High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
By
John E Gorzynski,
Hannah N De Jong,
David Amar,
Chris R Hughes,
Alexander Ioannidis,
Rob Bierman,
Darren Liu,
Yosuke Tanigawa,
Amy Kistler,
Jack Kamm,
Jaehee Kim,
Lorenzo Cappello,
Norma F. Neff,
Simone Rubinacci,
Olivier Delaneau,
Massa J. Shoura,
Kinya Seo,
Anna Kirillova,
Archana Raja,
Shirley Sutton,
ChunHong Huang,
Malaya K. Sahoo,
Kalyan C. Mallempati,
Gonzalo Montero-Martin,
Kazutoyo Osoegawa,
David Jimenez-Morales,
Nathaniel Watson,
Nathan Hammond,
Ruchi Joshi,
Marcelo Fernandez-Vina,
Jeffrey W. Christle,
Matthew T. Wheeler,
Phil Febbo,
Kyle Farh,
Gary Schroth,
F Desouza,
Julia Palacios,
Julia Salzman,
Benjamin A. Pinsky,
Manuel A Rivas,
Carlos D. Bustamante,
Euan A. Ashley,
Victoria N. Parikh
Posted 29 Jul 2020
medRxiv DOI: 10.1101/2020.07.27.20163147
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.
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