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

We used CATCH to design a probe set that targets all viral species reported to infect humans (V ALL ), which could be used to achieve more sensitive metagenomic sequencing of viruses from human samples. V ALL encompasses 356 species (86 genera, 31 families), and we designed it using genomes available from NCBI GenBank 35, 36 (Supplementary Table 1 ). We constrained the number of probes to 350,000, significantly fewer than the number used in studies with comparable goals 24, 25 , reducing the cost of synthesizing probes that target diversity across hundreds of viral species. The design output by CATCH contained 349,998 probes (Fig. 1c ). This design represents comprehensive coverage of the input sequence diversity under conservative choices of parameter values, e.g., tolerating few mismatches between probe and target sequence (Fig. 1d) . To compare the performance of V ALL against probe sets with lower complexity, we separately designed three focused probe sets for commonly co-circulating viral infections: measles and mumps viruses (V MM ; 6,219 probes), Zika and chikungunya viruses (V ZC ; 6,171 probes), and a panel of 23 species (16 genera, 12 families) circulating in West Africa (V WAFR ; 44,995 probes) ( Supplementary Fig. 3 , Supplementary Table 1) . These probe sets are publicly available (see Methods for link).