NYU Dataset

Sequencing Data for a Delta-Omicron Recombinant in an Immunosuppressed Transplant Recipient Treated with Monoclonal Antibody Sotrovimab

UID: 10454
* Corresponding Author
A Delta-Omicron recombinant of the SARS-CoV-2 virus was sequenced and isolated from an immunosuppressed and unvaccinated male kidney transplant patient who received Sotrovimab for treatment of COVID-19. Further clinical details and medical history of the patient are described in the associated publication. Sotrovimab is a therapeutic monoclonal antibody (mAb) used to treat infections by the BA.1 Omicron lineage. It was observed that the Delta-Omicron recombinant found in this patient was resistant to neutralization by Sotrovimab. Genomic analysis of the SARS-CoV-2-positive nasopharyngeal swab specimen revealed an unusual SARS-CoV-2 sequence with outlier Omicron BA.1 placement in a global phylogenetic tree and high number of mutations.
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A GISAID account is required to access the sequencing data shared in the GISAID repository. Users must complete a Database Access Agreement and Registration Form to obtain credentials. Raw FASTQ files have been shared in the Sequence Read Archive (SRA), accessible through BioProject.
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Virus sequencing data
Accession #: EPI_ISL_10792641

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Raw sequence reads
Accession #: PRJNA915368

Associated Publications
Data Type
Equipment Used
bioMerieux NucliSENS easyMAG
Illumina NovaSeq 6000
Thermo Scientific Ion S5 XL
Software Used
bcl2fastq v2.20
BEAST v1.10.5
ChimeraX v1.3
GraphPad Prism v8.0
IQ-TREE v2.2.0
Nextclade v1.14
Nextstrain CLI v6.0.0
Pangolin v3.1.19
Sambamba v0.6.8
Trimmomatic v0.36
Study Type
Dataset Format(s)
Grant Support
G0E1420N/Research Foundation - Flanders
G098321N/Research Foundation - Flanders
C14/18/094/Internal Funds KU Leuven
V420922N/Research Foundation Flanders
Jan Vilcek/David Goldfarb Fellowship Endowment Fund/NYU Langone Health
Other Resources
ncov2019-artic-nf Pipeline

Consensus genome


Fully automated protein structure homology-modelling server


Ultrafast Sample placement on Existing tRee