Identification of a Pangolin Niche for a 2019-nCoV-like Coronavirus via an Extensive Meta-metagenomic Search

Lamia Wahba; Nimit Jain; Andrew Z. Fire; Massa J. Shoura; Karen L. Artiles; Matthew J. McCoy; Dae-Eun Jeong

The abundance and homology of viruses within a metagenomic sample are of The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939660 doi: bioRxiv preprint this thread and appear to have encountered it through a more targeted search than ours (this 206 study has since been posted online in bioRxiv) (13). As noted by Wong et al. (13) The availability of numerous paths (both targeted and agnostic) toward identification 221 of natural niches for pathogenic sequences will remain useful to the scientific community and 222 to public health, as will vigorous sharing of ideas, data, and discussion of potential origins 223 and modes of spread for epidemic pathogens. Metagenomic datasets with k=32-mer matches to MN908947.3 2019-nCoV Details of search and are described in legend to Table S1 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939660 doi: bioRxiv preprint SRR10168377. This plot addresses several challenges associated with the limited sequencing data 302 available by attempting to provide the most favorable alignment of that sequence possible. To 303 maximize sensitivity in detecting potential recombination, ambiguities in which two or more reads 304 apparently disagreed (which were rare; approximately 1.2% of assigned bases) were resolved in favor 305