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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Pathogen diversity</title>
<meta name="author" content="Trevor Bedford">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
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<body>
<div style="position: absolute; top:10px; left:10px; z-index:100;">
<a href="/sismid/pathogens/">
<i class="fa fa-times-circle" style="color: #bbb; opacity: 0.1;"></i>
</a>
</div>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section data-background="#5BA6A7">
<h1 class="title">Pathogen diversity</h1>
</section>
<section>
<h3>A pathogen is a disease-causing biological entity capable of replication within a host and transmission between hosts</h3>
</section>
<section>
<h3>Broad categories</h3>
<p>
<ol>
<li>RNA viruses</li>
<li>DNA viruses</li>
<li>Bacteria</li>
<li>Parasites and fungi</li>
</ol>
</section>
<section>
<h3>Mutation rate varies with genome size</h3>
<img class="stretch" src="images/mutation_rate_genome_size.jpg">
</section>
<section>
<h3>Viroids are parasitic functionless RNA</h3>
<img class="stretch" src="images/viroid.jpg">
</section>
<section>
<h3>Baltimore classification system describes virus groups</h3>
<img class="stretch" src="images/baltimore_classification.png">
</section>
<section>
<h3>RNA virus lifecycle, internal vs surface proteins</h3>
<img class="stretch" src="images/measles_lifecycle.png">
<div class="citation">
<a href="http://femsre.oxfordjournals.org/content/36/3/649">
Griffin et al. 2012
</a>
</div>
</section>
<section>
<img class="stretch" src="images/positive_sense_vs_negative_sense.png">
<div class="citation">
<a href="https://dx.doi.org/10.1128%2FMMBR.00059-12">
Li et al. 2013
</a>
</div>
</section>
<section>
<h3>Negative-sense RNA virus phylogeny</h3>
<img class="stretch" src="images/ns_rna_virus_tree.png">
<div class="citation">
<a href="https://elifesciences.org/content/4/e05378">
Li et al. 2015
</a>
</div>
</section>
<section>
<h3>Negative-sense RNA virus phylogeny</h3>
<img class="stretch" src="images/ns_rna_virus_tree_2.jpg">
<div class="citation">
<a href="http://www.nature.com/nature/journal/v468/n7325/full/468773a.html">
Rey 2010
</a>
</div>
</section>
<section style="text-align: left;">
<h3>Negative-sense RNA viruses</h3>
<p>
<ul>
<li>Influenza</li>
<li>Measles</li>
<li>Ebola</li>
<li>Rabies</li>
<li>Lassa</li>
<li>Hanta</li>
<li>Respiratory syncytial virus (RSV)</li>
</ul>
</section>
<section style="text-align: left;">
<h3>Positive-sense RNA viruses</h3>
<p>
<ul>
<li>Flaviviruses: Yellow fever, West Nile, Dengue, Zika, HCV</li>
<li>Coronaviruses, including SARS-CoV-2</li>
<li>Rhinovirus</li>
<li>Polio</li>
<li>Norovirus</li>
<li>Chikungunya</li>
</ul>
</section>
<section>
<h3>Retrovirus lifecycle</h3>
<img class="stretch" src="images/hiv_lifecycle.jpg">
<div class="citation">
<a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(14)60164-1/">
Maartens et al. 2014
</a>
</div>
</section>
<section>
<h3>DNA virus genomes</h3>
<img class="stretch" src="images/herpes_genome.png">
<div class="citation">
<a href="http://szparalab.psu.edu/hsv-diversity/">
Szpara et al. 2013
</a>
</div>
</section>
<section>
<h3>Bigger genome allows for more functions</h3>
<img class="stretch" src="images/herpes_immune_modulation.jpg">
<div class="citation">
<a href="http://journal.frontiersin.org/article/10.3389/fmicb.2012.00044/full">
Lee et al. 2012
</a>
</div>
</section>
<section style="text-align: left;">
<h3>DNA viruses</h3>
<p>
<ul>
<li>Herpesviruses: HSV, Epstein–Barr virus (EBV), Varicella, Cytomegalovirus (CMV), Kaposi's sarcoma-associated herpesvirus (KSHV)</li>
<li>Papillomavirus (HPV)</li>
<li>Smallpox, monkeypox</li>
</ul>
</section>
<section>
<h3>Bacterial cell</h3>
<img class="stretch" src="images/bacterial_cell.jpg">
</section>
<section>
<h3>Bacterial diversity</h3>
<img class="stretch" src="images/bacterial_phylogeny.png">
<div class="citation">
<a href="https://www.nature.com/articles/nmicrobiol201648">
Hug et al. 2016
</a>
</div>
</section>
<section>
<h3>Core vs pangenome</h3>
<img class="stretch" src="images/pangenome.png">
<div class="citation">
<a href="https://www.nature.com/articles/nmicrobiol201740">
McInerney et al. 2017
</a>
</div>
</section>
<section>
<h3>Divergent evolutionary histories between core chromosome and plasmids</h3>
<img class="stretch" src="images/plasmid_trees.png">
<div class="citation">
<a href="https://www.biorxiv.org/content/10.1101/2022.10.27.514108v2">
Müller et al. 2023
</a>
</div>
</section>
<section>
<h3>Recombination is often rampant</h3>
<img class="stretch" src="images/bacterial_recombination.png">
<div class="citation">
<a href="https://elifesciences.org/articles/65366">
Sakoparnig et al. 2021
</a>
</div>
</section>
<section style="text-align: left;">
<h3>Bacterial pathogens</h3>
<p>
<ul>
<li>C. difficile</li>
<li>Cholera</li>
<li>Klebsiella</li>
<li>Neisseria gonorrhoeae</li>
<li>S. aureus (MRSA)</li>
<li>Shigella</li>
<li>Streptococcus pneumoniae</li>
<li>Tuberculosis</li>
<li>Typhoid</li>
<li>Y. pestis</li>
</ul>
</section>
<section>
<h3>Parasites</h3>
<img class="stretch" src="images/cryptosporidium_lifecycle.png">
</section>
<section style="text-align: left;">
<h3>Parasite lifecycle</h3>
<p>
<ul>
<li>Malaria</li>
<li>Cryptosporidium</li>
<li>Trypanosomes</li>
<li>Giardia</li>
<li>Leishmaniasis</li>
</ul>
</section>
<section data-background="#4988C5">
<h1 class="title">Influenza</h1>
<p class="title">Prototypical antigenically evolving pathogen</p>
</section>
<section>
<h3>Influenza virion</h3>
<img class="stretch" src="images/virion.jpg">
</section>
<section>
<h3>Influenza life cycle</h3>
<img class="stretch" src="images/lifecycle.jpg">
</section>
<section data-background="images/sneeze.jpg">
</section>
<section>
<h3>1918 "Spanish flu"</h3>
<img class="stretch" src="images/1918_cases.png">
<div class="citation">
<a href="http://jid.oxfordjournals.org/content/202/4/567.abstract">
Chowell et al. 2010
</a>
</div>
</section>
<section data-background="images/1918_beds.png">
</section>
<section>
<h4>Flu pandemics caused by host switch events</h4>
<img class="stretch" src="images/pandemics.png">
</section>
<section>
<h4>Host switch events often occur through reassortment</h4>
<img class="stretch" src="images/reassortment.png">
</section>
<section>
<h4>Host switch events often occur through reassortment</h4>
<img class="stretch" src="images/reassortment_swine.png">
<div class="citation">
<a href="http://jid.oxfordjournals.org/content/202/4/567.abstract">
Neumann et al. 2009
</a>
</div>
</section>
<section>
<h4>Reassortment creates different histories</h4>
<img class="stretch" src="images/pandemics_na.png">
</section>
<section>
<h4>Influenza B does not have pandemic potential</h4>
<img class="stretch" src="images/pandemics_b.png">
</section>
<section>
<h4>Phylogenetic trees of different influenza lineages</h4>
<img class="stretch" src="images/flu_trees.png">
</section>
<section data-background="#CBB742">
<h1 class="title">SARS-CoV-2</h1>
</section>
<section>
<h3>Genetic relationships of globally sampled SARS-CoV-2 to present</h3>
<img class="stretch" src="images/ncov_variants_tree_unrooted.png">
<div class="citation">
<a href="https://nextstrain.org/ncov/gisaid/global/all-time?l=unrooted">nextstrain.org</a>
</div>
</section>
<section>
<h3>New variants rapidly replace existing diversity</h3>
<img class="stretch" src="images/ncov_tree_freq.png">
<div class="citation">
<a href="https://nextstrain.org/ncov/gisaid/global/all-time">nextstrain.org</a>
</div>
</section>
<section>
<h3>S1 evolution remarkably fast relative to seasonal influenza</h3>
<img class="stretch" src="images/adaptive_evolution_rates_comparison.png">
<div class="citation">
<a href="https://bedford.io/papers/kistler-atlas-viral-evolution/">Kistler and Bedford. 2023</a>
</div>
</section>
</div>
</div>
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