Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Chantal B. F. Vogels; Mallery I. Breban; Isabel M. Ott; Tara Alpert; Mary E. Petrone; Anne E. Watkins; Chaney C. Kalinich; Rebecca Earnest; Jessica E. Rothman; Jaqueline Goes de Jesus; Ingra Morales Claro; Giulia Magalhães Ferreira; Myuki A. E. Crispim; Brazil-UK CADDE Genomic Network; Lavanya Singh; Houriiyah Tegally; Ugochukwu J. Anyaneji; Network for Genomic Surveillance in South Africa; Emma B. Hodcroft; Christopher E. Mason; Gaurav Khullar; Jessica Metti; Joel T. Dudley; Matthew J. MacKay; Megan Nash; Jianhui Wang; Chen Liu; Pei Hui; Steven Murphy; Caleb Neal; Eva Laszlo; Marie L. Landry; Anthony Muyombwe; Randy Downing; Jafar Razeq; Tulio de Oliveira; Nuno R. Faria; Ester C. Sabino; Richard A. Neher; Joseph R. Fauver; Nathan D. Grubaugh

doi:10.1371/journal.pbio.3001236

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Methods and Resources report novel methods, substantial improvements to current methodologies, or informational datasets.

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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Chantal B. F. Vogels ,

Contributed equally to this work with: Chantal B. F. Vogels, Mallery I. Breban

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: chantal.vogels@yale.edu (CBFV); joseph.fauver@yale.edu (JRF); nathan.grubaugh@yale.edu (NDG)

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0003-0027-6480

⨯
Mallery I. Breban ,

Contributed equally to this work with: Chantal B. F. Vogels, Mallery I. Breban

Roles Formal analysis, Investigation, Validation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Isabel M. Ott,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Tara Alpert,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0003-3582-1047

⨯
Mary E. Petrone,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Anne E. Watkins,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Chaney C. Kalinich,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0001-9675-0065

⨯
Rebecca Earnest,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0001-6555-8409

⨯
Jessica E. Rothman,

Roles Formal analysis, Investigation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0002-9961-1092

⨯
Jaqueline Goes de Jesus,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil

https://orcid.org/0000-0002-5404-272X

⨯
Ingra Morales Claro,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
⨯
Giulia Magalhães Ferreira,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliations Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil, Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil

https://orcid.org/0000-0003-0444-4592

⨯
Myuki A. E. Crispim,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
⨯
Brazil-UK CADDE Genomic Network ,

¶Membership of the Brazil-UK CADDE Genomic Network and the Network for Genomic Surveillance in South Africa (NGS-SA) is provided in the Acknowledgments.
⨯
Lavanya Singh,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa

https://orcid.org/0000-0002-1726-4454

⨯
Houriiyah Tegally,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
⨯
Ugochukwu J. Anyaneji,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
⨯
Network for Genomic Surveillance in South Africa ,

¶Membership of the Brazil-UK CADDE Genomic Network and the Network for Genomic Surveillance in South Africa (NGS-SA) is provided in the Acknowledgments.
⨯
Emma B. Hodcroft,

Roles Investigation, Visualization, Writing – review & editing

Affiliation Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
⨯
Christopher E. Mason,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America

https://orcid.org/0000-0002-1850-1642

⨯
Gaurav Khullar,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America
⨯
Jessica Metti,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America
⨯
Joel T. Dudley,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America

https://orcid.org/0000-0002-7036-6492

⨯
Matthew J. MacKay,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America
⨯
Megan Nash,

Roles Investigation, Resources, Writing – review & editing

Affiliation Tempus Labs, Chicago, Illinois, United States of America
⨯
Jianhui Wang,

Roles Investigation, Resources, Writing – review & editing

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Chen Liu,

Roles Investigation, Resources, Writing – review & editing

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Pei Hui,

Roles Investigation, Resources, Writing – review & editing

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Steven Murphy,

Roles Investigation, Resources, Writing – review & editing

Affiliation Murphy Medical Associates, Greenwich, Connecticut, United States of America
⨯
Caleb Neal,

Roles Investigation, Resources, Writing – review & editing

Affiliation Murphy Medical Associates, Greenwich, Connecticut, United States of America
⨯
Eva Laszlo,

Roles Investigation, Resources, Writing – review & editing

Affiliation Murphy Medical Associates, Greenwich, Connecticut, United States of America
⨯
Marie L. Landry,

Roles Investigation, Resources, Writing – review & editing

Affiliation Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
⨯
Anthony Muyombwe,

Roles Investigation, Resources, Writing – review & editing

Affiliation Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
⨯
Randy Downing,

Roles Investigation, Resources, Writing – review & editing

Affiliation Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
⨯
Jafar Razeq,

Roles Investigation, Resources, Writing – review & editing

Affiliation Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
⨯
Tulio de Oliveira,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
⨯
Nuno R. Faria,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliations Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil, MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom, Department of Zoology, University of Oxford, Oxford, United Kingdom

https://orcid.org/0000-0001-8839-2798

⨯
Ester C. Sabino,

Roles Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliation Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
⨯
Richard A. Neher,

Roles Conceptualization, Formal analysis, Investigation, Writing – review & editing

Affiliations Biozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland
⨯
Joseph R. Fauver ,

Roles Conceptualization, Formal analysis, Investigation, Methodology, Supervision, Validation, Writing – review & editing

* E-mail: chantal.vogels@yale.edu (CBFV); joseph.fauver@yale.edu (JRF); nathan.grubaugh@yale.edu (NDG)

¶‡ These authors are joint senior authors on this work.

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
[ ... ],
Nathan D. Grubaugh

Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: chantal.vogels@yale.edu (CBFV); joseph.fauver@yale.edu (JRF); nathan.grubaugh@yale.edu (NDG)

¶‡ These authors are joint senior authors on this work.

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
⨯
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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Chantal B. F. Vogels,
Mallery I. Breban,
Isabel M. Ott,
Tara Alpert,
Mary E. Petrone,
Anne E. Watkins,
Chaney C. Kalinich,
Rebecca Earnest,
Jessica E. Rothman,
Jaqueline Goes de Jesus

Published: May 7, 2021
https://doi.org/10.1371/journal.pbio.3001236

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