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A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways Open Access (recommended)


Resource type(s)
Viral load
Viral genotype
Whole genome sequencing
Attribution-NonCommercial-NoDerivs 3.0 United States

Lorenzo Redondo, Ramon
Nam, Hannah H
Roberts, Scott C
Simons, Lacy Marie
Jennings, Lawrence J
Qi, Chao
Achenbach, Chad J
Hauser, Alan R
Ison, Michael G
Hultquist, Judd Franklin
Ozer, Egon Anderson
Background: The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of distinct viral clades, though their clinical significance remains unclear. Here, we aimed to investigate the phylogenetic characteristics of SARS-CoV-2 infections in Chicago, Illinois, and assess their relationship to clinical parameters. Methods: We performed whole-genome sequencing of SARS-CoV-2 isolates collected from COVID-19 patients in Chicago in mid-March, 2020. Using these and other publicly available sequences, we performed phylogenetic, phylogeographic, and phylodynamic analyses. Patient data was assessed for correlations between demographic or clinical characteristics and virologic features. Findings: The 88 SARS-CoV-2 genome sequences in our study separated into three distinct phylogenetic clades. Clades 1 and 3 were most closely related to viral sequences from New York and Washington state, respectively, with relatively broad distributions across the US. Clade 2 was primarily found in the Chicago area with limited distribution elsewhere. At the time of diagnosis, patients infected with Clade 1 viruses had significantly higher average viral loads in their upper airways relative to patients infected with Clade 2 viruses, independent of disease severity. Interpretation: These results show that multiple variants of SARS-CoV-2 were circulating in the Chicago area in mid-March 2020 that differed in their relative viral loads in patient upper airways. These data suggest that differences in virus genotype can impact viral load and may influence viral spread.
Original Bibliographic Citation
Lorenzo-Redondo R, Nam HH, Roberts SC, Simons LM, Jennings LJ, Qi C, Achenbach CJ, Hauser AR, Ison MG, Hultquist JF, Ozer EA. A Clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways. Ebiomedicine. 2020;62:10.
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Date Created
Original Identifier
(PMID) 33186810
Subject: MESH
Viral Load
Whole Genome Sequencing
Genome, Viral
Subject: Geographic Name

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