CoV-Spectrum LAPIS API

Name: CoV-Spectrum LAPIS API API
Brand: CoV-Spectrum LAPIS API
Availability: InStock

★ Only Publicly Available SpecHealthcareClinical 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.

Quickstart

Get started with CoV-Spectrum LAPIS API in minutes using your preferred integration method.

# Add to your MCP client config (Claude Desktop, Cursor, Windsurf)
{
  "jentic": {
    "url": "https://api.jentic.com/mcp",
    "auth": "oauth"
  }
}

# Then ask your agent:
"aggregate SARS-CoV-2 sample counts by lineage"

# → Jentic returns the GET /events tool with parameter schema, agent executes.

Capabilities

What an agent can do with CoV-Spectrum LAPIS API 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

GET STARTED

Start building with CoV-Spectrum LAPIS API API

Explore with Jentic

View OpenAPI Spec

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.

Jentic publishes the only available OpenAPI specification for CoV-Spectrum LAPIS API, keeping it validated and agent-ready.

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.

Use Cases

Patterns agents use CoV-Spectrum LAPIS API 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

Why though 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.

Complementary

NCBI Datasets API

Reference genomes and bulk genomic data downloads from NCBI

Use NCBI Datasets to pull reference genomes that complement the SARS-CoV-2 sample data from LAPIS

Complementary

Clinical Tables API

Lookup of medical codes and conditions hosted by the NIH

Use Clinical Tables to enrich epidemiology dashboards with standardised condition or drug codes

Complementary

NLM API

National Library of Medicine reference data services

Use NLM endpoints alongside cov-spectrum for cross-referencing biomedical literature with surveillance data

FAQs

Specific to using CoV-Spectrum LAPIS API 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.