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:

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 descriptions

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

Citations

Citation key Reference
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