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

While our conclusions here are based on whole genome capture of viruses, CATCH is a versatile approach that can be applied to capture of non-viral microbial genomes and to the design of oligonucleotide sequences for uses other than whole genome enrichment. Because CATCH scales well with our growing knowledge of genomic diversity 26, 27 , it is particularly wellsuited for designing against any class of input from microbes that have a high degree of diversity. Capture-based approaches have successfully been used to enrich whole genomes of eukaryotic parasites such as Plasmodium 58 and Babesia 59 , as well as bacteria 60 . Many bacteria, like viruses, have high variation even within species 61 , and CATCH can enable efficient and sensitive enrichment of these bacterial genomes or even of combinations of viral and bacterial targets. Beyond microbes, CATCH can benefit studies in other areas that use capture-based approaches, such as the detection of previously characterized fetal and tumor DNA from cell-free material 62, 63 , in which known targets of interest may represent a small fraction of all material and for which it may be useful to rapidly design new probe sets for enrichment as novel targets are discovered. Moreover, CATCH can identify conserved regions or regions suitable for differential identification, which can help in the design of PCR primers and CRISPR-Cas13 crRNA guides for nucleic acid diagnostics.