Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets

Abstract

The compounding challenges of low signal, high background, and uncertain targets plague many sequencing efforts, including monitoring potential zoonotic resevoirs. One solution has been targeted DNA capture, where probes are designed to hybridize with target sequences, enriching them relative to the background. We have developed the HUBDesign pipeline which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and potentially novel sequences. We validated HUBDesign by generating a probe set targeting the breadth of coronavirus diversity. We demonstrated significant enrichment of SARS-CoV-2 and HCoV-NL63 from a human background, without interference between the two viruses, nor background enrichment. This probe set will be of use in identifying coronavirus co-infections and surveillance of coronaviruses resevoirs. HUBDesign has broad applicability wherever there are multiple organisms of interest, such as ancient DNA, and host specific microbiomes.Funding Statement: This work was partially supported by CIHR COVID-19 Rapid Response funding to MSM. MSM was supported in part by a CIHR New Investigator Award and an Early Career Researcher Award from the Government of Ontario. This work was partially funded by a CIHR COVID grant to Principal applicant KM and co-applicant AB. AB, HP, GBG, and ZWD were funded through Natural Sciences and Engineering Research Council of Canada.HP was generously funded by the Boris Family Fund, the Micheal G. DeGroote Institute for Infectious Disease Research.Declaration of Interests: None to declareEthics Approval Statement: Work with SARS-CoV-2 was performed in a containment level 3 laboratory and all protocols were approved by the McMaster Presidential Biosafety Advisory Committee.