Shortcomings of SARS-CoV-2 genomic metadata

Objective: The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was sequenced, and is integral to epidemiological efforts and public health direction. Here, we interrogate some shortcomings of metadata within the GISAID database to raise awareness of common errors and inconsistencies that may affect data-driven analyses and provide possible avenues for resolutions. Results: Our analysis reveals a startling prevalence of spelling errors and inconsistent naming conventions, which together occur in an estimated similar to 9.8% and similar to 11.6% of originating lab and submitting lab GISAID metadata entries respectively. We also find numerous ambiguous entries which provide very little information about the actual source of a sample and could easily associate with multiple sources worldwide. Importantly, all of these issues can impair the ability and accuracy of association studies by deceptively causing a group of samples to identify with multiple sources when they truly all identify with one source, or vice versa.

Automated summary

The SARS-CoV-2 pandemic has led to extensive genomic sequencing efforts, but the metadata in the GISAID database shows a high prevalence of spelling errors, inconsistent naming conventions, and ambiguous entries, which could affect the accuracy of data-driven analyses.