DOI: 10.5281/zenodo.17725054
title: Scaling Lassa Virus Dynamics within Anthropogenic Ecosystems (SCAPES) Study Protocol: a mixed-methods observational cohort study of humans, rodents, and landscapes in Nigeria.

description: General Information

This repository contains the processed, anonymised datasets underlying the analysis presented in the associated publication. The data focuses on household demographics, rodent interactions, and serological evidence of Lassa fever exposure in Benue, Cross River and Ebonyi States, Nigeria.

Data Processing and Anonymisation Statement

To protect participant privacy and comply with ethical requirements regarding Participant Identifiable Information (PII), the following processing steps have been applied to the raw data:





Pseudonymisation: All original identifiers (Household IDs, Individual IDs, Names) have been stripped. A randomised, non-identifiable linkage key (public_hh_id and public_ind_id) was generated to allow linkage between tables without revealing the original survey sequence.




Geomasking: Spatial coordinates (latitude, longitude) have been subjected to random displacement (jittering) of up to 500m to prevent the precise location of households from being identified while preserving regional spatial patterns for analysis.




Attribute Suppression: Free-text fields containing potential identifiers (names, specific notes) have been removed. Age has been top-coded at 90 years.



Due to these privacy measures, the raw code used for data cleaning is not included. However, the analysis code provided in this repository is fully reproducible using these processed datasets.

File Overview

The repository consists of three comma-separated value (CSV) files:





households_anon.csv: Household-level demographic, structural, and risk-factor data.




individuals_anon.csv: Individual-level demographic, behavioural, and knowledge data.




serology_anon.csv: Laboratory results from IgG ELISA assays.





Data Dictionary

1. households_anon.csv

Linkage Key:





public_hh_id: Unique, randomised alphanumeric identifier for the household. Used to join with individuals_anon.csv.



Temporal & Spatial:





date_visit: Date the questionnaire was administered (YYYY-MM-DD).




latitude: Geomasked latitude (WGS84). Coordinates have been randomly displaced.




longitude: Geomasked longitude (WGS84). Coordinates have been randomly displaced.



Demographics:





n_people: Number of individuals living within the household.




multiple_family_household: Binary indicator if multiple families reside in the household (1 = Yes, 0 = No).




household_ethnicity: Primary ethnicity of the household.





Codes: igbo_izzi, igbo_other, membe, tiv, other.






household_religion: Primary religion of the household.





Codes: christian, muslim, traditionalist, other.





Housing Structure:





n_compound: Number of structures within the compound.




n_individual_buildings: Number of individual buildings used regularly by the household.




building_owned: Ownership status of the buildings.





Codes: own_themselves, own_family, rented, other.






n_single_room: Number of single-room buildings used.




n_multi_room: Number of multi-room buildings used.




toilet: Type of toilet facility used.





Codes: field_defecation (Open/Bush), open_system (Trench), pit_latrine, toilet_plumbing, other.





Domestic Animals & Risk Factors:





livestock: Does the household own livestock? (1 = Yes, 0 = No).




livestock_animals: Types of animals owned (multiple options separated by space/comma).





Codes: chicken, goat, cow, pig, duck, other.






cats: Does the household keep cats? (1 = Yes, 0 = No).




cats_inside: Do cats ever enter the buildings? (1 = Yes, 0 = No).



Rodent Interactions & Control:





rodent_removal_home_method: Methods used to remove rats from the home.





Codes: traps, poison, gumtrap, sticks, cat, dog, other.






rodent_remove_use: Disposal method of removed rats.





Codes: eat_them, sell_them, dispose_them, feed_them_to_animals, no_contact.






rodent_mitigation_method: Structural methods used to prevent rodent entry/damage.





Codes: containers, seal_burrows, convert_door (metal doors), upgrade_structure (concrete), cats, dogs, none.





Food Security:





food_resources: In the past 30 days, was there no food due to lack of resources? (1 = Yes, 0 = No).




food_sleep: In the past 30 days, did a member sleep hungry? (1 = Yes, 0 = No).




food_day: In the past 30 days, did a member go a whole day/night without eating? (1 = Yes, 0 = No).





2. individuals_anon.csv

Linkage Keys:





public_ind_id: Unique, randomised identifier for the study participant.




public_hh_id: Identifier of the household the participant belongs to (links to households_anon.csv).



Demographics:





sex: Sex of the participant (0 = Male, 1 = Female).




age: Age in years (Top-coded at 90 for privacy).




education: Highest level of education attained.





Codes: none, primary, junior_secondary, senior_secondary, undergraduate, postgraduate, other.






income_bracket: Self-reported monthly income (Anonymised/Categorical representation of raw integer data).



Residence & Movement:





village_residence_status: Is the participant a permanent resident of the village? (Yes/No).




months_residence_in_year: Number of months per year spent in the community (1-12).




sleep_elsewhere: Does the participant regularly sleep in a different location? (Yes/No).




field_work_freq: Months per year spent working in agricultural fields (1-12).




forest_entry_freq: Months per year spent accessing forested areas (1-12).



Dietary Behaviours (Zoonotic Risk):





meat_consumption_freq: Frequency of domestic meat consumption.





Codes: few_life, few_year, few_month, few_week, daily.






bushmeat_consumption: Does the participant eat meat from wild animals? (Yes/No).




bushmeat_freq: Frequency of bushmeat consumption (same codes as domestic meat).




rodent_consumption_history: Has the participant ever eaten rat? (Yes/No).




current_rodent_consumption: Does the participant currently eat rat? (Yes/No).



Lassa Fever Knowledge & Risk:





lassa_disease_aware: Has the participant heard of Lassa fever? (Yes/No).




lassa_source: Source of information regarding Lassa fever.





Codes: radio, television, hospital_or_health_centre, community, etc.






rodent_contact_lassa: Knowledge of transmission routes (e.g., consumption_rat, contact_excreta).





3. serology_anon.csv

Identifiers:





sample: Internal sample identifier used for laboratory tracking.




public_ind_id: Linkage key to individuals_anon.csv.



Assay Metadata:





experiment_batch: Laboratory batch identifier.



Results (ELISA):





OD450: Optical Density at 450nm.




OD630: Optical Density at 630nm (Reference).




Delta: Calculated difference (OD450 - OD630).




cut_off: Calculated threshold for positivity for the specific plate/batch.




index_value: Normalised index value (Delta / cut_off).




interpretation: Final result classification (Positive/Negative/Equivocal).



Quality Control:





valid_pc: Validity status of the Positive Control well.




valid_nc: Validity status of the Negative Control well.