Identification of potential SARS-CoV-2 genetic markers resulting from host domestication.
Wisniewski, J.; CHEN, H.-C.
Show abstract
We developed a k-mer-based pipeline, namely the Pathogen Origin Recognition Tool using Enriched K-mers (PORT-EK) to identify genomic regions enriched in the respective hosts after the comparison of metagenomes of isolates between two host species. Using it we identified thousands of k-mers enriched in US white-tailed deer and betacoronaviruses in bat reservoirs while comparing them with human isolates. We demonstrated different coverage landscapes of k-mers enriched in deer and bats and unraveled 148 mutations in enriched k-mers yielded from the comparison of viral metagenomes between bat and human isolates. We observed that the third position within a genetic codon is prone to mutations, resulting in a high frequency of synonymous mutations of amino acids harboring the same physicochemical properties as unaltered amino acids. Finally, we classified and predicted the likelihood of host species based on the enriched k-mer counts. Altogether, PORT-EK showcased its feasibility for identifying enriched viral genomic regions, illuminating the different intrinsic tropisms of coronavirus after host domestication. TeaserA measure of enriched viral genomic correlates resulting from host domestication as a potential predictor of zoonotic risk.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A Protein Language Model for Exploring Viral Fitness Landscapes 95%
- Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions 95%
- No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2 95%
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
- SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery 94%
- Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks 94%
- In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs 94%
Similar papers in this journal
- Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses 95%
- Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19 94%
- A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.