exclude: true --- class: top left hide-count background-image: url(img/sarscov2_cdc_blur_crop.png) background-size: cover .move-top20[ .title-text[<span style='font-size:1.0em'>COVID-19</span>] .title-subtext[<span style='font-size:1.0em'>The Promise & Problems of Genomic Epidemiology</span>] ] .callout-url-leftcorner[ .title-nametext[ Brendan J. Kelly, MD, MS Infectious Diseases, Epidemiology & Microbiology University of Pennsylvania 29 November 2022 ] ] .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</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</div></div> <div class="extension-tile gridset-c animated bounceInDown"><div>Omicron<br>Origins</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</div></div> <div class="extension-tile gridset-grey"><div>Omicron<br>Origins</div></div> </div> --- ## Genomic Epidemiology .pad-left[ - __Epidemiology__: - study of the distribution and determinants of health-related outcomes in a specified population - the application of this study to improve health - __Genomic Epidemiology__: - use of pathogen genomic data to determine the distribution and spread of an infectious disease in a specified population - the application of this information to improve health ] .footnote-left[[CDC COVID-19 Genomic Epidemiology Toolkit 1.1](https://www.cdc.gov/amd/pdf/slidesets/toolkitmodule_1.1-508c.pdf)] --- ## 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</div></div> <div class="extension-tile gridset-grey"><div>Omicron<br>Origins</div></div> </div> --- .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;" /> ] --- 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</div></div> <div class="extension-tile gridset-c"><div>Omicron<br>Origins</div></div> </div> --- ## 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)] --- ## 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)] --- 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</div></div> <div class="extension-tile gridset-c animated bounceInDown"><div>Omicron<br>Origins</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> ]