Table 16.1 Classification of viruses based on nucleic acid composition. Note that NCBI BioProject accessions begin PRJNA and typically encompass several segments. Adapted from Schaechter et al. (1999) with permission from Wolters Kluwer and with data from NCBI. Nucleic acid Strands Family Example Accession Base pairs RNA Single Picornaviridae Human poliovirus 1 NC_002058.3 7,440 Togaviridae Rubella virus NC_001545.2 9,762 Flaviviridae Yellow fever virus NC_002031.1 10,862 Coronaviridae Coronavirus NC_002645.1 27,317 Rhabdoviridae Rabies virus NC_001542.1 11,932 Paramyxoviridae Measles virus NC_001498.1 15,894 Orthomyxoviridae PRJNA14892 13,498 Bunyaviridae Tula virus (a hantavirus) PRJNA14936 12,066 Arenaviridae Lassa fever virus PRJNA14864 10,681 Retroviridae HIV NC_001802.1 9,181 Double Reoviridae Rotavirus C PRJNA16140 17,910 DNA Single Parvoviridae Parvovirus H1 NC_001358.1 5,176 Mixed Hepadnaviridae Hepatitis B NC_003977.1 3,215 Double Papovaviridae JC virus NC_001699.1 5,130 Adenoviridae Human adenovirus, type 17 AC_000006.1 35,100 Herpesviruses Human herpesvirus 1 NC_001806.1 152,261 Poxviridae Vaccinia NC_006998.1 194,711 tables 92
Table 16.2 Vaccine-preventable viral diseases. Data from http://www.cdc.gov/ vaccines/vpd-vac/default.htm (WebLink 16.26). Disease Virus Comment Hepatitis A Hepatitis A virus Causes liver disease Hepatitis B Hepatitis B virus Causes liver disease Influenza Influenza type A or B Causes 20,000 deaths per year (US) Measles Measles virus See below Mumps Rubulavirus A disease of the lymph nodes Poliomyelitis Poliovirus (three serotypes) Inflammation of the gray matter of the spinal cord; kills neurons Rotavirus Rotavirus Most common cause of diarrhea in children; kills 600,000 children annually worldwide Rubella Genus rubivirus Also called German measles Smallpox Variola virus Eradicated in 1977 Varicella Varicella zoster virus About 75% of all children contract varicella by age 15 tables 93
Table 16.3 Seven viruses that cause cancer in humans. Note that EBV is also called human herpesvirus 4 (HHV-4). Adapted from Moore and Chang (2010) with permission from Macmillan Publishers. Virus Genome Notable cancers Epstein Barr virus (EBV) Double stranded DNA Most Buritt s lymphoma and nasopharyngeal herpesvirus carcinoma; most lymphoproliferative disorders; some Hodgkin s disease; some nonhodgkin s lymphoma; some gastrointestinal lymphoma Hepatitis B virus (HBV) Single stranded and doublestranded DNA hepadenovirus Human T lymphotropic virus-i (HTLV-I) High-risk human papillomaviruses (HPV) 16 and HPV 18 (some other α HPV types are also carcinogens) Hepatitis C virus (HCV) Kaposi s sarcoma herpesvirus (KSHV; also known as human herpesvirus 8 (HHV 8)) Merkel cell polyomavirus (MCV) Positive-strand, single-stranded RNA retrovirus Double stranded DNA papillomavirus Positive strand, single stranded RNA flavivirus Double stranded DNA herpesvirus Double stranded DNA polyomavirus Some hepatocellular carcinoma 1965 Adult T cell leukaemia 1980 Most cervical cancer and penile cancers and some other anogenital and head and neck cancers Some hepatocellular carcinoma and some lymphomas Kaposi s sarcoma, primary effusion lymphoma and some multicentric Castleman s disease Year first described 1964 1983 1984 1989 1994 Most Merkel cell carcinoma 2008 tables 94
Table 16.4 Influenza viruses: examples of family Orthomyxoviridae complete genomes. Virus Source information Segments Influenzavirus A Length (nt) Proteins (A/Goose/Guangdong/1/1996(H5N1)) (A/Hong Kong/1073/99(H9N2)) (A/Korea/426/1968(H2N2)) (A/New York/392/2004(H3N2)) (A/Puerto Rico/8/1934(H1N1)) Strain: A/Goose/Guangdong/1/96(H5N1) Serotype: H9N2; Strain: A/Hong Kong/1073/99 Serotype: H2N2; Strain: A/Korea/426/68 Serotype: H3N2; Strain: A/New York/392/2004 Serotype: H1N1; Strain: A/Puerto Rico/8/34 8 13,590 12 8 13,460 12 8 13,460 12 8 13,627 12 8 13,588 12 Influenzavirus B Influenza B virus Strain: B/Lee/40 8 14,452 11 Influenzavirus C Influenza C virus Strain: C/Ann Arbor/1/50 7 12,555 9 Isavirus Infectious salmon anemia virus Isolate: CCBB 8 12,716 10 Thogotovirus Thogoto virus Strain: SiAr 126 6 10,461 7 Source: NCBI Genomes, NCBI ( http://www.ncbi.nlm.nih.gov/genomes/genomesgroup.cgi?taxid=11308, WebLink 16.27). tables 95
Table 16.5 Genes in a representative complete genome (A/Puerto Rico/8/34(H1N1)), taxonomy identifier 211044. Gene Segment Protein Accession Length (amino acids) Name PB2 1 NP_040987 759 RNA dependent RNA polymerase subunit PB2 PB1 2 NP_040985 757 RNA dependent RNA polymerase subunit PB1 PB1 F2 2 YP_418248 87 PB1 F2 protein PA 3 NP_040986 716 RNA dependent RNA polymerase subunit PA PA X 3 YP_006495785 252 RNA dependent RNA polymerase subunit PA X HA 4 NP_040980 566 Haemagglutinin NP 5 NP_040982 498 Nucleocapsid protein NA 6 NP_040981 454 Neuraminidase M2 7 NP_040979 97 Matrix protein 2 M1 7 NP_040978 252 Matrix protein 1 NS1 8 NP_040984 230 Nonstructural protein NS1 NS2 8 NP_040983 121 Nonstructural protein NS2 Source: NCBI Genomes, NCBI ( http://www.ncbi.nlm.nih.gov/genome/proteins/10290?project_id=15521). tables 96
Table 16.6 Largest virus genomes. All are double-stranded DNA (no RNA stage). The order Megavirales has been proposed to reflect the genome size of at least 1 megabase. Genus, species Accession Base pairs Acanthamoeba polyphaga NC_020104.1 1,021,348 moumouvirus Acanthamoeba polyphaga mimivirus NC_014649.1 1,181,549 Acanthamoeba castellanii mamavirus JF801956.1 1,191,693 Megavirus chiliensis NC_016072.1 1,259,197 Pandoravirus dulcis NC_021858.1 1,908,524 Pandoravirus salinus NC_022098.1 2,473,870 tables 97
Table 16.7 Virus resources available on web. Resource Description URL ICTVdb Universal virus database http://ictvonline.org/ All the Virology on the Provides many virology links and http://www.virology.net/ WWW resources The Big Picture Book of Viruses VIrus Particle ExploreER (VIPER) Viral Bioinformatics Resource Center Virusworld Stanford HIV Drug Resistance Database General virus resource High resolution virus structures in the Protein Data Bank (PDB) Databases and software to analyze viruses A research institute at the University of Wisconsin Madison A curated database with information on drug targets http://www.virology.net/big_virology/ BVHomePage.html http://viperdb.scripps.edu/ http://athena.bioc.uvic.ca/ http://www.virology.wisc.edu/ virusworld/viruslist.php http://hivdb.stanford.edu/ tables 98