THEME 2: VIRUS STRUCTURE & EVOLUTION

Polyphyletic origin of viruses

Viruses originated multiple times from different ancestors

Regressive evolution theory

Viruses evolved from degenerate cellular life forms

Cellular origin theory

Viruses originated from subcellular elements that escaped cells

Independent entity theory

Viruses evolved independently from self-replicating molecules in the RNA world

Main drivers of viral diversity

Multiple origins and rapid evolution

Key factors influencing viral genetic variability

Replication fidelity, replication rate, population size, transmission, co-infection

Main mechanisms of viral genetic diversification

Mutation, recombination, reassortment

Definition of mutation

Changes in nucleotide sequence such as insertions, deletions or mismatches

Mutation rate

Number of mutations per nucleotide per replication cycle

Substitution rate

Rate at which mutations become fixed in populations

Polymerases lacking proofreading

RNA-dependent RNA polymerase and reverse transcriptase

Viruses with highest mutation rates

RNA viruses and retroviruses

Error threshold

Maximum mutation rate allowing genetic information transmission

Definition of recombination

Exchange of genetic material between nucleic acid molecules

Requirement for recombination

Co-infection of the same cell

Evolutionary impact of recombination

Rapid and drastic genetic changes

Definition of reassortment

Exchange of genome segments in segmented viruses

Virus showing reassortment

Influenza virus

Consequence of reassortment

Antigenic shift

Quasispecies theory

Viral populations exist as dynamic mutant swarms

Scientist who proposed quasispecies theory

Manfred Eigen

Reason RNA viruses form quasispecies

High mutation rate and short generation time

Definition of quasispecies

Closely related viral genomes under collective selection

Master sequence

Most frequent genome in a quasispecies

Consensus sequence

Average sequence of the population

Effect of quasispecies diversity

Increases adaptability and virulence

Population bottleneck

Loss of viral diversity during transmission

Examples of natural bottlenecks

Aerosol, fecal–oral, vector transmission

Effect of bottlenecks on fitness

Reduction in viral fitness

Population diversity as virulence determinant

Diverse populations cause more severe disease

Virus taxonomy authority

ICTV

Current ICTV classification levels

Realms, kingdoms, phyla, classes, orders, families, genera, species

Baltimore classification basis

Genome type and replication strategy

Baltimore class I

Double-stranded DNA viruses

Baltimore class II

Single-stranded DNA viruses

Baltimore class III

Double-stranded RNA viruses

Baltimore class IV

Positive-sense single-stranded RNA viruses

Baltimore class V

Negative-sense single-stranded RNA viruses

Baltimore class VI

Single-stranded RNA with reverse transcription

Baltimore class VII

Double-stranded DNA with reverse transcription

General structure of viruses

Nucleic acid genome surrounded by capsid

Definition of capsid

Protein shell protecting viral genome

Definition of capsomere

Morphological subunit of the capsid

Definition of nucleocapsid

Genome plus capsid

Definition of envelope

Host-derived lipid bilayer with viral glycoproteins

Definition of virion

Complete infectious virus particle

Role of viral glycoproteins

Host recognition and antigenicity

Host proteins in viral envelope

May be incorporated during budding

Structural proteins

Form capsid and envelope

Enzymatic viral proteins

Required for replication

Viruses resistant to environment

Naked icosahedral viruses

Viruses sensitive to environment

Enveloped viruses

Subviral particles

Viroids, satellites, prions

Possible viral genome forms

DNA or RNA, ss or ds, linear or circular

Multipartite genome

Genome divided into multiple segments

Helical capsid structure

Single protein type arranged around nucleic acid

Genome type in helical viruses

Usually single-stranded RNA

Example of helical virus

Tobacco mosaic virus

Shape of helical viruses

Rod-shaped or filamentous

Icosahedral symmetry

Regular capsid with 20 triangular faces

Capsomer arrangement

Pentamers and hexamers

T-number definition

Determines number of capsid proteins

Capsid protein formula

60 × T proteins

Example of T-number

Hepatitis B virus has T=4

Example of icosahedral virus

Picornaviridae

Complex symmetry viruses

Neither purely helical nor icosahedral

Example of complex virus

Bacteriophages

Structural features of complex viruses

Icosahedral head and helical tail

Example of complex eukaryotic virus

Poxvirus

Giant viruses

Large DNA viruses infecting amoebae

Examples of giant viruses

Mimivirus, Pandoravirus, Marseillevirus

Unique feature of giant viruses

Comparable in size to bacteria