by Carl Zimmer
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 APOBEC3 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.
McFadden, G. 2010. Killing a killer: What next for smallpox? PLoS Pathogens 6 (1): e1000727.
Shchelkunov, S. N. 2009. How long ago did smallpox virus emerge? Archives of Virology 154:1865–71.
EPILOGUE
Claverie, J.-M., and C. Abergel. 2009. Mimivirus and its virophage. Annual Review of Genetics 43:49–66.
Forterre, P. 2010. Defining life: The virus viewpoint. Origins of Life and Evolution of Biospheres 40:151–60.
Moreira, D., and C. Brochier-Armanet. 2008. Giant viruses, giant chimeras: The multiple evolutionary histories of mimivirus genes. BMC Evolutionary Biology 8:12.
Moreira, D., and P. Lopez-Garcia. 2009. Ten reasons to exclude viruses from the tree of life. Nature Reviews Microbiology 7:306–11.
Ogata, H., and J. M. Claverie. 2008. How to infect a mimivirus. Science 321:1305.
Raoult, D., and P. Forterre. 2008. Redefining viruses: Lessons from mimivirus. Nature Reviews Microbiology 6:315–19.
Raoult, D., B. La Scola, and R. Birtles. 2007. The discovery and characterization of mimivirus, the largest known virus and putative pneumonia agent. Clinical Infectious Diseases 45:95–102.
Credits
Introduction: tobacco mosaic viruses, © Dennis Kunkel Microscopy, Inc. Chapter 1: rhinovirus, copyright © 2010 Photo Researchers, Inc. (all rights reserved). Chapter 2:influenza virus, by Frederick Murphy, from the PHIL, courtesy of the CDC. Chapter 3: human papillomavirus, copyright © 2010 Photo Researchers, Inc. (all rights reserved). Chapter 4: bacteriophages, courtesy of Graham Colm. Chapter 5: marine phage, courtesy of Willie Wilson. Chapter 6: avian leukosis virus, courtesy of Dr. Venugopal Nair and Dr. Pippa Hawes, Bioimaging group, Institute for Animal Health. Chapter 7: human immunodeficiency virus, by P. Goldsmith, E. L. Feorino, E. L. Palmer, and W. R. McManus, from the PHIL, courtesy of the CDC. Chapter 8: West Nile virus, by P. E. Rollin, from the PHIL, courtesy of the CDC. Chapter 9: Ebola virus, by Cynthia Goldsmith, from the PHIL, courtesy of the CDC. Chapter 10: smallpox virus, by Frederick Murphy, from the PHIL, courtesy of the CDC. Epilogue: mimivirus, courtesy of Dr. Didier Raoult, Research Unit in Infectious and Tropical Emergent Diseases (URMITE).
Index
AIDS. See HIV
&nb
sp; algae, climate and, 43
allergies, immune system and, 13
Andromeda Strain, The (film), 74
antibiotics: discovery of, 36–37; drug resistance and, 39; overprescription of, 11–12
antiviral medications, 84
APOBEC3 protein, 52
Arrowsmith (Lewis), 36
avian leukosis, 46, 48–49. See also retroviruses
bacteria: biofilm and, 39; drug resistant, 12, 38, 39; photosynthetic, 43, 45; size of, 5. See also bacteriophages
bacteriophages: abundance of, 43; debates over, 35–36, 37–38; discovery of, 34; genetic engineering and, 38–39; lytic, 35–36; in marine environment, 42–43; as medicine, 36, 37–39; picture of, 32; temperate, 35–36, 44; ubiquity of, 37–38. See also bacteria
bats, animal-to-human leap of viruses and, 75, 76
Beijerinck, Martinus, 4
Bieniasz, Paul, 51–52
biological weapons, smallpox as, 82, 86
birds: influenza and, 17–19; West Nile virus and, 65–69
Bordet, Jules, 35–36
Boylston, Zabdiel, 83
Bradfordcoccus, 90
Bronx Zoo, 65
bubonic plague, bacteriophages and, 36
Cameroon, origins of HIV and, 75
cancer, 24, 29, 48–51
Carlos (king of Spain), 84
Cave of Crystals, 1–2
Centers for Disease Control and Prevention, 55
Central America, smallpox in, 83
chickens, avian leukosis in, 48–49
chimpanzees, HIV and, 74–75
China: SARS and, 75–77; smallpox prevention in, 83
cholera: bacteriophages and, 36, 43; cause of, 43, 45
civets, SARS and, 76–77
climate: marine organisms and, 43; West Nile virus and, 69–70
cloning, 47
Collins, James, 38–39
Columbus, Christopher, 66, 82
common cold, 9–13. See also rhinovirus
coronaviruses, 76
cough syrup, dangers of, 11
Crohn disease, immune system and, 13
cystic fibrosis, virus-hunting expedition and, 2–3
cytokines, common cold and, 11
Darwin, Charles, 45
Dede (Indonesian boy), 24–25, 27
Delbruck, Max, 38
Democratic Republic of Congo, HIV and, 59–60
DNA: avian leukosis and, 48–49; bacteriophages and, 35–36, 38–39, 44–45; cell division and, 26; cervical tumors and, 25; cystic fibrosis studies and, 2; endogenous retroviruses and, 50, 51–52; human evolution and, 28; human reproduction and, 18, 47; jumping, 52; mimiviruses and, 92; origins of life and, 93–94; protein-coding genes in, 52; virus genomes and, 91
Dochez, Alphonse, 10
Dover, White Cliffs of, 43
dysentery, bacteriophages and, 34, 36
Ebers Papyrus, 9, 11
Ebola virus: outbreaks of, 77; picture of, 72
E. coli. See Escherichia coli
Egypt, ancient medical texts and, 9
Eliava Institute of Bacteriophage, Microbiology, and Virology, 37, 38
Emiliania huxleyi virus, picture of, 40
encephalitis, West Nile virus and, 68
epidemics: bacteriophages and, 43; HIV as mystery and, 57
Escherichia coli: bacteriophages and, 35, 36, 38, 39; picture of, 32
Ethiopia, smallpox in, 86
evolution: animal-to-human leap of viruses and, 74–75; bacteriophages and, 38; HIV and, 61–62; human papillomavirus and, 27, 30; of influenza, 17–20; marine microbes and, 45; marine viruses and, 43, 44; of rhinovirus, 12
Food and Drug Administration, 11
Forterre, Patrick, 93
García-Ruiz, Juan Manuel, 2
genetics: genetic engineering and, 38–39; gene transfer and, 44–45, 47, 50; history of genes and, 45; identity and, 47; influenza and, 18; viruses in human genome and, 47–48
Global Viral Forecasting Initiative (GVFI), 74, 77
Gottschling, Marc, 27
Goulder, Philip, 62
Gustave Roussy Institute, 51
GVFI (Global Viral Forecasting Initiative). See Global Viral Forecasting Initiative (GVFI)
H1N1 virus, 19–20
H5N1 virus, 17
Haiti, HIV and, 60
Heidmann, Thierry, 51, 52
Herelle, Felix d’, 34–37, 42–43
HERV-K[con] virus, 52
Hill, Leonard, 10, 11
Hippocrates, 10
HIV: death toll of, 56; early recognition of, 55–56, 57; effects of, 56–57; evolution and, 61–62; genome of, 89; global spread of, 59–60, 66, 77; mutations and, 61–62; origins of, 57, 58–60, 74–75; picture of, 54; prevention and treatment of, 60–61; transmission of, 56
Ho, David, 59
horses, papillomavirus in, 27
host cells: alteration of by viruses, 25–26, 45; cancer and, 48; picture of, 32; production of viruses and, 5, 10–11, 13, 18, 26–27, 44, 48
human immunodeficiency viruses. See HIV
human papillomavirus: cervical cancer and, 25–26; evolution of, 30; global distribution of, 66; history of, 27–29; horned rabbits and, 23–25; incidence of, 28–29; picture of, 22; reproduction of, 25–27; vaccine for, 29–30
hunting, testing for viruses and, 73–74, 77–78
immune system: avian leukosis, 49; common cold and, 11, 13; influenza and, 16–17; West Nile virus and, 67–68. See also specific immune disorders, vaccinations
influenza: death toll of, 15–16, 75; etymology of word and, 15; evolution of, 17–20; genome of, 91; manufactured, 85; migration and, 66; natural history of, 15, 17–19; picture of, 14; secondary infections and, 16; transmission of, 16, 18, 19–20; vaccines and, 20. See also specific strains of
Intensified Smallpox Eradication Programme, 85
International Committee on Taxonomy of Viruses, 92
Israel, West Nile virus in, 68
jackalope, 23–24, 30, 48
Jenner, Edward, 83–84
Joseph I (emperor of Austria), 82
Katzourakis, Aris, 50
Kruse, Walter, 10
La Scola, Bernard, 90–91, 92
lentiviruses, 58
leukocytes, avian. See avian leukosis
Lewis, Sinclair, 36
life, origins of, 93
Lipkin, Ian, 12, 66
L’Oreal, 36
Los Alamos National Laboratory, 59
Lu, Tim, 38–39
Luria, Salvador, 38
Lwoff, Andre, 92
Mackay, Ian, 12
Malaysia, avian leukosis and, 49
marine viruses, 41–45
Marx, Preston, 58
Mary II (queen of England), 82
Mayer, Adolph, 3–4
McNamara, Tracey, 65–66
Merck (pharmaceutical company), HIV vaccine and, 61
Mexico: Cave of Crystals in, 1–2; swine flu and, 19–20
microbes, as geoengineers, 43
migration: human papillomavirus and, 27, 66; Old and New World and, 66–67, 68–69, 82–83; West Nile virus and, 66–67, 68
mimiviruses, 88, 89–94
monkeys, testing for viruses and, 73–74, 77
Morbidity and Mortality Weekly Report, 55–56
mosquitoes, West Nile virus and, 67–68, 69
mutations: APOBEC3 protein and, 52; drug resistance and, 38; HIV and, 61–62; HPV and, 29–30; influenza and, 17, 19; retroviruses and, 50, 51; rhinoviruses and, 12–13; viruses hobbled by, 44, 50
Native Americans, migration and disease and, 66, 82
Nelmes, Sarah, 83–84
Netherlands, tobacco mosaic disease in, 3
Nipah virus, 77