BACKGROUND: Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories around the globe generated new sequences at unprecedented speed and volume and bioinformaticians developed new tools and dashboards to analyze this wealth of data. However, a major challenge that remains is the lack of simple and efficient approaches for accessing and processing sequencing data. RESULTS: The Lightweight API for Sequences (LAPIS) facilitates rapid retrieval and analysis of genomic sequencing data through a REST API. It supports complex mutation- and metadata-based queries and can perform aggregation operations on massive datasets. LAPIS is optimized for typical questions relevant to genomic epidemiology. Using a newly-developed in-memory database engine, it has a high speed and throughput: between 25 January and 4 February 2023, the SARS-CoV-2 instance of LAPIS, which contains 14.5 million sequences, processed over 20 million requests with a mean response time of 411 ms and a median response time of 1 ms. LAPIS is the core engine behind our dashboards on genspectrum.org and we currently maintain public LAPIS instances for SARS-CoV-2 and mpox. CONCLUSIONS: Powered by an optimized database engine and available through a web API, LAPIS enhances the accessibility of genomic sequencing data. It is designed to serve as a common backend for dashboards and analyses with the potential to be integrated into common database platforms such as GenBank.

SUMMARY: The CoV-Spectrum website supports the identification of new SARS-CoV-2 variants of concern and the tracking of known variants. Its flexible amino acid and nucleotide mutation search allows querying of variants before they are designated by a lineage nomenclature system. The platform brings together SARS-CoV-2 data from different sources and applies analyses. Results include the proportion of different variants over time, their demographic and geographic distributions, common mutations, hospitalization and mortality probabilities, estimates for transmission fitness advantage and insights obtained from wastewater samples. AVAILABILITY AND IMPLEMENTATION: CoV-Spectrum is available at https://cov-spectrum.org. The code is released under the GPL-3.0 license at https://github.com/cevo-public/cov-spectrum-website.