Items referring to sequence-level data, including genomics, microbiomics, proteomics, etc.

molecular

The fauna database stores viral sequences and serological data in RethinkDB. The current database and scripts are designed around influenza, Ebola and Zika viruses, but with the intention of provided a general purpose tool.

non-collection specific

(Simple) Released

JavaScript Object Notation: a lightweight text-based data interchange format.

JSON

FASTA: a text-based format for representing nucleotide or amino acid sequences.

FASTA

English

GNU AGPL v3

Charlton Callender

James Hadfield

Trevor Bedford

ORCID

Barney Potter

Jover Lee

Sarah Murata

Richard Neher

Eden Berga

Louise H Moncla

John Huddleston

Python is a high-level, interpreted programming language known for its readability and broad applicability in web development, data science, and automation.

Python

nextstrain: fauna

A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis.

Severe acute respiratory syndrome coronavirus 2

SARS-CoV2

An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.

host organism

Host

Homo sapiens

A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

disease

Disease

A disease whose physical basis is an infectious disorder

infectious disease

Infectious Disease

Yellow fever (YF), caused by YF virus, is a zoonotic disease characterized by fever and constitutional symptoms, with the potential to progress to severe and fatal viral hemorrhagic fever with shock and multi-organ system failure.

yellow fever

Yellow Fever Virus Infection

A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.

COVID-19

The type species of MORBILLIVIRUS and the cause of the highly infectious human disease MEASLES, which affects mostly children.

Measles morbillivirus

Measles virus

The type species of the genus ALPHAINFLUENZAVIRUS that causes influenza and other diseases in humans and animals. Antigenic variation occurs frequently between strains, allowing classification into subtypes and variants. Transmission is usually by aerosol (human and most non-aquatic hosts) or waterborne (ducks). Infected birds shed the virus in their saliva, nasal secretions, and feces.

Influenza A virus

A species of the genus FLAVIVIRUS which causes an acute febrile and sometimes hemorrhagic disease in man. Dengue is mosquito-borne and four serotypes are known.

Dengue virus

viral Infectious disease

Viruses Infection

sequence collection

Sequence Collection

A genus in the family FILOVIRIDAE consisting of several distinct species of Ebolavirus, each containing separate strains. These viruses cause outbreaks of a contagious, hemorrhagic disease (HEMORRHAGIC FEVER, EBOLA) in humans, usually with high mortality.

Ebolavirus

The type species of RUBULAVIRUS that causes an acute infectious disease in humans, affecting mainly children. Transmission occurs by droplet infection.

Mumps orthorubulavirus

Mumps virus

Dengue fever (DF), caused by dengue virus, is an arboviral disease characterized by an initial non-specific febrile illness that can sometimes progress to more severe forms manifesting capillary leakage and hemorrhage (dengue hemorrhagic fever, or DHF) and shock (dengue shock syndrome, or DSS).

dengue disease

Dengue

An arbovirus in the FLAVIVIRUS genus of the family FLAVIVIRIDAE. Originally isolated in the Zika Forest of UGANDA it has been introduced to Asia and the Americas.

Zika virus

A contagious viral infection caused by the mumps virus. Symptoms include swollen and tender parotid glands, fever, muscle aches and fatigue. Due to vaccination programs, mumps has become a rare disease.

mumps infectious disease

Mumps

A highly contagious viral infection caused by the measles virus. Symptoms appear 8-12 days after exposure and include a rash, cough, fever and muscle pains that can last 4-7 days. Measles vaccines are available to provide prophylaxis, usually combined with mumps and rubella vaccines (MMR).

measles

Measles

A viral hemorrhagic fever that is caused by the Ebola virus, which is transmitted by contact with infected animals or humans; it is characterized by high fever, unexplained bleeding, and a high mortality rate.

Ebola hemorrhagic fever

Ebola

An acute viral infection of the respiratory tract, occurring in isolated cases, in epidemics, or in pandemics; it is caused by serologically different strains of viruses (influenzaviruses) designated A, B, and C, has a 3-day incubation period, and usually lasts for 3 to 10 days. It is marked by inflammation of the nasal mucosa, pharynx, and conjunctiva; headache; myalgia; often fever, chills, and prostration; and occasionally involvement of the myocardium or central nervous system.

influenza

Influenza

An infectious disease where a pathogen is carried and transmitted by another organism that acts as disease vector.

vector-borne disease

Vector-borne Infection

A viral infectious disease caused by RNA viruses in the Arenaviridae, Bunyaviridae, Filoviridae, or Flaviviridae family, and characterized by a severe multisystem syndrome, with damage to the vascular system and hemorrhaging.

viral hemorrhagic fever

Viral Hemorrhagic Fever

Mosquito-born virus disease characterized by a clinical course that may be asymptomatic or mild with fever, conjunctivitis, muscle and joint pain, headache, exanthema, but may also be associated with severe neurological (meningitis, meningoencephalitis and myelitis) and auto-immune (Guillain-Barre syndrome) complications, as well as a potential increase of birth defects (microcephaly) if the infection occurs during pregnancy.

Zika virus infectious disease

Zika

A respiratory tract infection caused by a virus. Viruses represent the most common causes of upper and lower respiratory tract infections and include rhinoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial virus.

viral respiratory tract infection

Viral Respiratory Tract Infection

Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.

Viruses

Unidentified influenza virus is a species of ssRNA(-) virus in the family Orthomyxoviridae.

unidentified influenza virus

Influenza virus

Species of the genus BETAINFLUENZAVIRUS that cause HUMAN INFLUENZA and other diseases primarily in humans. Antigenic variation is less extensive than in type A viruses (INFLUENZA A VIRUS) and consequently there is no basis for distinct subtypes or variants. Epidemics are less likely than with INFLUENZA A VIRUS and there have been no pandemics. Previously only found in humans, Influenza B virus has been isolated from seals which may constitute the animal reservoir from which humans are exposed.

Influenza B virus

The type species of PNEUMOVIRUS and an important cause of lower respiratory disease in infants and young children. It frequently presents with bronchitis and bronchopneumonia and is further characterized by fever, cough, dyspnea, wheezing, and pallor.

human respiratory syncytial virus

Infection by an etiologic agent that can be passed between animals and humans.

Zoonotic Infection

Zoonotic infection

The type species of the FLAVIVIRUS genus. Principal vector transmission to humans is by AEDES spp. mosquitoes.

Yellow fever virus

Neglected tropical diseases (NTDs) are a diverse group of conditions caused by a variety of pathogens (including viruses, bacteria, parasites, fungi and toxins) and associated with devastating health, social and economic consequences.

neglected tropical disease

Neglected Tropical Disease

Vaccine preventable diseases are those infectious diseases that can be prevented by vaccination

vaccine-preventable Disease

Vaccine-Preventable Disease

An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.

pathogen

Pathogen

A collection of information in various types of structured or non-structured formats.

repository

The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability

about-property-structure

Apache 2.0

Schema.org vocabulary for structured data on the web

Schema.org

A structured data markup specification for describing datasets in the life sciences, extending schema.org Dataset

Bioschemas Dataset Profile

Dublin Core Metadata Initiative Terms - refined elements for precise resource description

DCMI Metadata Terms

W3C Data Catalog Vocabulary for describing data catalogs

Data Catalog Vocabulary

DataCite metadata schema for research data citation

DataCite Metadata Schema

W3C Provenance Ontology for describing provenance information

PROV Ontology

Provenance, Authoring and Versioning ontology for metadata about web resources

PAV Ontology

Custom MIDAS vocabulary for epidemiological data and modeling

MIDAS Metadata Vocabulary

OBO Foundry ontologies for life sciences and biomedical research

Open Biological and Biomedical Ontology

Health Level 7 Fast Healthcare Interoperability Resources

HL7 FHIR

Systematized Nomenclature of Medicine Clinical Terms

SNOMED Clinical Terms

LOINC database for laboratory and clinical observations

Logical Observation Identifiers Names and Codes

JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records

MIDAS Catalog JSON-LD Schema

Landing page where users can browse and download dataset files in various formats.

Identifier	URL: https://github.com/nextstrain/fauna
Type	Repository
Topics/About	Disease Infectious Disease Neglected Tropical Disease Dengue Vaccine-Preventable Disease COVID-19 Dengue Ebola Influenza Measles Mumps Yellow Fever Virus Infection Vector-borne Infection Dengue Yellow Fever Virus Infection Zika Viruses Infection Dengue Measles Mumps Viral Hemorrhagic Fever Ebola Viral Respiratory Tract Infection COVID-19 Influenza Yellow Fever Virus Infection Zika Zoonotic infection Ebola Influenza Yellow Fever Virus Infection Zika Host Homo sapiens Pathogen Viruses Dengue virus Ebolavirus human respiratory syncytial virus Influenza A virus Influenza B virus Influenza virus Measles virus Mumps virus SARS-CoV2 Yellow fever virus Zika virus Sequence Collection
Language	English
License	GNU AGPL v3
Accessible For Free	TRUE
Biological Scale	molecular
Software Language	Python
File Format	JSON, FASTA
Version	unspecified
HTTP Status Code	200
HTTP Checked On	2026/09/13