Viruses (2) Eukaryotic microorganisms and viruses. RNA viruses. Classification of viruses

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1 Viruses (2) Eukaryotic microorganisms and viruses Classification of viruses RNA viruses

2 Virus diversity: Retrovirus (Reverse Transcriptase Onkovirus) Structure of a retrovirus (e.g. Human immunodefiency virus HIV, genus: Lentivirus) 2 copies of (+) ssrna Virus carries enzyme for reverse transcription Envelope consists of lipid membrane and specific proteins Structure and genomic map of a retrovirus Coding sequences gag: pol: env: internal structure proteins - reverse transcriptase - integrase - RNAse H (degrades RNA of DNA/RNAhybrid double-strands) envelope proteins r/ltr: long terminal repeats, regulation of viral genes

3 Retrovirus: Replication Enzyme: Reverse Transcriptase Enzyme: Integrase Retrovirus: Replication

4 Retrovirus: Replication Retrovirus: HIV (Human immunodeficiency virus) Lifecycle Infection of - helper T-cells - macrophages - dendritic cells Transmission by - sexual route - blood product route - mother to child

5 Retrovirus: History of HIV HIV originated in non-human primates in sub-saharan Africa. Transferred to humans in late 19 th or early 20 th century. HIV-1 appears to have originated in southern Cameroon through the evolution of the simian immunodeficiency virus (SIV) that infects wild chimpanzees. The closest relative of HIV-2 is a virus of the sooty mangabey (SIV,smm), living in West Africa. Humans who eat or have contact with bushmeat (from apes) commonly acquire SIV. AIDS (Acquired Immune Deficiency Syndrome) was first clinically observed between late 1980 and early Retrovirus: HIV and AIDS (Acquired Immune Deficiency Syndrome) Pandemic and distribution of subtypes A pandemic is an epidemic of infectious disease that is spreading through human populations across a large region; for instance a continent, or even worldwide. AIDS has killed more than 25 million people since its discovery in 1981!

6 Retrovirus: HIV Global prevalence of adult HIV positive individuals 2005 Retrovirus: Influenza A-virus Family: Orthomyxoviridae Genus: Influenzavirus A Species: Influenza A virus Causes avian flu, hosted by birds but can infect mammals (e.g. H5N1) Genome contains eight single (non-paired) RNA strands that encode eleven proteins Segmented nature of the genome allows exchange of entire genes between different viral strains

7 Retrovirus: Influenza A-virus Class V: - strand ssrna virus 8 RNA molecules associated with nucleoprotein (NP) Core is covered with a matrix (M) which is surrounded by lipid membrane Hemagglutinin A protein (HA) responsible for virulence HA is responsible for binding the virus to the cell. Hemagglutinin" comes from the protein's ability to cause that red blood cells (erythrocytes) clump together. Retrovirus: Influenza A-virus life cycle - Invasion of host by endocytose - Fusion with endosome (membrane bound compartment inside eukaryotic cells) - Unpacking and penetration of RNA into the nucleus - Transcription into (+) RNA strand and replication of viral RNA - Translation of viral proteins for virus synthesis - Assembling and coating with matrix protein - Release of an enveloped virion by budding

8 Retrovirus: Influenza A-virus Known outbreaks of highly pathogenic flu in poultry Year Area Affected Subtype 1959 Scotland chicken H5N England turkey H7N Ontario (Canada) turkey H5N Victoria (Australia) chicken H7N Germany chicken H7N England turkey H7N Pennsylvania (USA)* chicken, turkey H5N Ireland turkey H5N Victoria (Australia) chicken H7N England turkey H5N Victoria (Australia) chicken H7N Queensland (Australia) chicken H7N Pakistan* chicken H7N New South Wales (Australia) chicken H7N Hong Kong (China)* chicken H5N Italy chicken H5N Italy* turkey H7N Hong Kong (China) chicken H5N Chile chicken H7N Netherlands* chicken H7N7 *Outbreaks with significant spread to numerous farms, resulting in great economic losses, are increasing. Most other outbreaks involved little or no spread from the initially infected farms. Retrovirus: Influenza A-virus Countries with poultry or wild birds killed by H5N1. Countries with humans, poultry and wild birds killed by H5N1

9 Retrovirus: Influenza A-virus Increasing numbers of human cases of and deaths from H5N1 Ecology of viruses

10 The three domains of life Ecology of viruses Yet, 30,000-40,000 viruses are known But only 5000 have been characterized Only little is known about their ecological impact Influence on microbial food web and biogeochemical cycles still uncertain Effect on host diversity Important role in mediation of horizontal gene transfer between hosts

11 Ecology of viruses Problems to enumerate viruses in nature - they are tiny (average head size in nature nm) - occur intra- and extracellular - isolation depends on cultivation of the host (more than 90% of all bacteria are currently uncultured) - lack on information about their lifestyle - no functional gene that have all viruses in common (PCR is inappropriate to detect and quantify all viruses) Quantification of viruses: Plaque assay using the agar overlay technique Plaques are 1-2 mm in diameter

12 Quantification by transmission electron microscopy Water sample showing bacteria and viruses (negative-stained with uranylacetate). Bacterial cell infected with phages (negative-stained with uranylacetate). Quantification by epifluorescence microscopy Water sample showing bacteria and viruses. Both are stained with SYBRGreenI.

13 Quantification by flow cytometry Simplified illustration of flow cytometry Counting of microscopic particles by suspending them in a stream of fluid and passing them by an electronic detection apparatus. Allows simultaneous multiparametric analysis of physical and/or chemical characteristics of up to thousands of particles per second. Quantification of viruses

14 Different viral lifecycles have influence on microorganisms and environment Pseudolysogenic: Infection only of susceptible variants of the strain. Virus contribution to biogeochemical cycle

15 Virus contribution to biogeochemical cycle Virus diversity and abundance is even higher than those of bacteria! - up to 10 times higher abundance than bacteria - abundance depends on environmental conditions - up to 70% of marine bacteria may be infected by phages - influence on host diversity - concept of killing the winner allows losing competitors to co-exist

16 Classification of microorganisms in accordance to their growth temperature

17 Hot environments in Yellowstone NP Geysir Mud pot Fumerols Hot springs Diversity of thermophilic viruses Unusual morphologies

18 Diversity of thermophilic viruses Viruses of the thermophilic Crenarchaeon Sulfolobus Sulfolobus spec Fuselloviridae (circ ds DNA) Lipithrixviridae Rudiviridae (ds DNA)

19 Extracellular development of RM378 (host Rhodothermus marinus)