SGU SOM - T3 - Introduction to viruses

Viral mRNA

Can be processed with the same range of features that are round in eukaryotic RNA: - 5'-5' N⁷- methylguanosine- triphosphate CAP - poly A tail (100-200 adenosine residues) When Viruses replicate in the cytoplasm, they can either make their own 5' CAP or process a 3D RNA structure known as internal ribosomal entry site element (IRES)

Arenaviruses Bunaviruses

Group V (-ve) ssRNA - have ambisense genome where part of the ssRNA is negative

Viral protein phases

Immediate early phase proteins Early phase proteins Late phase proteins

Viroids

Plant pathogens - smallest infectious pathogen - composed of short strand of circular, single stranded RNA molecule that do no encode any protein - they are distributed from cell to cell through plasmodesmata - similar to each other suggesting close evolutionary origin (~246-375 nucleotides) - likely to interfere with RNA regulation such as siRNA causing - they are responsible for causing disease in a number of plants, including potatoes, tomatoes, cucumbers

Spontaneous prion disease

Rate of about 1 per million people usually late in health, or 1-2 million infected worldwide - the normal, innocuous protein (PrPc) can change its shape to a harmful, disease causing form PrPsc - this conversion procesds via a chian reaction - PrPsc proteins form long filamentous aggregates that gradually damage neuronal tissue

dsRNA viruses

Reoviruses

dsRNA

Reoviruses segmented genome

Positive ssRNA

Retroviruses (HIV-diploid genome)

Viron

a complete infectious form of virus outside the host cell (extracellular)

Viral envelope

a lipoprotein membrane derived from host membrane and can be: - cell plasma membrane + HIV; most of the enveloped viruses) - nuclear or other internal (endoplasmic reitculum) membranes + herpesviruses poor in host proteins, but rich in virus specific glycoproteins- viral attachment protein (VAP)

Prions mode of transmission

acquired through diet, transfusion, surgical procedures, and corneal transplants

DNA based genomes

always presented by single molecule, either dsDNA or ssDNA (+ve) or (-ve)

Negative strand

antisense strand - template strand

Hereditary prion disease

autosomal dominant mutation of PrP (chromosome 20)p - at least 10-15% of total human transmissible spongiform encephalopathy cases

RNA based genomes

can be presented by either single molecule (non-segmented) or several molecules (segmented)

Viral synthesis and growth

"One step viral growth cycle" - the time required for a single cycle of virus reproduction and yield per cell, or burst size - initial infection is followed by disappearance of all viral particles - eclipse phase - viral genome takes over the control of the host cell protein making machinery and direct the production towards viral components. this is known as latent period until new virion particles are assembled. ** latent period is different from latent infection

Positive strand

sense strand - coding sequence

ssDNa viruses

+ve strand or "sense" DNA - parvoviruses

+ve ssRNA viruses

+ve strand or sense - RNA - Picornaviruses - Togaviruses

ssRNA-RT viruses

+ve strand or sense - RNA with DNA intermediate in life-cycle - Retroviruses

Attachment

- The interaction between a virus and its target cell begins with attachment of the virus particle to a specific receptor on the cell - critical step as a determinant of target selections by many viruses - requires viral attachment protein and cellular receptors

Viral production with single function

- Transcription of individual monocistronic mRNA molecules from the genome - Segmented genome where each molecule gives single monocistronic mRNA - Production of a single long polyprotein that is later cleaved into individual functional peptides

Enveloped viruses

- Viral nucleocapsid is surrounded by a lipoprotein membrane derived from host cell membrane (measles virus) or nuclear (herpesvirus) or other internal membranes and contain virus specific glycoproteins - they are sensitive to inactivation by organic solvents (alcohol, chloroform, ether, etc) detergens, drying, acid, heat - usually transmitted by secretions, large droplets, blood, or sexual contact + Measles virus - usually spherical or pleomorphic in shape except rhabdovirus (rabies, bullet shaped) and poxvirus (smallpox, complex)

Helical capsid

- appear as rod-like, filamentous structures (may be rigid or flexible depending on the specific virus) - capsomers bind to the viral genome in a regular fashion - "open ended" and form around the genome. No empty capsids can form. - all known examples of animal viruses with helical symmetry contain RNA genomes and have flexible nucleocapsids wound into a ball and surrounded by envelope, except: Rhabdoviruses

Baltimore classification

- classification of viruses on a combo of their nucleic acid, strandedness, sense, and method of replication 1. dsDNA viruses 2. ssDNA viruses 3. dsRNA viruses 4. +ve ssRNA virsues 5. -ve ssRNA virsues 6. ssRNA-RT viruses 7. dsDNA-RT viruses

Icosahedral capsid

- few proteins assemble in a basic protomers - the amount of nucleic acid that can be packaged is limited by the size of the particle - form independently of the genome - the promoters assemble into a pentamer - has a complex 5-3-2 axes of symmetry (e.g. poliovirus)

Virus family nomenclature

- idae

virus subfamily nomenclature

- inae

Viral release

- newly formed virion can be released by different means: - exocytosis cause the viral capsid to grab cellular membrane in a form of an envelope which is laced with viral proteins. + commonly observed for enveloped viruses

Hepatits D Virus

- satellite viruses - very small single stranded RNA virus that can only infect in the presence of hepatitis B virus (HBV) (helper virus) - shows replication similarities with viroids in plants - produces an antigen termed "delta antigen" HDsAg - utilizes HBV surface antigen (HBsAg) for entry into host cell

Virus capsid

- serves to protect the nucleic acid genome - held together by non-covalent, reversible hydrophobic, or hydrogen bonds - consists of single or serval different subunits (capsomeres) that have variable sizes, have identifiable domains,and symmetry - proteins have various functions: + define tissue or species specific transmission by interaction with host receptors to facilitate the host cell entry + interact with the viral nucleic acid for packaging/ assembling the virus + assist in viral and/or host gene regulation + evades/ block host immune system, and other functions - icosahedral (roughly spherical) - helical - complex (nonsymmetrical)

Viral genomes

single stranded (ss) double stranded (ds) linear circular segmented haploid or diploid

Viral replication

- uncoating of the viral genome leads to the first steo of viral replication i.e. expression of mRNA (transcription) - translation of mRNA generates the so-called "early proteins" which often include synthesis of viral DNA or RNA polymerase and other proteins which play an important role in viral replication - viral genome replication leads to complementary strand synthesis and additional templates using nucleic acids - late mRNA synthesis generates "late proteins" (structural proteins) which participate in the formation of the viral capsomeres - capsid formation follows a self assembly mechanism in most of the cases - some viruses may use chaperons to fold the capsomeres - process of generating new genomes + special cases require specific viral enzymes: = RNA dependent DNA polymerase (reverse transcriptase) = RNA dependent RNA polymerase (RNA replicase)

Tropism

- viral glycoproteins (VAP) integrated in the outer coat: we either the capsid or the envelope that target receptors are acting as doors on the surface of the host cells (susceptibility) - presence of transcription factors allowing expression of viral genes - presence of cell enzyme pathways to produce viral proteins known as "premissivity"

Non-enveloped viruses

- viral nucleocapsid is naked - tough and relatively resistant to inactivation by organic solvents (alcohol, chloroform, ether, etc) detergens, drying, acid, and heat - transmitted by fecal/ oral route, fomites, or small droplets - released from infected cells by lysis + poliovirus + adenovirus

-ve ssRNA viruses

-ve strand or antisense - RNA - Orthomyxoviruses - Rhabdoviruses

virus genus

-virus

Stages in Viral replication

1. Attachment to specific host cell receptors - this binding determines what cell can be infected (tropism) 2. Penetration 3. Uncoating - release of nucleic acid 4. Macromolecular synthesis - Early mRNA and protein synthesis: + proteins to shut off host cell + proteins to replicate viral genome (if needed) - Replication of the genome - Late mRNA and protein synthesis: structural proteins 5. Post Translational modification of proteins 6. Assembly of new virus particles 7. Release (lysis of the cell or budding out)

Penetrating and Uncoating non-enveloped viruses

1. Direct entry across plasma membrane A. Virus attaches to host cell receptors B. sinks into cell membrane C. injects its genome through a pore into the cell - poliovirus

Penetration and Uncoating enveloped viruses

1. Fusion: Entry of enveloped virus by fusing with plasma membrane A. virus glycoproteins attach to host cell receptors B. envelope- membrane fusion occurs C. capsid enters, is coated and virus is released - e.g. Herpesvirus - Paramyxovirus - HIV

Bacteriophage life cycle

1. Virulent (lytic phage): kills the host following infection 2. Lysogenic (temperate) phage: undergoes lysogeny wherein the host is not immediately killed and the phase genome becomes a prophage (provirus) either by integration into the host chromosome or exist as an independent entity but replicating with the rate equal to the host genome multiplication

Non-enveloped endocytosis

A. Host cell cytoplasmic membrane wraps around virus B. brings it inside C. the capsid is uncoated D. the viral genome is released into the host cell - parvovirus

Enveloped Endocytosis and acidification

A. Host cell cytoplasmic membrane wraps around virus and brings it inside B. the capsid is uncoated and the viral genome is released into the host cell C. the viral genome is released into the host cell - e.g. influenza virus

dsDNA viruses

Adenoviruses Herpesviruses Poxviruses

Viral genome

All viruses all need to go through mRNA (+ve) strand synthesis to produce proteins: - Positive (+ve) nucleic acid (DNA or RNA) is the gene coding strand (or the actual gene sequence) - Negative (-ve) nucleic acid (DNA or RNA) is the complementary strand to the gene coding mRNA (the template strand) All viruses are haploid except retroviruses (HIV) have diploid genome

dsDNA-RT viruses

DNA with RNA intermediate in life cycle - Hepadnaviruses

Viral structure

Genome (nucleic acid) - either DNA or RNA Capsomere - viral (protein) subunits that assemble into capsid Nucleocapsid - genome assembled into the capsid Virus specific glycoproteins Envelope - outer layer that originates from the host membranes and covers the capsid to maintain aqueous solution Tegument - a cluster of proteins that line the space between the envelope and nucleocapsid

Viruses

Non-cellular organisms: - consists of either DNA or RNA that is surrounded by a protein coat - invisible by light microscopy with sizes ranging from 20-400nm - infect any living organism e.g. vertebrates, invertebrates, plants, bacteria, and fungi - obligate "intracellular parasites" that require a host cell for replication - individual viral components self assembly into a viron

Negative ssRNA

Paramyxoviruses (non-segemented genome) Orthomyxoviruses (segmented genome)

Viral attachment proteins

Peplomers - facilitate host cell entry + e.g. hemagglutinin on influenza virus which binds erythrocytes + VAP on Epstein- Barr virus (EBV) binds C3d receptor (CR2) on B cells

Defective viruses

Satellite viruses cannot replicate without a helper virus - up to 100 times more defective viruses are produced than normal viruses (100:1) due to genome mutations

Influenza A

Target cell: Epithelial cells Receptor: Sialic acid

HIV

Target cell: Helper T cell Receptor: CD4 molecule and chemokine coreceptor

Viral polymerase

present within the genome of viruses and involved in transcription and replication of viral genome

VIral mRNA Protease inhibitors

Viral proteases are essential targets in antiviral strategies - e.g. Boceprevir- mediated inhibition of Hepatitis C virus (polyprotein processing - e.g. Saquinavir-mediated inhibition of HIV gag and gag-pol polyprotein processing

Viruses with diploid genome

retroviruses - HIV

Bacteriophages

exhibit complex symmetry - bacterial viruses - head: nucleic acid and protein - tail and cotnractive sheath - tail fibers and tail pins - base/ end plate

Retroviruses

human immunodeficiency virus (HIV) - possess a distinctive cone-shaped capsid structure - positive ssRNA - diploid genome

Prions

infectious proteins - have no genome (RNA or DNA) - that adopt a modified structure/ folding compare to the non-infectious folding of the same protein First identified as "transmissible spongiform encephalopathies" causing: - loss of motor control - dementia - paralysis - encephalitis; widespread neuronal loss

Saquinavir

inhibition of HIV gag and gag-pol polyprotein processing

Boceprevir

inhibition of NS3/ NS4A protease on non structural proteins

Poxviruses

lack a typical capsid and are covered by a dense layer of lipoproteins - vaccinia virus exhibit complex symmetry

Viral tropism

limited to a single organ, tissue, specialized cell type, or range of different organs, and tissue

Frameshifting

may transcribe some viral genomes by shifting the read frame with one or two nucleotides and thus producing different mRNA and proteins

Rotaviruses

possess a 3 layer capside that contains 11 dsRNA

Matrix proteins

present between nucleocapsid and envelope, stabilize the organization of viral glycoprotein, directs the viral genome to intracellular sites of viral assembly, facilitate virus assembly and budding