Read A Planet of Viruses Online
Authors: Carl Zimmer
Drawing a bright line between life and nonlife can also make it harder to understand how life began in the first place. Scientists are still trying to work out the origin of life, but one thing is clear: it did not start suddenly with the flick of a great cosmic power switch. It’s likely that life emerged gradually, as raw ingredients like sugar and phosphate combined in increasingly complex reactions on the early Earth. It’s possible, for example, that single-stranded molecules of RNA gradually grew and acquired the ability to make copies of themselves. Trying to find a moment in time when such RNA-life abruptly became “alive” just distracts us from the gradual transition to life as we know it.
Banning viruses from the Life Club also deprives us of some of the most important clues to how life began. One of the great discoveries about viruses has been the tremendous diversity in their genes. Every time scientists find new viruses, most of their genes bear little resemblance to any gene ever found before. The genes of viruses are not a meager collection of DNA cast off in recent years from true living things. Many scientists now argue that viruses contain a genetic archive that’s been circulating the planet for billions of years. When they try to trace the common ancestry of virus genes, they often work their way back to a time before the common ancestor of all cell-based life. Viruses may have first evolved before the first true cells even existed. At the time, life may have consisted of little more than brief coalitions of genes, which sometimes thrived and sometimes were undermined by genes that acted like parasites. Patrick Forterre, a French virologist, has even proposed that in the RNA world, viruses invented the double-stranded DNA molecule as a way to protect their genes
from attack. Eventually their hosts took over their DNA, which then took over the world. Life as we know it, in other words, may have needed viruses to get its start.
At long last, we may be returning to the original two-sided sense of the word
virus
, which originally signified either a life-giving substance or a deadly venom. Viruses are indeed exquisitely deadly, but they have provided the world with some of its most important innovations. Creation and destruction join together once more.
A Planet of Viruses
was funded by the National Center for Research Resources at the National Institutes of Health through the Science Education Partnership Award (SEPA), grant no. R25 RR024267 (2007–2012), Judy Diamond, Moira Rankin and Charles Wood, principal investigators. Its content is solely the responsibility of the author and does not necessarily represent the official views of the NCRR or the NIH. I thank the many people who advised this project: Anisa Angeletti, Peter Angeletti, Aaron Brault, Ruben Donis, Ann Downer-Hazell, David Dunigan, Angie Fox, Laurie Garrett, Benjamin David Jee, Ian Lipkin, Ian Mackay, Grant McFadden, Nathan Meier, Abbie Smith, Gavin Smith, Philip W. Smith, Amy Spiegel, David Uttal, James L. Van Etten, Kristin Watkins, Willie Wilson, and Nathan Wolfe. I am particularly grateful to my SEPA program officer, L. Tony Beck, and to my editor at the University of Chicago Press, Christie Henry, for making this book possible.
INTRODUCTION
Bos, L. 1999. Beijerinck’ s work on tobacco mosaic virus: Historical context and legacy.
Philosophical Transactions of the Royal Society B: Biological Sciences
354:675.
Flint, S. J. 2009.
Principles of virology
. 3rd ed. Washington DC: ASM Press.
Willner D., M. Furlan, M. Haynes, et al. 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.
PLoS ONE
4 (10): e7370.
THE UNCOMMON COLD
Arden, K. E., and I. M. Mackay. 2009. Human rhinoviruses: Coming in from the cold.
Genome Medicine
1:44.
Briese, T., N. Renwick, M. Venter, et al. 2008. Global distribution of novel rhinovirus genotype.
Emerging Infectious Diseases
14:944.
Palmenberg, A. C., D. Spiro, R. Kuzmickas, et al. 2009. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution.
Science
324:55–59.
Simasek, M., and D. A. Blandino. 2007. Treatment of the common cold. American
Family Physician
75:515–20.
LOOKING DOWN FROM THE STARS
Barry, J. M. 2004.
The great influenza: The epic story of the deadliest plague in history
. New York: Viking.
Dugan, V. G., R. Chen, D. J. Spiro, et al. 2008. The evolutionary genetics and emergence of avian influenza viruses in wild birds.
PLoS Pathogens
4 (5): e1000076.
Rambaut, A., O. G. Pybus, M. I. Nelson, C. Viboud, J. K. Taubenberger, and E. C. Holmes. 2008. The genomic and epidemiological dynamics of human influenza A virus.
Nature
453:615–19.
Smith, G. J. D., D. Vijaykrishna, J. Bahl, et al. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
Nature
459:1122–25.
Taubenberger, J. K., and D. M. Morens. 2008. The pathology of influenza virus infections.
Annual Reviews of Pathology
3:499–522.
RABBITS WITH HORNS
Bravo, I. G., and Á. Alonso. 2006. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins.
Virus Genes
34:249–62.
Doorbar, J. 2006. Molecular biology of human papillomavirus infection and cervical cancer.
Clinical Science
110:525.
García-Vallvé, S., Á. Alonso, and I. G. Bravo. 2005. Papillomaviruses: Different genes have different histories.
Trends in Microbiology
13:514–21.
García-Vallvé, S., J. R. Iglesias-Rozas, Á. Alonso, and I. G. Bravo. 2006. Different papillomaviruses have different repertoires of transcription factor binding sites: Convergence and divergence in the upstream regulatory region.
BMC Evolutionary Biology
6:20.
Horvath, C. A. J., G. A. V. Boulet, V. M. Renoux, P. O. Delvenne, and J.-P. J. Bogers. 2010. Mechanisms of cell entry by human papillomaviruses: An overview.
Virology Journal
7:11.
Martin, D., and J. S. Gutkind. 2008. Human tumor-associated viruses and new insights into the molecular mechanisms of cancer.
Oncogene
27 (Suppl 2): S31–42.
Schiffman, M., R. Herrero, R. DeSalle, et al. 2005. The carcinogenicity of human papillomavirus types reflects viral evolution.
Virology
337:76–84.
THE ENEMY OF OUR ENEMY
Brussow, H. 2005. Phage therapy: The
Escherichia coli
experience.
Microbiology
151:2133.
Deresinski, S. 2009. Bacteriophage therapy: Exploiting smaller fleas.
Clinical
Infectious Diseases
48:1096–1101.
Sulakvelidze, A., Z. Alavidze, and J. G. Morris Jr. 2001. Bacteriophage therapy.
Antimicrobial Agents and Chemotherapy
45:649.
Summers, W. C. 2001. Bacteriophage therapy.
Annual Reviews in Microbiology
55:437–51.
THE INFECTED OCEAN
Angly, F. E., B. Felts, M. Breitbart, et al. 2006. The marine viromes of four oceanic regions.
PLoS Biology
4 (11): e368.
Brussaard, C. P. D., S. W. Wilhelm, F. Thingstad, et al. 2008. Global-scale processes with a nanoscale drive: The role of marine viruses.
ISME Journal
2:575–78.
Danovaro, R., A. Dell’ Anno, C. Corinaldesi, et al. 2008. Major viral impact on the functioning of benthic deep-sea ecosystems.
Nature
454:1084–87.
Desnues, C., B. Rodriguez-Brito, S. Rayhawk, et al. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites.
Nature
452:340–43.
Rohwer, F., and R. Vega Thurber. 2009. Viruses manipulate the marine environment.
Nature
459:207–12.
Suttle, C. A. 2007. Marine viruses—major players in the global ecosystem.
Nature Reviews Microbiology
5:801–12.
Van Etten, J. L., L. C. Lane, and R. H. Meints. 1991. Viruses and viruslike particles of eukaryotic algae.
Microbiology and Molecular Biology Reviews
55:586.
Williamson, S. J., S. C. Cary, K. E. Williamson, et al. 2008. Lysogenic virus–host interactions predominate at deep-sea diffuse-flow hydrothermal vents.
ISME Journal
2:1112–21.
OUR INNER PARASITES
Blikstad, V., F. Benachenhou, G. O. Sperber, and J. Blomberg. 2008. Evolution of human endogenous retroviral sequences: A conceptual account.
Cellular and Molecular Life Sciences
65:3348–65.
Dewannieux, M., F. Harper, A. Richaud, et al. 2006. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements.
Genome Research
16:1548–56.
Jern, P., and J. M. Coffin. 2008. Effects of retroviruses on host genome function.
Annual Review of Genetics
42:709–32.
Ruprecht, K., J. Mayer, M. Sauter, K. Roemer, and N. Mueller-Lantzsch. 2008. Endogenous retroviruses and cancer.
Cellular and Molecular Life Sciences
65:3366–82.
Tarlinton, R., J. Meers, and P. Young. 2008. Biology and evolution of the endogenous koala retrovirus.
Cellular and Molecular Life Sciences
65:3413–21.
Weiss, R. A. 2006. The discovery of endogenous retroviruses.
Retrovirology
3:67.
THE YOUNG SCOURGE
Fan, H. 2011.
AIDS: Science and society
. 6th ed. Sudbury, MA: Jones and Bartlett.
Gilbert, M. T. P., A. Rambaut, G. Wlasiuk, T. J. Spira, A. E. Pitchenik, and M. Worobey. 2007. The emergence of HIV/AIDS in the Americas and beyond.
Proceedings of the National Academy of Sciences
104:18566.
Keele, B. F. 2006. Chimpanzee reservoirs of pandemic and nonpandemic HIV-1.
Science
313:523–26.
Montagnier, L. 2010. 25 Years after HIV discovery: Prospects for cure and vaccine.
Virology
397:248–54.
Niewiadomska, A. M., and X.-F. Yu. 2009. Host restriction of HIV-1 by APOBEC
3
and viral evasion through Vif.
Current Topics in Microbiology and Immunology
339:1–25.
Worobey, M., M. Gemmel, D. E. Teuwen, et al. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.
Nature
455:661–64.
BECOMING AN AMERICAN
Brault, A. C. 2009. Changing patterns of West Nile virus transmission: Altered vector competence and host susceptibility.
Veterinary Research
40:43.
Diamond, M. S. 2009. Progress on the development of therapeutics against West Nile virus.
Antiviral Research
83:214–27.
Gould, E. A., and S. Higgs. 2009. Impact of climate change and other factors on emerging arbovirus diseases.
Transactions of the Royal Society of Tropical Medicine and Hygiene
103:109–21.
Hamer, G. L, U. D. Kitron, T. L. Goldberg, et al. 2009. Host selection by
Culex pipiens
mosquitoes and West Nile virus amplification.
American Journal of Tropical Medicine and Hygiene
80:268.
Sfakianos, J. N. 2009.
West Nile virus
. 2nd ed. New York: Chelsea House.
Venkatesan M., and J. L. Rasgon. 2010. Population genetic data suggest a role for mosquito-mediated dispersal of West Nile virus across the western United States.
Molecular Ecology
19:1573–84.
PREDICTING THE NEXT PLAGUE
Holmes, E. C., and A. Rambaut. 2004. Viral evolution and the emergence of SARS coronavirus.
Philosophical Transactions of the Royal Society B: Biological Sciences
359:1059–65.
Parrish, C. R., E. C. Holmes, D. M. Morens, et al. 2008. Cross-species virus transmission and the emergence of new epidemic diseases.
Microbiology and Molecular Biology Reviews
72:457–70.
Skowronski, D. M., C. Astell, R. C. Brunham, et al. 2005. Severe acute respiratory syndrome (SARS): A year in review.
Annual Review of Medicine
56:357–81.
Wolfe, N. 2009. Preventing the next pandemic.
Scientific American
, April 2009, 76–81.
THE LONG GOODBYE
Hughes, A. L., S. Irausquin, and R. Friedman. 2010. The evolutionary biology of poxviruses.
Infection, Genetics and Evolution
10:50–59.
Jacobs, B. L., J. O. Langland, K. V. Kibler, et al. 2009. Vaccinia virus vaccines: Past, present and future.
Antiviral Research
84:1–13.
Kennedy, R. B., I. Ovsyannikova, and G. A. Poland. 2009. Smallpox vaccines for biodefense.
Vaccine
27 (Suppl): D73–79.
Koplow, D. A. 2003.
Smallpox: The fight to eradicate a global scourge
. Berkeley: University of California Press.