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Open AccessArticle

Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis

National Institute for Infectious Diseases, L’Istituto Nazionale per le Malattie Infettive (INMI), “Lazzaro Spallanzani” Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00149 Rome, Italy
Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Università Degli Studi di Pavia, 27100 Pavia, Italy
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(9), 1302;
Received: 17 July 2020 / Revised: 22 August 2020 / Accepted: 24 August 2020 / Published: 26 August 2020
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution. View Full-Text
Keywords: coronavirus; variability; SARS-COV-2; COVID-19; quasispecies coronavirus; variability; SARS-COV-2; COVID-19; quasispecies
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Rueca, M.; Bartolini, B.; Gruber, C.E.M.; Piralla, A.; Baldanti, F.; Giombini, E.; Messina, F.; Marchioni, L.; Ippolito, G.; Di Caro, A.; Capobianchi, M.R. Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis. Microorganisms 2020, 8, 1302.

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