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Characterization of SARS-CoV-2 viral diversity within and across hosts

View ORCID ProfilePalash Sashittal, View ORCID ProfileYunan Luo, View ORCID ProfileJian Peng, View ORCID ProfileMohammed El-Kebir
doi: https://doi.org/10.1101/2020.05.07.083410
Palash Sashittal
1Dept. of Aerospace Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
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  • ORCID record for Palash Sashittal
Yunan Luo
2Dept. of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
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Jian Peng
2Dept. of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
3College of Medicine, University of Illinois at Urbana-Champaign, IL 61801, USA
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  • For correspondence: jianpeng@illinois.edu melkebir@illinois.edu
Mohammed El-Kebir
2Dept. of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
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  • For correspondence: jianpeng@illinois.edu melkebir@illinois.edu
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SUMMARY

In light of the current COVID-19 pandemic, there is an urgent need to accurately infer the evolutionary and transmission history of the virus to inform real-time outbreak management, public health policies and mitigation strategies. Current phylogenetic and phylodynamic approaches typically use consensus sequences, essentially assuming the presence of a single viral strain per host. Here, we analyze 621 bulk RNA sequencing samples and 7,540 consensus sequences from COVID-19 patients, and identify multiple strains of the virus, SARS-CoV-2, in four major clades that are prevalent within and across hosts. In particular, we find evidence for (i) within-host diversity across phylogenetic clades, (ii) putative cases of recombination, multi-strain and/or superinfections as well as (iii) distinct strain profiles across geographical locations and time. Our findings and algorithms will facilitate more detailed evolutionary analyses and contact tracing that specifically account for within-host viral diversity in the ongoing COVID-19 pandemic as well as future pandemics.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵‡ Lead contact

  • A few references and a short paragraph in the results section referring to Figure 3.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 13, 2020.
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Characterization of SARS-CoV-2 viral diversity within and across hosts
Palash Sashittal, Yunan Luo, Jian Peng, Mohammed El-Kebir
bioRxiv 2020.05.07.083410; doi: https://doi.org/10.1101/2020.05.07.083410
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Characterization of SARS-CoV-2 viral diversity within and across hosts
Palash Sashittal, Yunan Luo, Jian Peng, Mohammed El-Kebir
bioRxiv 2020.05.07.083410; doi: https://doi.org/10.1101/2020.05.07.083410

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