Viruses make mistakes in genome packing (virion assembly), genome replication, and even in other processes encompassed by the viral cycle.

Still, viruses survive and evolve!

John J. Holland: “I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.”.

Evolutionary Biology of Viruses

What is viral evolution?

The term usually (still) includes the origin (how viruses originated in the first place) and evolution of a virus (variability, mechanisms of evolution, natural history, phylogeography).

Viral origin hypotheses – no fossils available, except in the case of:

“Spanish flu”

ToMV (Tomato mosaic virus, Tobamoviridae)

1. Relics of the precellular (prebiotic, RNA) world

First there were RNAs as enzymes and information molecules (ribozymes)…than those associated with proteins into the first replicable entities - viruses (“virus first” hypothesis); or ribozymes invaded the first cellular life forms and acquired capsids(Picornaviridae, Parvoviridae?)

2. Runaway cell components (no cell control of their replication) –the “escape” or “endogenous” hypothesis

eukaryotic mRNAs

eukaryotic and prokaryotic DNAs–plasmids (F-pilus genes areplasmid genes « phage?)

eukaryotic and prokaryotic DNAs – transposons

eukaryotic DNA – retrotransposons (fungi, plants, invertebrates,vertebrates) « proviral form of a retrovirus; pararetroviruses?

3. Intracellular microorganisms – the “degenerative” ,“retrograde”,Green-Laidlaw hypothesis

independent prokaryotes turned endosymbionts (chloroplasts,mitochondria) and degenerated further to viruses or simpleintracellular parasitic prokaryotes degenerated into completedependents on the host cell (Mimivirus).

The origin of different viruses:

monophyletic (from a single ancestor) or polyphyletic?

HGT in viruses, certain types of hosts are infected in a majority of cases by viruses sharing similar characteristics (genome type, size, shape).

A virus has to replicate (produce progeny like cells do). A viral genome is a particular “bag of genes” that has the ability to replicateitself and be disseminated in nature.

New genome variants arise (genotypes) and some are even more successful than the parental variants in replication and dissemination, but being successful is a relative term…

Virus variability fuels the evolution process but the selection determines which variants are more successful and those to survive over time in the biosphere.

Sequencing of viral genes, genome fragments or full genomes enable better understanding of viral evolution.

Problems?

Viral genome sequencing projects including the most appropriate samples, developing hardware and software for analyses.

Phylogeny (phylogenetic trees for important viral genes or full genomes) is easier nowadays.

Phylogenetic trees (rooted!) suggest the most plausible evolutionary pathway (the time course of changes) and reveal ancestors and descendants.

Analytic tools for finding recombinants are also available.

What is a virus species, in evolutionary terms?

Criteria for differentiating virus species are complex: genomedifferences, capsid protein primary structure, serological andbiological features.

Virus variants – (isolates, mutants) have small genome changescompared to the original isolate (wild type, representative type)sometimes with accompanying “phenotype” changes (biologicalfeatures).

Virus strains – (types or serotypes) bigger genome changes withdifferences in host range, infectivity. Often isolated from differenthost species, patients, areas. The stability of virion is also changed,serological characteristics, sensitivity to chemical agents, drugsdepending on the genes that are changed.

It is not always easy to discern categories.

Virus Quasispecies

The term is not a synonym for heterogenic population structure of anRNA virus (a collection of variants) but includes both relatedness andinterdependency of genotypes within the population, and a certainerror threshold level a quasispecies can sustain before the informationis lost due to the sequence randomization (“melting point”).

Evolution of a new virus species – hypermutated genome (divergentenough) from the original variant able to replicate abundantly andsurvive in time and space.

relative abundance of a variant (n)

genomic variant

Molecular mechanisms of viral evolution:

“microevolution” – small gene, and genome, changes accumulate (substitutions, additions, deletions) over time;

“macroevolution” – sudden and larger genome changes:deletions or duplications of genes or genome fragments (geneblocks),recombination (between evolutionary close or remote viruses, evenwith the host genome – acquisition of host genes),reassortments of the genome fragments (where applicable).

• Mutations of a viral genome

• Induced mutations – physical or chemical agents

Mutagens in vitro – direct chemical modifications of a viral genome (nitrous acid, hydroxylamine, alkylating agents e.g. nitrosoguanidine).

R·NH2 + HNO2®R·OH + N2 + H2O C®U

G®xanthine

xanthylateribose

+ HNO2 ®

OH

(enol) (keto)

®

UCU (Ser) UUU (Phe)HNO2

CCU (Pro) UCU (Ser)HNO2

cytosine

Mutagenic agents in vivo – they affect replicating genomes because

modified bases are incorporated in newly synthesized strands.

Mutations occur in the subsequent rounds of replication.

Base analogues (5-bromouracil) - mismatches;

Intercalating agents (acridine dyes) - insertions, deletions;

UV irradiation – pyrimidine dimers are cut out and the damage repaired but often not correctly.

• Spontaneous mutations

Viruses have different mutation rates:

HIV 10-3-10-4 per incorporated nt; HIV-1 10-2/nt/y*,

106 x faster than mammalian genes ,

genome size 9.7 kb ® 0.9-9.7 mutations/genome copy;

herpesviruses 10-8-10-11;

RNA plant viruses (TMV) – 1 mutated out of 200;

phages – 1 mutant out of 107-109 virions.

*Sharp P. M. (2002) Origins of human virus diversity. Cell 108: 305-312; Cann, 2001; Juretić 2002.

High mutation rates are consequences of:

the genome replicating enzyme (RT, RdRp, DNApol), the replicationrate of the virus.

Mutations can affect genome parts outside the CP gene – the emergence of new TMV strains (naturally and experimentally):

Holmes or “masked” strain (TMV-M) infects tobacco systemically without symptoms (in tobacco and tomato 15 d.p.i. at 35°C), the same CP as the original TMV.

The yellow aucuba strain (TMV-YA) was found in natural infectionof tomato. The green aucuba strain (TMV-GA) was obtained fromYA in Nicotiana silvestris at 35°C. Both have 3 pairs of changedamino acids in comparison with wild type TMV-CP .

The selection pressure (environmental conditions) is important forthe emergence of new virus strains and species.

Large source of new variants is antigenic shift.

In viruses, homologous and non-homologous recombinations are possible, or “pseudo-recombinations” (genome fragment reassorting)- changes in 20-50% of the genome.

“Sudden” genome changes and consequential biological changes (phenotypic) like “jumping” to a new host, development of a new virus species.

1. Poxviridae:Family Subfamily Genus Virus Species

Poxviridae Chordopoxvirinae Avipoxvirus fowlpox

Capripoxvirus sheeppox

Leporipoxvirus myxoma

Molluscipoxvirus Molluscum contagiosum

Orthopoxvirus vaccinia

variola (major, minor)

Parapoxvirus orf,

pseudocowpox (pseudovaccinia)

Suipoxvirus swinepox

Yatapoxvirus Yaba monkey tumorvirus

Tanapox monkey virus

Entomopoxvirinae Entomopoxvirus A Melolontha melolonthaentomopoxvirus

Entomopoxvirus B Amsacta moorei entomopoxvirus

Entomopoxvirus C Chironomus luridus entomopoxvirus

Common features (monophyletic origin): virion shape, structure, related antigens, replication cycle, pathogenesis.Divergence into different species - specific adsorption conditions,replication conditions, not all are virulent in humans, the avenue forvaccine production.

The emergence of new virus species:

https://talk.ictvonline.org/ictv-reports/ictv_9th_report/dsdna-viruses-2011/w/dsdna_viruses/75/poxviridae-figures

2. Tobamoviridae:

TMV – tobacco mosaic, solanaceaeous species are susceptible, virion shape and size, extremely stable, 158 amino acids in CP, high titer in plant homogenate (1-2g/l), non-transmissible by insects.

Other family members:

ToMV (Tomato mosaic virus),

HRV (Holmes ribgrass virus),

CGMMV (Cucumber green mottle mosaic),

ORSV (Odontoglossum ringspot mosaic),

SHMV (Sunn-hemp=crotalaria mosaic virus, Fabaceae);

Differences in the CP exist but still they are serologically related.

3. Orthomyxoviridae – emergence of new subtypes

Influenzavirus A - 18 HA and 11 NA types. All 16 “old HA types” found in water birds (e.g. ducks), novel (17H10N, 18H11N) only in bats, so far...Human pandemic strains:

1930. (1918.) “Spanish flu”, H1N1-20 mil. (maybe 50?) victims

1957. “Asian flu”, H2N2, antigenic shift H1N1 from human and avian virus,

1968. “Hong-Kong flu”, H3N2 (from H2N2 and avian H3)

1961. H5A1 in some South African birds (non-transmissible to humans), …but in 1997, 18 people infected in Asia and 6 died (33% mortality rate at first).

2009-10. H1N1 swine flu (triple reasortant), swine H1N1, human, birdvirus.

NP-gene phylogenetic tree of influenza A (Strauss&Strauss, 2002).

Boxed isolates are reassortants. Color disparity for branches and NH types indicate the amount of reassortment.