High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs.
John E GorzynskiHannah N De JongDavid AmarChris R HughesAlexander G IoannidisRob BiermanDarren LiuYosuke TanigawaAmy L KistlerJack KammJaehee KimLorenzo CappelloNorma F NeffSimone RubinacciOlivier DelaneauMassa J ShouraKinya SeoAnna KirillovaArchana Natarajan RajaShirley C SuttonChunHong HuangMalaya Kumar SahooKalyan C MallempatiGonzalo Montero-MartinKazutoyo OsoegawaDavid Jimenez-MoralesNathaniel WatsonNathan HammondRuchi JoshiMarcelo Fernandez-VinaJeffrey W ChristleMatthew T WheelerPhil FebboKyle FarhGary P SchrothF DesouzaJulia PalaciosJulia SalzmanBenjamin A PinskyManuel A RivasCarlos D BustamanteEuan A AshleyVictoria N ParikhPublished in: medRxiv : the preprint server for health sciences (2020)
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.