AI-Assisted SARS-CoV-2 Variant Classification for Public Health

Pangolin is a bioinformatics tool used by the NYC Department of Health and Mental Hygiene to assign lineage names to SARS-CoV-2 genomic sequences. It classifies viral samples into named variants (such as Omicron or Delta) to support epidemiological tracking and public health reporting. The system processes viral genome data — not personal health information — and its outputs are used to understand how COVID-19 variants are spreading across the city. Results inform variant surveillance decisions made by public health professionals.