Cluster_59_linelist

Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient’s nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.Methods: Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases.

Data Dictionary:
Unit_of_Transmission: Hospital Unit where a infection prevention and control epidemiologist identified a possible transmission event.
Unit_Acquisition: Hospital Unit where a infection prevention and control epidemiologist identified a possible acquisition event.
Collection Date (yyyy-mm-dd, UTC): date at which a nasopharyngeal specimen was collected from a symptomatic case for SARS-CoV-2 molecular diagnostic testing using qRT-PCR.
log_GE: Logarithmic base ten genome-equivalents per millilitre of SARS-CoV-2 detected by envelope gene target using qRT-PCR.
Fold.Change.ace3: Relative gene expression data of ACE2 expression (full-length/ transmembrane transcript variant).
Linearge: SARS-CoV-2 viral lineage as classified by the PANGOLIN tool (Version 1.15.1), viral genome alignments are available on GISAID.