A Planet of Viruses - Carl Zimmer (2011)

Selected References

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 Sciences104:18566.

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.