Capturing diverse microbial sequence with comprehensive and scalable probe design

Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga

Here, we developed and implemented CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a method that yields scalable and comprehensive probe designs from any collection of target sequences. Using CATCH, we designed several multi-virus probe sets, and then synthesized and used them to enrich viral nucleic acid in sequencing libraries from patient and environmental samples across diverse source material. We evaluated their performance and investigated any biases introduced by capture with these probe sets. Finally, to demonstrate use in clinical and biosurveillance settings, we applied this platform to recover Lassa virus genomes in low titer clinical samples from the 2018 Lassa fever outbreak in Nigeria and to identify viruses in human and mosquito samples with unknown content.