An integrated genomic surveillance platform reveals multiple introductions of SARS-CoV-2

on YouTube ↗34m

" summary

A public genomic platform (CARD) collects >80,000 SARS‑CoV‑2 genomes and a Virus Genome Tracker that places any new sequence into global and USA phylogenies in minutes. Haplotype analysis of 4,200 California, 6,356 US and >80,000 global isolates reveals multiple introductions into California from other states and international travel, distinct Orange County clusters separate from Los Angeles, and 22,171 country‑private haplotypes (45.8%) rising from ~28–30% in Jan–Mar to ~46–60% in Apr–May.

AI-written summary · about

" chapters (7)

1. 0:00Introduction and platform overview
2. 3:10Genomic data collection and tools
3. 10:24California variant analysis results
4. 17:54Mutation trends and global spread
5. 23:20Transmission patterns in California
6. 27:05Los Angeles and local transmission
7. 31:54Q&A and closing remarks

" related talks

• 56mA Global Comparison of COVID-19 Variant Waves and Relationships with Clinical and...Sara del Valle · Epidemics and Information Diffusion (Simons Institute, 2022)
• 32mHow Do We Deliver Precision Health at Scale for All?Carlos Bustamante · Computational Challenges in Very Large-Scale 'Omics'
• 33mCOVIDcast: An ecosystem for COVID-19 tracking and forecastingRyan Tibshirani · AWS Machine Learning Summit 2021
• 24mUrban MetagenomicsKevin Slavin · DLD Munich 2016
• 38mCrime in the Pandemic A look at changes in Los Angeles crime during Covid-19Preet Singh · Data Con LA 2021
• 01h 19mOpportunities and risks of big data in disease surveillance.Leon Hempel, Tim Eckmanns, Ciro Cattuto, Jennifer Cole, Martin French, Edward Velasco · CPDP 2015
• 28mBiological Discovery and Consumer Genomics Databases Activate Latent Privacy Risk in...Steven Brenner · Computational Challenges in Very Large-Scale 'Omics'
• 34mLongitudinal Phenotypes and Disease Trajectories at Population ScaleSøren Brunak · Computational Challenges in Very Large-Scale 'Omics'