The primary goal of this report is to quantify the number of Spanish SARS-CoV-2 sequences uploaded to GISAID, which are available to researchers. To effectively monitor the pandemic, it is important for sequences to be uploaded as soon as possible after being obtained from patients. However, this is not always the case and we may find sequences that were uploaded recently but were actually obtained from patients two years ago.
To address this issue, we will download all Spanish patient sequences from GISAID and analyze the associated metadata, including the upload date, sampling date, location in the autonomous community, and lineage/variant of interest.
All data is available to researchers through the GISAID platform.
This report displays all sequences that were uploaded from the beginning of the pandemic until the time of its creation:
221,407 sequences from Spain available on 2023-04-08
To determine the effect of the delay in uploading sequences on epidemiological surveillance, we classified them based on the number of days between the date of sample collection and the date of upload to the database. This classification allowed us to divide the sequences into three levels.
The number of sequences for the 3 levels from the beginning of the pandemic are shown below: