exclude: true --- class: top left hide-count background-image: url(img/sarscov2_cdc_blur_crop.png) background-size: cover .move-top10[ .title-text[<span style='font-size:0.6em'>Molecular & Genomic<br> Epidemiology<br> of Infectious Diseases</span>] <hr> .title-subtext[<span style='font-size:1.0em'>Lessons and Directions<br>After COVID-19</span>] ] .callout-url-leftcorner[ .title-nametext[ Brendan J. Kelly, MD, MS Infectious Diseases, Epidemiology & Microbiology University of Pennsylvania 14 November 2023 <!-- 14 November 2023 --> ] ] .footnote-right[<span style='color: white'>photo: CDC @unsplash</span>] --- ## Disclosures .pad-left[ - No conflicts of interest. - Research supported by: - NIAID K23 AI121485 - CDC BAA 200-2021-10986 ] --- class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-a animated flipInY"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> </div> --- layout: false class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-a"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-b animated flipInX"><div>Biases<br>Limitations<br>& Unknowns</div></div> </div> --- layout: false class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-a"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-b"><div>Biases<br>Limitations<br>& Unknowns</div></div> <div class="extension-tile gridset-c animated bounceInDown"><div>COVID-19<br>Aftermath</div></div> </div> --- layout: false class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-a"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-grey"><div>Biases<br>Limitations<br>& Unknowns</div></div> <div class="extension-tile gridset-grey"><div>COVID-19<br>Aftermath</div></div> </div> --- ## Genomic Epidemiology .pad-left[ - __Epidemiology__: - study of the distribution and determinants of health-related outcomes in a specified population - __Molecular Epidemiology__: - joins understanding of disease at the molecular level with population-based study designs and approaches; links epidemiology with laboratory sciences - __Genomic Epidemiology__: - use of pathogen genomic data to determine the distribution and spread of an infectious disease in a specified population ] .footnote-left[[CDC COVID-19 Genomic Epidemiology Toolkit 1.1](https://www.cdc.gov/amd/pdf/slidesets/toolkitmodule_1.1-508c.pdf); Lash TL et al _Modern Epidemiology (4th ed)_] --- ## SARS-CoV-2 Genomic Epidemiology .pad-left[ - __SARS-CoV-2 Genomes__: - SARS-CoV-2 genome: ~ 30,000 nucleotides (~ 10,000 amino acids) - infer relatedness from phylogenetic distance - __RNA Genome Sequencing__: - extract RNA, reverse transcription, multiplex PCR, end repair & ligation indexing - short-read or long-read sequencing ] .footnote-left[[CDC COVID-19 Genomic Epidemiology Toolkit 1.1](https://www.cdc.gov/amd/pdf/slidesets/toolkitmodule_1.1-508c.pdf)] --- ## National & Local Applications .pad-left[ - **National**: - monitor emergence and movement of new strains - monitor trends after intervention (e.g., vaccination) - **Local**: - investigate clusters for transmission (workplace, healthcare, etc) - reveal unexpected clusters ] .footnote-left[[CDC COVID-19 Genomic Epidemiology Toolkit 1.1](https://www.cdc.gov/amd/pdf/slidesets/toolkitmodule_1.1-508c.pdf); [Washington Post](https://www.washingtonpost.com/graphics/2020/health/coronavirus-genetic-code/)] --- exclude: false ## International Collaboration .center[ <iframe src="https://gisaid.org/" width="95%" height="400px" data-external="1"></iframe> ] .footnote-left[https://gisaid.org/] --- exclude: false ## International Collaboration .center[ <img src="figs/nextstrain_ncov_screenshot.png" width="60%" style="display: block; margin: auto;" /> ] .footnote-left[https://nextstrain.org/ncov/open/global/all-time] --- ## Variants of Concern .center[ <iframe src="https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html" width="95%" height="400px" data-external="1"></iframe> ] .footnote-left[https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html] --- exclude: false ## Local Tracking .center[ <iframe src="https://microb120.med.upenn.edu/data/SARS-CoV-2" width="95%" height="400px" data-external="1"></iframe> ] .footnote-left[https://microb120.med.upenn.edu/data/SARS-CoV-2] --- layout: false class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-grey"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-b"><div>Biases<br>Limitations<br>& Unknowns</div></div> <div class="extension-tile gridset-grey"><div>COVID-19<br>Aftermath</div></div> </div> --- ## Biases: SARS-CoV-2 "Viral Load" .pad-left[ - The number of virions detectable in respiratory secretions varies between individuals and over the course of infection: - high viral loads are required for most sequencing-preparation pipelines - coverage/quality may be poor if viral loads are low - What are the consequences of excluding low-viral-load samples from genomic epidemiology surveillance? ] --- .center[ <img src="./figs//p_ct_distribution_ridgeplot_flip.png" width="80%" style="display: block; margin: auto;" /> ] --- .center[ <img src="./figs/p_ct_distribution_ridgeplot_with_seqbar_flip.png" width="80%" style="display: block; margin: auto;" /> ] --- ## Limitations: SARS-CoV-2 vs Population Immunity .pad-left[ - Molecular evolution occurs in the context of increasingly complex and heterogeneous population immunity: - waves of SARS-CoV-2 variants with different immune epitopes - the introduction of vaccines - How best to measure SARS-CoV-2 molecular evolution in this context? (e.g., how best to perform "antigenic cartography"?) ] .footnote-left[Mykytyn AZ et al _Science Immunology_ 2022] --- ## SARS-CoV-2 Molecular Evolution .pad-left[ - How do we measure SARS-CoV-2 genome change? - daily, weekly, monthly? - nucleotide, dN/dS, AA, gene? - how to pool within codons, genes? - covariance across genome? - How does genomic change relate to changes in incidence? ] --- ## Genomic Positional Diversity .pad-left[ - Shannon diversity: `$$H' = - \sum{ p_{i} * \log_{b}{(p_{i})} }$$` <center>(note: typically natural log or base 2 are used)</center> - richness: how many nucleotide variants are there? - evenness: how are variants distributed? ] --- ## Aside on Information Theory .pad-left[ - Shannon diversity: `$$H' = - \sum{ p_{i} * \log_{b}{(p_{i})} }$$` - Claude Shannon & information entropy: `$$H(p) = - \sum{ p_{i} * \log_{b}{(p_{i})} }$$` - **"The uncertainty contained in a probability distribution is the average log-probability of an event."** ] .footnote[McElreath _Statistical Rethinking, 2nd_ 2020] --- exclude: true background-image: url(figs/scv2_snv_diversity_per_position_and_time_clear.gif) background-size: contain --- exclude: true background-image: url(figs/scv2_snv_diversity_per_position_and_time_shadow.gif) background-size: contain --- <img src="figs/scv2_snv_diversity_per_position_and_time_clear_color.gif" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/scv2_snv_diversity_per_position_and_time_shadow_color.gif" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/scv2_peptide_diversity_per_position_and_time_clear.gif" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/scv2_peptide_diversity_per_position_and_time_shadow.gif" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/p_phl_cases.png" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/p_lm_logdiff_peptide_color.png" width="100%" style="display: block; margin: auto;" /> --- <img src="figs/p_lm_logdiff_peptide_color_tag.png" width="100%" style="display: block; margin: auto;" /> --- exclude: false ## The Canyon Hypothesis .pad-left[ - SARS-CoV-2 molecular evolution & the "Canyon Hypothesis": - highly conserved cell entry mechanism mediated by the spike protein (S gene) - spike engages angiotensin converting enzyme 2 (ACE2) & host proteases enable efficient membrane fusion between virions and target cells - a model by which sarbecoviruses are activated for fusion competency and interplay between humoral immunity and the molecular evolution ] .footnote[Wolf et al *mBio* 2022; Rossman et al *J Biol Chem* 1989] --- exclude: false ## The Canyon Hypothesis .pad-left[ - during circulation in populations with high rates of humoral immunity, viral entry proteins favor predominantly closed RBD configurations - immediately after spillover into a population that lacks immunity, the newly emergent virus remains closely related to its ancestor - during sustained transmission between seronegative individuals, wide transmission bottlenecks facilitate rapid emergence of variants that favor open RBD configurations to spread rapidly - as humoral immunity expands, it gradually leads to a return to closed RBDs as repeat exposures facilitate the affinity maturation of expansive antibody repertoires that are disproportionately costly to open RBD configurations ] .footnote[Wolf et al *mBio* 2022; Rossman et al *J Biol Chem* 1989] --- ## The Canyon Hypothesis .center[ <img src="./figs/canyon_hypothesis_rbd_open_closed.png" width="80%" style="display: block; margin: auto;" /> ] .footnote[Wolf et al *mBio* 2022; Rossman et al *J Biol Chem* 1989] --- exclude: false ## The Canyon Hypothesis .pad-left[ - most changes in S prior to the emergence of the Omicron variant appear to have been driven by selection for improved transmission between immunologically naive hosts - S:D614G spike mutation improved ACE2 affinity but also made RBDs were more likely to hold the open conformation - cryo-EM studies of the Omicron S protein suggest that while the Delta Spike predominantly occupies conformations with 1 or more RBDs open simultaneously, the Omicron Spike appears to prefer conformations with 0 or 1 open RBD - antigenicity of stabilizing elements & tendency of primary immune responses to generate a limited repertoire of antibodies may explain the selection for open RBDs early in the pandemic & shift in the selective landscape that led to the Omicron variant’s emergence and rapid sweep ] .footnote[Wolf et al *mBio* 2022; Rossman et al *J Biol Chem* 1989] --- exclude: true .center[ <img src="./figs//p_ct_distribution_ridgeplot_flip.png" width="80%" style="display: block; margin: auto;" /> ] --- exclude: true .center[ <img src="./figs/p_ct_distribution_ridgeplot_with_seqbar_flip.png" width="80%" style="display: block; margin: auto;" /> ] --- .center[ <img src="./figs/alpha_delta_omicron_ct_comparison.png" width="80%" style="display: block; margin: auto;" /> ] --- ## Unknowns: Where did 'weird' Omicron come from? .center[ <img src="./figs/new_long_branch_screenshot.png" width="80%" style="display: block; margin: auto;" /> ] .footnote-left[[Kupferschmidt K *Science* 1 Dec 2021](https://www.science.org/content/article/where-did-weird-omicron-come)] --- ## Unknowns: Where did 'weird' Omicron come from? .center[ <img src="./figs/three_explanations_screenshot.png" width="80%" style="display: block; margin: auto;" /> ] .footnote-left[[Kupferschmidt K *Science* 1 Dec 2021](https://www.science.org/content/article/where-did-weird-omicron-come)] --- ## Pennsylvania Deer .center[ <img src="./figs/mbio.02101-22-f005.gif" width="80%" style="display: block; margin: auto;" /> ] .footnote-left[[Marques AD et al *mBio* 2022](http://dx.doi.org/10.1128/mbio.02101-22)] --- layout: false class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-grey"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-grey"><div>Biases<br>Limitations<br>& Unknowns</div></div> <div class="extension-tile gridset-c"><div>COVID-19<br>Aftermath</div></div> </div> --- ## Lessons & Directions After COVID-19 .pad-left[ - What has come of this unprecedented investment in molecular/genomic epidemiology? - unprecedented pathogen sequencing capacity - novel methods of population surveillance: wastewater surveillance - political animus against CDC & resulting budget cuts ] --- ## Ongoing SARS-CoV-2 Variant Tracking .center[ <iframe src="https://covid.cdc.gov/covid-data-tracker/#variant-proportions" width="95%" height="400px" data-external="1"></iframe> ] .footnote[[https://covid.cdc.gov/covid-data-tracker/#variant-proportions](https://covid.cdc.gov/covid-data-tracker/#variant-proportions)] --- ## Wastewater SARS-CoV-2 Surveillance .center[ <iframe src="https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance" width="95%" height="400px" data-external="1"></iframe> ] .footnote[[https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance](https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance)] --- ## Centers for Pathogen Genomics .center[ <iframe src="https://www.cdc.gov/media/releases/2022/p0920-PGCoE-network.html" width="95%" height="400px" data-external="1"></iframe> ] .footnote[[https://www.cdc.gov/media/releases/2022/p0920-PGCoE-network.html](https://www.cdc.gov/media/releases/2022/p0920-PGCoE-network.html)] --- ## NWSS: National Wastewater Surveillance System .center[ <iframe src="https://www.cdc.gov/nwss/index.html" width="95%" height="400px" data-external="1"></iframe> ] .footnote[[https://www.cdc.gov/nwss/index.html](https://www.cdc.gov/nwss/index.html)] --- ## CDC Budget Cuts .pad-left[ - CDC and NIH have become political targets: - $1.3 billion (~18%) cut from CDC as part of debt ceiling agreement - some budget proposals for FY2024 include a total $11.5 billion ($2.8 billion increase from FY2023) - other budget proposals for FY2024 include additional 20-30% cuts ] --- ## Lessons & Directions After COVID-19 .pad-left[ - What has come of this unprecedented investment in molecular/genomic epidemiology? - unprecedented pathogen sequencing capacity - novel methods of population surveillance: wastewater surveillance - political animus against CDC & resulting budget cuts - **Will re-investment come before or after the next pandemic?** ] --- exclude: true ## Acknowledgements .pull-left[ - __ARES Group @ Penn__ Laurel Glaser, Kyle Rodino, Sean Loughrey, Laura Cowden, Magda Wernovsky, Jessie Gunoskey, Jennifer Han, Erik Clarke, Michael David, Matt Ziegler, Lauren Dutcher, Ebbing Lautenbach, Jim Harrigan - __Bushman Laboratory @ Penn__ Arwa Abbas, Aoife Roche, Andrew Marques, Aubrey Bailey, John Everett, Rick Bushman - __PennCHOP Microbiome Program__ Lisa Mattei, Casey Hofstaedter, Huanjia Zhang, Kyle Bittinger ] .pull-right[ - __Collman Laboratory @ Penn__ Ize Imai, Aurea Simon Soro, John McGinniss, Ron Collman - __Division of ID @ Penn__ Ian Frank, Pablo Tebas, Robert Gross, Emily Blumberg - __Rutgers University & Penn DBEI__ Jason Roy, Arman Oganisian - __CDC Prevention Epicenters__ Clifford McDonald, Alison Laufer Halpin - __Funding__ <u>CDC</u>: BAAs 200-2016-91964, 200-2018-02919, 200-2021-10986, 200-2021-10986 & <u>NIAID</u>: K23 AI121485 ] .center[ ### brendank@pennmedicine.upenn.edu ] --- class: full-screen hide-count <div class="grid-3-1"> <div class="extension-tile gridset-a animated flipInY"><div>COVID-19<br>Genomic<br>Epidemiology</div></div> <div class="extension-tile gridset-b animated flipInX"><div>Biases<br>Limitations<br>& Unknowns</div></div> <div class="extension-tile gridset-c animated bounceInDown"><div>COVID-19<br>Aftermath</div></div> </div> --- class: middle center hide-count background-image: url(img/sarscov2_cdc_blur_crop.png) background-size: cover .title-subtext[Questions?] --- exclude: true class: middle center hide-count background-image: url(img/sarscov2_cdc_blur_crop.png) background-size: cover .title-subtext[Questions?] .callout-url-bottom[ .fade-in[<span style="font-size:0.5em; color:white">slides ↓ </span>] <span style="link-color:white">[bjklab.org](http://www.bjklab.org)</span> ]