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Yip M, Chen J, Zhi Y, Tran NT, Namkung S, Pastor E, Gao G, Tai PWL. Querying Recombination Junctions of Replication-Competent Adeno-Associated Viruses in Gene Therapy Vector Preparations with Single Molecule, Real-Time Sequencing. Viruses 2023; 15:1228. [PMID: 37376529 DOI: 10.3390/v15061228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/20/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Clinical-grade preparations of adeno-associated virus (AAV) vectors used for gene therapy typically undergo a series of diagnostics to determine titer, purity, homogeneity, and the presence of DNA contaminants. One type of contaminant that remains poorly investigated is replication-competent (rc)AAVs. rcAAVs form through recombination of DNA originating from production materials, yielding intact, replicative, and potentially infectious virus-like virions. They can be detected through the serial passaging of lysates from cells transduced by AAV vectors in the presence of wildtype adenovirus. Cellular lysates from the last passage are subjected to qPCR to detect the presence of the rep gene. Unfortunately, the method cannot be used to query the diversity of recombination events, nor can qPCR provide insights into how rcAAVs arise. Thus, the formation of rcAAVs through errant recombination events between ITR-flanked gene of interest (GOI) constructs and expression constructs carrying the rep-cap genes is poorly described. We have used single molecule, real-time sequencing (SMRT) to analyze virus-like genomes expanded from rcAAV-positive vector preparations. We present evidence that sequence-independent and non-homologous recombination between the ITR-bearing transgene and the rep/cap plasmid occurs under several events and rcAAVs spawn from diverse clones.
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Affiliation(s)
- Mitchell Yip
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jing Chen
- Spirovant Sciences, Inc., Philadelphia, PA 19104, USA
| | - Yan Zhi
- Spirovant Sciences, Inc., Philadelphia, PA 19104, USA
| | - Ngoc Tam Tran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Suk Namkung
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Eric Pastor
- Spirovant Sciences, Inc., Philadelphia, PA 19104, USA
| | - Guangping Gao
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute of Rare Diseases Research, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute of Rare Diseases Research, UMass Chan Medical School, Worcester, MA 01605, USA
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2
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Morsli M, Kerharo Q, Delerce J, Roche PH, Troude L, Drancourt M. Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report. Pathogens 2021; 10:461. [PMID: 33921275 DOI: 10.3390/pathogens10040461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes.
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Tran NT, Heiner C, Weber K, Weiand M, Wilmot D, Xie J, Wang D, Brown A, Manokaran S, Su Q, Zapp ML, Gao G, Tai PW. AAV-Genome Population Sequencing of Vectors Packaging CRISPR Components Reveals Design-Influenced Heterogeneity. Mol Ther Methods Clin Dev 2020; 18:639-651. [PMID: 32775498 PMCID: PMC7397707 DOI: 10.1016/j.omtm.2020.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
The gene therapy field has been galvanized by two technologies that have revolutionized treating genetic diseases: vectors based on adeno-associated viruses (AAVs), and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene-editing tools. When combined into one platform, these safe and broadly tropic biotherapies can be engineered to target any region in the human genome to correct genetic flaws. Unfortunately, few investigations into the design compatibility of CRISPR components in AAV vectors exist. Using AAV-genome population sequencing (AAV-GPseq), we previously found that self-complementary AAV vector designs with strong DNA secondary structures can cause a high degree of truncation events, impacting production and vector efficacy. We hypothesized that the single-guide RNA (sgRNA) scaffold, which contains several loop regions, may also compromise vector integrity. We have therefore advanced the AAV-GPseq method to also interrogate single-strand AAV vectors to investigate whether vector genomes carrying Cas9-sgRNA cassettes can cause truncation events. We found that on their own, sgRNA sequences do not produce a high degree of truncation events. However, we demonstrate that vector genome designs that carry dual sgRNA expression cassettes in tail-to-tail configurations lead to truncations. In addition, we revealed that heterogeneity in inverted terminal repeat sequences in the form of regional deletions inherent to certain AAV vector plasmids can be interrogated.
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Affiliation(s)
- Ngoc Tam Tran
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Cheryl Heiner
- Pacific Biosciences, Inc., Menlo Park, CA 94025, USA
| | | | | | - Daniella Wilmot
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Alexander Brown
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sangeetha Manokaran
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Maria L. Zapp
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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Nicholls SM, Quick JC, Tang S, Loman NJ. Ultra-deep, long-read nanopore sequencing of mock microbial community standards. Gigascience 2019; 8:giz043. [PMID: 31089679 PMCID: PMC6520541 DOI: 10.1093/gigascience/giz043] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition. FINDINGS We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning. CONCLUSIONS We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.
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Affiliation(s)
- Samuel M Nicholls
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Joshua C Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Shuiquan Tang
- Zymo Research Corporation, 17062 Murphy Ave., Irvine, CA 92614, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Sissoko D, Keïta M, Diallo B, Aliabadi N, Fitter DL, Dahl BA, Akoi Bore J, Raymond Koundouno F, Singethan K, Meisel S, Enkirch T, Mazzarelli A, Amburgey V, Faye O, Alpha Sall A, Magassouba N, Carroll MW, Anglaret X, Malvy D, Formenty P, Bruce Aylward R, Keïta S, Harouna Djingarey M, Loman NJ, Günther S, Duraffour S. Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child. Clin Infect Dis 2017; 64:513-516. [PMID: 27940938 PMCID: PMC5404930 DOI: 10.1093/cid/ciw793] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 07/05/2016] [Accepted: 11/30/2016] [Indexed: 12/03/2022] Open
Abstract
A 9-month-old infant died from Ebola virus (EBOV) disease with unknown epidemiological link. While her parents did not report previous illness, laboratory investigations revealed persisting EBOV RNA in the mother’s breast milk and the father’s seminal fluid. Genomic analysis strongly suggests EBOV transmission to the child through breastfeeding.
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Affiliation(s)
- Daouda Sissoko
- INSERM U1219, Bordeaux University, Bordeaux, France.,Bordeaux University Hospital, Bordeaux, France
| | - Mory Keïta
- World Health Organization, Conakry, Guinea
| | | | - Negar Aliabadi
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David L Fitter
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin A Dahl
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joseph Akoi Bore
- European Mobile Laboratory Consortium, Hamburg, Germany.,Ministry of Health, Conakry, Guinea
| | - Fara Raymond Koundouno
- European Mobile Laboratory Consortium, Hamburg, Germany.,Ministry of Health, Conakry, Guinea
| | - Katrin Singethan
- European Mobile Laboratory Consortium, Hamburg, Germany.,Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich
| | - Sarah Meisel
- European Mobile Laboratory Consortium, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Theresa Enkirch
- European Mobile Laboratory Consortium, Hamburg, Germany.,Paul-Ehrlich-Institut, Division of Veterinary Medicine, Langen, Germany
| | - Antonio Mazzarelli
- European Mobile Laboratory Consortium, Hamburg, Germany.,National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Victoria Amburgey
- Sandia National Laboratories, Albuquerque, New Mexico.,Ratoma Ebola Diagnostic Center, Conakry, Guinea
| | | | | | - N'Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Miles W Carroll
- European Mobile Laboratory Consortium, Hamburg, Germany.,Public Health England, Porton Down, Salisbury.,University of Southampton, South General Hospital, Southampton, United Kingdom
| | - Xavier Anglaret
- INSERM U1219, Bordeaux University, Bordeaux, France.,PAC-CI, ANRS Research Site, Treichville University Hospital, Abidjan, Côte d'Ivoire
| | - Denis Malvy
- INSERM U1219, Bordeaux University, Bordeaux, France.,Bordeaux University Hospital, Bordeaux, France
| | | | | | | | | | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, United Kingdom
| | - Stephan Günther
- European Mobile Laboratory Consortium, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sophie Duraffour
- European Mobile Laboratory Consortium, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S. Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days. Clin Infect Dis 2016; 63:1353-1356. [PMID: 27585800 PMCID: PMC5091350 DOI: 10.1093/cid/ciw601] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [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: 07/05/2016] [Accepted: 08/17/2016] [Indexed: 11/17/2022] Open
Abstract
We report on an Ebola virus disease (EVD) survivor who showed Ebola virus in seminal fluid 531 days after onset of disease. The persisting virus was sexually transmitted in February 2016, about 470 days after onset of symptoms, and caused a new cluster of EVD in Guinea and Liberia.
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Affiliation(s)
| | - Daouda Sissoko
- INSERM U1219, Bordeaux University.,Bordeaux University Hospital, France
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, United Kingdom
| | - Hadja Aïssatou Bah
- Laboratoire des Fièvres Hémorragiques en Guinée, Hôpital Donka et N'Zérékoré
| | - Hawa Bah
- World Health Organization, Conakry, Guinea
| | - Mary Claire Worrell
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,Center for Global Health, CDC, Atlanta, Georgia
| | | | | | | | | | | | - Ngozi A Erondu
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry
| | - Benjamin A Dahl
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,Center for Global Health, CDC, Atlanta, Georgia
| | - Susann Handrick
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, United Kingdom.,Department of Public Health, University of Makeni, Sierra Leone
| | - Luke W Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, United Kingdom.,Department of Public Health, University of Makeni, Sierra Leone
| | - Matthew Cotten
- Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Umaru Jah
- Department of Public Health, University of Makeni, Sierra Leone
| | - Raoul Emeric Guetiya Wadoum
- Department of Public Health, University of Makeni, Sierra Leone.,Department of Biology, University of Rome II "Tor Vergata," Italy
| | - Pierre Rollin
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,National Center for Emerging and Zoonotic Infectious Diseases, CDC, Atlanta, Georgia
| | - N'Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Guinea
| | - Denis Malvy
- INSERM U1219, Bordeaux University.,Bordeaux University Hospital, France
| | - Xavier Anglaret
- INSERM U1219, Bordeaux University.,Programme ANRS Coopération Côte d'Ivoire, Agence Nationale de Recherche sur le Sida Research Site, Treichville University Hospital, Abidjan, Côte d'Ivoire
| | - Miles W Carroll
- European Mobile Laboratory Consortium.,Public Health England, Porton Down, Salisbury.,University of Southampton, South General Hospital, United Kingdom
| | | | | | | | | | | | - Stephan Günther
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andrew Rambaut
- Institute for Evolutionary Biology, Centre for Infection, Immunity and Evolution, Ashworth Laboratories, University of Edinburgh, United Kingdom
| | - Sophie Duraffour
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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