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SARS-CoV-2 wastewater and epidemiological data from Kisumu Kenya

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posted on 2025-04-02, 21:46 authored by Bhagya Galkissa DewageBhagya Galkissa Dewage, Samuel DorevitchSamuel Dorevitch, Abhilasha ShresthaAbhilasha Shrestha, Jared Oremo, Simon Bunde, Oscar Oluoch Akello, Naomy Onyuka, Jeremiah Ongwara

This data repository contains wastewater-based and epidemiological data collected in Kisumu, Kenya, between March 29, 2022 and March 8, 2023. Wastewater-based data was generated from samples (n=161) collected and extracted by trained professionals from centralized wastewater treatment sites (n=41) and from decentralized sites: hospitals (n=50), public toilets in markets (n=31), and public toilets at transportation hubs (n=39). The presence or absence of SARS-CoV-2 RNA and its concentration if present were measured using RT-qPCR. Epidemiological data was gathered from two sources, COVID-Dx platform and the Kisumu County Health Information Office. This epidemiological data includes the number of SARS-CoV-2 tests conducted, the number of positive tests, and the number of COVID-19 related admissions from the four largest hospitals in Kisumu: JOOTRH, Kisumu County Referral Hospital, Avenue Hospital, and Aga Khan Hospital. The odds of detecting one or more COVID-19 cases within 4-7 days after a positive WBS sample were 9 times higher than on days with negative WBS samples.

T_min : Minimum daily temperature

T_max: Maximum daily temperature

Average_WBS_conc : Average Wastewater based SARS CoV-2 concentration Gene copies/ml

Cat_WBS : Absence or presence of SARS CoV-2 in Wastewater samples

logconc : Log concentration

WWTP : Average WBS concentration in wastewater treatment plant samples

Transport_public_toilets : Average WBS concentration in bus terminal wastewater samples

Market_public_toilets : Average WBS concentration in market wastewater samples

Hospitals : Average WBS concentration in hospital wastewater samples

Total_tests : Total number of COVID-19 tests conducted in the four hospitals

Total_positives : Total number of positive COVID-19 tests from the four hospitals

Total_admissions : Total number of COVID-19 related admissions in the four hospitals

Cum_pos_3daysbefore : Cumulative number of positive COVID-19 tests within 3 days before a wastewater sample collection date

Cum_pos_7daysbefore: Cumulative number of positive COVID-19 tests within 7 days before a wastewater sample collection date

Cum_pos_15daysbefore : Cumulative number of positive COVID-19 tests within 15 days before a wastewater sample collection date

Cum_pos_3daysafter : Cumulative number of positive COVID-19 tests within 3 days after a wastewater sample collection date

Cum_pos_7daysafter : Cumulative number of positive COVID-19 tests within 7 days after a wastewater sample collection date

Cum_pos_15daysafter : Cumulative number of positive COVID-19 tests within 15 days after a wastewater sample collection date


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