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Genetics and Evolution of Infectious Diseases
This page intentionally left blank
Genetics and Evolution
of Infectious Diseases

Second Edition

Michel Tibayrenc

AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD

PARIS • SAN DIEGO • SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO
Elsevier
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The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
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Copyright © 2017, 2011 Elsevier Inc. All rights reserved.

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ISBN: 978-0-12-799942-5

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Contents

List of Contributors xiii

1 Recent Developments in the Definition and Official Names

of Virus Species 1
M.H.V. Van Regenmortel
1. Introduction 1
2. The Logic of Hierarchical Virus Classification 3
3. Bionominalism: Are Species Classes or Individuals? 4
4. The Virus Species Problem 5
5. Properties Used for Defining Virus Species and Identifying
Individual Viruses 8
6. A Virus Species Cannot Be Defined Solely by the Properties
of Viral Genomes 9
7. The New ICTV Definition of Virus Species 11
8. Non-Latinized Binomial Names for Virus Species 14
9. Discussion 17
References 18

2 A Theory-Based Pragmatism for Discovering and Classifying

Newly Divergent Species of Bacterial Pathogens 25
F.M. Cohan, Sarah Kopac
1. Introduction 25
2. Ecological Breadth of Recognized Species 30
3. The Stable Ecotype Model of Bacterial Speciation 33
4. Demarcating Putative Ecotypes From Sequence Data 35
5. Ecological Diversity Within Putative Ecotypes 36
6. Models of Frequent Speciation 38
7. Other Models Where Ecotypes Are Not Discernible
as Sequence Clusters 40
8. Are Bacterial Ecotypes Cohesive? 41
9. Incorporating Ecology Into Bacterial Systematics 43
Acknowledgments 44
References 44
vi Contents

3 Population Structure of Pathogenic Bacteria 51

C.P. Andam, L. Challagundla, T. Azarian, W.P. Hanage, D.A. Robinson
1. Introduction 51
2. Recombination in Bacterial Populations 52
3. Evolutionary Processes Shape Intra- and Interhost Bacterial
Population Structure 58
4. Genomic Analysis Tools for Studying Bacterial Population
Structure 61
5. Conclusions 63
References 64

4 Epidemiology and Evolution of Fungal Pathogens in Plants

and Animals 71
P. Gladieux, E.J. Byrnes III, G. Aguileta, M. Fisher, R.B. Billmyre,
J. Heitman, T. Giraud
1. Introduction 71
2. New and Emerging Mycoses 74
3. Plant Pathogenic Fungi 77
4. New and Emerging Plant Diseases 78
5. Modern Molecular Epidemiological Tools for Investigating Fungal
Diseases 79
6. Population Genetics of Pathogenic Fungi 80
7. Genomics of Fungi: What Makes a Fungus Pathogenic? 86
8. Conclusion 88
References 88

5 Clonal Evolution
ˇ 99
T. de Meeus, F. Prugnolle
1. Introduction 99
2. Definitions 99
3. The Origin of Life, the Origin of Propagation, and Recombination 101
4. Clonal Modes 102
5. Quantifying the Importance of Asexuality in the Biosphere 103
6. Genetic Consequences of Asexuality 103
7. Evolution and the Paradox of Sex 105
8. Clonal Microevolution 106
9. Conclusions 109
Abbreviation List 109
Acknowledgments 110
References 110

6 Coevolution of Host and Pathogen 115

A.D. Morgan, B. Koskella
1. Coevolution of Host and Pathogen 115
2. The Process of Antagonistic Coevolution 121
Contents vii

3. Testing for HostePathogen Coevolution 124

4. Implications of Coevolution 130
5. Summary/Future Outlook 131
References 132

7 Microbes as Tracers of Past Human Demography and Migrations 141

J.-P. Rasigade, A. Gilabert, T. Wirth
1. Introduction 141
2. Using Pathogens as Genetic Tracers for Host History 142
3. Candidates 144
4. Conclusion 159
Abbreviations 159
References 160

8 Phylogenetic Analysis of Pathogens 167

D.A. Morrison
1. Introduction 167
2. The Uses of Phylogenies 168
3. The Logic of Phylogeny Reconstruction 169
4. Characters and Samples 171
5. The Practice of Phylogeny Reconstruction 174
6. Choosing a Method 179
7. Representing Phylogenies: Trees 181
8. Phylogenetic Networks 184
References 188

9 Evolutionary Responses to Infectious Disease 195

G. Cochran, H. Harpending
1. Introduction 195
2. Parasites as Our Friends 197
3. Demography and Parasites 197
4. Agriculture 198
5. Some Lessons From Malaria 199
6. Disease and Standard of Living in Preindustrial Societies:
A Simple Model 202
7. Population Limitation 203
8. Disease, Mating, and Reproductive Strategy 206
9. Prosperity and the Postindustrial Era Mortality Decline 207
References 208

10 Infectious Disease Genomics 211

Y.-T. Liu
1. Introduction 211
2. Vaccine Target 214
3. New Drug Discovery 214
viii Contents

4. Drug Target 215

5. Therapeutic Response and Drug Resistance 216
6. Vector Control 217
7. Clinical Application 218
8. Conclusion 219
References 220

11 Proteomics and HostePathogen Interactions: A Bright Future? 227

D.G. Biron, D. Nedelkov, D. Missé, P. Holzmuller
1. Introduction 227
2. Interest of Proteomics to Study HostePathogen Interactions 228
3. Retrospective Analysis of Previous Proteomics Studies 229
4. Toward New Conceptual Approaches to Decipher the Hoste
Parasite Interactions for Parasites With Simple or Complex
Life Cycle 236
5. Population Proteomics: An Emerging Discipline to Study
HosteParasite Interactions 240
6. Conclusion 247
References 248

12 The Evolution of Antibiotic Resistance 257

F. Gonzalez-Candelas, I. Comas, J.L. Martínez, J.C. Galan, F. Baquero
1. Introduction 257
2. Mechanisms and Sources of Antibiotic Resistance 260
3. Evolution of Antibiotic-Resistance Genes 264
4. Limitations to Adaptation and the Cost of Resistance 269
5. Can the Evolution of Antibiotic Resistance be Predicted? 274
6. Conclusions and Perspectives 275
Glossary 276
List of Abbreviations 276
Acknowledgments 277
References 277

13 Modern Morphometrics of Medically Important Arthropods 285

J.-P. Dujardin
1. Introduction 285
2. Landmark-Based Geometric Morphometry 285
3. Pseudo-Landmark-Based Shape 288
4. Allometry 289
5. Measurement Error 289
6. Some Considerations About the Genetics of Metric Change 290
7. Phenotypic Plasticity 293
8. A Special Case of Shape Change: the Character Displacement 293
9. The Regulation of Phenotype 294
10. Applications in Medical Entomology 296
Contents ix

Glossary 302
Acknowledgments 302
References 302

14 Evolution of Resistance to Insecticide in Disease Vectors 313

P. Labbé, J.-P. David, H. Alout, P. Milesi, L. Djogbénou,
N. Pasteur, M. Weill
1. Introduction 313
2. Insecticide Resistance: Definition and History 314
3. Mechanisms of Resistance 318
4. Conclusion 328
References 329

15 Genetics of Major Insect Vectors 341

P.L. Dorn, S. Justi, E.S. Krafsur, G.C. Lanzaro, A.J. Cornel,
Y. Lee, C.A. Hill
1. Introduction 341
2. Genetics of Tsetse Flies and African Trypanosomiasis 343
3. Genetics of the Triatominae (Hemiptera, Reduviidae) and Chagas
Disease 351
4. The Anopheles gambiae Complex 361
5. Genetics of the Order Ixodida 367
Glossary 371
Acknowledgments 372
References 372

16 Multilocus Sequence Typing of Pathogens: Methods, Analyses,

and Applications 383
M. Pérez-Losada, M. Arenas, E. Castro-Nallar
1. Introduction 383
2. Molecular Design and Development of Multilocus Sequence
Typing 384
3. Multilocus Sequence Typing Databases 388
4. Advantages and Disadvantages of Multilocus Sequence Typing 389
5. Analytical Approaches 390
6. Applications of Multilocus Sequence Typing 395
7. Conclusions and Prospects 397
Acknowledgments 397
References 398

17 Next-Generation Sequencing, Bioinformatics, and Infectious Diseases 405

R. van Aerle, M. van der Giezen
1. Analyzing Big Data 405
2. Comparative Genomics 405
3. Transcriptomics 409
x Contents

4. Single-Cell Technologies 411

5. High-Throughput Sequencing 413
6. De Novo Genome Assembly 414
7. Whole-Genome Sequence Analysis 414
8. RNA-Seq (Transcriptomics) 415
9. Concluding Remarks 416
References 417

18 Genomics of Infectious Diseases and Private Industry 421

G. Vernet
1. Introduction 421
2. Technologies and Instrument Platforms 423
3. Customers and Their Needs 428
4. Industry Landscape 430
5. Conclusion 433
References 433

19 Current Progress in the Pharmacogenetics of Infectious

Disease Therapy 435
E. Elliot, T. Mahungu, A. Owen
1. Introduction 435
2. Pharmacogenetics of HIV Therapy 435
3. Pharmacogenetics of Antimalarial Therapy 442
4. Pharmacogenetics of Antituberculous Therapy 444
5. Summary and Perspective 446
References 446

20 Genetic Exchange in Trypanosomatids and Its Relevance

to Epidemiology 459
W. Gibson, M.D. Lewis, M. Yeo, M.A. Miles
1. Introduction 459
2. Trypanosoma brucei 459
3. Trypanosoma cruzi 465
4. Leishmania 474
Abbreviations 476
Acknowledgments 477
References 477

21 Genomic Insights Into the Past, Current, and Future Evolution

of Human Parasites of the Genus Plasmodium 487
C.J. Sutherland, S.D. Polley
1. Introduction 487
2. Evolution of Plasmodium: The Last 10 Million Years 491
3. Evolution of Plasmodium: The 21st Century in Three Courses 496
4. Evolution of Plasmodium, and the Eradication Agenda 501
References 502
Contents xi

22 Integrated Genetic Epidemiology of Chagas Disease 509

M. Tibayrenc, M.A. Shaw
1. What Is Integrated Genetic Epidemiology? 509
2. Chagas Disease: A Major Health Problem in Latin America
and Other Countries 509
3. The Chagas Disease Cycle 510
4. Host Genetic Susceptibility to Chagas Disease 510
5. Vector Genetic Diversity 517
6. Parasite Genetic Diversity 517
7. Concluding Remarks 521
Glossary 522
References 522

23 Adaptive Evolution of the Mycobacterium tuberculosis Complex

to Different Hosts 529
E. Broset, J. Gonzalo-Asensio
1. Overview: Disease and Mycobacterial Genetics 529
2. HostePathogen Coevolution of the Tubercle Bacillus 531
3. Evolution of the Mycobacterium tuberculosis Complex From
a Genomic Perspective 538
4. Evolution in the Laboratory Environment and In Vitro Attenuation
of Bacteria From the Mycobacterium tuberculosis Complex 540
5. Short-Term Evolution of Mycobacterium tuberculosis During
Infection, Drug Treatment, and Disease 542
6. Adaptive Cues of the Mycobacterium tuberculosis Complex
As the Most Successful Pathogens 544
7. Pending Questions and Concluding Remarks 547
References 548

24 The Evolution and Dynamics of Methicillin-Resistant

Staphylococcus aureus 553
M.M.H. Abdelbary, P. Basset, D.S. Blanc, E.J. Feil
1. Introduction 553
2. The Staphylococcal Cassette Chromosome mec 553
3. Evolution of Staphylococcus aureus and MRSA 556
4. Molecular Epidemiology of MRSA 561
5. Conclusion 564
References 565

25 Origin and Emergence of HIV/AIDS 573

M. D’arc, L. Etienne, E. Delaporte, M. Peeters
1. History of AIDS 573
2. Human Immunodeficiency Viruses Are Closely Related to Simian
Immunodeficiency Virus From Nonhuman Primates 575
xii Contents

3. HIV-1 Is Derived From Simian Immunodeficiency Viruses

Circulating Among African Apes 581
4. Origin of HIV-2: Another Emergence, Another Epidemic 585
5. Ongoing Exposure of Humans to a Large Diversity of Simian
Immunodeficiency Viruses: Risk for a Novel HIV? 587
6. Conclusion 591
References 592

26 Evolution of SARS Coronavirus and the Relevance of Modern

Molecular Epidemiology 601
Z. Shi, L.-F. Wang
1. A Brief History of SARS 601
2. SARS Coronavirus 603
3. The Animal Link 605
4. Natural Reservoirs of SARS-CoV 606
5. Molecular Evolution of SARS-CoV in Humans and Animals 610
6. Coronavirus Surveillance in Wildlife Animals 614
7. Concluding Remarks 614
References 615

27 Ecology and Evolution of Avian Influenza Viruses 621

A.C. Hurt, R.A.M. Fouchier, D. Vijaykrishna
1. Introduction to Influenza A Virus 621
2. Influenza Viruses in Birds 624
3. Evolutionary Genetics of Avian Influenza Viruses 629
4. Future Perspective 633
Acknowledgments 634
References 635

Index 641
List of Contributors

M.M.H. Abdelbary Centre Hospitalier Universitaire Vaudois and University

Hospital of Lausanne, Lausanne, Switzerland
G. Aguileta Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParis-
Tech, Université Paris-Saclay, Orsay, France
H. Alout Institut des Sciences de l’Evolution de Montpellier (UMR 5554, CNRS-
UM-IRD-EPHE), Université de Montpellier, Montpellier, France; Colorado State
University, Fort Collins, CO, United States
C.P. Andam Harvard T. H. Chan School of Public Health, Boston, MA, United
States
M. Arenas University of Porto, Porto, Portugal; Institute of Molecular Pathology
and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
T. Azarian Harvard T. H. Chan School of Public Health, Boston, MA, United States
F. Baquero CIBER en Epidemiología y Salud P
ublica, Madrid, Spain; IRYCIS-
Hospital Ram

on y Cajal, Madrid, Spain
P. Basset Centre Hospitalier Universitaire Vaudois and University Hospital of
Lausanne, Lausanne, Switzerland
R.B. Billmyre Duke University Medical Center, Durham, NC, United States
D.G. Biron Laboratoire Microorganismes: Génome et Environnement, UMR
CNRS/UBP/UDA 6023, Aubiere Cedex, France
D.S. Blanc Centre Hospitalier Universitaire Vaudois and University Hospital of
Lausanne, Lausanne, Switzerland
E. Broset Universidad de Zaragoza, Zaragoza, Spain; CIBERes, Instituto de Salud
Carlos III, Madrid, Spain
E.J. Byrnes III Duke University Medical Center, Durham, NC, United States
E. Castro-Nallar Universidad Andrés Bello, Santiago, Chile
L. Challagundla University of Mississippi Medical Center, Jackson, MS, United
States
G. Cochran University of Utah, Salt Lake City, UT, United States
xiv List of Contributors

F.M. Cohan Wesleyan University, Middletown, CT, United States

I. Comas FISABIO/CSISP-UV/Instituto Cavanilles, Valencia, Spain; CIBER en
Epidemiología y Salud P

ublica, Madrid, Spain; IBV-CSIC, Valencia, Spain
A.J. Cornel University of California at Davis, Davis, CA, United States; Mosquito
Control Research Lab, Parlier, CA, United States
M. D’arc UMI 233, Institut de Recherche pour le Développement (IRD), INSERM
U1175 and Université de Montpellier, Montpellier, France; Instituto Nacional de
ˇ
Cancer, Rio de Janeiro, Brazil
J.-P. David Laboratoire d’Ecologie Alpine (UMR 5553 CNRS-UGA), Université
GrenobleeAlpes, Grenoble, France
E. Delaporte UMI 233, Institut de Recherche pour le Développement (IRD),
INSERM U1175 and Université de Montpellier, Montpellier, France
ˇ
T. de Meeus UMR 177 IRD e CIRAD INTERTRYP, Campus International de
Baillarguet, Montpellier, France
L. Djogbénou Université d’Abomey Calavi, Cotonou, Benin
P.L. Dorn Loyola University New Orleans, New Orleans, LA, United States
J.-P. Dujardin CIRAD-IRD, Baillarguet, France
E. Elliot University of Liverpool, Liverpool, United Kingdom
L. Etienne UMI 233, Institut de Recherche pour le Développement (IRD), INSERM
U1175 and Université de Montpellier, Montpellier, France; International Center for
Infectiology Research, INSERM U1111, Ecole Normale Supérieure de Lyon, Univer-
sité Claude Bernard Lyon 1, CNRS UMR 5308, 69364, Lyon, France
E.J. Feil University of Bath, Bath, United Kingdom
M. Fisher Imperial College London, London, United Kingdom
R.A.M. Fouchier Erasmus Medical Center, Rotterdam, the Netherlands
J.C. Gal
an CIBER en Epidemiología y Salud P

ublica, Madrid, Spain; IRYCIS-
Hospital Ram

on y Cajal, Madrid, Spain
W. Gibson University of Bristol, Bristol, United Kingdom
A. Gilabert Laboratoire MIVEGEC, UMR 5290, IRD-CNRS-UM, Montpellier,
France
T. Giraud Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParis-
Tech, Université Paris-Saclay, Orsay, France
P. Gladieux Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParis-
Tech, Université Paris-Saclay, Orsay, France
List of Contributors xv

F. Gonz

alez-Candelas FISABIO/CSISP-UV/Instituto Cavanilles, Valencia, Spain;
CIBER en Epidemiología y Salud P

ublica, Madrid, Spain
J. Gonzalo-Asensio Universidad de Zaragoza, Zaragoza, Spain; CIBERes, Instituto
de Salud Carlos III, Madrid, Spain; Hospital Universitario Miguel Servet, Zaragoza,
Spain
W.P. Hanage Harvard T. H. Chan School of Public Health, Boston, MA, United
States
H. Harpending University of Utah, Salt Lake City, UT, United States
J. Heitman Duke University Medical Center, Durham, NC, United States
C.A. Hill Purdue University, West Lafayette, IN, United States
ˇ
P. Holzmuller UMR CIRAD-INRA Controle des maladies exotiques émergentes
(CMAEE), Montpellier Cedex, France
A.C. Hurt WHO Collaborating Centre for Reference and Research on Influenza,
VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC,
Australia; University of Melbourne, Parkville, VIC, Australia
S. Justi University of Vermont, Burlington, VT, United States
Sarah Kopac University of Rhode Island, Kingston, RI, United States
B. Koskella University of California, Berkeley, CA, United States
E.S. Krafsur Iowa State University, Ames, IA, United States
P. Labbé Institut des Sciences de l’Evolution de Montpellier (UMR 5554, CNRS-
UM-IRD-EPHE), Université de Montpellier, Montpellier, France
G.C. Lanzaro University of California at Davis, Davis, CA, United States
Y. Lee University of California at Davis, Davis, CA, United States
M.D. Lewis London School of Hygiene and Tropical Medicine (LSHTM), London,
United Kingdom
Y.-T. Liu University of California San Diego, La Jolla, CA, United States
T. Mahungu Royal Free London NHS Foundation Trust, London, United Kingdom
J.L. Martínez CNB-CSIC, Madrid, Spain
M.A. Miles London School of Hygiene and Tropical Medicine (LSHTM), London,
United Kingdom
P. Milesi Institut des Sciences de l’Evolution de Montpellier (UMR 5554, CNRS-
UM-IRD-EPHE), Université de Montpellier, Montpellier, France
D. Missé Laboratoire MIVEGEC, UMR CNRS 5290/IRD 224/UM, Montpellier
Cedex, France
xvi List of Contributors

A.D. Morgan University of Edinburgh, Edinburgh, United Kingdom

D.A. Morrison Uppsala University, Uppsala, Sweden
D. Nedelkov Arizona State University, Tempe, AZ, United States
A. Owen University of Liverpool, Liverpool, United Kingdom
N. Pasteur Institut des Sciences de l’Evolution de Montpellier (UMR 5554, CNRS-
UM-IRD-EPHE), Université de Montpellier, Montpellier, France
M. Peeters UMI 233, Institut de Recherche pour le Développement (IRD), INSERM
U1175 and Université de Montpellier, Montpellier, France
M. Pérez-Losada George Washington University, Ashburn, VA, United States;
Universidade do Porto, Vair~ao, Portugal; Children’s National Medical Center,
Washington, DC, United States
S.D. Polley Hospital for Tropical Diseases, London, United Kingdom
F. Prugnolle Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et
ˇ
Controle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier,
France
J.-P. Rasigade Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres, Paris,
France; CIRI, International Center for Infectiology Research, INSERM U1111-CNRS
UMR5308, ENS Lyon-Université Lyon 1, Hospices Civils de Lyon, Lyon, France
D.A. Robinson University of Mississippi Medical Center, Jackson, MS, United
States
M.A. Shaw University of Leeds, St James’s University Hospital, Leeds, United
Kingdom
Z. Shi Chinese Academy of Sciences (CAS), Wuhan, China
C.J. Sutherland London School of Hygiene & Tropical Medicine, London, United
Kingdom
M. Tibayrenc Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et
ˇ
Controle MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD, Montpellier, France
R. van Aerle Centre for Environment, Fisheries and Aquaculture Science,
Weymouth, United Kingdom
M. van der Giezen University of Exeter, Exeter, United Kingdom
M.H.V. Van Regenmortel Université de Strasbourg-CNRS, Illkirch Cedex, France
G. Vernet Centre Pasteur, Yaoundé, Cameroon
D. Vijaykrishna Duke-NUS Graduate Medical School, Singapore, Singapore
L.-F. Wang Duke-NUS Medical School, Singapore, Singapore
List of Contributors xvii

M. Weill Institut des Sciences de l’Evolution de Montpellier (UMR 5554,

CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, France
T. Wirth Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres, Paris, France;
Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum
National d’Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des
Hautes Etudes, Sorbonne Universités, Paris, France
M. Yeo London School of Hygiene and Tropical Medicine (LSHTM), London,
United Kingdom
This page intentionally left blank
Recent Developments in the
Definition and Official Names of 1
Virus Species*
M.H.V. Van Regenmortel
Université de Strasbourg-CNRS, Illkirch Cedex, France

1. Introduction
Classification deals with abstract classes and taxonomy deals with classes called taxa.
Viral taxonomy refers both to the scientific discipline of virus classification and to the
outcome of a classification activity involving viruses.
Virus classification deals with abstract classes of viruses that are conceptual con-
structions of the mind. The most important characteristic of such classes is that they
have members that are the concrete viral objects studied by virologists. Every mem-
bership condition determines a class and if a virus has a monopartite negative strand
RNA genome, it automatically becomes a member of the Mononegavirales, which is
a class known as an order.1 Such a class is not physically real and must not be
confused with the viruses themselves. Similarly, the abstract concept of a virus spe-
cies as a class of viruses should not be confused with the viruses that are the concrete
members of the species. Confusions between different logical categories have been a
fertile source of misunderstandings in viral taxonomy. It has been claimed, for
instance, that the name tobacco mosaic virus is an abstraction because only its par-
ticles can be handled.2,3 Such a claim arose because the term “virus” was not recog-
nized to be what logicians call a general term, that is, a word that denotes any number
of concrete entities.4(pp. 90 105)
The species taxon was introduced in virus classification as late as 1991 when it was
endorsed by the International Committee on Taxonomy of Viruses (ICTV), which is
the body empowered by the International Union of Microbiologial Societies (IUMS)
to make decisions on matters of virus classification and nomenclature.5 The official
definition of virus species was as follows: “A virus species is a polythetic class of vi-
ruses that constitute a replicating lineage and occupy a particular ecological niche.” Its
key feature was that it incorporated the notion of polythetic class also known as a clus-
ter class. While monothetic classes are defined by one or a few properties that are both
necessary and sufficient for membership in the class, polythetic classes are defined by a
variable set of statistically covariant properties, none of which is a defining property

* A very similar version of this chapter with the title: “Classes, taxa and categories in hierarchical virus
classification: a review of current debates on definitions and names of virus species” appeared in Bio-
nomina 2016, Dumerilia, 10: 1e20. copyright M. Van Regenmortel.

Genetics and Evolution of Infectious Diseases. http://dx.doi.org/10.1016/B978-0-12-799942-5.00001-9

Copyright © 2017 Elsevier Inc. All rights reserved.
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