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Viral Genomics

Viral Genomics. Outline of today’s lecture. Introduction Classification of Viruses Diversity and Evolution of Viruses Metagenomics and Virus Diversity Bioinformatics Approaches to Problems in Virology Influenza Virus Herpesvirus: From Phylogeny to Gene Expression

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Viral Genomics

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  1. Viral Genomics

  2. Outline of today’s lecture Introduction Classification of Viruses Diversity and Evolution of Viruses Metagenomics and Virus Diversity Bioinformatics Approaches to Problems in Virology Influenza Virus Herpesvirus: From Phylogeny to Gene Expression Human Immunodeficiency Virus Bioinformatic Approaches to HIV-1 Measles Virus

  3. Learning objectives for today’s lecture • Describe how viruses are classified • Explain bioinformatics approaches to virology • Describe the influenza virus genome including the new H1N1 virus • Provide a descriptio of the Herpesviruses • Use NCBI and LANL resources to identify the function and evolution of Human Immunodeficiency Virus (HIV-1)

  4. Introduction to viruses Viruses are small, infectious, obligate intracellular parasites. They depend on host cells to replicate. Because they lack the resources for independent existence, they exist on the borderline of the definition of life. The virion (virus particle) consists of a nucleic acid genome surrounded by coat proteins (capsid) that may be enveloped in a host-derived lipid bilayer. Viral genomes consist of either RNA or DNA. They may be single-, double, or partially double stranded. The genomes may be circular, linear, or segmented. Page 567

  5. Introduction to viruses Viruses have been classified by several criteria: -- based on morphology (e.g. by electron microscopy) -- by type of nucleic acid in the genome -- by size (rubella is about 2 kb; HIV-1 about 9 kb; poxviruses are several hundred kb). Mimivirus (for Mimicking microbe) has a double-stranded circular genome of 1.2 megabases (Mb). -- based on human disease Page 568

  6. Fig. 14.1 Page 569

  7. The International Committee on Taxonomy of Viruses (ICTV) offers a website, accessible via NCBI’s Entrez site http://www.ncbi.nlm.nih.gov/ICTVdb/ Fig. 14.2 Page 570

  8. Mimivirus: mimicking microbe Mimivirus is the sole member of the Mimiviridae family of nucleocytoplasmic large DNA viruses (NCLDVs). It was isolated from amoebae growing in England. The mature particle has a diameter of ~400 nanometers, comparable to a small bacterium (e.g. a mycoplasma). Thus, mimivirus is by far the largest virus identified to date. Page 569

  9. Mimivirus: mimicking microbe The mimivirus genome is 1.2 Mb (1,181,404 base pairs). It is a double-stranded DNA virus. ► Two inverted repeats of 900 base pairs at the ends (thus it may circularize) ► 72% AT content (~28% GC content) ► 1262 putative open-reading frames (ORFs) of length >100 amino acids. 911 of these are predicted to be protein-coding genes ► Unique features include genes predicted to encode proteins that function in protein translation. The inability to perform protein synthesis has been considered a prime feature of viruses, in contrast to most life forms. See Raoult D et al. (2004) Science 306:1344. Page 569

  10. Viral metagenomics Viral metagenomics refers to the sampling of representative viral genomes from the environment. A typical viral genome is ~50 kilobases (in comparison, a typical microbial genome is ~2.5 megabases). A sample is collected (e.g. seawater, fecal material, or soil). Cellular material is excluded. Viral DNA is extracted, cloned, and sequenced. Page 573

  11. Comparison of viral metagenomic libraries to the GenBank non-redundant database. Viral metagenomic sequences from human faeces, a marine sediment sample and two seawater samples were compared to the GenBank non-redundant database at the date of publication and in December 2004. The percentage of each library that could be classified as Eukarya, Bacteria, Archaea, viruses or showed no similarities (E-value >0.001) is shown. Edwards RA, Rohwer F. Nature Reviews Microbiology3, 504-510 (2005)

  12. “The Phage Proteomic Tree is a whole-genome-based taxonomy system that can be used to identify similarities between complete phage genomes and metagenomic sequences. This new version of the tree contains 167 phage genomes. Phages in black cannot be classified into any clade. In the key, each phage is defined in a clockwise direction.” Edwards RA, Rohwer F. Nature Reviews Microbiology3, 504-510 (2005)

  13. Genomic overview of the uncultured viral community from human feces based on TBLASTX sequence similarities. (A) Numbers of sequences with significant matches (E values of <0.001) in GenBank. (B) Distribution of significant matches among major classes of biological entities. (C) Types of mobile elements recognized in the library. (D) Families of phages identified in the fecal library. Mya Breitbart M. et al. (2003) Metagenomic Analyses of an Uncultured Viral Community from Human Feces. J Bacteriol. 185: 6220–6223.

  14. Categories of phage proteins with significant matches in the uncultured human fecal viral library Mya Breitbart M. et al. (2003) Metagenomic Analyses of an Uncultured Viral Community from Human Feces. J Bacteriol. 185: 6220–6223.

  15. Human disease relevance of viruses Vaccine-preventable viral diseases include: Hepatitis A Hepatitis B Influenza Measles Mumps Poliomyelitis Rubella Smallpox Page 571 Source: Centers for Disease Control website

  16. Human disease relevance of viruses DiseaseVirus Hepatitis A Hepatitis A virus Hepatitis B Hepatitis B virus Influenza Influenza type A or B Measles Measles virus Mumps Rubulavirus Poliomyelitis Poliovirus (three serotypes) Rotavirus Rotavirus Rubella Genus Rubivirus Smallpox Variola virus Varicella Varicella-zoster virus Page 571 Source: Centers for Disease Control website

  17. Outline of today’s lecture Introduction Classification of Viruses Diversity and Evolution of Viruses Metagenomics and Virus Diversity Bioinformatics Approaches to Problems in Virology Influenza Virus Herpesvirus: From Phylogeny to Gene Expression Human Immunodeficiency Virus Bioinformatic Approaches to HIV-1 Measles Virus

  18. Bioinformatic approaches to viruses Some of the outstanding problems in virology include: -- Why does a virus such as HIV-1 infect one species (human) selectively? -- Why do some viruses change their natural host? In 1997 a chicken influenza virus killed six people. -- Why are some viral strains particularly deadly? -- What are the mechanisms of viral evasion of the host immune system? -- Where did viruses originate? Page 574

  19. Diversity and evolution of viruses • The unique nature of viruses presents special challenges • to studies of their evolution. • viruses tend not to survive in historical samples • viral polymerases of RNA genomes typically lack • proofreading activity • viruses undergo an extremely high rate of replication • many viral genomes are segmented; shuffling may occur • viruses may be subjected to intense selective pressures • (host immune respones, antiviral therapy) • viruses invade diverse species • the diversity of viral genomes precludes us from • making comprehensive phylogenetic trees of viruses Page 574

  20. viruses SARS influenza archaea bacteria eukaryota viruses

  21. Overview of viral complete genomes PASC ►

  22. PASC: pairwise sequence comparison of viruses

  23. Overview of viral complete genomes

  24. Outline of today’s lecture Introduction Classification of Viruses Diversity and Evolution of Viruses Metagenomics and Virus Diversity Bioinformatics Approaches to Problems in Virology Influenza Virus Herpesvirus: From Phylogeny to Gene Expression Human Immunodeficiency Virus Bioinformatic Approaches to HIV-1 Measles Virus

  25. Influenza virus Influenza virus leads to 200,000 hospitalizations and ~36,000 deaths in the U.S. each year. Influenza viruses belong to the family Orthomyxoviridae. The viral particles are about 80-120 nm in diameter and can be spherical or pleiomorphic. They have a lipid membrane envelope that contains the two glycoproteins: hemagglutinin (H) and neuraminidase (N). These two proteins determine the subtypes of Influenza A virus. Influenza A Page 574

  26. Influenza virus Since 1976, the H5N1 avian influenza virus has infected at least 232 people (mostly in Asia), of whom 134 have died. A major concern is that a human influenza virus and the H5N1 avian influenza strain were to combine, a new lethal virus could emerge causing a human pandemic. In a pandemic, 20% to 40% of the population is infected per year. ►The 1918 Spanish influenza virus killed tens of millions of people (H1N1 subtype). ►1957 (H2N2) ► 1968 (H3N2) ► Asia 2003-2005 (H5N1) ► Current, 2009 (H1N1, “swine flu”) Page 575

  27. Influenza virus There are three types: A, B, C ► A and B cause flu epidemics ► Influenza A: 20 subtypes; occurs in humans, other animals. For example, in birds there are nine subtypes based on the type of neuraminidase expressed (group 1: N1, N4, N5, N8; group 2: N2, N3, N6, N7, N9). The structure of H5N1 avian influenza neuraminidase has been reported (Russell RJ et al., Nature 443:45, 2006). ► Influenza A genome consists of eight, single negative-strand RNAs (from 890 to 2340 nucleotides). Each RNA segment encodes one to two proteins. Page 575

  28. Page 576

  29. NCBI offers an Influenza Virus Resource (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html)

  30. Growth of Influenza Virus Sequences in GenBank 10/08 http://www.ncbi.nlm.nih.gov/genomes/FLU/growth.html

  31. Large-scale influenza virus genome analysis Holmes et al. (2005) performed phylogenetic analyses of 156 complete genomes of human H3N2 influenza A viruses collected over time (1999-2004) in one location (New York State). Phylogenetic analysis revealed multiple reassortment events. One clade of H3N2 virus, present since 2002, is the source for the HA gene in all subsequently sampled viruses. Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep;3(9):e300. Page 576

  32. Evolutionary Relationships of Concatenated Major Coding Regions of Influenza A Viruses Sampled in New York State during 1999–2004. The maximum likelihood phylogenetic tree is mid-point rooted for purposes of clarity, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for key nodes. Isolates assigned to clade A (light blue), clade B (yellow), and clade C (red) are indicated, as are those isolates involved in other reassortment events: A/New York/11/2003 (orange), A/New York/182/2000 (dark blue), and A/New York/137/1999 and A/New York/138/1999 (green). Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep;3(9):e300.

  33. Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep;3(9):e300.

  34. Large-scale influenza virus genome analysis Ghedin et al. (2005) sequenced 209 complete genomes of human influenza A virus (sequencing 2,821,103 nucleotides). See Nature 437:1162.

  35. Each row represents a single amino acid position in one protein. Amino acids (single-letter abbreviations are used) are colour-coded as shown in the key, so that mutations can be seen as changes in colour when scanning from left to right along a row. For simplicity, only amino acids that showed changes in at least three isolates are shown. Each column represents a single isolate, and columns are only a few pixels wide in order to display all 207 H3N2 isolates in this figure. Isolates are ordered along the columns chronologically according to the date of collection; boundaries between influenza seasons are indicated by gaps between columns. A more detailed version of this figure, showing positions that experienced any amino acid change and showing identifiers for the isolates in each column, is available as Supplementary Fig. 1. Ghedin E, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 2005 Oct 20;437(7062):1162-6.

  36. amino acid positions in influenza proteins 207 H3N2 isolates

  37. Outline of today’s lecture Introduction Classification of Viruses Diversity and Evolution of Viruses Metagenomics and Virus Diversity Bioinformatics Approaches to Problems in Virology Influenza Virus Herpesvirus: From Phylogeny to Gene Expression Human Immunodeficiency Virus Bioinformatic Approaches to HIV-1 Measles Virus

  38. Herpesvirus Herpesviruses are double-stranded DNA viruses that include herpes simplex, cytomegalovirus, and Epstein-Barr. The genomic DNA is packed inside an icosahedral capsid; with a lipid bilayer the diameter is ~200 nanometers. Page 578

  39. Herpesvirus Phylogenetic analysis suggests three major groups that originated about 180-220 MYA. Mammalian herpesviruses are in all three subfamilies. Avian and reptilian herpesviruses are all in the Alphaherpesvirinae. Page 578

  40. Herpesvirus: three main groups Millions of years before present Fig. 14.6 Page 578

  41. Herpesvirus taxonomy McGeoch et al. (Virus Res. 117:90-104, 2006) describe a new herpesvirus taxonomy. Family Herpesviridae Subfamilies Alpha-, Beta-, Gammaherpesvirinae New family Alloherpesviridae (piscine, amphibian herpesviruses) Page 578

  42. Alphaherpesvirinae Gammaherpesvirinae protein-coding regions Betaherpesvirinae Blocks of core genes (I–VII) Alloherpesviridae (piscine, amphibian) putative ATPase subunit of the terminase Malacoherpesviridae (invertebrate HV) McGeoch DJ et al. (Virus Res. 117:90-104, 2006)

  43. Herpesvirus taxonomy Genome sizes range from 124 kb (simian varicella virus from Alphaherpesvirinae) to 241 kb (chimpanzee cytomegalovirus from Betaherpesvirinae). ► GC content ranges from 32% to 75%. ►Protein-coding regions occur at a density of one gene per 1.5 to 2 kb of herpesvirus DNA. ► There are immediate-early genes, early genes (nucleotide metabolism, DNA replication), and late genes (encoding proteins comprising the virion). ►Introns occur in some herpesvirus genes. ► Noncoding RNAs have been described (e.g. latency-associated transcripts in HSV-1).

  44. Bioinformatic approaches to herpesvirus Consider human herpesvirus 8 (HHV-8)(family Herpesviridae; subfamily Gammaherpesvirinae). Its genome is ~140,000 base pairs and encodes ~80 proteins. Its RefSeq accession number is NC_003409. We can explore this virus at the NCBI website. Try NCBI  Entrez  Genomes  viruses (this is on the right sidebar)  dsDNA Page 579

  45. NCBI virus site includes tools (e.g. “Protein clusters”) to analyze herpesviruses clusters► Page 579

  46. NCBI virus site includes tools (e.g. “Protein clusters”) to analyze herpesviruses Fig. 14.7 Page 579

  47. Viruses can acquire host genes HHV-8 proteins include structural and metabolic proteins. There are also viral homologs of human host proteins such as the apoptosis inhibitor Bcl-2, an interleukin receptor, and a neural cell adhesion-related adhesin. Mechanisms by which viruses may acquire host proteins include recombination, transposition, splicing. A blastp search using HHV-8 interleukin IL-8 receptor as a query reveals several other viral IL-8 receptor molecules. Page 579

  48. Fig. 14.11 Page 581

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