Ecology and Evolutionary Biology

of Viruses
 SOME CONSEQUENCES AND
EFFECTS OF VIRUS INFECTION
• Like other life forms, viruses promote the
propagation of their own kind
• Like other life forms, viruses evolve in
response to selection pressure
• Viruses are major factors in promoting the
evolution of higher organisms
• Viruses help control populations of their hosts,
including humans
 Host properties influence the virus
types found in that host group

• Vertebrates have broad range of viruses

• Plants have mostly small RNA viruses
• Fungi have mostly dsRNA viruses
• Single-celled organisms have mostly
large dsDNA viruses
 • True Fungi Overview of Virus
– RNA – 2.5-28 kb
– DNA – none
– Enveloped ones have no capsid
– Little genome complexity
– Little morphological complexity
– Some divided genomes
• Prokaryote
– RNA – 5-8 kb
– DNA – 10-200 kb
– Few enveloped
– Range of complexity
– Range of morphologies
– Few divided genomes
• Plant
Properties – RNA – 0.3-28 kb
– DNA – 3-10 kb
– Few enveloped
– Little genome complexity
– Little morphological complexity
• Animal – Many divided genomes
– RNA – 5-30 kb
– DNA: 5-350 kb
– Many enveloped
– Range of complexity
– Range of morphologies • Lower eukaryote
– Some divided genomes – RNA – 5-10 kb
– DNA – 180-1200 kb
– Internal envelope
– Range of complexity
– Range of morphologies
– No divided genomes
 Virus transmission
• Animal viruses are transmitted through air,
through wounds, through orifices, or by vectors
• Most plant viruses are transmitted by vectors,
especially homopterous insects
• Most fungal viruses are transmitted horizontally
only by hyphal fusion
• Bacterial viruses are transmitted by attachment of
free virus to bacterial cell walls or pili; injection of
nucleic acid
• How do these transmission modes affect their
ecology and evolutionary biology?
 Virus Evolution
• Viruses origins are unknown
• Theories of virus origin:
– Regressive evolution: viruses degenerated from previously
independent life forms, lost many functions required by
cellular organisms
– Cellular origins: viruses assembled from cellular
components into independent entities capable of moving
cell-to-cell and, later, gaining ability capacity for
transmission
– Independent entities: viruses evolved independently and in
parallel with complex organisms from self-replicating
molecules in the primordial RNA world
• These theories are not mutually exclusive – different
virus lineages may have different origins
 Virus evolution
• Virus evolution is contemporary and observable
• Large numbers of progeny contribute to potential
high rate of evolution of viruses
• Mutation rate is higher for RNA than for DNA
• Evolution rate does not necessarily reflect mutation
rate
• Mutation rate for a particular virus may be different
in different tissues
• Different parts of viral genomes evolve at different
rates
• Ability to generate large amounts of sequence data
has greatly enhanced ability to study evolution
Sequence variation during virus replication
• Intrinsic error rates of polymerases are difficult to
quantify
• DNA polymerase has proof-reading capability;
intrinsic error rate is low, usually ~ 10 -6 to 10-5
• RNA polymerase has no proof-reading capability;
intrinsic error rate is high, usually ~ 10 -4 to 10-3
• Error rates may be different in different genome
regions, e.g., “hotspots”
• Homologous or non-homologous recombination
may occur in RNA or DNA viruses
• Change of templates is referred to as copy choice
 Means of RNA virus evolution
• Minor replication error (substitution, single
base change) – no error correction by RdRp
• Major replication error (deletion)
• Intragenomic gene duplication
• Intergenomic recombination
– gene duplication
– acquisition of additional genes
– coding sequence or noncoding sequence
substitution
• Virus evolution may be accelerated by co-
infection
 Positive-strand RNA virus evolution
• Positive-strand RNA viruses evolve rapidly; only
important functional domains are conserved
• RNA viruses are made up of a limited number of
building blocks; only RdRp is required and is the
ultimate basis of rational phylogenies
• Evolution of RNA viruses involves conservation of
required genes and recombination/shuffling of gene
blocks
• Widespread recombination of a relatively small
number of genes makes it impossible to generate
single phylogenetic trees (reticulate evolution)
• Basic RNA virus replication machinery likely evolved
more than once
Positive-strand RNA virus evolution

A. Organization of conserved replication-associated genes of major

groups of positive-sense RNA viruses; B. Phylogenetic reconstruction
of selected alphaviruses based on RdRp gene.
From your text: Flint et al., 2004
Viruses closely related to RNA bacteriophages (Leviviridae)

Virus Location Host Capsid?

OMV4 (2.6 kb) Mito Fungus No
*
CMV1/NB631 (2.7 kb) * Mito Fungus No

SNV/23S (2.9 kb) * Cyto Yeast No

Qβ (3.6 kb) (Cyto) Bacterium Yes

*

TBSV (4.8 kb) * Cyto Plant Yes

PEMV (4.2 kb) * Cyto Plant No

DRV (4.1 kb) * Cyto Fungus No

= stop codon position

* = core RNA-dependent RNA polymerase domain
= capsid protein gene
Genome organizations of negative-sense RNA viruses, and homologies among genes

From text: Flint et al., 2004

 Mechanisms of recombination
of viral RNAs
Left: Generalized viral RNA recombination.

Bottom: Three classes of intergenomic RNA

recombination: 1) Requiring substantial base
pairing but no identifiable RNA secondary
structures or regulatory elements; 2) Occurring
in association with identifiable RNA ,structures
or regulatory elements, but not requiring
substantial base pairing; 3) A combination of 1
and 2.

From your text: Flint et al., 2004

 Variation among viral sequences
• The term “quasi species” is used predominately for RNA
viruses
• Because of absence of proofreading, many variants are
found in an RNA virus population; the “quasi-species
cloud” is the mutant spectrum derived from the
dominant master copy
• A genetic bottleneck occurs when a virus population is
constrained, resulting in loss of diversity – can be
because of:
– vector constraints
– host defense constraints
• A small founder population coming through a genetic
bottleneck may give rise to a skewed population
Viral quasispecies, population size, bottlenecks, and fitness

From your text: Flint et al., 2004

 Intrinsic mutation rates among RNA viruses vary

In the absence of selection,

spontaneous mutation rates of
different viral RNA polymerases
are high, and vary by ~10 fold.

From Drake & Holland, 1999, PNAS 96:13909