引言 有传染性的活液
Bos, L. 1999. Beijerinck's work on tobacco mosaic virus: Historical context and legacy. Philosophical Transactions of the Royal Society B:Biological Sciences354:675.
Flint, S. J. 2009. Principles of Virology. 3rd ed. Washington, DC: ASM Press.
Kay, L. E. 1986. W. M. Stanley's crystallization of the tobacco mosaic virus, 1930–1940. Isis77:450–72.
Willner D., M. Furlan, M. Haynes, et al. 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and noncystic fibrosis individuals.PLoS ONE4（10）:e7370.
1 并不普通的感冒
Arden, K. E., and I. M. Mackay. 2009. Human rhinoviruses: Coming in from the cold. Genome Medicine1:44.
Briese, T., N. Renwick, M. Venter, et al. 2008. Global distribution of novel rhinovirus genotype. Emerging Infectious Diseases14:944.
Fashner, J., K. Ericson, and S. Werner. 2012. Treatment of the common cold in children and adults. American Family Physician86:153–59.
Palmenberg, A. C., D. Spiro, R. Kuzmickas, et al. 2009. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science324:55–59.
2 祈求星星的照看
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 Pathogens4（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.Nature453:615–19.
Smith, G. J. D., D. Vijaykrishna, J. Bahl, et al. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature459:1122–25.
Taubenberger, J. K., and D. M. Morens. 2008. The pathology of influenza virus infections. Annual Reviews of Pathology3:499–522.
3 长角的兔子
Bravo, I. G., and Á. Alonso. 2006. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins. Virus Genes34:249–62.
Doorbar, J. 2006. Molecular biology of human papillomavirus infection and cervical cancer. Clinical Science110:525.
García-Vallvé, S., Á. Alonso, and I. G. Bravo. 2005. Papillomaviruses:Different genes have different histories. Trends in Microbiology13:514–21.
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 Biology6:20.
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 Journal7:11.
Martin, D., and J. S. Gutkind. 2008. Human tumor-associated viruses and new insights into the molecular mechanisms of cancer. Oncogene27（Suppl2）:S31–42.
Orlando, P. A., R. A. Gatenby, A. R. Giuliano, and J. S. Brown.2012. Evolutionary ecology of human papillomavirus: trade-offs,coexistence, and origins of high-risk and low-risk types. Journal ofInfectious Diseases205:272–79.
Schiffman, M., R. Herrero, R. DeSalle, et al. 2005. The carcinogenicity of human papillomavirus types reflects viral evolution.Virology337:76–84.
Shulzhenko, N., H. Lyng, G. F. Sanson, and A. Morgun. 2014. Ménage à trois: An evolutionary interplay between human papillomavirus, a tumor, and a woman. Trends in Microbiology22:345–53.
4 敌人的敌人
Adhya, S., C. R. Merril, and B. Biswas. 2014. Therapeutic and prophylactic applications of bacteriophage components in modern medicine. Cold Spring Harbor Perspectives in Medicine4:a012518.
Brussow, H. 2005. Phage therapy: The Escherichia coli experience. Microbiology151:2133.
Deresinski, S. 2009. Bacteriophage therapy: Exploiting smaller fleas.Clinical Infectious Diseases48:1096–101.
Summers, W. C. 2001. Bacteriophage therapy. Annual Reviews in Microbiology55:437–51.
5 感染的海洋
Angly, F. E., B. Felts, M. Breitbart, et al. 2006. The marine viromes of four oceanic regions. PLoS Biology4 （11）:e368.
Breitbart, M. 2012. Marine viruses: Truth or dare. Annual Review of Marine Sciences4:425–48.
Brussaard, C. P. D., S. W. Wilhelm, F. Thingstad, et al. 2008. Global-scale processes with a nanoscale drive: The role of marine viruses. ISMEJournal2:575–78.
Danovaro, R., A. Dell'Anno, C. Corinaldesi, et al. 2008. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature454:1084–87.
Desnues, C., B. Rodriguez-Brito, S. Rayhawk, et al. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites.Nature452:340–43.
Keen, E.C. 2015. A century of phage research: Bacteriophages and the shaping of modern biology. Bioessays37:6–9.
Rohwer, F., and R. Vega Thurber. 2009. Viruses manipulate the marine environment. Nature459:207–12.
Rohwer, F., M. Youle, H. Maughan, and N. Hisakawa. 2015. Life in OurPhage World. San Diego: Wholon.
Suttle, C. A. 2007. Marine viruses—major players in the global ecosystem. Nature Reviews Microbiology5:801–12.
Van Etten, J. L., L. C. Lane, and R. H. Meints. 1991. Viruses and viruslike particles of eukaryotic algae. Microbiology and Molecular Biology Reviews55:586.
6 人体里的“寄生者”
Blikstad, V., F. Benachenhou, G. O. Sperber, and J. Blomberg. 2008.Evolution of human endogenous retroviral sequences: A conceptual account. Cellular and Molecular Life Sciences65:3348–65.
Dewannieux, M., F. Harper, A. Richaud, et al. 2006. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Research16:1548–56.
Jern, P., and J. M. Coffin. 2008. Effects of retroviruses on host genome function. Annual Review of Genetics42:709–32.
Lavialle, C., G. Cornelis, A. Dupressoir, et al. 2013. Paleovirology of“syncytins,” retroviral env genes exapted for a role in placentation.Philosophical Transactions of the Royal SocietyB: Biological Sciences368:20120507.
Lee, A., A. Nolan, J. Watson, and M. Tristem. 2013. Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals. Philosophical Transactions of the Royal SocietyB:Biological Sciences368:20120503.
Ruprecht, K., J. Mayer, M. Sauter, K. Roemer, and N. Mueller-Lantzsch.2008. Endogenous retroviruses and cancer. Cellular and MolecularLife Sciences65:3366–82.
Tarlinton, R., J. Meers, and P. Young. 2008. Biology and evolution of the endogenous koala retrovirus. Cellular and Molecular Life Sciences65:3413–21.
Weiss, R. A. 2006. The discovery of endogenous retroviruses. Retrovirology3:67.
Weiss, R. A. 2013. On the concept and elucidation of endogenous retroviruses. Philosophical Transactions of the Royal SocietyB: Biological Sciences368:20120494.
7 新的灾难
D'arca, M., A. Ayoubaa, A. Estebana, et al. 2015. Origin of the HIV-1 group O epidemic in western lowland gorillas. Proceedings of the National Academy of SciencesPublished ahead of print, March 2, 2015.doi:10.1073/pnas.1502022112.
Fan, H. 2011. AIDS: Science and Society. 6th ed. Sudbury, MA: Jones and Bartlett.
Faria, N. R., A. Rambaut, M. A. Suchard, et al. 2014. The early spread and epidemic ignition of HIV-1 in human populations. Science346:56–61.
Fauci, A. S., and H. D. Marston. 2014. Ending AIDS–is an HIV vaccine necessary? New England Journal of Medicine370:495–98.
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 Sciences104:18566.
Keele, B. F. 2006. Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science313:523–26.
Montagnier, L. 2010. 25 Years after HIV discovery: Prospects for cure and vaccine. Virology397:248–54.
Worobey, M., M. Gemmel, D. E. Teuwen, et al. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature455:661–64.
8 融入美国
Brault, A. C. 2009. Changing patterns of West Nile virus transmission:Altered vector competence and host susceptibility. Veterinary Research40:43.
Diamond, M. S. 2009. Progress on the development of therapeutics against West Nile virus. Antiviral Research83:214–27.
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 Hygiene103:109–21.
Hamer, G. L, U. D. Kitron, T. L. Goldberg, et al. 2009. Host selection by Culex pipiens mosquitoes and West Nile virus amplification.AmericanJournal of Tropical Medicine and Hygiene80:268.
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 Ecology19:1573–84.
9 预测下一场瘟疫
Holmes, E. C., and A. Rambaut. 2004. Viral evolution and the emergence of SARS coronavirus. Philosophical Transactions of the Royal Society B: Biological Sciences359:1059–65.
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 Reviews72:457–70.
Pigott, D. M., N. Golding, A. Mylne, et al. 2014. Mapping the zoonotic niche of Ebola virus disease in Africa. Elife3:e04395.
Piot, P. 2013. No Time to Lose: A Life in Pursuit of Deadly Viruses. New York: W. W. Norton.
Quammen, D. 2012. Spillover: Animal Infections and the Next Human Pandemic. New York: W. W. Norton.
Raj, V. S., A. D. Osterhaus, R. A. Fouchier, and B. L. Haagmans. 2014.MERS: Emergence of a novel human coronavirus. Current Opinion inVirology5:58–62.
Sack, K., S. Fink, P. Belluck, and A. Nossiter. 2014. Ebola's deadline escape. New York Times, December 30, 2014, D1.
Skowronski, D. M., C. Astell, R. C. Brunham, et al. 2005. Severe acute respiratory syndrome （SARS）: A year in review. Annual Review ofMedicine56:357–81.
WHO Ebola Response Team. 2014. Ebola virus disease in West Africa—the first 9 months of the epidemic and forward projections.New England Journal of Medicine371:1481–95.
Wolfe, N. 2009. Preventing the next pandemic. Scientific America, April 2009, 76–81.
10 漫长的告别
Damon, I. K., C. R. Damaso, and G. McFadden. 2014. Are we there yet?The smallpox research agenda using variola virus. PLoS Pathogens10:e1004108.
Dormitzer, P. R., P. Suphaphiphat, D. G. Gibson, et al. 2013. Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Science Translational Medicine5:185ra68.
Hughes, A. L., S. Irausquin, and R. Friedman. 2010. The evolutionary biology of poxviruses. Infection, Genetics and Evolution10:50–59.
Jacobs, B. L., J. O. Langland, K. V. Kibler, et al. 2009. Vaccinia virus vaccines: Past, present and future. Antiviral Research84:1–13.
Kennedy, R. B., I. Ovsyannikova, and G. A. Poland. 2009. Smallpox vaccines for biodefense. Vaccine27 （Suppl）:D73–79.
Koplow, D. A. 2003. Smallpox: The Fight to Eradicate a Global Scourge.Berkeley: University of California Press.
Kosuri, S., and G. M. Church. 2014. Large-scale de novo DNA synthesis:Technologies and applications. Nature Methods11:499–507.
Mariner, J. C., J. A. House, C. A. Mebus, et al. 2012. Rinderpest eradication: Appropriate technology and social innovations. Science337:1309–12.
Reardon, S. 2014. “Forgotten” NIH smallpox virus languishes on death row. Nature514:544.
Shchelkunov, S. N. 2009. How long ago did smallpox virus emerge? Archives of Virology154:1865–71.
Wimmer, E. 2006. The test-tube synthesis of a chemical called poliovirus.EMBO Reports7:S3–9.
尾声 冷却塔中的“外来客”
Abrahão, J. S., F. P. Dornas, L. C. F. Silva, et al 2014. Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries. Virology Journal11:120.
Claverie, J. M., and C. Abergel. 2013. Open questions about giant viruses.Advances in Virus Research85:25-56.
Forterre, P. 2010. Defining life: The virus viewpoint.Origins of Life andEvolution of Biospheres40:151–60.
Forterre, P., M. Krupovic, and D. Prangishvili. 2014. Cellular domains and viral lineages. Trends in Microbiology22:554–58.
Katzourakis, A., and A. Aswad. 2014. The origins of giant viruses,virophages and their relatives in host genomes. BMC Biology12:51.
Koonin, E. V., and V. V. Dolja. 2014. Virus world as an evolutionary network of viruses and capsidless selfish elements.Microbiology andMolecular Biology Reviews78:278–303.
Moreira, D., and C. Brochier-Armanet. 2008. Giant viruses, giant chimeras: The multiple evolutionary histories of mimivirus genes.BMC Evolutionary Biology8:12.
Moreira, D., and P. Lopez-Garcia. 2009. Ten reasons to exclude viruses from the tree of life. Nature Reviews Microbiology7:306–11.
Ogata, H., and J. M. Claverie. 2008. How to infect a mimivirus. Science321:1305.
Raoult, D., and P. Forterre. 2008. Redefining viruses: Lessons from mimivirus. Nature Reviews Microbiology6:315–19.
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 Diseases45:95–102.