CoV-Spectrum LAPIS API
★ Only Publicly Available OpenAPI DocumentHealthcareClinical Datanone40 EndpointsREST
For Agents
Query SARS-CoV-2 sequence data, mutations, insertions, phylogenetic subtrees, and sample metadata from the open CoV-Spectrum LAPIS backend with no authentication.
Use for: I need to fetch aligned nucleotide sequences for a SARS-CoV-2 lineage, Get amino acid mutations for samples from a country and date range, Retrieve a phylogenetic subtree as Newick text, Find the most recent common ancestor for a set of samples
Not supported: Does not provide patient-level clinical data, hospital outcomes, or non-SARS-CoV-2 pathogens — use for SARS-CoV-2 sequence and aggregate metadata queries only.
The CoV-Spectrum LAPIS API is the open data backend behind cov-spectrum.org, exposing 40 endpoints for querying SARS-CoV-2 sequence and metadata aggregates. Endpoints cover aligned and unaligned nucleotide sequences, aligned amino acid sequences per gene, nucleotide and amino acid mutations and insertions, phylogenetic subtrees, most-recent common ancestor lookups, sample details and aggregations, and a generic /query/parse helper. The base URL is the open v2 LAPIS endpoint and no authentication is required, making it suitable for public health dashboards, research pipelines, and academic agents that need bulk SARS-CoV-2 surveillance data.
Install Jentic One Beta
Connect the CoV-Spectrum LAPIS API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the CoV-Spectrum LAPIS API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.
Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.
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Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register # connects your agent to your Jentic One instanceJentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.
Capabilities
What an agent can do with CoV-Spectrum LAPIS API.
Retrieve aligned or unaligned nucleotide sequences for filtered samples
Retrieve aligned amino acid sequences across all genes or by specific gene
Pull nucleotide and amino acid mutations and insertions as CSV or JSON
Generate phylogenetic subtrees in Newick format
Find the most recent common ancestor for a sample selection
Aggregate sample counts grouped by date, lineage, or country
Look up sample-level details for filtered cohorts
Use Cases
Patterns agents use CoV-Spectrum LAPIS API for, with concrete tasks.
★ Variant Surveillance Dashboard
Power a public-facing or institutional SARS-CoV-2 variant tracker that shows lineage prevalence over time and geography. The /sample/aggregated endpoint returns counts grouped by date, country, or lineage, which is the core query a surveillance dashboard runs every few hours. Because the API is open, dashboards can run client-side without a credential proxy.
Call POST /sample/aggregated with a filter on country and a groupBy of pangoLineage and date to refresh a variant prevalence chart
Genomic Research Pipeline
Pull aligned nucleotide and amino acid sequences for a defined sample cohort into a downstream phylogenetics or mutation-analysis pipeline. /sample/alignedNucleotideSequences returns the aligned sequences and /sample/alignedAminoAcidSequences/{gene} narrows to a specific gene such as Spike. Together with /sample/nucleotideMutations and /sample/aminoAcidMutations, an agent can prepare a clean dataset for analysis without manual export.
Call GET /sample/alignedAminoAcidSequences/S filtered to a date range, then GET /sample/aminoAcidMutations to pull the mutation set for the same cohort
Phylogenetic Context Lookup
Place a sample or set of samples in their phylogenetic context by fetching a Newick subtree or the most recent common ancestor. /sample/phyloSubtree returns Newick text suitable for visualisation libraries, and /sample/mostRecentCommonAncestor returns the MRCA for a query selection. Useful for researchers writing case reports or evolutionary analyses.
Call POST /sample/phyloSubtree with a country and lineage filter, then render the returned Newick string in a tree viewer
AI Agent Public Health Q&A
Let an AI agent answer epidemiological questions like 'how prevalent is XBB in Switzerland' by calling LAPIS through Jentic. The agent searches by intent, executes the matching aggregate or details query, and returns structured counts. Because LAPIS is open, no credential is needed but Jentic still standardises the request shape and response handling.
Use Jentic to search 'aggregate SARS-CoV-2 sample counts', load the schema for POST /sample/aggregated, and execute it with country and lineage filters
Key Endpoints
40 endpoints — the cov-spectrum lapis api is the open data backend behind cov-spectrum.
METHOD
PATH
DESCRIPTION
POST
/sample/aggregated
Aggregate sample counts grouped by fields
GET
/sample/details
List per-sample metadata for a filtered cohort
POST
/sample/nucleotideMutations
Get nucleotide mutations for a cohort
POST
/sample/aminoAcidMutations
Get amino acid mutations for a cohort
POST
/sample/alignedNucleotideSequences
Fetch aligned nucleotide sequences
GET
/sample/alignedAminoAcidSequences/{gene}
Fetch aligned amino acid sequences for a gene
POST
/sample/phyloSubtree
Get a phylogenetic subtree as Newick
POST
/sample/mostRecentCommonAncestor
Get the MRCA for a sample selection
POST
/sample/aggregated
Aggregate sample counts grouped by fields
GET
/sample/details
List per-sample metadata for a filtered cohort
POST
/sample/nucleotideMutations
Get nucleotide mutations for a cohort
POST
/sample/aminoAcidMutations
Get amino acid mutations for a cohort
POST
/sample/alignedNucleotideSequences
Fetch aligned nucleotide sequences
GET
/sample/alignedAminoAcidSequences/{gene}
Fetch aligned amino acid sequences for a gene
POST
/sample/phyloSubtree
Get a phylogenetic subtree as Newick
POST
/sample/mostRecentCommonAncestor
Get the MRCA for a sample selection
Why Jentic?
Three things that make agents converge on Jentic-routed access.
Credential isolation
LAPIS is open and requires no credential, so Jentic forwards requests directly. There are no tokens to vault, rotate, or scope.
Intent-based discovery
Agents search Jentic with intents like 'aggregate SARS-CoV-2 samples by lineage' or 'get amino acid mutations for Spike' and Jentic returns the matching LAPIS operation with its parameter schema, so the agent calls the right endpoint without reading the spec.
Time to first call
Direct integration: 1-2 days to learn the LAPIS query model and handle large response payloads. Through Jentic: under 1 hour to search, load, and execute.
Related APIs
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using CoV-Spectrum LAPIS API through Jentic.
What authentication does the CoV-Spectrum LAPIS API use?
The open LAPIS endpoint at https://lapis.cov-spectrum.org/open/v2 requires no authentication. All 40 endpoints are publicly accessible. When called via Jentic, no credential is provisioned for this API.
Can I download aligned amino acid sequences for a specific gene?
Yes. GET /sample/alignedAminoAcidSequences/{gene} returns aligned amino acid sequences for the specified gene, for example /sample/alignedAminoAcidSequences/S for the Spike gene. Filter parameters narrow the cohort by date, country, or lineage.
How do I aggregate sample counts by lineage?
POST /sample/aggregated with a `groupBy` parameter listing fields such as `pangoLineage` and `date`. The response is a JSON array of grouped counts, suitable for variant prevalence dashboards.
What are the rate limits for the LAPIS API?
The open LAPIS instance is provided as a public research utility and does not advertise hard rate limits. Heavy users (large bulk sequence pulls or repeated multi-million-row aggregations) should batch requests and cache results to remain a good citizen on shared infrastructure.
How do I get a phylogenetic subtree through Jentic?
Search Jentic for 'get a SARS-CoV-2 phylogenetic subtree', load the schema for POST /sample/phyloSubtree, and execute it with country and lineage filters. The response is a Newick string ready for tree-viewer libraries.
Does the API include patient-level clinical data?
No. LAPIS exposes anonymised genomic and metadata fields like collection date, country, and lineage. It does not include patient identifiers, hospital outcomes, or individual case clinical data.
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