Introduction to Virology

1. Introduction to virology

1.1 Definition and scope of virology

•Definition= the study of virus biology as well as interaction to their host

•A virus is a very small, non cellular parasite of cells. Its genome is either DNA or RNA and enclosed in a protein coat.

•Scope = virus biology, mechanisms for easy identification, control and treatment.

Introduction to virology

1.2 Position of viruses in the living world• “Viruses belong to biology b/c they posses genes,

replicate, evolve, and are adapted to particular hosts, biotic habitats and ecological niches. However,… they are nonliving infectious entities lead a kind of borrowed life.”-Regenmortel and Mahy

• Rickettsiae and Chlamydiae- obligate intracellular parasitic bacteria.– Virus particles product of assemblage of preformed

components– Do not grow or undergo division– Lack gene for metabolic energy/ protein synthesis


Growth on artificial media

Division by binary fission

Contain DNA and RNA

Contain protein synthesis machinery

Sensitive to antibiotics

Bacteria Often Yes Yes Yes Yes

Virus Never No Either DNA or RNA not both

No No

*viruses are on the boundary between living and nonliving


• Other infectious entities

– Viroids• very small (200–400 nucleotides)• circular RNA with a rod-like secondary structure.• no capsid or envelope • associated with certain plant diseases.


– Virusoids• satellite, viroid-like molecules• larger than Viroids• dependent on virus replication for multiplication,• packaged into virus capsids as passengers.


– Prions• single type protein molecule• no nucleic acid component.• (confusion =prion protein and the gene that encodes it

are also found in normal ‘uninfected’ cells).

2. Virus structure and composition

• Some terminologies:– Virion= (virus particle) a gene delivery system; containing

virus genome, and its functions are to protect the genome and to aid its entry into a host cell

– Capsid= The protein coat that encloses the nucleic acid of a virus

– Capsomere= A discrete component of a capsid, constructed from several identical protein molecules

– Nuclocapsid= genome + capsid– Envelope = A lipid bilayer and associated protein forming

the outer component of an enveloped virion

Virus structure and composition

• Virus genome– RNA or DNA– Single stranded or double stranded – Four categories of genome (dsDNA, ssDNA, dsRNA

and ssRNA)– Linear or circular, strand end– Seven categories



• Virus protein– Genome size increase- protein species– Structural protein =component of virions • Protection of genome• Attachment to host cell

– Non structural protein• Enzymes• Transcription factors • primer for nucleic acid replication


– Nomenclature of virus proteins • No standard system • Most virus proteins number system large to small

– Structural protein= virus protein (VP1, VP2..)– Non-structural protein =NSP1, NSP2,…

• Abbreviation – Structural characteristics

» G(glycoprotein)» P (phosphoprotein)

– Function » F (fusion)» P (polymerase)» RT (reverse transcriptase)


• Capsids – Protection of genome – Recognition and attachment– One/few protein species – Form symmetrical structure • Capsids with helical structure

– ssRNA viruses – Few DNA viruses– Length of the helix determined by length of genome – Eg. Influenza, tobacco mosaic virus ,filamentous phages



• Capsids with icosahedral structure – 20 faces, each equilateral triangles – 12 vertices , each vertices are five triangles meet – 30 edges– 5,3, 0r 2 fold axis– Eg. satellite tobacco mosaic virus(60 proteins), cowpea

mosaic virus (12*5 +20*3), herpesvirus, adenovirus




– Tailed bacteriophages» dsDNA » Eg phage lamda, phage T4

– Conical and rod shaped capsids» HIV-1 , baculovirus,



• Envelope – Derived from host cell, undergo modification– more than one host cells-composition vary• Indicate the origin of the virus• Common in animal viruses, rare in plant viruses and

very rare in prokaryotic

3. Classification

• Early classification-host, disease and vector• Characters used – DNA or RNA – Single or double– Genome is segmented or not – Size of virion – Capsid symmetry – Enveloped or not– Nature of the host

Classification

• Naming and classification=international committee for taxonomy of viruses (ICTV)– Order, Family, Subfamily, Genus, Species– Virus strains, serotypes and genotypes – First letter capital, name italic

• Phylogenetic tree – Based on genome sequence – Relationships of viruses – Rooted, un-rooted

Classification

Classification

• Baltimore classification of viruses– genome multiplication – mRNA transcription – Seven classes

Classification

Classification

Classification

• ICTV classify viruses into three orders,56 families, 9 subfamilies,233 genera and 1,550 viruses species.

• Caudovirales=I-III• Monegavirales= IV• Nidovirales=V-VII

Infection and replication– 7 steps:• Attachment to a cell• Entry into a cell• Transcription to mRNA • Translation to proteins• Genome replication• Assembly of protein and genome• Exit of virion from cell

– 3 steps • Initiation of infection• Replication and expression of virus genome• Release of mature virions from the infected cell

Infection and replication

– Basis of selectivity for specific host cell• vector (organism)

– High degree of specificity between vector and virus transmitted by the vector

– Greater in plant virus and vector than animal virus and vector– The only factor for plant viruses

• cell receptor (cell surface molecules) and co-receptor– Virion attaches to specific molecules on the surface of the

host– Cell surface molecules- receptors-usually glycoproteins(3D) – Recognition of a receptor by a virion is highly specific– have cell function


• Their function:– acting as receptors for chemokines and growth factors– mediating cell-to-cell contact and adhesion

• Evidence for a cell surface molecule as virus receptor– Soluble derivatives of the molecule block virus binding– The normal ligand for the molecule blocks virus binding– Inserting gene encoding the molecule and expression in virus

resistant cells makes them susceptible to infection.


• Availability of cell proteins(transcription factors and enzymes)• Lack defense against the virus

– Prokaryotes- restriction endonucleases to degrade foreign DNA

– Vertebrates-produce cytokines(interferon, interleukins and tumor necrosis factor) which trigger a range of antiviral defenses.

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Introduction to Virology