Whole-genome analysis of SARS-CoV-2 samples indicate no tissue specific genetic adaptation of the virus in COVID-19 patients' upper and lower respiratory tract

Claudia Wylezich; Tina Schaller; Rainer Claus; Klaus Hirschbühl; Bruno Märkl; Elisabeth Kling; Oliver Spring; Dirk Höper; Jürgen Schlegel; Martin Beer; Sebastian Dintner

doi:10.1016/j.diagmicrobio.2021.115520

Whole-genome analysis of SARS-CoV-2 samples indicate no tissue specific genetic adaptation of the virus in COVID-19 patients' upper and lower respiratory tract

Diagn Microbiol Infect Dis. 2021 Dec;101(4):115520. doi: 10.1016/j.diagmicrobio.2021.115520. Epub 2021 Aug 20.

Authors

Affiliations

¹ Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany. Electronic address: claudia.wylezich@fli.de.
² Department of General Pathology and Molecular Diagnostics, University of Augsburg, Augsburg, Germany.
³ Department of Hematology and Oncology, University of Augsburg, Augsburg, Germany.
⁴ Department of Microbiology, University of Augsburg, Augsburg, Germany.
⁵ Anesthesiology and Operative Intensive Care Medicine,University of Augsburg, Augsburg, Germany.
⁶ Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
⁷ Department of Neuropathology, School of Medicine, Institute of Pathology, Technical University Munich, Munich, Germany.

Abstract

Sample panels of SARS-CoV-2 cases were retrospectively whole-genome sequenced. In three individuals, samples of upper and lower respiratory tract resulted in identical sequences suggesting virus stability including the spike protein cleavage site. In a fourth case, low-level intra-host genomic evolution and a unique 5-nucleotide deletion was observed.

Keywords: Intra-host virus evolution; ORF8 5-nucleotide deletion; Postmortem; S-614D; SARS-CoV-2 genome sequences; Upper and lower respiratory tract.

Publication types

Case Reports

MeSH terms

Adaptation, Physiological / genetics*
COVID-19 / virology*
Genome, Viral
Humans
Respiratory System / virology*
Retrospective Studies
SARS-CoV-2 / isolation & purification*
Tissue Distribution
Whole Genome Sequencing*