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Khan D, Thomas SA, Tientcheu PE, Suso SMS, Dupont C, Kwambana-Adams B, Mohammed NI, Nicol MP, Antonio M. Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal/oropharyngeal samples. PLoS One 2023; 18:e0289557. [PMID: 37535692 PMCID: PMC10399880 DOI: 10.1371/journal.pone.0289557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
INTRODUCTION Several important human pathogens that cause life-threatening infections are asymptomatically carried in the Nasopharynx/Oropharynx (NP/OP). DNA extraction is a prerequisite for most culture-independent techniques used to identify pathogens in the NP/OP. However, components of DNA extraction kits differ thereby giving rise to differences in performance. We compared the DNA concentration and the detection of three pathogens in the NP/OP using the discontinued DNeasy PowerSoil Kit (Kit DP) and the DNeasy PowerLyzer PowerSoil Kit (Kit DPP). METHODS DNA was extracted from the same set of 103 NP/OP samples using the two kits. DNA concentration was measured using the Qubit 2.0 Fluorometer. Real-time Polymerase Chain reaction (RT-PCR) was done using the QuantStudio 7-flex system to detect three pathogens: S. pneumoniae, H. influenzae, and N. meningitidis. Bland-Altman statistics and plots were used to determine the threshold cycle (Ct) value agreement for the two kits. RESULTS The average DNA concentration from kit DPP was higher than Kit DP; 1235.6 ng/ml (SD = 1368.3) vs 884.9 ng/ml (SD = 1095.3), p = 0.002. Using a Ct value cutoff of 40 for positivity, the concordance for the presence of S. pneumoniae was 82% (84/102); 94%(96/103) for N. meningitidis and 92%(95/103) for H. influenzae. Kit DP proportionately resulted in higher Ct values than Kit DPP for all pathogens. The Ct value bias of measurement for S. pneumoniae was +2.4 (95% CI, 1.9-3.0), +1.4 (95% CI, 0.9-1.9) for N. meningitidis and +1.4 (95% CI, 0.2-2.5) for H. influenzae. CONCLUSION The higher DNA concentration obtained using kit DPP could increase the chances of recovering low abundant bacteria. The PCR results were reproducible for more than 90% of the samples for the gram-negative H. influenzae and N. meningitidis. Ct value variations of the kits must be taken into consideration when comparing studies that have used the two kits.
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Affiliation(s)
- Dam Khan
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Shola-Able Thomas
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Peggy-Estelle Tientcheu
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sambou M S Suso
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nuredin Ibrahim Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mark P Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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2
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Dunne EM, Hua Y, Salaudeen R, Hossain I, Ndiaye M, Ortika BD, Mulholland EK, Hinds J, Manna S, Mackenzie GA, Satzke C. Insights into pneumococcal pneumonia using lung aspirates and nasopharyngeal swabs collected from pneumonia patients in The Gambia. J Infect Dis 2020; 225:1447-1451. [PMID: 32319524 PMCID: PMC9016440 DOI: 10.1093/infdis/jiaa186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background We investigated the pathogenesis of pneumococcal pneumonia using clinical specimens collected for pneumonia surveillance in The Gambia. Methods Lung aspirates and nasopharyngeal swabs from 31 patients were examined by culture, quantitative polymerase chain reaction (qPCR), whole genome sequencing, serotyping, and reverse-transcription qPCR. Results Five lung aspirates cultured pneumococci, with a matching strain identified in the nasopharynx. Three virulence genes including ply (pneumolysin) were upregulated >20-fold in the lung compared with the nasopharynx. Nasopharyngeal pneumococcal density was higher in pediatric pneumonia patients compared with controls (P < .0001). Conclusions Findings suggest that changes in pneumococcal gene expression occurring in the lung environment may be important in pathogenesis.
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Affiliation(s)
- Eileen M Dunne
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Yinglei Hua
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Rasheed Salaudeen
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ilias Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Malick Ndiaye
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Belinda D Ortika
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia
| | - E Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom.,BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Sam Manna
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Grant A Mackenzie
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.,Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
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3
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Chan J, Nguyen CD, Dunne EM, Kim Mulholland E, Mungun T, Pomat WS, Rafai E, Satzke C, Weinberger DM, Russell FM. Using pneumococcal carriage studies to monitor vaccine impact in low- and middle-income countries. Vaccine 2019; 37:6299-6309. [PMID: 31500968 DOI: 10.1016/j.vaccine.2019.08.073] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/13/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022]
Abstract
Pneumococcal disease is a leading cause of childhood mortality, globally. The pneumococcal conjugate vaccine (PCV) has been introduced to many countries worldwide. However there are few studies evaluating PCV impacts in low- and middle-income countries (LMIC) because measuring the impact of PCV on pneumococcal disease in LMICs is challenging. We review the role of pneumococcal carriage studies for the evaluation of PCVs in LMICs and discuss optimal methods for conducting these studies. Fifteen carriage studies from 13 LMICs quantified the effects of PCV on carriage, and identified replacement carriage serotypes in the post-PCV era. Ten studies reported on the indirect effects of PCV on carriage. Results can be used to inform cost-effectiveness evaluations, guide policy decisions on dosing and product, and monitor equity in program implementation. Critically, we highlight gaps in our understanding of serotype replacement disease in LMICs and identify priorities for research to address this gap.
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Affiliation(s)
- Jocelyn Chan
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Cattram D Nguyen
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Eileen M Dunne
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - E Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tuya Mungun
- National Center of Communicable Diseases (NCCD), Ministry of Health, Ulaanbaatar, Mongolia
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Infection and Immunity Unit, Goroka, Papua New Guinea; Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Eric Rafai
- Ministry of Health and Medical Services, Suva, Fiji
| | - Catherine Satzke
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Fiona M Russell
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
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4
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
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Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK. The PneuCarriage Project: A Multi-Centre Comparative Study to Identify the Best Serotyping Methods for Examining Pneumococcal Carriage in Vaccine Evaluation Studies. PLoS Med 2015; 12:e1001903; discussion e1001903. [PMID: 26575033 PMCID: PMC4648509 DOI: 10.1371/journal.pmed.1001903] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/09/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. METHODS AND FINDINGS Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. CONCLUSIONS Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail:
| | - Eileen M. Dunne
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Barbara D. Porter
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - E. Kim Mulholland
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Single-plex quantitative assays for the detection and quantification of most pneumococcal serotypes. PLoS One 2015; 10:e0121064. [PMID: 25798884 PMCID: PMC4370668 DOI: 10.1371/journal.pone.0121064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/27/2015] [Indexed: 12/04/2022] Open
Abstract
Streptococcus pneumoniae globally kills more children than any other infectious disease every year. A prerequisite for pneumococcal disease and transmission is colonization of the nasopharynx. While the introduction of pneumococcal conjugate vaccines has reduced the burden of pneumococcal disease, understanding the impact of vaccination on nasopharyngeal colonization has been hampered by the lack of sensitive quantitative methods for the detection of >90 known S. pneumoniae serotypes. In this work, we developed 27 new quantitative (q)PCR reactions and optimized 26 for a total of 53 qPCR reactions targeting pneumococcal serotypes or serogroups, including all vaccine types. Reactions proved to be target-specific with a limit of detection of 2 genome equivalents per reaction. Given the number of probes required for these assays and their unknown shelf-life, the stability of cryopreserved reagents was evaluated. Our studies demonstrate that two-year cryopreserved probes had similar limit of detection as freshly-diluted probes. Moreover, efficiency and limit of detection of 1-month cryopreserved, ready-to-use, qPCR reaction mixtures were similar to those of freshly prepared mixtures. Using these reactions, our proof-of-concept studies utilizing nasopharyngeal samples (N=30) collected from young children detected samples containing ≥2 serotypes/serogroups. Samples colonized by multiple serotypes/serogroups always had a serotype that contributes at least 50% of the pneumococcal load. In addition, a molecular approach called S6-q(PCR)2 was developed and proven to individually detect and quantify epidemiologically-important serogroup 6 strains including 6A, 6B, 6C and 6D. This technology will be useful for epidemiological studies, diagnostic platforms and to study the pneumobiome.
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Abstract
Since the introduction of 7-valent pneumococcal conjugate vaccine (PCV7), PCVs with extended coverage have become available, and there is emerging global evidence that these vaccines, in particular PCV13, have further reduced rates of invasive pneumococcal disease compared with PCV7. The present article aims to address emerging topics related to PCV13 use in routine clinical practice; specifically: (1) the potential role of high-valent PCVs in reducing pneumococcal disease burden; (2) the impact of PCVs on nasopharyngeal carriage and how this may contribute to reductions in otitis media and pneumonia, as well as the prevalence of resistant pneumococcal strains; (3) new PCV13 indications and (4) importance of schedule adherence for PCV in the prevention of cases of vaccine serotype-specific invasive pneumococcal disease. The beneficial effects of PCVs in protecting individuals from a wide spectrum of pneumococcal diseases can be increased by improving the vaccine coverage and adhering to the recommended vaccination schedules. There is increasing evidence that PCV13 has reduced much of the post-PCV7 burden of pneumococcal diseases in the pediatric community, including reducing pneumococcal colonization and the incidence of invasive pneumococcal disease and mucosal diseases. This has also led to a reduction in antibiotic-resistant pneumococcal diseases. The role of PCV13 in clinical practice is evolving, with PCV13 now available for children and adolescents between the ages of 6 weeks and 17 years, thus ensuring that children in all age groups can be protected against vaccine-serotype pneumococcal diseases. Continued surveillance is warranted to monitor the impact of PCV13 on disease burden.
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9
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Howie SRC, Morris GAJ, Tokarz R, Ebruke BE, Machuka EM, Ideh RC, Chimah O, Secka O, Townend J, Dione M, Oluwalana C, Njie M, Jallow M, Hill PC, Antonio M, Greenwood B, Briese T, Mulholland K, Corrah T, Lipkin WI, Adegbola RA. Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples. Clin Infect Dis 2014; 59:682-5. [PMID: 24867789 PMCID: PMC4130311 DOI: 10.1093/cid/ciu384] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcuspneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.
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Affiliation(s)
| | | | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University, New York, New York
| | | | | | - Readon C Ideh
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Osaretin Chimah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Ousman Secka
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - John Townend
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Michel Dione
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | | | - Malick Njie
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Mariatou Jallow
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Martin Antonio
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Brian Greenwood
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Kim Mulholland
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Tumani Corrah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Richard A Adegbola
- Medical Research Council Unit, Fajara, Republic of The Gambia GlaxoSmithKline Vaccines, Wavre, Belgium
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Kaslow RA, Stanberry LR, Le Duc JW. Diagnosis, Discovery and Dissection of Viral Diseases. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7122662 DOI: 10.1007/978-1-4899-7448-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard A. Kaslow
- Department of Epidemiology, University of Alabama, Birmingham School of Public Health, Birmingham, Alabama USA
| | - Lawrence R. Stanberry
- Departmant of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York USA
| | - James W. Le Duc
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas USA
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