Edward C. Holmes - The Evolution and Emergence of RNA Viruses (Oxford Series in Ecology and Evolution)

The Evolution and Emergence of RNA Viruses

Oxford Series in Ecology and Evolution Edited by Paul H. Harvey and Robert M. May

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The Evolution and Emergence of RNA Viruses

Edward C. Holmes

The Evolution and

Emergence of RNA

Viruses

EDWARD C. HOLMES

Center for Infectious Disease Dynamics,

Department of Biology, The Pennsylvania State University,Pennsylvania, USA and Fogarty International Center,National Institutes of Health, Bethesda, USA

Great Clarendon Street, Oxford OX2 6DP

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Edward C. Holmes 2009

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First published 2009

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ISBN 9780199211128 (Hbk.)

ISBN 9780199211135 (Pbk.)

10 9 8 7 6 5 4 3 2 1

Everyone knows that pestilences have a way of recurring in the world; yet somehow we fi nd it hard to believe in ones that crash down on our heads from a blue sky.

Albert Camus, La Peste

For Rachel and Scott.

Preface

Hurricanes are not good for much. This book was conceived in a hotel room in Valladolid, Mexico, during October 2005 where my wife and I had taken shelter from Hurricane Wilma, a category 5 storm responsible for the lowest pressure ever recorded in the Caribbean. With little else to do for 3 days, I set about planning the book that Paul Harvey and Bob May, the series editors, had generously asked me to write. As the good citizens of Cancn, Cozumel, Playa del Carmen, and Tulum will testify, I escaped lightly.

I wish to thank the following people who graciously commented on various chapters: Siobain Duffy, Adrian Gibbs, John McCauley, Andrs Moya, Cadhla Ramsden, and Rafa Sanjun. The text was greatly improved by their diligent reading, intelligent criticism, and sound ideas. As should go without saying, any errors that remain are entirely my own doing. In addition, I benefi ted greatly from numerous discussions with John Aaskov, Elodie Ghedin, Bryan Grenfell, Oliver Pybus, Andrew Rambaut, Tony Schmitt, Laura Shackelton, and Paolo Zanotto. I am also grateful to Helen Eaton and Ian Sherman at Oxford University Press for their relaxed encouragement. Finally, I am indebted to my wife Rachel for her patience, support, and willingness to leave me alone on Saturday mornings.

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Contents

xContents

Contentsxi

xiiContents

Viral diseases, particularly the exotic and the fatal, hold a unique fascination to scientists and the general public alike. Because of books like The Hot Zone (Preston 1994), which glamorizes outbreaks of highly virulent fi loviruses, the public image of RNA viruses is a complex combination of the frightening and the alluring. While this has certainly given them name recognition, the accounts of RNA viruses that are increasingly commonplace in the popular media are also frustratingly inaccurate, as they are often given capabilities that could never have arisen through evolution by natural selection.

The marginalization of viruses also occurs to some extent in evolutionary biology.

Although abundant in nature, viruses are sometimes not considered as worthy items for scientifi c endeavour as the venerable