Taj Azarian:
ORCID: https://orcid.org/0000-0002-8611-5241
Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole:
ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review
& editing
Pamela P. Martinez:
ORCID: https://orcid.org/0000-0002-3607-0938
Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole:
ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original
draftRole: Writing – review & editing
Brian J. Arnold: Role: ConceptualizationRole: Formal analysisRole: VisualizationRole: Writing – review
& editing
Xueting Qiu:
ORCID: https://orcid.org/0000-0001-6810-7304
Role: Data curationRole: InvestigationRole: ValidationRole: Writing – review & editing
Lindsay R. Grant: Role: InvestigationRole: MethodologyRole: ResourcesRole: Writing – review & editing
Jukka Corander:
ORCID: https://orcid.org/0000-0002-7752-1942
Role: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing
– review & editing
Christophe Fraser:
ORCID: https://orcid.org/0000-0003-2399-9657
Role: InvestigationRole: MethodologyRole: ValidationRole: Writing – review & editing
Nicholas J. Croucher:
ORCID: https://orcid.org/0000-0001-6303-8768
Role: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review &
editing
Laura L. Hammitt:
ORCID: https://orcid.org/0000-0001-6051-1484
Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole:
Writing – review & editing
Raymond Reid: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole:
Writing – review & editing
Mathuram Santosham: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing
– review & editing
Robert C. Weatherholtz: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole:
SupervisionRole: ValidationRole: Writing – review & editing
Stephen D. Bentley: Role: InvestigationRole: MethodologyRole: Writing – review & editing
Katherine L. O’Brien: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole:
ValidationRole: Writing – review & editing
Marc Lipsitch:
ORCID: https://orcid.org/0000-0003-1504-9213
Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole:
InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole:
Writing – original draftRole: Writing – review & editing
William P. Hanage:
ORCID: https://orcid.org/0000-0002-6319-7336
Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole:
Project administrationRole: SupervisionRole: ValidationRole: Writing – original draftRole:
Writing – review & editing
J. Arjan G. M. de Visser: Role: Academic Editor
Journal ID (nlm-ta): PLoS Biol
Journal ID (iso-abbrev): PLoS Biol
Journal ID (publisher-id): plos
Journal ID (pmc): plosbiol
Title:
PLoS Biology
Publisher:
Public Library of Science
(San Francisco, CA USA
)
ISSN
(Print):
1544-9173
ISSN
(Electronic):
1545-7885
Publication date
(Electronic):
22
October
2020
Publication date Collection:
October
2020
Publication date PMC-release: 22
October
2020
Volume: 18
Issue: 10
Electronic Location Identifier: e3000878
Affiliations
[1
]
Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida,
United States of America
[2
]
Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School
of Public Health, Harvard University, Boston, Massachusetts, United States of America
[3
]
Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health,
Baltimore, Maryland, United States of America
[4
]
Helsinki Institute for Information Technology, Department of Mathematics and Statistics,
University of Helsinki, Helsinki, Finland
[5
]
Department of Biostatistics, University of Oslo, Oslo, Norway
[6
]
Infection Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, United Kingdom
[7
]
Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford,
United Kingdom
[8
]
MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease
Epidemiology, Imperial College London, London, United Kingdom
[9
]
World Health Organization, Geneva, Switzerland
[10
]
Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health,
Harvard University, Boston, Massachusetts, United States of America
Wageningen University, NETHERLANDS
Author notes
I have read the journal’s policy and the authors of this manuscript have the following
competing interests. ML has consulted for Pfizer, Affinivax, and Merck and has received
grant support not related to this paper from Pfizer and PATH Vaccine Solutions. WPH,
ML, and NJC have consulted for Antigen Discovery Inc. The authors have declared that
no competing interests exist. KLOB has received grant support for pneumococcal work
not related to this paper from Pfizer, GSK, and Gavi. KLOB has consulted for Merck
and Sanofi Pasteur. LRG, LLH, and RCW have received grant support not related to this
paper from Pfizer, Merck, and GSK.
[¤a]
Current address: Department of Microbiology, University of Illinois at Urbana Champaign,
Illinois, United States of America.
‡ TA and PPM are joint first authors on this work. ML and WPH are joint senior authors
on this work.
Author information
Article
Publisher ID:
PBIOLOGY-D-20-00582
DOI: 10.1371/journal.pbio.3000878
PMC ID: 7580979
PubMed ID: 33091022
SO-VID: 3e4d6e7b-f9e5-412f-abea-f8d576b7efcb
Copyright © © 2020 Azarian et al
License:
This is an open access article distributed under the terms of the
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided
the original author and source are credited.
Funded by: National Institutes of Health (US)
Award ID: R01 AI106786
Award Recipient
:
ORCID: https://orcid.org/0000-0002-6319-7336
William P. Hanage
Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
Award ID: R01 AI048935
Award Recipient
:
ORCID: https://orcid.org/0000-0002-6319-7336
William P. Hanage
Funded by: funder-id http://dx.doi.org/10.13039/100004440, Wellcome Trust;
Award ID: 104169/Z/14/A
Award Recipient
:
ORCID: https://orcid.org/0000-0001-6303-8768
Nicholas J. Croucher
Funded by: funder-id http://dx.doi.org/10.13039/100010663, H2020 European Research Council;
Award ID: 742158
Award Recipient
:
ORCID: https://orcid.org/0000-0002-7752-1942
Jukka Corander
TA and WPH were funded by NIH grant R01 AI106786. TA, PPM, and ML were funded by NIH
grant R01 AI048935. XQ was supported by the National Institute of General Medical
Sciences of NIH under Award Number U54GM088558. NJC was funded by a Sir Henry Dale
fellowship and jointly funded by the Wellcome Trust and Royal Society (Grant Number
104169/Z/14/A). JC was funded by European Research Council grant number 742158. The
funders had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.
Subject:
Research Article
Subject:
Biology and Life Sciences
Subject:
Genetics
Subject:
Genomics
Subject:
Medicine and Health Sciences
Subject:
Medical Conditions
Subject:
Infectious Diseases
Subject:
Infectious Disease Control
Subject:
Vaccines
Subject:
Biology and Life Sciences
Subject:
Immunology
Subject:
Vaccination and Immunization
Subject:
Medicine and Health Sciences
Subject:
Immunology
Subject:
Vaccination and Immunization
Subject:
Medicine and Health Sciences
Subject:
Public and Occupational Health
Subject:
Preventive Medicine
Subject:
Vaccination and Immunization
Subject:
Medicine and Health Sciences
Subject:
Medical Conditions
Subject:
Infectious Diseases
Subject:
Infectious Disease Control
Subject:
Vaccines
Subject:
Conjugate Vaccines
Subject:
Biology and Life Sciences
Subject:
Microbiology
Subject:
Bacteriology
Subject:
Bacterial Genetics
Subject:
Bacterial Genomics
Subject:
Biology and Life Sciences
Subject:
Genetics
Subject:
Microbial Genetics
Subject:
Bacterial Genetics
Subject:
Bacterial Genomics
Subject:
Biology and Life Sciences
Subject:
Genetics
Subject:
Genomics
Subject:
Microbial Genomics
Subject:
Bacterial Genomics
Subject:
Biology and Life Sciences
Subject:
Microbiology
Subject:
Microbial Genomics
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Bacterial Genomics
Subject:
Biology and Life Sciences
Subject:
Genetics
Subject:
Genetic Loci
Subject:
Biology and Life Sciences
Subject:
Organisms
Subject:
Bacteria
Subject:
Streptococcus
Subject:
Pneumococcus
Subject:
Biology and Life Sciences
Subject:
Microbiology
Subject:
Medical Microbiology
Subject:
Microbial Pathogens
Subject:
Bacterial Pathogens
Subject:
Streptococcus
Subject:
Pneumococcus
Subject:
Medicine and Health Sciences
Subject:
Pathology and Laboratory Medicine
Subject:
Pathogens
Subject:
Microbial Pathogens
Subject:
Bacterial Pathogens
Subject:
Streptococcus
Subject:
Pneumococcus
Subject:
Biology and Life Sciences
Subject:
Evolutionary Biology
Subject:
Evolutionary Systematics
Subject:
Phylogenetics
Subject:
Biology and Life Sciences
Subject:
Taxonomy
Subject:
Evolutionary Systematics
Subject:
Phylogenetics
Subject:
Computer and Information Sciences
Subject:
Data Management
Subject:
Taxonomy
Subject:
Evolutionary Systematics
Subject:
Phylogenetics
