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

Abstract

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.

Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

“…The Spike Y839 variant was most likely imported from Italy in mid-late February 2020, as first detected genomes were all collected from individuals from the Northern region of Portugal that contacted (primarily or secondarily) with epidemiologically linked infected individuals that had been in Milan for an international trade fair during the third week of February 2020. Concordantly, the first D839Y genome sequence reported worldwide was collected in Italy (Lombardy) on 21 February (Italy/PV-5314-N/2020; GISAID accession number EPI_ISL_451307) (Table S2) [ 26 ], being identical (i.e, Nextstrain clade 20A background plus the G24077 T SNP) to the “founder” Spike Y839 variant genome sequences detected in Portugal ( https://insaflu.insa.pt/covid19 ). So far, current data and ongoing epidemiological investigations support a single origin (Milan, Italy) and, although there was a substantial representation of Portuguese companies in this event, available data links the introduction of the Y839 variant in Portugal to a single industrial area in the North of Portugal.…”

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis

“…In addition to interhost SNP analysis, we performed iSNVs analysis on published sequencing data (for specifics, see “Materials and Methods”) to trace the evolutionary dynamics of the mutants. We performed analyses of the SARS-CoV-2 sequencing data ( supplementary table S3, Supplementary Material online) collected from six patients ( Rueca et al. 2020 ), but observed no allele change event in a single patient.…”

“…First, we tried to calculate the variation of identified mutants in one single host. We analyzed 13 consensus genomes of SARS-CoV-2 extracted from six patients with COVID-19 ( Rueca et al. 2020 ).…”

New Insights Into the Physiopathology of COVID-19: SARS-CoV-2-Associated Gastrointestinal Illness

“…Beside the hamster lungs, among non-respiratory tract tissues only the intestinal tissues demonstrated viral antigen expression in association with severe epithelial cell necrosis, intestinal villi damage and increased lamina propria mononuclear or neutrophilic cell infiltration. Next generation sequencing (NGS) was used to study SARS-CoV-2 intra-host variability and identify possible tissue-specific patterns and signature of variant selection for upper (URT) and lower respiratory tract (LRT) from six COVID-19 patients ( 75 ). The presence of quasispecies was observed in this study with differences between the URT and LRT variants indicating a quasispecies compartmentalization.…”