Nucleic acid Strands Family Example Accession Base pairs

Transcription

1 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_ ,440 Togaviridae Rubella virus NC_ ,762 Flaviviridae Yellow fever virus NC_ ,862 Coronaviridae Coronavirus NC_ ,317 Rhabdoviridae Rabies virus NC_ ,932 Paramyxoviridae Measles virus NC_ ,894 Orthomyxoviridae PRJNA ,498 Bunyaviridae Tula virus (a hantavirus) PRJNA ,066 Arenaviridae Lassa fever virus PRJNA ,681 Retroviridae HIV NC_ ,181 Double Reoviridae Rotavirus C PRJNA ,910 DNA Single Parvoviridae Parvovirus H1 NC_ ,176 Mixed Hepadnaviridae Hepatitis B NC_ ,215 Double Papovaviridae JC virus NC_ ,130 Adenoviridae Human adenovirus, type 17 AC_ ,100 Herpesviruses Human herpesvirus 1 NC_ ,261 Poxviridae Vaccinia NC_ ,711 tables 92

2 Table 16.2 Vaccine-preventable viral diseases. Data from 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

3 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 Most Merkel cell carcinoma 2008 tables 94

4 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/ , , , , , Influenzavirus B Influenza B virus Strain: B/Lee/ , Influenzavirus C Influenza C virus Strain: C/Ann Arbor/1/ ,555 9 Isavirus Infectious salmon anemia virus Isolate: CCBB 8 12, Thogotovirus Thogoto virus Strain: SiAr ,461 7 Source: NCBI Genomes, NCBI ( WebLink 16.27). tables 95

5 Table 16.5 Genes in a representative complete genome (A/Puerto Rico/8/34(H1N1)), taxonomy identifier Gene Segment Protein Accession Length (amino acids) Name PB2 1 NP_ RNA dependent RNA polymerase subunit PB2 PB1 2 NP_ RNA dependent RNA polymerase subunit PB1 PB1 F2 2 YP_ PB1 F2 protein PA 3 NP_ RNA dependent RNA polymerase subunit PA PA X 3 YP_ RNA dependent RNA polymerase subunit PA X HA 4 NP_ Haemagglutinin NP 5 NP_ Nucleocapsid protein NA 6 NP_ Neuraminidase M2 7 NP_ Matrix protein 2 M1 7 NP_ Matrix protein 1 NS1 8 NP_ Nonstructural protein NS1 NS2 8 NP_ Nonstructural protein NS2 Source: NCBI Genomes, NCBI ( tables 96

6 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_ ,021,348 moumouvirus Acanthamoeba polyphaga mimivirus NC_ ,181,549 Acanthamoeba castellanii mamavirus JF ,191,693 Megavirus chiliensis NC_ ,259,197 Pandoravirus dulcis NC_ ,908,524 Pandoravirus salinus NC_ ,473,870 tables 97

7 Table 16.7 Virus resources available on web. Resource Description URL ICTVdb Universal virus database All the Virology on the Provides many virology links and 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 BVHomePage.html virusworld/viruslist.php tables 98