ZOO 405 Week 2, Lecture 4 ZOO405 by Rania Baleela is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License

This week Ebola continued Viruses

Fig. 3 Molecular dating of the 2014 outbreak Fig. 3 Molecular dating of the 2014 outbreak.(A) BEAST dating of the separation of the 2014 lineage from central African lineages [SL, Sierra Leone; GN, Guinea; DRC, Democratic Republic of Congo; time of most recent common ancestor (tMRCA), September 2004; 95% highest posterior density (HPD), October 2002 to May 2006]. Molecular dating of the 2014 outbreak.(A) BEAST dating of the separation of the 2014 lineage from central African lineages [SL, Sierra Leone; GN, Guinea; DRC, Democratic Republic of Congo; time of most recent common ancestor (tMRCA), September 2004; 95% highest posterior density (HPD), October 2002 to May 2006]. (B) BEAST dating of the tMRCA of the 2014 West African outbreak (23 February; 95% HPD, 27 January to 14 March) and the tMRCA of the Sierra Leone lineages (23 April; 95% HPD, 2 April to 13 May). Probability distributions for both 2014 divergence events are overlaid below. Posterior support for major nodes is shown. Time of most recent common ancestor (tMRCA), September 2004; 95% highest posterior density (HPD), October 2002 to May 2006]. (B) BEAST dating of the tMRCA of the 2014 West African outbreak (23 February; 95% HPD, 27 January to 14 March) and the tMRCA of the Sierra Leone lineages (23 April; 95% HPD, 2 April to 13 May). Probability distributions for both 2014 divergence events are overlaid below. Posterior support for major nodes is shown. S K Gire et al. Science 2014;345:1369-1372 Published by AAAS

Fig. 4 Viral dynamics during the 2014 outbreak Fig. 4 Viral dynamics during the 2014 outbreak.(A) Mutations, one patient sample per row; beige blocks indicate identity with the Kissidougou Guinean sequence (GenBank accession KJ660346). top row = type of mutation (green, synonymous; pink, nonsynonymous; gray, intergenic), with genomic locations indicated above. (B) Number of EVD-confirmed patients per day, colored by cluster. Arrow indicates the first appearance of the derived allele at position 10,218, distinguishing clusters 2 and 3. (C) Intrahost frequency of SNP 10,218 in all 78 patients (absent in 28 patients, polymorphic in 12, fixed in 38). (D and E) Twelve patients carrying iSNV 10,218 cluster geographically and temporally (HCW-A = unsequenced health care worker; Driver drove HCW-A from Kissi Teng to Jawie, then continued alone to Mambolo; HCW-B treated HCW-A). KGH = location of Kenema Government Hospital. (F) Substitution rates within the 2014 outbreak and between all EVD outbreaks. (G) Proportion of nonsynonymous changes observed on different time scales (green, synonymous; pink, nonsynonymous). (H) Acquisition of genetic variation over time. Fifty mutational events (short dashes) and 29 new viral lineages (long dashes) were observed (intrahost variants not included). Viral dynamics during the 2014 outbreak.(A) Mutations, one patient sample per row; beige blocks indicate identity with the Kissidougou Guinean sequence (GenBank accession KJ660346). The top row shows the type of mutation (green, synonymous; pink, nonsynonymous; gray, intergenic), with genomic locations indicated above. Cluster assignments are shown at the left. (B) Number of EVD-confirmed patients per day, colored by cluster. Arrow indicates the first appearance of the derived allele at position 10,218, distinguishing clusters 2 and 3. (C) Intrahost frequency of SNP 10,218 in all 78 patients (absent in 28 patients, polymorphic in 12, fixed in 38). (D and E) Twelve patients carrying iSNV 10,218 cluster geographically and temporally (HCW-A = unsequenced health care worker; Driver drove HCW-A from Kissi Teng to Jawie, then continued alone to Mambolo; HCW-B treated HCW-A). KGH = location of Kenema Government Hospital. (F) Substitution rates within the 2014 outbreak and between all EVD outbreaks. (G) Proportion of nonsynonymous changes observed on different time scales (green, synonymous; pink, nonsynonymous). (H) Acquisition of genetic variation over time. Fifty mutational events (short dashes) and 29 new viral lineages (long dashes) were observed (intrahost variants not included). S K Gire et al. Science 2014;345:1369-1372 Published by AAAS

What is a virus? = a small infectious agent that can ONLY replicate inside organisms. Viruses are obligatory intracellular Viruses cannot produce energy or synthesize proteins independently, the host cell machinery is needed Viral genome may be RNA or DNA Viruses have a naked capsid (protein coat) or are enveloped Viruses do not replicate by division, their components must self assemble Viruses must encode any required processes not provided by host cell

structure Protein capsid Genome (DNA or RNA) ± Lipid envelope ± Enzymes

4 main morphological types 1. Helical Single type of capsomer (a morphological unit of the capsid of a virus) stacked around a central axis (rod-shaped or filamentous virions). Single-stranded RNA (ssDNA in some cases). e.g. Tobacco mosaic virus.

Human adenovirus C causes acute upper respiratory tract 2. Icosahedral a regular polyhedron with 20 identical equilateral triangular faces Most animal viruses. Icosahedron is the optimum way of forming a closed shell from identical sub-units. e.g. adenoviruses. Human adenovirus C causes acute upper respiratory tract

3. Envelope Enveloped in a modified form of one of the cell membranes => outer lipid bilayer. Most enveloped viruses are dependent on the envelope for their infectivity. E.g. Herpes viruses& HIV Epstein-Barr virus (EBV) cancer-causing virus Varicella zoster virus (VZV) causes chickenpox

4. Complex Possess a capsid that is neither purely helical, nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. The tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell. e.g. some bacteriophages.

What is a retrovirus? enveloped RNA viruses

Family: Retroviruses Are defined by common taxonomic denominators that include structure, composition, and replicative properties. The shape and location of the internal protein core are characteristic for various genera of the family. The hallmark of the family is its replicative strategy which includes as essential steps reverse transcription of the virion RNA into linear dsDNA and the subsequent integration of this DNA into the genome of the cell. The name is derived from the fact that the virus particle contains an RNA dependent DNA Polymerase (Reverse transcriptase). This enzyme converts the RNA genome into DNA, which then integrates into the host chromosomal DNA. The reverse transcriptase is highly error prone and rapid genetic variation is a feature of this group of viruses.

The virions are 80–100 nm in diameter, and their outer lipid envelope incorporates and displays the viral glycoproteins. The virion RNA = 7–12 kb, linear, positive ssRNA

Classification of RNA viruses

Retroviruses are currently classified into 7 genera. Classification of Retroviral Families.   Major classification systems of the retroviruses and the family systems as arranged by computer analysis of genomes https://web.stanford.edu/group/nolan/tutorials/retcl_1_classification.html

Structure HIV1 HTLV1

Genome organization Retroviruses have a diploid genome (2x RNA). The genome codes for at least 3 genes: gag (Group- specific AntiGen), pol, env. LTR - Long terminal repeat - non coding regulatory sequences at each end of the genome, which are necessary for: (1) integration into host chromosome and (2) control gene expression. gag - codes for the core proteins, structural virion components pol - reverse transcriptase (polymerase) env - envelope glycoprotein onc - oncogene

The pol gene products Reverse transcriptase: a polymerase that copies RNA to DNA; b) Integrase: integrates the viral genome into the host genome; c) RNase H:  cleaves the RNA as the DNA is transcribed so that RT can make the second complementary strand of DNA; d) Protease: cleaves the polyproteins translated from mRNAs from the gag & pol genes. Protease This virally encoded protease is the target of a new generation of anti-viral drugs.

Replication

Replication of RNA viruses RNA viruses that do not have a DNA phase need an RNA-dependent RNA-polymerase to replicate their RNA RNA viruses which copy their RNA into DNA -encode reverse transcriptase (RT).

Influenza A virus replication cycle

Replication of DNA viruses The virus needs to make mRNAs that can be translated into protein by the host cell translation machinery. Host enzymes for mRNA synthesis and DNA replication are nuclear (except for those in mitochondrion).

Herpes simplex virus Early gene expression (enzymes and protein that start viral replication) Late gene expression (protein synthesis)

Cell cycle M- mitosis G1 - cells grow S - DNA synthesis G2 - growth and preparation for mitosis G1/S decision point for going to dividing state Problem for DNA viruses that need S phase machinery.

Cell cycle control proteins Activation of cell cycle progression => cyclins, cyclin dependent protein kinases (Cdks), Cdk inhibitors Inhibitors of cell cycle progression => tumor suppressors

Is the uncontrolled growth of abnormal cells in the body. Cancer Is the uncontrolled growth of abnormal cells in the body.

Viruses can give rise to a tumor by Bring an oncogene into the cell = V-onc Or Can take control of a cellular proto-oncogene = proto/C-onc