Data collected for Mollentze et al. (2020). Virulence mismatches in index hosts shape the outcomes of cross-species transmission. PNAS (in press).
Two versions of the data are available:
cleaned_consolidated_data.csv
- cleaned / processed data, including consolidated disease progression timings. Generated by GenerateReleaseData.R
.raw_data.csv
- raw data, as entered. Note that this dataset contains a few data-entry errors and other inconsistencies, and should not be used directly. See PrepareData.R
for the corrections applied prior to use in the present study.Each row in the data represents a single inoculated animal. All available data were recorded, as long as it could be unequivocally linked to a single animal. When multiple sets of data could not be linked up to individual animals, preference was given to recording data on disease progression timings.
Column name | Data type | Description | Notes |
---|---|---|---|
CitationKey | text | Bibtex citation key for the publication relating to this record (see “data_references.bib”). | |
ExperimentID | text | Unique identifier for a discrete experiment (some publications report multiple experiments). | |
ResultGroup | text | Unique identifier for groups of related records, representing a group of animals for which some data were reported only in aggregated form (e.g. a range of survival times for all animals receiving a given treatment). | |
AnimalID | text | Unique identifier for the animal represented by this inoculation record. If a publication reports animal identifiers, that identifier will form part of this unique identifier. | |
SourceSpecies | text | Species from which the virus inoculum was derived. | |
SourceSubSpecies | text | Subspecies from which the virus inoculum was derived, where available. | Present in clean data only – raw data contains this information as part of the “SourceSpecies” column. |
SourceKnownHost | boolean | Is the stated virus source a known reservoir of rabies? | |
InoculatedSpecies | text | Species of the inoculated animal. | |
InculatedSubSpecies | text | Subspecies of the inoculated animal, where available. | Present in clean data only – raw data contains this information as part of the “InoculatedSpecies” column. |
InoculatedKnownHost | boolean | Is the inoculated species a known reservoir of rabies? | |
InoculatedCommonName | text | Common name of the inoculated species, as reported. | |
InoculatedAge | text | Age category of the inoculated animal, as reported. | |
InoculatedSex | text | Sex of the inoculated animal. | |
InoculumID | text | Unique identifier for the specific virus inoculum used. Different experiments and publications may re-use the same inoculum. | See “InoculumData.csv” for more details on each inoculum. |
InoculumType | text | Tissue from which the inoculum was prepared – values are “SalivaryGland”, “Brain” or “Supernatant” (representing cell culture supernatant). | Present in clean data only (derived from “InoculumData.csv”) |
PassageHost | text | Animal species or type of cell culture in which virus was passaged prior to inoculation. | |
PassageNumber | numeric | Number of passages the virus was subjected to prior to the present inoculation. | |
InoculationRoute_raw | text | Inoculation route, as reported. | Named “InoculationRoute” in raw data. |
InoculationRoute_cat | text | Inoculation route, reclassified into a set of defined categories. | Present in clean data only. |
InoculationPropDist | numeric | Proportional inoculation distance for this inoculation route category. | Present in clean data only. |
Dose | numeric | Dose used in this inoculation. | |
TitrationMethod | text | Method used to determine the inoculated dose. This determines the units for the “Dose” column. | |
CauseOfDeath | text | Cause of death, as a free text field. Records with “NA” survived until the end of their respective experiments (see “ExperimentLength”); “unknown” means the animal died during the experiment, but a cause was either not reported, or not known. | |
RabiesConfirmed | boolean | Was a rabies infection confirmed by at least one diagnostic method? | |
ConfirmationMethod | text | Diagnostic method(s) used to test whether animal was infected with rabies. FAT = fluorescent antibody test, MIT = mouse inoculation test, IC = intracranial inoculation of mice (but not reported by the authors as an MIT). | |
RabiesClinicalDiagnosis | boolean | Did the original authors consider this a case of rabies based on disease presentation? | |
OtherCOD | boolean | Was the animal reported to have died of a cause unrelated to rabies? | |
ExperimentLength | numeric | Length of the experiment (or observation period for this specific animal), in days post infection. In some experiments, animals were euthanised at different times over the course of the experiment. In such cases, “ExperimentLength” will differ for animals in the same experiment. | |
days_survived_lower | numeric | Number of days between inoculation and death (lower bound). | Consolidated variable, present in clean data only. |
days_survived_upper | numeric | Number of days between inoculation and death (upper bound). | Consolidated variable, present in clean data only. |
incubation_lower | numeric | Inocubation period duration, in days (lower bound). | Consolidated variable, present in clean data only. |
incubation_upper | numeric | Inocubation period duration, in days (upper bound). | Consolidated variable, present in clean data only. |
clinical_lower | numeric | Clinical period duration, in days (lower bound). | Consolidated variable, present in clean data only. |
clinical_upper | numeric | Clinical period duration, in days (upper bound). | Consolidated variable, present in clean data only. |
VirusInSalivaryGlands | boolean | Was virus detected in salivary glands post mortem? | |
VirusExcreted_FirstDay_Lower | numeric | First day on which virus was detected in saliva samples (lower bound). | |
VirusExcreted_FirstDay_Upper | numeric | First day on which virus was detected in saliva samples (lower bound). | |
ExcretionConfirmationMethod | text | Method used to detect virus in saliva samples. | |
SalivaTitre_Max | numeric | Maximum virus titre observed in saliva samples over the course of infection, in mouse LD50. Note that experiments differed in the frequency with which saliva samples were taken. | |
GlandTitre | numeric | Virus titre in salivary glands post mortem, in mouse LD50. | |
DiseaseManifestation | text | Manifestation of disease, as reported. | |
AntibodyResponse | boolean | Did the animal show an antibody response at any time during the infection? “NA” means not tested, while “FALSE” means the animal was tested, but negative. | |
Inoculum_Notes | text | Notes about the inoculum used. | Present in clean data only (derived from “InoculumData.csv”) |
Comments | text | General comments about this animal / inoculation record. | |
RowID | numeric | Unique identifier for this inoculation record. | Present in clean data only. |
DaysSurvived | numeric | Number of days survived, if reported. | Available only when directly reported, present in raw data only. |
DaysSurvived_Lower | numeric | Lower limit of days survived, if reported. | Available only when directly reported, present in raw data only. |
DaysSurvived_Upper | numeric | Upper limit of days survived, if reported. | Available only when directly reported, present in raw data only. |
IncubationPeriod_Lower | numeric | Lower limit of incubation period, if reported. | Available only when directly reported, present in raw data only. |
IncubationPeriod_Upper | numeric | Upper limit of incubation period, if reported. | Available only when directly reported, present in raw data only. |
IncubationPeriod_Median | numeric | Median incubation period for this result group, if reported. | Available only when directly reported, present in raw data only. |
MorbidityPeriod_Lower | numeric | Lower limit of clinical period, if reported. | Available only when directly reported, present in raw data only. |
MorbidityPeriod_Upper | numeric | Upper limit of clinical period, if reported. | Available only when directly reported, present in raw data only. |
MorbidityPeriod_Median | numeric | Median clinical period for this result group, if reported. | Available only when directly reported, present in raw data only. |
CitationTitle | text | Title of study reporting this inoculation, as in the original meta-analysis search results. | Present in raw data only. |
SourceOrder | text | Taxonomic order of the virus source (the reservoir). | May not match latest taxonomy, present in raw data only |
SourceSubOrder | text | Taxonomic sub-order of the virus source. | May not match latest taxonomy, present in raw data only |
SourceFamily | text | Taxonomic family of the virus source. | May not match latest taxonomy, present in raw data only |
SourceGenus | text | Taxonomic genus of the virus source. | May not match latest taxonomy, present in raw data only |
InoculatedOrder | text | Taxonomic order of the inoculated animal. | May not match latest taxonomy, present in raw data only |
InoculatedSubOrder | text | Taxonomic sub-order of the inoculated animal. | May not match latest taxonomy, present in raw data only |
InoculatedFamily | text | Taxonomic family of the inoculated animal. | May not match latest taxonomy, present in raw data only |
InoculatedGenus | text | Taxonomic genus of the inoculated animal. | May not match latest taxonomy, present in raw data only |
Citation key | Reference |
---|---|
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