined that DENV-reactive IgA class-switched antibodies represent a significant fraction of DENV-reactive Igs generated in response to DENV infection, and that they exhibit a comparable epitope specificity to DENV-reactive IgG antibodies. These results provide insight into the molecular-level diversity of DENV-elicited humoral immunity and identify a heretofore unappreciated IgA plasmablast response to DENV infection.
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Affiliation(s)
- Adam T Waickman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
| | - Gregory D Gromowski
- 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
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Hayden Siegfried
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Kaitlin Victor
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Caitlin Kuklis
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Methee Gomootsukavadee
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Michael K McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Benjamin Gabriel
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Anuja Mathew
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | | | | | - Jenny Liang
- Integral Molecular, Philadelphia, PA, United States
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Anon Srikiatkhachorn
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States; Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Timothy Endy
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Stephen J Thomas
- Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Damon Ellison
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Alan L Rothman
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Heather Friberg
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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10
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Maljkovic Berry I, Rutvisuttinunt W, Sippy R, Beltran-Ayala E, Figueroa K, Ryan S, Srikanth A, Stewart-Ibarra AM, Endy T, Jarman RG. The origins of dengue and chikungunya viruses in Ecuador following increased migration from Venezuela and Colombia. BMC Evol Biol 2020; 20:31. [PMID: 32075576 PMCID: PMC7031975 DOI: 10.1186/s12862-020-1596-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/12/2019] [Accepted: 02/11/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND In recent years, Ecuador and other South American countries have experienced an increase in arboviral diseases. A rise in dengue infections was followed by introductions of chikungunya and Zika, two viruses never before seen in many of these areas. Furthermore, the latest socioeconomic and political instability in Venezuela and the mass migration of its population into the neighboring countries has given rise to concerns of infectious disease spillover and escalation of arboviral spread in the region. RESULTS We performed phylogeographic analyses of dengue (DENV) and chikungunya (CHIKV) virus genomes sampled from a surveillance site in Ecuador in 2014-2015, along with genomes from the surrounding countries. Our results revealed at least two introductions of DENV, in 2011 and late 2013, that initially originated from Venezuela and/or Colombia. The introductions were subsequent to increases in the influx of Venezuelan and Colombian citizens into Ecuador, which in 2013 were 343% and 214% higher than in 2009, respectively. However, we show that Venezuela has historically been an important source of DENV dispersal in this region, even before the massive exodus of its population, suggesting already established paths of viral distribution. Like DENV, CHIKV was introduced into Ecuador at multiple time points in 2013-2014, but unlike DENV, these introductions were associated with the Caribbean. Our findings indicated no direct CHIKV connection between Ecuador, Colombia, and Venezuela as of 2015, suggesting that CHIKV was, at this point, not following the paths of DENV spread. CONCLUSION Our results reveal that Ecuador is vulnerable to arbovirus import from many geographic locations, emphasizing the need of continued surveillance and more diversified prevention strategies. Importantly, increase in human movement along established paths of viral dissemination, combined with regional outbreaks and epidemics, may facilitate viral spread and lead to novel virus introductions. Thus, strengthening infectious disease surveillance and control along migration routes and improving access to healthcare for the vulnerable populations is of utmost importance.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army institute of Research, Silver Spring, MD, USA.
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army institute of Research, Silver Spring, MD, USA
| | - Rachel Sippy
- Institute for Global Health and Translational Science, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Efrain Beltran-Ayala
- Department of Medicine, Technical University of Machala, Machala, El Oro, Ecuador
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army institute of Research, Silver Spring, MD, USA
| | - Sadie Ryan
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Abhinaya Srikanth
- Viral Diseases Branch, Walter Reed Army institute of Research, Silver Spring, MD, USA
| | - Anna M Stewart-Ibarra
- Institute for Global Health and Translational Science, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Montevideo, InterAmerican Institute for Global Change Research (IAI), Montevideo, Uruguay
| | - Timothy Endy
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army institute of Research, Silver Spring, MD, USA
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11
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Guan M, Hall JS, Zhang X, Dusek RJ, Olivier AK, Liu L, Li L, Krauss S, Danner A, Li T, Rutvisuttinunt W, Lin X, Hallgrimsson GT, Ragnarsdottir SB, Vignisson SR, TeSlaa J, Nashold SW, Jarman R, Wan XF. Aerosol Transmission of Gull-Origin Iceland Subtype H10N7 Influenza A Virus in Ferrets. J Virol 2019; 93:e00282-19. [PMID: 30996092 PMCID: PMC6580963 DOI: 10.1128/jvi.00282-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/19/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023] Open
Abstract
Subtype H10 influenza A viruses (IAVs) have been recovered from domestic poultry and various aquatic bird species, and sporadic transmission of these IAVs from avian species to mammals (i.e., human, seal, and mink) are well documented. In 2015, we isolated four H10N7 viruses from gulls in Iceland. Genomic analyses showed four gene segments in the viruses were genetically associated with H10 IAVs that caused influenza outbreaks and deaths among European seals in 2014. Antigenic characterization suggested minimal antigenic variation among these H10N7 isolates and other archived H10 viruses recovered from human, seal, mink, and various avian species in Asia, Europe, and North America. Glycan binding preference analyses suggested that, similar to other avian-origin H10 IAVs, these gull-origin H10N7 IAVs bound to both avian-like alpha 2,3-linked sialic acids and human-like alpha 2,6-linked sialic acids. However, when the gull-origin viruses were compared with another Eurasian avian-origin H10N8 IAV, which caused human infections, the gull-origin virus showed significantly higher binding affinity to human-like glycan receptors. Results from a ferret experiment demonstrated that a gull-origin H10N7 IAV replicated well in turbinate, trachea, and lung, but replication was most efficient in turbinate and trachea. This gull-origin H10N7 virus can be transmitted between ferrets through the direct contact and aerosol routes, without prior adaptation. Gulls share their habitat with other birds and mammals and have frequent contact with humans; therefore, gull-origin H10N7 IAVs could pose a risk to public health. Surveillance and monitoring of these IAVs at the wild bird-human interface should be continued.IMPORTANCE Subtype H10 avian influenza A viruses (IAVs) have caused sporadic human infections and enzootic outbreaks among seals. In the fall of 2015, H10N7 viruses were recovered from gulls in Iceland, and genomic analyses showed that the viruses were genetically related with IAVs that caused outbreaks among seals in Europe a year earlier. These gull-origin viruses showed high binding affinity to human-like glycan receptors. Transmission studies in ferrets demonstrated that the gull-origin IAV could infect ferrets, and that the virus could be transmitted between ferrets through direct contact and aerosol droplets. This study demonstrated that avian H10 IAV can infect mammals and be transmitted among them without adaptation. Thus, avian H10 IAV is a candidate for influenza pandemic preparedness and should be monitored in wildlife and at the animal-human interface.
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Affiliation(s)
- Minhui Guan
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jeffrey S Hall
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Xiaojian Zhang
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Robert J Dusek
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Alicia K Olivier
- Department of Population and Pathobiology Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Liyuan Liu
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Lei Li
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Angela Danner
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiaoxu Lin
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Josh TeSlaa
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Sean W Nashold
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiu-Feng Wan
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
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12
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Chang D, Sanders‐Buell E, Bose M, O'Sullivan AM, Pham P, Kroon E, Colby DJ, Sirijatuphat R, Billings E, Pinyakorn S, Chomchey N, Rutvisuttinunt W, Kijak G, de Souza M, Excler J, Phanuphak P, Phanuphak N, O'Connell RJ, Kim JH, Robb ML, Michael NL, Ananworanich J, Tovanabutra S. Molecular epidemiology of a primarily MSM acute HIV-1 cohort in Bangkok, Thailand and connections within networks of transmission in Asia. J Int AIDS Soc 2018; 21:e25204. [PMID: 30601598 PMCID: PMC6282942 DOI: 10.1002/jia2.25204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Thailand plays a substantial role in global HIV-1 transmission of CRF01_AE. Worldwide, men who have sex with men (MSM) are at elevated risk for HIV-1 infection. Hence, understanding HIV-1 diversity in a primarily Thai MSM cohort with acute infection, and its connections to the broader HIV-1 transmission network in Asia is crucial for research and development of HIV-1 vaccines, treatment and cure. METHODS Subtypes and diversity of infecting viruses from individuals sampled from 2009 to 2015 within the RV254/SEARCH 010 cohort were assessed by multiregion hybridization assay (MHAbce), multiregion subtype-specific PCR assay (MSSPbce) and full-length single-genome sequencing (SGS). Phylogenetic analysis was performed by maximum likelihood. Pairwise genetic distances of envelope gp160 sequences obtained from the cohort and from Asia (Los Alamos National Laboratory HIV Database) were calculated to identify potential transmission networks. RESULTS MHAbce/MSSPbce results identified 81.6% CRF01_AE infecting strains in RV254. CRF01_AE/B recombinants and subtype B were found at 7.3% and 2.8% respectively. Western subtype B strains outnumbered Thai B' strains. Phylogenetic analysis revealed one C, one CRF01_AE/CRF02_AG recombinant and one CRF01_AE/B/C recombinant. Asian network analysis identified one hundred and twenty-three clusters, including five clusters of RV254 participants. None of the RV254 sequences clustered with non-RV254 sequences. The largest international cluster involved 15 CRF01_AE strains from China and Vietnam. The remaining clusters were mostly intracountry connections, of which 31.7% included Thai nodes and 43.1% included Chinese nodes. CONCLUSION While the majority of strains in Thailand are CRF01_AE and subtype B, emergence of unique recombinant forms (URFs) are found in a moderate fraction of new HIV-1 infections. Approaches to vaccine design and immunotherapeutics will need to monitor and consider the expanding proportion of recombinants and the increasing genetic diversity in the region. Identified HIV-1 transmission networks indicate ongoing spread of HIV-1 among MSM. As HIV-1 epidemics continue to expand in other Asian countries, transmission network analyses can inform strategies for prevention, intervention, treatment and cure.
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Affiliation(s)
- David Chang
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Eric Sanders‐Buell
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Meera Bose
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Anne Marie O'Sullivan
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Phuc Pham
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | | | | | - Rujipas Sirijatuphat
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- Department of MedicineFaculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Erik Billings
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Suteeraporn Pinyakorn
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | | | - Wiriya Rutvisuttinunt
- Department of RetrovirologyArmed Forces Research Institute of Medical SciencesBangkokThailand
- Viral Diseases BranchWalter Reed Army Institute of ResearchSilver SpringMDUSA
| | - Gustavo Kijak
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
- Present address:
GSK VaccinesRockvilleMDUSA
| | - Mark de Souza
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
- SEARCHBangkokThailand
| | - Jean‐Louis Excler
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | | | | | - Robert J O'Connell
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- Department of RetrovirologyArmed Forces Research Institute of Medical SciencesBangkokThailand
| | - Jerome H Kim
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- International Vaccine InstituteSeoulSouth Korea
| | - Merlin L Robb
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Nelson L Michael
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
| | - Jintanat Ananworanich
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
- SEARCHBangkokThailand
- Department of Global HealthAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sodsai Tovanabutra
- United States Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMDUSA
- The Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
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Rutvisuttinunt W, Klungthong C, Thaisomboonsuk B, Chinnawirotpisan P, Ajariyakhajorn C, Manasatienkij W, Phonpakobsin T, Lon C, Saunders D, Wangchuk S, Shrestha SK, Velasco JMS, Alera MTP, Simasathien S, Buddhari D, Jarman RG, Macareo LR, Yoon IK, Fernandez S. Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010-2013. J Clin Virol 2017; 94:91-99. [PMID: 28779659 PMCID: PMC7106496 DOI: 10.1016/j.jcv.2017.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 12/16/2016] [Revised: 06/29/2017] [Accepted: 07/08/2017] [Indexed: 01/15/2023]
Abstract
Next-generation Sequencing (NGS) was adopted in routine respiratory pathogen surveillance from South/South East (S/SE) Asia during 2010–2013. From 12,865 respiratory collections from ILI patients, 324 CPE-positive from 4,478 viral isolations were negative by standard assays. The CPE-positive samples were pooled, screened using NGS and validated the presence of the pathogens identified from NGS. Herpes simplex virus type 1, parainfluenza, adenovirus, coronavirus, human metapneumovirus, mumps virus and enterovirus genus were detected. NGS on pooled samples can be applied to surveillance work, identifying medically important viruses which may have missed by conventional methods.
Background Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010–2013. Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. Objective To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. Study design The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2–26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. Results WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%).
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand; Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal.
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Piyawan Chinnawirotpisan
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Chuanpis Ajariyakhajorn
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Thipwipha Phonpakobsin
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Chanthap Lon
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - David Saunders
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Sonam Wangchuk
- Royal Centre for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Sanjaya K Shrestha
- Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal; Center for International Health, University of Bergen, Norway
| | - John Mark S Velasco
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Maria Theresa P Alera
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | | | - Darunee Buddhari
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Richard G Jarman
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Louis R Macareo
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand.
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Alera MT, Hermann L, Tac-An IA, Klungthong C, Rutvisuttinunt W, Manasatienkij W, Villa D, Thaisomboonsuk B, Velasco JM, Chinnawirotpisan P, Lago CB, Roque VG, Macareo LR, Srikiatkhachorn A, Fernandez S, Yoon IK. Zika virus infection, Philippines, 2012. Emerg Infect Dis 2015; 21:722-4. [PMID: 25811410 PMCID: PMC4378478 DOI: 10.3201/eid2104.141707] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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15
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Buathong R, Hermann L, Thaisomboonsuk B, Rutvisuttinunt W, Klungthong C, Chinnawirotpisan P, Manasatienkij W, Nisalak A, Fernandez S, Yoon IK, Akrasewi P, Plipat T. Detection of Zika Virus Infection in Thailand, 2012-2014. Am J Trop Med Hyg 2015; 93:380-383. [PMID: 26101272 PMCID: PMC4530765 DOI: 10.4269/ajtmh.15-0022] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [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: 01/09/2015] [Accepted: 04/06/2015] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV) is an emerging mosquito-borne pathogen with reported cases in Africa, Asia, and large outbreaks in the Pacific. No autochthonous ZIKV infections have been confirmed in Thailand. However, there have been several cases reported in travelers returning from Thailand. Here we report seven cases of acute ZIKV infection in Thai residents across the country confirmed by molecular or serological testing including sequence data. These endemic cases, combined with previous reports in travelers, provide evidence that ZIKV is widespread throughout Thailand.
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Affiliation(s)
| | - Laura Hermann
- *Address correspondence to Laura Hermann, Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6 Rajvithi Road, Bangkok 10400, Thailand. E-mail:
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16
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Rutvisuttinunt W, Chinnawirotpisan P, Thaisomboonsuk B, Rodpradit P, Ajariyakhajorn C, Manasatienkij W, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Viral subpopulation diversity in influenza virus isolates compared to clinical specimens. J Clin Virol 2015; 68:16-23. [PMID: 26071329 DOI: 10.1016/j.jcv.2015.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 01/03/2015] [Revised: 03/17/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Influenza virus (IFV) isolates obtained from mammalian cell cultures are valuable reagents used for vaccine production, antigenic characterization, laboratory assays, and epidemiological and evolutionary studies. Complete genomic comparison of IFV isolates with their original clinical specimens provides insight into cell culture-driven genomic changes which may sequentially alter the virus phenotype. OBJECTIVES The genome of the viral isolates and of the viruses in the clinical specimens was examined by deep sequencing in order to determine nucleotide heterogeneity (measured number of variances or numbers of mixed bases) as a marker for IFV population diversity. STUDY DESIGN Clinical respiratory specimens were collected between July and October 2012 and identified by RT-PCR as positive for influenza A H3N2 or H1N1, or influenza B. The viruses in the clinical specimens were amplified using mammalian cell culture. Next generation sequencing (NGS) was used to investigate genomic differences between IFV isolates and their corresponding clinical specimens. RESULTS There was less nucleotide heterogeneity in 5 of 6 viral isolates compared to the corresponding clinical specimens, especially for influenza B. A phylogenetic analysis of the hemagglutinin (HA) gene consensus sequences obtained from deep and Sanger sequencing showed that the viral isolates and their corresponding clinical specimens contained the same IFV strains with less than 5% pair-wise genetic distance. CONCLUSION The IFV sequence data analysis detected a substantial decrease in nucleotide heterogeneity from clinical specimens to viral cultures in 5 out of 6 investigated cases.
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Affiliation(s)
- W Rutvisuttinunt
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - P Chinnawirotpisan
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - B Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - P Rodpradit
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - C Ajariyakhajorn
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - W Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | | | - S K Shrestha
- Walter Reed/ AFRIMS Research Unit Nepal, Kathmandu, Nepal.
| | - I K Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - C Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
| | - S Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajavithi Road, 10400 Bangkok, Thailand.
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Leelawiwat W, Rutvisuttinunt W, Arroyo M, Mueanpai F, Kongpechsatit O, Chonwattana W, Chaikummao S, de Souza M, vanGriensven F, McNicholl JM, Curlin ME. Increasing HIV-1 molecular complexity among men who have sex with men in Bangkok. AIDS Res Hum Retroviruses 2015; 31:393-400. [PMID: 25366819 DOI: 10.1089/aid.2014.0139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In Thailand, new HIV-1 infections are largely concentrated in certain risk groups such as men who have sex with men (MSM), where annual incidence may be as high as 12% per year. The paucity of information on the molecular epidemiology of HIV-1 in Thai MSM limits progress in understanding the epidemic and developing new prevention methods. We evaluated HIV-1 subtypes in seroincident and seroprevalent HIV-1-infected men enrolled in the Bangkok MSM Cohort Study (BMCS) between 2006 and 2011. We characterized HIV-1 subtype in 231 seroprevalent and 194 seroincident subjects using the multihybridization assay (MHA). Apparent dual infections, recombinant strains, and isolates found to be nontypeable by MHA were further characterized by targeted genomic sequencing. Most subjects were infected with HIV-1 CRF01_AE (82%), followed by infections with recombinants (11%, primarily CRF01_AE/B recombinants), subtype B (5%), and dual infections (2%). More than 11 distinct chimeric patterns were observed among CRF01B_AE/B recombinants, most involving recombination within integrase. A significant increase in the proportion of nontypeable strains was observed among seroincident MSM between 2006 and 2011. CRF01_AE and subtype B were the most and least common infecting strains, respectively. The predominance of CRF01_AE among HIV-1 infections in Thai MSM participating in the BMCS parallels trends observed in Thai heterosexuals and injecting drug users. The presence of complex recombinants and a significant rise in nontypeable strains suggest ongoing changes in the genetic makeup of the HIV-1 epidemic in Thailand, which may pose challenges for HIV-1 prevention efforts and vaccine development.
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Affiliation(s)
- Wanna Leelawiwat
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Wiriya Rutvisuttinunt
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Miguel Arroyo
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Famui Mueanpai
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Oranuch Kongpechsatit
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Wannee Chonwattana
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Supaporn Chaikummao
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Mark de Souza
- SEARCH Thailand, Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Frits vanGriensven
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Divisions of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Janet M. McNicholl
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Divisions of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Marcel E. Curlin
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Divisions of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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Rutvisuttinunt W, Chinnawirotpisan P, Klungthong C, Shrestha SK, Thapa AB, Pant A, Yingst SL, Yoon IK, Fernandez S, Pavlin JA. Evidence of West Nile virus infection in Nepal. BMC Infect Dis 2014; 14:606. [PMID: 25427544 PMCID: PMC4265323 DOI: 10.1186/s12879-014-0606-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 03/25/2014] [Accepted: 10/31/2014] [Indexed: 12/03/2022] Open
Abstract
Background Acute febrile illness is common among those seeking medical care and is frequently treated empirically with the underlying illness remaining undiagnosed in resource-poor countries. A febrile illness study was conducted 2009-2010 to identify known and unknown pathogens circulating in Nepal. Method Study methods included diagnostic testing and preliminary ELISA screening of acute and convalescent samples for diseases both known and unknown to be circulating in Nepal, including West Nile virus (WNV). The molecular assays including Polymerase Chain Reaction (PCR), Sanger sequencing and ultra deep sequencing on MiSeq Illumina Platform were conducted to further confirm the presence of WNV. Results The study enrolled 2,046 patients presenting undifferentiated febrile illness with unknown etiology. Sera from 14 out of 2,046 patients were tested positive for west nile virus (WNV) by nested Reverse Transcription-Polymerase Chain Reaction (RT-PCR). Only two out of 14 cases were confirmed for the presence of WNV by sequencing and identified as WNV lineage 1 phylogentically. The two patients were adult males with fever and no neurological symptoms from Kathmandu and Bharatpur, Nepal. Conclusion Two out of 2,046 serum samples contained fragments of WNV genome resembling WNV lineage 1, which is evidence of the continued spread of WNV which should be considered a possible illness cause in Nepal. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0606-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Arjun Pant
- Sukra Raj Tropical Infectious Diseases Hospital, Kathmandu, Nepal.
| | - Samuel L Yingst
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
| | - In-Kyu Yoon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
| | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
| | - Julie A Pavlin
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA.
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Rutvisuttinunt W, Leelawiwat W, Chinnawirotpisan P, Mueanpai F, Kongpechsatit O, Klungthong C, O'Connell R, de Souza M, Yoon IK, Curlin M, Fernandez S. Metagenomics Analysis of Plasma in HIV-infected Men Who Have Sex with Men in Bangkok, Thailand. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5393.abstract] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Wanna Leelawiwat
- The Thai Ministry of Public Health – U.S. Centers for Disease Prevention Collaboration, Nonthaburi, Thailand
| | | | - Famui Mueanpai
- The Thai Ministry of Public Health – U.S. Centers for Disease Prevention Collaboration, Nonthaburi, Thailand
| | - Oranuch Kongpechsatit
- The Thai Ministry of Public Health – U.S. Centers for Disease Prevention Collaboration, Nonthaburi, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Robert O'Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mark de Souza
- South-East Asian Research Collaboration with Hawaii, Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Marcel Curlin
- The Thai Ministry of Public Health – U.S. Centers for Disease Prevention Collaboration, Nonthaburi, Thailand
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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Sanders-Buell E, Rutvisuttinunt W, Todd CS, Nasir A, Bradfield A, Lei E, Poltavee K, Savadsuk H, Kim JH, Scott PT, de Souza M, Tovanabutra S. Hepatitis C genotype distribution and homology among geographically disparate injecting drug users in Afghanistan. J Med Virol 2014; 85:1170-9. [PMID: 23918535 DOI: 10.1002/jmv.23575] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2013] [Indexed: 01/25/2023]
Abstract
Hepatitis C virus (HCV) prevalence is high among injecting drug users in Afghanistan, but transmission dynamics are poorly understood. Samples from HCV-infected injecting drug users were sequenced to determine circulating genotypes and potential transmission linkages. Serum samples were obtained from injecting drug user participants in Hirat, Jalalabad, and Mazar-i-Sharif between 2006 and 2008 with reactive anti-HCV rapid tests. Specimens with detected HCV viremia were amplified and underwent sequence analysis. Of 113 samples evaluated, 25 samples (35.2%) were only typeable in NS5B, nine samples (12.7%) were only typeable in CE1, and 37 samples (52.1%) were genotyped in both regions. Of those with typeable HCV, all were Afghan males with a mean age of 31.1 (standard deviation [SD] ± 8.0) years and mean duration of injecting of 3.9 (SD ± 4.3) years. Most reported residence outside Afghanistan in the last decade (90.1%) and prior incarceration (76.8%). HCV genotypes detected were: 1a, (35.2%, n = 25), 3a (62.0%, n = 44), and 1b (2.8%, n = 2). Cluster formation was detected in NS5B and CE1 and were generally from within the same city. All participants within clusters reported being a refugee in Iran compared to 93.5% of those outside clusters. Only 22.2% (4/11) of those within clusters had been refugees in Pakistan and these four individuals had also been refugees in Iran. Predominance of genotype 3a and the association between HCV viremia and having been a refugee in Iran potentially reflects migration between Afghanistan and Iran among IDUs from Mazar-i-Sharif and Hirat and carry implications for harm reduction programs for this migratory population.
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Affiliation(s)
- Eric Sanders-Buell
- Department of Molecular Virology and Pathogenesis, United States Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods 2013; 193:394-404. [PMID: 23856301 DOI: 10.1016/j.jviromet.2013.07.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 11/30/2022]
Abstract
Active global surveillance and characterization of influenza viruses are essential for better preparation against possible pandemic events. Obtaining comprehensive information about the influenza genome can improve our understanding of the evolution of influenza viruses and emergence of new strains, and improve the accuracy when designing preventive vaccines. This study investigated the use of deep sequencing by the next-generation sequencing (NGS) Illumina MiSeq Platform to obtain complete genome sequence information from influenza virus isolates. The influenza virus isolates were cultured from 6 respiratory acute clinical specimens collected in Thailand and Nepal. DNA libraries obtained from each viral isolate were mixed and all were sequenced simultaneously. Total information of 2.6 Gbases was obtained from a 455±14 K/mm2 density with 95.76% (8,571,655/8,950,724 clusters) of the clusters passing quality control (QC) filters. Approximately 93.7% of all sequences from Read1 and 83.5% from Read2 contained high quality sequences that were ≥Q30, a base calling QC score standard. Alignments analysis identified three seasonal influenza A H3N2 strains, one 2009 pandemic influenza A H1N1 strain and two influenza B strains. The nearly entire genomes of all six virus isolates yielded equal or greater than 600-fold sequence coverage depth. MiSeq Platform identified seasonal influenza A H3N2, 2009 pandemic influenza A H1N1and influenza B in the DNA library mixtures efficiently.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
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Rutvisuttinunt W, Sirivichayakul S, Oota S, Assawadarachai V, Poltavee K, Savadsuk H, Pattanachaiwit S, Chaemchuen S, Arroyo MA, Paris RM, Michael NL, Kim JH, Ruxrungtham K, de Souza M, Phanuphak P, Tovanabutra S. Two unique recombinant forms identified in incident HIV type 1 infections in Thai blood donors. AIDS Res Hum Retroviruses 2012; 28:1703-11. [PMID: 22587412 DOI: 10.1089/aid.2011.0339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 genetic diversity of recently seroconverting (<12 months) Thai repeated blood donors attending the National Blood Centre, Thai Red Cross Society (NBC, TRCS) from September 2007 until March 2008 was assessed. Ten HIV-1 recent seroconvertors (10/239,134 donations) were identified during the study period. The estimated median time to seroconversion was 67.3 days (range: 45.5-102.0 days), and viral load ranged from 307 to 341,805 copies HIV-1 RNA/ml. MHAbce, a real-time-based PCR genotyping assay, identified six CRF01_AE, two CRF01_AE/B recombinants, one subtype B, and one CRF01_AE/B dual infection. Nine samples were further characterized by full genome sequencing, identifying CRF01_AE (N=6), unique CRF01_AE/B recombinants (N=2), and subtype B (N=1). One recombinant contained 13 breakpoints located in gag, pol, vif, vpr, env, and nef while the other recombinant contained 10 breakpoints located in pol, vif, env, and nef. This study found two unique CRF01B recombinants circulating in 10 recent HIV-1-positive subjects from a blood donor population in Thailand.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sineenart Oota
- National Blood Centre, Thai Red Cross Society, Bangkok, Thailand
| | | | - Kultida Poltavee
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Hathairat Savadsuk
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Suwittra Chaemchuen
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Miguel A. Arroyo
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Robert M. Paris
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Kiat Ruxrungtham
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Mark de Souza
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Praphan Phanuphak
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
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23
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Rutvisuttinunt W, Chaorattanakawee S, Tyner SD, Teja-Isavadharm P, Se Y, Yingyuen K, Chaichana P, Bethell D, Walsh DS, Lon C, Fukuda M, Socheat D, Noedl H, Schaecher K, Saunders DL. Optimizing the HRP-2 in vitro malaria drug susceptibility assay using a reference clone to improve comparisons of Plasmodium falciparum field isolates. Malar J 2012; 11:325. [PMID: 22974086 PMCID: PMC3489509 DOI: 10.1186/1475-2875-11-325] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022] Open
Abstract
Background Apparent emerging artemisinin-resistant Plasmodium falciparum malaria in Southeast Asia requires development of practical tools to monitor for resistant parasites. Although in vitro anti-malarial susceptibility tests are widely used, uncertainties remain regarding interpretation of P. falciparum field isolate values. Methods Performance parameters of the W2 P. falciparum clone (considered artemisinin “sensitive”) were evaluated as a reference for the HRP-2 immediate ex vivo assay. Variability in W2 IC50s was assessed, including intra- and inter-assay variability among and between technicians in multiple experiments, over five freeze-thaw cycles, over five months of continuous culture, and before and after transport of drug-coated plates to remote field sites. Nominal drug plate concentrations of artesunate (AS) and dihydroartemisinin (DHA) were verified by LC-MS analysis. Plasmodium falciparum field isolate IC50s for DHA from subjects in an artemisinin-resistant area in Cambodia were compared with W2 susceptibility. Results Plate drug concentrations and day-to-day technical assay performance among technicians were important sources of variability for W2 IC50s within and between assays. Freeze-thaw cycles, long-term continuous culture, and transport to and from remote sites had less influence. Despite variability in W2 susceptibility, the median IC50s for DHA for Cambodian field isolates were higher (p <0.0001) than the W2 clone (3.9 nM), both for subjects with expected (less than 72 hours; 6.3 nM) and prolonged (greater or equal to 72 hours; 9.6 nM) parasite clearance times during treatment with artesunate monotherapy. Conclusion The W2 reference clone improved the interpretability of field isolate susceptibility from the immediate ex vivo HRP-2 assay from areas of artemisinin resistance. Methods to increase the reproducibility of plate coating may improve overall assay interpretability and utility.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Immunology and Medicine, US Army Medical Corps, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
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24
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Tyner SD, Lon C, Se Y, Bethell D, Socheat D, Noedl H, Sea D, Satimai W, Schaecher K, Rutvisuttinunt W, Fukuda MM, Chaorattanakawee S, Yingyuen K, Sundrakes S, Chaichana P, Saingam P, Buathong N, Sriwichai S, Chann S, Timmermans A, Saunders DL, Walsh DS. Ex vivo drug sensitivity profiles of Plasmodium falciparum field isolates from Cambodia and Thailand, 2005 to 2010, determined by a histidine-rich protein-2 assay. Malar J 2012; 11:198. [PMID: 22694953 PMCID: PMC3403988 DOI: 10.1186/1475-2875-11-198] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [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: 04/02/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022] Open
Abstract
Background In vitro drug susceptibility assay of Plasmodium falciparum field isolates processed “immediate ex vivo” (IEV), without culture adaption, and tested using histidine-rich protein-2 (HRP-2) detection as an assay, is an expedient way to track drug resistance. Methods From 2005 to 2010, a HRP-2 in vitro assay assessed 451 P. falciparum field isolates obtained from subjects with malaria in western and northern Cambodia, and eastern Thailand, processed IEV, for 50% inhibitory concentrations (IC50) against seven anti-malarial drugs, including artesunate (AS), dihydroartemisinin (DHA), and piperaquine. Results In western Cambodia, from 2006 to 2010, geometric mean (GM) IC50 values for chloroquine, mefloquine, quinine, AS, DHA, and lumefantrine increased. In northern Cambodia, from 2009–2010, GM IC50 values for most drugs approximated the highest western Cambodia GM IC50 values in 2009 or 2010. Conclusions Western Cambodia is associated with sustained reductions in anti-malarial drug susceptibility, including the artemisinins, with possible emergence, or spread, to northern Cambodia. This potential public health crisis supports continued in vitro drug IC50 monitoring of P. falciparum isolates at key locations in the region.
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Affiliation(s)
- Stuart D Tyner
- Department of Immunology and Medicine, US Army Medical Corps, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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25
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Ananworanich J, Schuetz A, Vandergeeten C, Sereti I, de Souza M, Rerknimitr R, Dewar R, Marovich M, van Griensven F, Sekaly R, Pinyakorn S, Phanuphak N, Trichavaroj R, Rutvisuttinunt W, Chomchey N, Paris R, Peel S, Valcour V, Maldarelli F, Chomont N, Michael N, Phanuphak P, Kim JH. Impact of multi-targeted antiretroviral treatment on gut T cell depletion and HIV reservoir seeding during acute HIV infection. PLoS One 2012; 7:e33948. [PMID: 22479485 PMCID: PMC3316511 DOI: 10.1371/journal.pone.0033948] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/20/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Limited knowledge exists on early HIV events that may inform preventive and therapeutic strategies. This study aims to characterize the earliest immunologic and virologic HIV events following infection and investigates the usage of a novel therapeutic strategy. METHODS AND FINDINGS We prospectively screened 24,430 subjects in Bangkok and identified 40 AHI individuals. Thirty Thais were enrolled (8 Fiebig I, 5 Fiebig II, 15 Fiebig III, 2 Fiebig IV) of whom 15 completed 24 weeks of megaHAART (tenofovir/emtricitabine/efavirenz/raltegravir/maraviroc). Sigmoid biopsies were completed in 24/30 at baseline and 13/15 at week 24. At baseline, the median age was 29 years and 83% were MSM. Most were symptomatic (87%), and were infected with R5-tropic (77%) CRF01_AE (70%). Median CD4 was 406 cells/mm(3). HIV RNA was 5.5 log(10) copies/ml. Median total blood HIV DNA was higher in Fiebig III (550 copy/10(6) PBMC) vs. Fiebig I (8 copy/10(6) PBMC) (p = 0.01) while the median %CD4+CCR5+ gut T cells was lower in Fiebig III (19%) vs. Fiebig I (59%) (p = 0.0008). After 24 weeks of megaHAART, HIV RNA levels of <50 copies were achieved in 14/15 in blood and 13/13 in gut. Total blood HIV DNA at week 0 predicted reservoir size at week 24 (p<0.001). Total HIV DNA declined significantly and was undetectable in 3 of 15 in blood and 3 of 7 in gut. Frequency of CD4+CCR5+ gut T cells increased from 41% at baseline to 64% at week 24 (p>0.050); subjects with less than 40% at baseline had a significant increase in CD4+CCR5+ T cells from baseline to week 24 (14% vs. 71%, p = 0.02). CONCLUSIONS Gut T cell depletion and HIV reservoir seeding increases with progression of AHI. MegaHAART was associated with immune restoration and reduced reservoir size. Our findings could inform research on strategies to achieve HIV drug-free remission.
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Rutvisuttinunt W, Arroyo MA, Assawadarachai V, Poltavee K, McCutchan FE, Tovanabutra S, Kijak G, Kim JH, Paris RM, de Souza M. Use of dried blood spots for HIV-1 genotyping in Southeast Asia: Thailand experience. Southeast Asian J Trop Med Public Health 2012; 43:333-339. [PMID: 23082585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The multi-region hybridization assay (MHAbce) for genotyping HIV-1 subtypes B, C and circulating recombinant form (CRF01_AE) was evaluated on paired plasma and dried blood spots (DBS) collected from 68 HIV-1 infected individuals in Thailand. CRF01_AE was the predominant subtype identified using plasma samples (51/62) and DBS (24/27). There was no discordance in subtype designations between plasma and DBS.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
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27
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Noedl H, Se Y, Sriwichai S, Schaecher K, Teja-Isavadharm P, Smith B, Rutvisuttinunt W, Bethell D, Surasri S, Fukuda MM, Socheat D, Chan Thap L. Artemisinin resistance in Cambodia: a clinical trial designed to address an emerging problem in Southeast Asia. Clin Infect Dis 2010; 51:e82-9. [PMID: 21028985 DOI: 10.1086/657120] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Increasing rates of failure of artemisinin-based combination therapy have highlighted the possibility of emerging artemisinin resistance along the Thai-Cambodian border. We used an integrated in vivo-in vitro approach to assess the presence of artemisinin resistance in western Cambodia. This article provides additional data from a clinical trial that has been published in The New England Journal of Medicine. METHODS Ninety-four adult patients from Battambang Province, western Cambodia, who presented with uncomplicated falciparum malaria were randomized to receive high-dose artesunate therapy (4 mg/kg/day orally for 7 days) or quinine-tetracycline. Plasma concentrations of dihydroartemisinin, in vitro drug susceptibility, and molecular markers were analyzed. Cases meeting all the following criteria were classified as artemisinin resistant: failure to clear parasites within 7 days of treatment or reemergence of parasites within 28 days of follow-up; adequate plasma concentrations of dihydroartemisinin; prolonged parasite clearance; and increased in vitro drug susceptibility levels for dihydroartemisinin. RESULTS Two (3.3%) of 60 artesunate-treated patients were classified as artemisinin resistant. Their parasite clearance times were prolonged (133 and 95 h, compared with a median of 52.2 h in patients who were cured). These patients had 50% inhibitory concentrations of dihydroartemisinin that were almost 10 times higher than the reference clone W2. Resistance did not appear to be mediated by the pfmdr1 copy number or selected PfATPase6 polymorphisms previously proposed to confer artemisinin resistance. CONCLUSION Artemisinin resistance has emerged along the Thai-Cambodian border. The potentially devastating implications of spreading resistance to a drug that currently has no successor call for further studies of this emerging problem. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov identifier NCT00479206.
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Affiliation(s)
- Harald Noedl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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Bogani F, Corredeira I, Fernandez V, Sattler U, Rutvisuttinunt W, Defais M, Boehmer PE. Association between the herpes simplex virus-1 DNA polymerase and uracil DNA glycosylase. J Biol Chem 2010; 285:27664-72. [PMID: 20601642 DOI: 10.1074/jbc.m110.131235] [Citation(s) in RCA: 31] [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: 12/30/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) is a large dsDNA virus that encodes its own DNA replication machinery and other enzymes involved in DNA transactions. We recently reported that the HSV-1 DNA polymerase catalytic subunit (UL30) exhibits apurinic/apyrimidinic and 5'-deoxyribose phosphate lyase activities. Moreover, UL30, in conjunction with the viral uracil DNA glycosylase (UL2), cellular apurinic/apyrimidinic endonuclease, and DNA ligase IIIalpha-XRCC1, performs uracil-initiated base excision repair. Base excision repair is required to maintain genome stability as a means to counter the accumulation of unusual bases and to protect from the loss of DNA bases. Here we show that the HSV-1 UL2 associates with the viral replisome. We identified UL2 as a protein that co-purifies with the DNA polymerase through numerous chromatographic steps, an interaction that was verified by co-immunoprecipitation and direct binding studies. The interaction between UL2 and the DNA polymerase is mediated through the UL30 subunit. Moreover, UL2 co-localizes with UL30 to nuclear viral prereplicative sites. The functional consequence of this interaction is that replication of uracil-containing templates stalls at positions -1 and -2 relative to the template uracil because of the fact that these are converted into non-instructional abasic sites. These findings support the existence of a viral repair complex that may be capable of replication-coupled base excision repair and further highlight the role of DNA repair in the maintenance of the HSV-1 genome.
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Affiliation(s)
- Federica Bogani
- Department of Basic Medical Sciences, The University of Arizona College of Medicine, Phoenix, Arizona 85004, USA
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29
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Rutvisuttinunt W, Meyer PR, Scott WA. Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template. PLoS One 2008; 3:e3561. [PMID: 18974785 PMCID: PMC2570493 DOI: 10.1371/journal.pone.0003561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 10/09/2008] [Indexed: 11/18/2022] Open
Abstract
Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Peter R. Meyer
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Walter A. Scott
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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30
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Meyer PR, Rutvisuttinunt W, Matsuura SE, So AG, Scott WA. Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer-template controlled by binding deoxynucleoside triphosphates or foscarnet. J Mol Biol 2007; 369:41-54. [PMID: 17400246 PMCID: PMC1986715 DOI: 10.1016/j.jmb.2007.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 02/28/2007] [Accepted: 03/02/2007] [Indexed: 11/30/2022]
Abstract
Binding of the next complementary dNTP by the binary complex containing HIV-1 reverse transcriptase (RT) and primer-template induces conformational changes that have been implicated in catalytic function of RT. We have used DNase I footprinting, gel electrophoretic mobility shift, and exonuclease protection assays to characterize the interactions between HIV-1 RT and chain-terminated primer-template in the absence and presence of various ligands. Distinguishable stable complexes were formed in the presence of foscarnet (an analog of pyrophosphate), the dNTP complementary to the first (+1) templating nucleotide or the dNTP complementary to the second (+2) templating nucleotide. The position of HIV-1 RT on the primer-template in each of these complexes is different. RT is located upstream in the foscarnet complex, relative to the +1 complex, and downstream in the +2 complex. These results suggest that HIV-1 RT can translocate along the primer-template in the absence of phosphodiester bond formation. The ability to form a specific foscarnet complex might explain the inhibitory properties of this compound. The ability to recognize the second templating nucleotide has implications for nucleotide misincorporation.
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Affiliation(s)
- Peter R Meyer
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
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Subramanian K, Rutvisuttinunt W, Scott W, Myers RS. The enzymatic basis of processivity in lambda exonuclease. Nucleic Acids Res 2003; 31:1585-96. [PMID: 12626699 PMCID: PMC152868 DOI: 10.1093/nar/gkg266] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Accepted: 01/28/2003] [Indexed: 11/12/2022] Open
Abstract
Lambda exonuclease is a highly processive 5'-->3' exonuclease that degrades double-stranded (ds)DNA. The single-stranded DNA produced by lambda exonuclease is utilized by homologous pairing proteins to carry out homologous recombination. The extensive studies of lambda biology, lambda exonuclease enzymology and the availability of the X-ray crystallographic structure of lambda exonuclease make it a suitable model to dissect the mechanisms of processivity. lambda Exonuclease is a toroidal homotrimeric molecule and this quaternary structure is a recurring theme in proteins engaged in processive reactions in nucleic acid metabolism. We have identified residues in lambda exonuclease involved in recognizing the 5'-phosphate at the ends of broken dsDNA. The preference of lambda exonuclease for a phosphate moiety at 5' dsDNA ends has been established in previous studies; our results indicate that the low activity in the absence of the 5'-phosphate is due to the formation of inert enzyme-substrate complexes. By examining a lambda exonuclease mutant impaired in 5'-phosphate recognition, the significance of catalytic efficiency in modulating the processivity of lambda exonuclease has been elucidated. We propose a model in which processivity of lambda exonuclease is expressed as the net result of competition between pathways that either induce forward translocation or promote reverse translocation and dissociation.
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Affiliation(s)
- Krithika Subramanian
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33136-6129, USA
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