Principles of Virology, Volume 1. Jane Flint

virus. Some of the important landmarks and achievements in the field of virology are summarized in Fig. 1.14. It is apparent that much has been discovered about the biology of viruses and about host defenses against them. Yet the more we learn, the more we realize that much is still unknown.

      In the first edition of this textbook (published in 2000), we noted that the most recent (1995) report of the ICTV listed 71 different virus families, which covered most new isolates. We speculated therefore that: “As few new virus families had been identified in recent years, it seems likely that a significant fraction of all existing virus families are now known.” In the intervening years, this prediction has been shattered, not only by the discovery of new families of viruses, including giant viruses with genome sizes that surpass those of some bacteria, but also by results from metagenomic analyses. For example, the fact that a high percentage (93%) of protein-coding sequences in the genomes of the giant Pandoraviruses have no homologs in the current databases was totally unexpected. The unusual morphological features and atypical reproduction process of these viruses were also surprising. In addition, it is mind-boggling to contemplate that of almost 900,000 viral sequences identified in samples of only one type of ecosystem (raw sewage), more than 66% bore no relationship to any viral family in the current database. From these analyses, and similar studies of other ecosystems (i.e., oceans and soil), it has been estimated that only a minor percentage of extant viral diversity has been explored to date. Clearly, the viral universe is far more vast and diverse than suspected only a decade ago, and there is much fertile ground for gaining a deeper understanding of the biology of viruses and their host cells and organisms.

Figure 1.13 Viral families sorted according to the nature of the viral genomes. A wide variety of sizes and shapes are illustrated for the families of viruses that infect vertebrates. Families are identified by Latinized names and organized in seven distinct classes, based on the nature of their genomes. Genome replication cycles are illustrated in the column at the left. Similar diversity exists for the families of viruses that infect other life forms, but the chart lists only the approximate number found to date in each class. As noted in the 9th and 10th ICTV Reports, in some cases there are as yet no examples. Data from King AMQ et al. 2012. Virus Taxonomy: The Classification and Nomenclature of Viruses (https://talk.ictvonline.org/ictv-reports/), with assistance from Dr. Elliot J. Lefkowitz, Department of Microbiology, Director of Informatics, UAB Center for Clinical and Translational Science, Birmingham, AL (http://www.uab.edu/bioinformatics/).

Figure 1.14 Landmarks in the study of viruses. Key discoveries and technical advances are listed for each time interval. The pace of discovery has increased exponentially over time. Abbreviations: AAV, adenovirus-associated virus; EU, European Union; EMA, European Medical Association; FDA, U.S. Food and Drug Administration; FMDV, foot-and-mouth disease virus; HAART, highly active antiretroviral therapy; HCV, hepatitis C virus; HHV-8, human herpesvirus 8; HIV-1, human immunodeficiency virus type 1; HPV, human papillomavirus; MHC, major histocompatibility complex; RSV, Rous sarcoma virus; SV40, simian virus 40; TBSV, tomato bushy stunt virus; TMV, tobacco mosaic virus; WHO, World Health Organization.

REFERENCES

       Books

      Barry JM. 2005. The Great Influenza. Penguin Books, New York, NY.

      Brock TD. 1990. The Emergence of Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

      Brothwell D, Sandison AT (ed). 1967. Diseases in Antiquity. Charles C Thomas, Publisher, Springfield, IL.

      Cairns J, Stent GS, Watson JD (ed). 1966. Phage and the Origins of Molecular Biology. Cold Spring Harbor Laboratory for Quantitative Biology, Cold Spring Harbor, NY.

      Creager ANH. 2002. The Life of a Virus: Tobacco Mosaic Virus as an Experimental Model, 1930–1965. University of Chicago Press, Chicago, IL.

      Denniston K, Enquist L. 1981. Recombinant DNA. Benchmark Papers in Microbiology, vol 15. Dowden, Hutchinson and Ross, Inc, Stroudsburg, PA.

      Hughes SS. 1977. The Virus: a History of the Concept. Heinemann Educational Books, London, United Kingdom.

      Karlen A. 1996. Plague’s Progress, a Social History of Man and Disease. Indigo, Guernsey Press Ltd, Guernsey, Channel Islands.

      Knipe DM, Howley PM (ed). 2013. Fields Virology, 6th ed. Lippincott Williams & Wilkins, Philadelphia, PA.

      Luria SE. 1953. General Virology. John Wiley & Sons, Inc, New York, NY.

      Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Rasmussen N. 1997. Picture Control: the Electron Microscope and the Transformation of Biology in America 1940–1960. Stanford University Press, Stanford, CA.

      Oldstone MBA. 2010. Viruses, Plagues, & History: Past, Present, and Future. Oxford University Press, New York, NY.

       Papers of Special Interest

      Boylston AW. 2018. The myth of the milkmaid. N Engl J Med 378:414–415.

       A delightful scientific historian’s report on research that debunks the much-cited notion that Edward Jenner was inspired to test the benefits of cowpox by the comments of a milkmaid who claimed to be immune to smallpox because she had had cowpox.

      Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. 2002. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99:14250–14255.

       Early use of metagenomic analysis to identify viruses in natural marine environments. One of the first to identify these agents using these methods, and to reveal the enormity in number of previously unknown viruses in these environments.

      Crick FHC, Watson JD. 1956. Structure of small viruses. Nature 177:473– 475.

       Authors deduce from X-ray crystal analysis of plant virus particles that virus shells (capsids) are composed of a large number of identical protein molecules, of small or moderate size, packed together in a regular manner.

      Murray NE, Gann A. 2007. What has phage lambda ever done for us? Curr Biol 17:R305–R312.

       The authors describe how study of the bacteriophage lambda has contributed to an understanding of the molecular basis of numerous fundamental biological processes.

      Suttle CA. 2007. Marine viruses—major players in the global ecosystem.

      Nat Rev Microbiol 5:801–812.

       Suttle describes the unappreciated yet enormous contribution that the huge numbers of marine viruses make to the earth’s marine and global ecosystems.

       Websites

      https://talk.ictvonline.org/taxonomy/