Items corresponding to entire populations or subpopulations. Might be geographically or temporally temporally limited.

population

The dataset contains 382 transmission trees with outbreak size from 2 to 286 for 16 directly-transmitted infectious diseases including COVID-19 (256 trees), H1N1, EBOLA, etc. most of which are caused by viruses. The trees are directly download but also can be explore on the website directly and can contains information on context of suspected transmission event (family, household, meal, hospital, etc.), sex, age, location, quarantine status, occupation, relationship, strain sequence, information regarding certainty/knowledge of transmission pattern (probabilistic vs epidemiologic, or source of transmission link if tree constructed from multiple sources), and duration of exposure period, if known.

non-collection specific

(Simple) Released

R serialized data file (.rds) containing a single saved R object.

Country

Earth

English

CC BY 4.0

Paige B. Miller

John M. Drake

Juliana C. Taube

Outbreak Trees: A database of infectious disease transmission trees for public use

A disease or disorder that involves the digestive system.

digestive system disorder

Digestive System Disorder

The condition of having at least three loose or liquid bowel movements each day.

diarrheal disease

Diarrhea

Actions of groups of people in response to outbreaks.

behavior

Behavior

Frequency of interactions between individuals in different settings, at different times...

contact rates

Contact Rates

Any disorder that results from the consumption of food contaminated with an infectious agent or toxin.

Foodborne Illness

Acute inflammation of the liver caused by the hepatitis A virus. It is highly contagious and usually contracted through close contact with an infected individual or their feces, contaminated food or water.

hepatitis A virus infection

Hepatitis A Infection

One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal.

Bacteria

An active inflammatory process affecting the liver for more than six months. Causes include viral infections, autoimmune disorders, drugs, and metabolic disorders.

hepatitis

Hepatitis

A species of gram-negative, aerobic bacteria that is the causative agent of WHOOPING COUGH. Its cells are minute coccobacilli that are surrounded by a slime sheath.

Bordetella pertussis

An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections.

bacterial infectious disease

Bacterial Infection

A census that is the specific outcome of a population demographic survey.

population demographic census

Population Demographic

A contagious bacterial respiratory infection caused by Bordetella pertussis. It is characterized by severe and uncontrollable cough, resulting in a whooping sound during breathing following the cough.

pertussis

Pertussis

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

The type species of VARICELLOVIRUS causing CHICKENPOX (varicella) and HERPES ZOSTER (shingles) in humans.

Human alphaherpesvirus 3

Varicella-zoster virus

A strain of HEPATITIS A VIRUS which causes hepatitis in humans. The virus replicates in hepatocytes and is presumed to reach the intestine via the bile duct. Transmission occurs by the fecal-oral route.

Human hepatitis A virus

The type (and only) species of RUBIVIRUS causing acute infection in humans, primarily children and young adults. Humans are the only natural host. A live, attenuated vaccine is available for prophylaxis.

Rubella virus

An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.

phenotypic sex

age-stratified

Age-Stratified

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

vaccine-preventable Disease

Vaccine-Preventable Disease

A contagious childhood disorder caused by the varicella zoster virus. It is transmitted via respiratory secretions and contact with chickenpox blister contents. It presents with a vesicular skin rash, usually associated with fever, headache, and myalgias. The pruritic fluid-filled vesicles occur 10-21 days after exposure and last for 3-4 days. An additional 3-4 days of malaise follows before the affected individual feels better. An individual is contagious 1-2 days prior to the appearance of the blisters until all blisters are crusted over. Generally, healthy individuals recover without complications.

chickenpox

Varicella

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 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

A viral infection caused by the rubella virus. It is initially manifested with flu-like symptoms that last one or two days, followed by the development of a characteristic red rash which lasts from one to five days. The rash first appears in the neck and face. It subsequently spreads to the rest of the body.

rubella

Rubella Infection

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 chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use.

tuberculosis

Tuberculosis

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

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

viral Infectious disease

Viruses Infection

A species of gram-positive, aerobic bacteria that produces TUBERCULOSIS in humans, other primates, CATTLE; DOGS; and some other animals which have contact with humans. Growth tends to be in serpentine, cordlike masses in which the bacilli show a parallel orientation.

Mycobacterium tuberculosis

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

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

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

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

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

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

Zoonotic Infection

Zoonotic infection

A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.

data set

Topic

Digital Object Type

Geographic Resolution

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

GeoNames 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

Searchable collection of curated datasets and software resources for infectious disease modeling, filterable by disease, topic, location, and time period.

MIDAS Catalog

Data for OutbreakTrees database and to reproduce results in "An open-access database of infectious disease transmission trees to explore superspreader epidemiology"

Identifier	URL: https://outbreaktrees.ecology.uga.edu/
Type	Data Set
Topics/About	Behavior Contact Rates Disease Digestive System Disorder Diarrhea Foodborne Illness Hepatitis A Infection Hepatitis Hepatitis A Infection Infectious Disease Bacterial Infection Pertussis Tuberculosis Vaccine-Preventable Disease COVID-19 Ebola Hepatitis A Infection Influenza Measles Pertussis Rubella Infection Tuberculosis Varicella Viruses Infection Hepatitis A Infection Measles Rubella Infection Varicella Viral Hemorrhagic Fever Ebola Viral Respiratory Tract Infection COVID-19 Influenza Zoonotic infection Ebola Influenza Host Homo sapiens Pathogen Bacteria Bordetella pertussis Mycobacterium tuberculosis Viruses Ebolavirus Human hepatitis A virus Influenza A virus Influenza B virus Influenza virus Measles virus Rubella virus SARS-CoV2 Varicella-zoster virus Population Demographic Age-Stratified Sex
Language	English
License	CC BY 4.0
Accessible For Free	TRUE
Biological Scale	population
Geographical Scope	Earth
Geographical Resolution	Country
Start Date	1946/01/01
End Date	2020/12/31
Collection End Date	2020/07/06
File Format	RDS
Version	unspecified
HTTP Status Code	200
HTTP Checked On	2026/09/27