The first case of Omicron in Kisumu Country, collected 4 days earlier than the first Omicron reported nationally. The patient had indicated presence of clinical symptoms by December 8, which is only 2 weeks after South Africa reported the first Omicron case to WHO (November 24, 2021). This very early detection of Omicron in Kisumu underscores the value of a County-wide digital epidemic preparedness and monitoring system. In recognition of this, the COVID-Dx is currently being rolled out in all 14 Counties of the Lake Region Economic Bloc.
Gregory Ganda1, Emmanuel Milimo2, Robert Aroka2, Alloys K’Oloo2, Nathalie Houben2, Santa Kratule3, Cem Koyuncu3, Simon Onsongo4, Shem Sam2,5, Tobias F. Rinke de Wit4
- Department of Health, Kisumu County Government P.O. Box 2738-40100, Kisumu, Kenya
- PharmAccess Foundation Kenya Office, Cairo Road, Milimani, 40100, Kisumu, Kenya
- PharmAccess Foundation, Amsterdam Office, Paasheuvelweg 25, 1105 BP, Amsterdam, the Netherlands
- Aga Khan Hospital Kisumu, Kisumu, Kenya
- Lake Region Economic Bloc Eminent Persons Committee, Prosperity House, 9th Floor, Kisumu, Kenya
All correspondence related to this manuscript can be directed towards G. Ganda, Department of Health, Kisumu County Government P.O. Box 2738-40100, Kisumu, Kenya. firstname.lastname@example.org, +254726991098
Early 2021, the Department of Health (DoH) of Kisumu County with technical assistance of the Dutch NGO PharmAccess established a digital COVID-19 epidemic preparedness and monitoring system, named COVID-Dx. This system is fully in sync with the Kenyan National COVID-19 Case Identification format and digitalizes important patient information including socio-demographics, vaccination status, clinical symptoms, comorbidities, occupation, geographical location, reason(s) for testing. Core to COVID-Dx is a digitalized SARS-CoV-2 test result, either obtained through the whole genome sequencing service offered by the KEMRI-Walter Reed Project in Kondele Kisumu or de-centrally at 32 participating Kisumu healthcare providers by RDTs, fully according to Kenyan guidelines. COVID-Dx is built on an initiative in Kisumu that started timely in May 2020, when first COVID cases had to be detected by testing and contact tracing. It built a unique public-private partnership model to supplement ongoing efforts by department of health with the capacity of 9 key private healthcare providers in the County, to best prepare for the imminent COVID-19 outbreak in the region
From the onset of the 5th wave in Kisumu, nasal samples from patients who tested positive for COVID-19 were sequenced. Here we report on the first case of Omicron in Kisumu in a 25 year-old male patient.
The patient reported first symptoms on December 8, 2021 and was admitted in a hospital in Kisumu city December 10, with a positive RDT (Abbott Binax Now). The patient had no travel history, came from Kisumu East, was not vaccinated, though indicating he was willing to. The patient had difficulty in breathing, chest pain, headache, nausea and vomiting, low grade fever and normal SPO2. On December 10, an additional nasal swab was collected and tested for SARS-CoV-2 by qPCR and then sequenced at KEMRI-Walter Reed Project in Kondele Kisumu. The virus was identified as B.1.1.529, the Omicron variant of concern. The patient recovered and released from hospital December 13. This is expected to significantly contribute to the epidemic preparedness of West Kenya.
Screenshots of the COVID-Dx dashboard.
 Kenya M. COVID-19 Antigen Rapid Diagnostic Testing Interim Guide KENYA: Kenya Ministry of Health 2020.
 Sequencing data provided as public health service by Basic Science Lab, Kenya Medical Research Institute (KEMRI), Kisumu Field Station, Kenya