TY - JOUR
T1 - Compartmentalized replication of sars-cov-2 in upper vs. Lower respiratory tract assessed by whole genome quasispecies analysis
AU - Rueca, Martina
AU - Bartolini, Barbara
AU - Gruber, Cesare Ernesto Maria
AU - Piralla, Antonio
AU - Baldanti, Fausto
AU - Giombini, Emanuela
AU - Messina, Francesco
AU - Marchioni, Luisa
AU - Ippolito, Giuseppe
AU - Di Caro, Antonino
AU - Capobianchi, Maria Rosaria
PY - 2020/9
Y1 - 2020/9
N2 - 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.
AB - 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.
KW - Coronavirus
KW - COVID-19
KW - Quasispecies
KW - SARS-COV-2
KW - Variability
UR - http://www.scopus.com/inward/record.url?scp=85089834267&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85089834267&partnerID=8YFLogxK
U2 - 10.3390/microorganisms8091302
DO - 10.3390/microorganisms8091302
M3 - Article
AN - SCOPUS:85089834267
VL - 8
SP - 1
EP - 12
JO - Microorganisms
JF - Microorganisms
SN - 2076-2607
IS - 9
M1 - 1302
ER -