OxRML/AgentSLR huggingface dataset:
Pathogen: Lassa mammarenavirus
Parameter class: Reproduction number
Parameter type: Reproduction number (Basic R0)
Parameter value: 1.1868
Unit: No units
Value type: Unspecified
Epidemic phase: Endemic
Reproduction number method: Next generation matrix
Reproduction number pathway: Other
Population group: Persons under investigation
Sample type: Population based
Sex: Unspecified
Country: Nigeria
Study period:   2018 to   2022
Pathogen: Lassa mammarenavirus
Parameter class: Reproduction number
Parameter type: Reproduction number (Basic R0)
Parameter value: 1.1299
Unit: No units
Value type: Unspecified
Epidemic phase: Unspecified
Reproduction number method: Next generation matrix
Reproduction number pathway: Other
Population group: Persons under investigation
Sample type: Population based
Sex: Unspecified
Country: Nigeria
Study period: 3 Jan 01 2021 to 19 May 05 2021
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 19
Unit: Percentage (%)
Value type: Unspecified
Lower bound: 16
Upper bound: 31
Bounds: 16 - 31
CFR/IFR numerator: 12
CFR/IFR denominator: 62
CFR/IFR method: Unspecified
Epidemic phase: Endemic
Disaggregated by: Occupation, Other
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Sample size: 62
Country: Nigeria
Location: Ebonyi State
Study period: 1 Jan 01 2018 to 31 Mar 03 2018
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - incubation period
Parameter value: 7
Unit: Days
Value type: Unspecified
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Sample size: 62
Country: Nigeria
Location: Ebonyi State
Study period: 1 Jan 01 2018 to 31 Mar 03 2018
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - Unspecified
Parameter value: 15.5
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR numerator: 15
CFR/IFR denominator: 97
Epidemic phase: Unspecified
Disaggregated by: Age, Occupation, Sex
Population group: Mixed groups
Sample type: Trade / business based
Sex: Both
Minimum age: 3
Maximum age: 56
Sample size: 97
Country: Nigeria
Location: Pankshin, Plateau State
Study period:  Aug 08 1976 to  Aug 08 1976
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IFA
Unit: Percentage (%)
Lower bound: 0
Upper bound: 52
Bounds: 0 - 52
Epidemic phase: Endemic
Disaggregated by: Age, Region, Sex
Population group: General population
Sample type: Community based
Sex: Both
Country: Sierra Leone
Location: Palima, Semewabu, Konia, Tongola, Njakundoma, Niahun, Kpandebu, Neama, Lowoma, Landoma, Bomie, Yengema, Kamethe, Kamabunyele, Kathumpe
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 63
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR numerator: 36
CFR/IFR denominator: 57
CFR/IFR method: Unspecified
Epidemic phase: Endemic
Population group: Children
Sample type: Hospital based
Sex: Both
Minimum age: 0
Maximum age: 18
Sample size: 57
Country: Sierra Leone
Location: Kenema District Of Eastern Province
Study period: 1 Jan 01 2012 to 31 Dec 12 2018
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Endemic
Risk factor: Age;Other;Sex
Risk factor outcome: Death
Risk factor significance: Not significant
Risk factor adjustment: Not adjusted
Population group: Children
Sample type: Hospital based
Sex: Both
Minimum age: 0
Maximum age: 18
Sample size: 57
Country: Sierra Leone
Location: Kenema District Of Eastern Province
Study period: 1 Jan 01 2012 to 31 Dec 12 2018
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Endemic
Risk factor: Other
Risk factor outcome: Death
Risk factor significance: Significant
Risk factor adjustment: Not adjusted
Population group: Children
Sample type: Hospital based
Sex: Both
Minimum age: 0
Maximum age: 18
Sample size: 57
Country: Sierra Leone
Location: Kenema District Of Eastern Province
Study period: 1 Jan 01 2012 to 31 Dec 12 2018
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 36
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR numerator: 4
CFR/IFR denominator: 11
CFR/IFR method: Naive
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Minimum age: 20
Maximum age: 56
Sample size: 11
Country: Liberia
Location: Zorzor
Study period:  Mar 03 1972 to  Apr 04 1972
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - incubation period
Unit: Days
Lower bound: 1
Upper bound: 24
Bounds: 1 - 24
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Minimum age: 20
Maximum age: 56
Sample size: 11
Country: Liberia
Location: Zorzor
Study period:  Mar 03 1972 to  Apr 04 1972
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - symptom onset>admission to care
Parameter value: 4
Unit: Days
Value type: Mean
Uncertainty type: Range
Uncertainty lower value: 0
Uncertainty upper value: 7
Combined uncertainty: 0 - 7 (Range)
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Minimum age: 20
Maximum age: 56
Sample size: 11
Country: Liberia
Location: Zorzor
Study period:  Mar 03 1972 to  Apr 04 1972
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - symptom onset>discharge/recovery
Parameter value: 14
Unit: Days
Value type: Mean
Uncertainty type: Range
Uncertainty lower value: 11
Uncertainty upper value: 21
Combined uncertainty: 11 - 21 (Range)
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Minimum age: 20
Maximum age: 56
Sample size: 11
Country: Liberia
Location: Zorzor
Study period:  Mar 03 1972 to  Apr 04 1972
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - symptom onset>death
Parameter value: 12
Unit: Days
Value type: Mean
Uncertainty type: Range
Uncertainty lower value: 12
Uncertainty upper value: 15
Combined uncertainty: 12 - 15 (Range)
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Minimum age: 20
Maximum age: 56
Sample size: 11
Country: Liberia
Location: Zorzor
Study period:  Mar 03 1972 to  Apr 04 1972
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
CFR/IFR numerator: 54
CFR/IFR denominator: 400
CFR/IFR method: Adjusted
Epidemic phase: Unspecified
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Sample size: 400
Country: Nigeria
Location: Edo, Ebonyi, Ondo, Kebbi
Study period:   2017 to   2020
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Other
Risk factor outcome: Death
Risk factor significance: Significant
Risk factor adjustment: Not adjusted
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Country: Nigeria
Location: Edo, Ebonyi, Ondo, Kebbi
Study period:   2017 to   2020
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Age;Other;Sex
Risk factor outcome: Death
Risk factor significance: Not significant
Risk factor adjustment: Not adjusted
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Country: Nigeria
Location: Edo, Ebonyi, Ondo, Kebbi
Study period:   2017 to   2020
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Other
Risk factor outcome: Death
Risk factor significance: Significant
Risk factor adjustment: Adjusted
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Country: Nigeria
Location: Edo, Ebonyi, Ondo, Kebbi
Study period:   2017 to   2020
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Age;Other
Risk factor outcome: Death
Risk factor significance: Not significant
Risk factor adjustment: Adjusted
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Country: Nigeria
Location: Edo, Ebonyi, Ondo, Kebbi
Study period:   2017 to   2020
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: L segment
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: S segment
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: GPC
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: L
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: NP
Pathogen: Lassa mammarenavirus
Parameter class: Mutations
Parameter type: Mutations - evolutionary rate
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 151
Country: Benin, Côte d'Ivoire, Ghana, Guinea, Liberia, Mali, Nigeria, Sierra Leone, Togo
Study period:   1974 to   2018
Genome site: Z
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IgG
Parameter value: 25.9
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR denominator: 751
Epidemic phase: Unspecified
Disaggregated by: Age
Population group: Other
Sample type: Other
Sex: Both
Sample size: 751
Country: Nigeria
Study period:   2011 to   2018
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IgG
Parameter value: 49.6
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR denominator: 589
Epidemic phase: Unspecified
Disaggregated by: Age
Population group: Other
Sample type: Other
Sex: Both
Sample size: 589
Country: Sierra Leone
Study period:   2011 to   2018
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IgG
CFR/IFR numerator: 0
CFR/IFR denominator: 117
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 117
Country: United States
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 35.3
Unit: Percentage (%)
Value type: Unspecified
Lower bound: 19.4
Upper bound: 42.9
Bounds: 19.4 - 42.9
CFR/IFR numerator: 107
CFR/IFR method: Adjusted
Epidemic phase: Unspecified
Disaggregated by: Age
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Country: Nigeria
Location: Isth
Study period:   2011 to   2018
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 64.8
Unit: Percentage (%)
Value type: Unspecified
Lower bound: 45.8
Upper bound: 73.3
Bounds: 45.8 - 73.3
CFR/IFR numerator: 70
CFR/IFR denominator: 108
CFR/IFR method: Adjusted
Epidemic phase: Unspecified
Disaggregated by: Age
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Sample size: 108
Country: Sierra Leone
Location: Kgh
Study period:   2011 to   2016
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Other
Risk factor outcome: Death
Risk factor significance: Significant
Risk factor adjustment: Not adjusted
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Country: Nigeria, Sierra Leone
Location: Isth, Kgh
Study period:   2011 to   2018
Pathogen: Lassa mammarenavirus
Parameter class: Risk factors
Parameter type: Risk factors
Epidemic phase: Unspecified
Risk factor: Age;Other
Risk factor outcome: Death
Risk factor significance: Not significant
Risk factor adjustment: Not adjusted
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Country: Nigeria, Sierra Leone
Location: Isth, Kgh
Study period:   2011 to   2018
Pathogen: Lassa mammarenavirus
Parameter class: Reproduction number
Parameter type: Reproduction number (Effective, Re)
Parameter value: 1.82
Unit: No units
Value type: Median
Uncertainty type: 90% CrI
Uncertainty lower value: 0.311
Uncertainty upper value: 3.09
Combined uncertainty: 0.311 - 3.09 (90% CrI)
Epidemic phase: Endemic
Reproduction number method: Next generation matrix
Reproduction number pathway: Human-human
Population group: Persons under investigation
Sample type: Population based
Sex: Unspecified
Country: Nigeria
Study period: 7 Jan 01 2018 to 12 Jul 07 2020
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - symptom onset>admission to care
Parameter value: 6
Unit: Days
Value type: Median
Uncertainty type: IQR
Uncertainty lower value: 3
Uncertainty upper value: 9
Combined uncertainty: 3 - 9 (IQR)
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Sample size: 192
Country: Liberia
Study period:   2016 to   2021
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 44.8
Unit: Percentage (%)
Value type: Unspecified
Lower bound: 0
Upper bound: 77.8
Bounds: 0 - 77.8
CFR/IFR numerator: 86
CFR/IFR denominator: 192
CFR/IFR method: Adjusted
Epidemic phase: Endemic
Disaggregated by: Age, Other, Region, Sex, Time
Population group: Persons under investigation
Sample type: Population based
Sex: Both
Sample size: 192
Country: Liberia
Study period:   2016 to   2021
Pathogen: Lassa mammarenavirus
Parameter class: Reproduction number
Parameter type: Reproduction number (Basic R0)
Parameter value: 1.395
Unit: No units
Value type: Unspecified
Epidemic phase: Endemic
Reproduction number method: Next generation matrix
Reproduction number pathway: Other
Population group: Persons under investigation
Sample type: Population based
Sex: Unspecified
Country: Nigeria
Study period:  Jan 01 2019 to  Dec 12 2019
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IFA
CFR/IFR numerator: 8
CFR/IFR denominator: 1898
Epidemic phase: Unspecified
Population group: Unspecified
Sample type: Unspecified
Sex: Unspecified
Sample size: 1898
Country: Central African Republic
Location: Savannah And Forest Galley Areas
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Unit: Percentage (%)
Lower bound: 12.5
Upper bound: 78
Bounds: 12.5 - 78
CFR/IFR numerator: 56
CFR/IFR denominator: 137
CFR/IFR method: Adjusted
Epidemic phase: Endemic
Disaggregated by: Other
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Sample size: 137
Country: Sierra Leone
Study period:   1977 to   1977
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IgM
Parameter value: 67
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR denominator: 137
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Sample size: 137
Country: Sierra Leone
Study period:   1977 to   1977
Pathogen: Lassa mammarenavirus
Parameter class: Seroprevalence
Parameter type: Seroprevalence - IgG
Parameter value: 53
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR denominator: 137
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Hospital based
Sex: Unspecified
Sample size: 137
Country: Sierra Leone
Study period:   1977 to   1977
Pathogen: Lassa mammarenavirus
Parameter class: Human delay
Parameter type: Human delay - admission to care>discharge/recovery
Parameter value: 11
Unit: Days
Value type: Mean
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Minimum age: 1
Maximum age: 60
Sample size: 27
Country: Nigeria
Location: Atbuth, Bauchi
Study period:  Oct 10 2016 to  Apr 04 2018
Pathogen: Lassa mammarenavirus
Parameter class: Severity
Parameter type: Severity - case fatality rate (CFR)
Parameter value: 44.4
Unit: Percentage (%)
Value type: Unspecified
CFR/IFR numerator: 12
CFR/IFR denominator: 27
CFR/IFR method: Unspecified
Epidemic phase: Endemic
Population group: Persons under investigation
Sample type: Hospital based
Sex: Both
Minimum age: 1
Maximum age: 60
Sample size: 27
Country: Nigeria
Location: Atbuth, Bauchi
Study period:  Oct 10 2016 to  Apr 04 2018
Pathogen: Lassa mammarenavirus
Parameter class: Reproduction number
Parameter type: Reproduction number (Basic R0)
Parameter value: 1.32
Unit: No units
Value type: Unspecified
Epidemic phase: Endemic
Reproduction number method: Next generation matrix
Reproduction number pathway: Other
Population group: Persons under investigation
Sample type: Population based
Sex: Unspecified
Country: Nigeria
Study period:  Jan 01 2020 to   2021