---
title: "Viral diversity"
author: "Duncan Golicher"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
  slidy_presentation: default
  ioslides_presentation: default
  beamer_presentation: default
link-citations: yes
bibliography:
- mendeley_7_4_2021.bib
- epidemics.bib
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE,message = FALSE)
library(mapview)
load("rmap.rda")
```

# What is known about viruses?

- Example textbook. Field's virology 
- Well over 2000 pages per volume (2 volumes)
- Each chapter apologises for what is **not** included
- Uncertainties, known unknowns, unknown unknowns: but very few known knowns
- Most chapters focus on pathology and molecular biology
- **Ecology** of viruses remains poorly understood

# Web of science

- The pandemic has brought viruses into the news
- However there is a shortage of literature on the **ecology** of viruses
- Search terms "virus" + "ecology"
- Search term "coronavirus"

![](figs/wos1.png) ![](figs/wos2.png)


# Quick history

- Viruses not recognised until 1880s
- Adolf Meyer working on tobacco at Wageningen identified TMV
- Clearly an infectious agent, but could not fulfill Koch's postulates as only cultivable in living cells: 
- The issue with Koch's postulate continues to muddy some debates to this day
- Beijerinck named the agent a "contagium vivum luidum"" or a contagious living liquid. 
- d’Herelle developed the plaque assay in 1917 
- First electron micrographs were taken of tobacco mosaic virus (TMV) in 1939.

# Tobacco mosaic virus

- Remains a key experimental organism 
- Plant viruses are possibly more diverse than higher animal viruses (more species of plant)
- Plant viruses have a different set of challenges (movement through an organism with cell walls)
- Plant viruses are not thought to infect animals directly (possible exceptions)

![](figs/tmv.png)

# Bacteriophages 

- Lytic (pathogneic) and lysogenic (non pathogenic) infections identified in 1900s
- Experiments with viruses resulted in the discovery of mRNA and the role of DNA
- First complete nucleotide sequence of an RNA virus genome was the bacteriophage MS2 (1976)
- Most abundant "organisms" on the planet
- Present at roughly $10^7/mL$  in coastal seawater 
- Around $10^{31}$ individual tailed phage virions on the planet
- If all the tailed phages were laid end to end, they would extend for 200 million light years into intergalactic space.

# Phage seen through electron microspope

![](figs/phage1.png)

# Insect viruses

- Abundant, ubiquitous and highly diverse
- Mammalian and avian viruses may have evolved in insects
- Insects are also vectors for both animal and plant viruses
- Can play a role in very complex life histories
- Some extremely complex symbiotic relationships

# Parasitic wasps use viruses as "venom"

![](figs/wasp.png)

# Mammalian viruses

- Experiments on viruses of animals used immortalised human cell lines and monkey kidney cells
- Polio virus was an early focal virus
- Virology allowed key insights into oncology and cancer
- Cellular receptors began to be identified and studied in depth
- Attention mainly on pathogenic viruses of humans (and some of rodents and domestic animals)
- Full diversity of mammalian viruses remains unknown

![](figs/oncology.png)

# Viral evolution

- Fundamental aspects of viral evolution remains unknown, contentious, or both
- Precise estimates of mutation rates unknown
- Deep origins of viruses still uncertain 
- Did viruses predate cellular organisms?
- "Escaped gene theory" vs "RNA first" theory
- Did the earliest replicators resemble what we now know as viruses?
- Should viruses even be classified as life?

# Evolution and phylogeny

- Viruses generally evolve at high rates, following basic and extended Darwinian principles 
- Evolutionary time frame much shorter than that of any other organism. 
- Species concept cannot be uncontentiously applied.
- True antiquity of currently circulating viruses still vague. 
- No fossil record

# Baltimore classification

Highest level of classification of viruses

- Split into 7 groups based on type of genetic material
- DNA viruses (single and double stranded)
- RNA viruses (double stranded, single stranded positive and negative sense )
- Reverse transcribing viruses

# Number of viral species

- Perhaps over one million viruses of vertebrates
- ~20 different viruses in each of the 50,000 vertebrates 
- "Minimum of 320,000 mammalian viruses awaiting discovery" [@Anthony2013]
 

# Species concept as applied to viruses

- Importance of species in biology derives from their importance in systematics
- Prior to the 1980s the notion of viral "species" was rejected by most of the scientific community 
- Clearly could not apply Ernst Mayr's definition(*"species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups"*)
- Concepts of species, strains, variants and viral isolates caused confusion [@Alimpiev2019]
- 1982 International Committee on Taxonomy of Viruses(ICTV): species = "a cluster of strains from a variety of sources, or a population of strains from a particular source, which **have in common a set of stable properties** that separate **the cluster** from other **clusters of strains.**"

# Modified definitions

- Van Regenmortel: "a polythetic class of viruses (*strains*) that constitute a replicating lineage and occupy a particular ecological niche"
- Polythetic is defined as "characteristics which occur commonly in members of a group or class, **none of which is essential** for membership of that group or class."
- 2012 ICTV viral species definition based on shared ancestry. "A monophyletic **group of viruses (strains)** whose properties can be distinguished from those of other species by multiple criteria"
- Can be used to define any virus **taxon**. (I.e. not just a species)
- Current definition essentially defines virus species (clades) based **only on their genomic sequence**
- However genetic sequences are a continuum, with no naturally defined breaks

# Time since divergence

Knowing time since divergence key to understanding viral evolution and viral "novelty".

- Three approaches

 1. Find a good match between the phylogenetic tree of viruses and that of their hosts. Assume co-divergence (not usually possible as few viruses are narrowly host specific .. can work for DNA viruses .. not generally RNA) 
2. Find endogenous genome copies within the host: Use the substitution rate of the host (similar to 1)
3. **Measure current evolution (i.e mutations fixed during time frame of human observation)**


# RNA viruses

- Particularly difficult to produce phylogenies
- Rarely strictly host specific
- Very fast rates of mutation
- Many RNA virus populations thought to exist as **quasispecies**
- Swarms of individual viral genomes where every member is unique. 

 
# Molecular clock

- Rate of evolution has been estimated for polio (short RNA ~7500 base pairs)
- Estimated that there is one synonymous substitution per 100 base pairs per year [@Jorba2008]
- Non-synonymous substitutions constrained by purifying selection
- However, these measurements were on a population with low prevalence 
- Hard to generalise, as rate of evolution depends on number of infections

 

# Evolution involves the host

- Experimental approaches using in vitro and in vivo **laboratory models**  focus on short-term **intrahost evolutionary mechanisms** 
- These may not always be relevant to natural systems.
- Should consider data collected over multiple cycles of virus–host transmission. [@Geoghegan2018]
- Evolution can take place at different rates and follow different lines in different host populations

# @Geoghegan2018

![](figs/evol.png)



# Quasispecies evolution

- Mutation–selection balance in which a distribution of variant viral genomes is ordered around the fittest, or “master,” sequence. 
- Mutation rates in RNA viruses are so high that the frequency of any variant is not only a function of its own replication rate (fitness), but also of the mutation of other variants in the population derived from the original sequences
- “Mutational coupling” leads to a distribution of evolutionarily interlinked viral genomes
- Entire mutant distribution behaves as a single unit
- Natural selection acts on the mutant distribution as a whole, rather than on individual variants.
- The "quasispecies"" as a whole evolves to maximize its average fitness. 
- Has been applied to SARS-Cov-1 [@Xu2004] and SARS-CoV-2 [@Jary2020]

# Quasispecies evolution

![](figs/evol2.png)

# Recombination

- Many, many examples of hybridisation in plants
- Some examples in well known animals (e.g edible frogs)
- Can be very difficult to establish as hybrids unless the sequences of all species involved are known.
- The equivalent of Tigons, Ligers and edible frogs also exist in the world of viruses: 
- Known as **Recombinants**
- The result of simultaneous infection with different viral sequences



# "Hybrid viruses": Influenza

- Influenza A, B, C and D are genera
- Enveloped negative sense single strand RNA viruses with a segmented genome
- Cell entry through glycoproteins: haemagglutinin (HA) and neuraminidase (NA)
- 16 antigenically different HA and 9 antigenically different NA serotypes
- Interchange, of genomic RNA segments occurs when two viruses of the same type infect the same cell.

# Recombination is SIV (simian IV) and Ebola

- SIVcpz represents a complex mosaic, generated by **recombination** of two lineages of SIVs that infect monkeys [@Sharp2011]
- Multiple ebola recombinants in simians [@Wittmann2007]

![](figs/siv.png)

# Coronavirus subgenomic RNA

- Coronavirus viral RNA synthesis involves the transcription of multiple sub-genomic RNAs 
- Potential for recombination unclear, but highly likely

![](figs/subgenomic.png)


# Putative phylogeny of SARS-CoV-2 clades

- Divergence based on assumptions regarding conserved characteristics of the sequence.
- Dates rely on assumed molecular clock
- Most sequences have gone extinct
- Extant (still circulating) sequences appear to have reduced virulence

# Putative phylogeny of SARS-CoV-2 clades

![](figs/next_strain.png)




# References
