Re-purposing ILRI labs to support national COVID-19 testing in Kenya

Re-purposing ILRI labs to support national COVID-19 testing in Kenya

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  This document islicensed for use under the Creative Commons Attribution 4.0 International Licence. August 2020 § ILRI has a rich history of animal health biotech research, including molecular diagnostics § ILRI has invested in different levels of bio-secure facilities, including a high-containment BSL-3 lab § The generic nature of ILRI’s modern bioscience facilities and expertise allowed us to rapidly re- purpose for COVID-19 testing under safe and secure conditions § Over 10,000 samples have been tested for presence of SARS-CoV-2 viral RNA so far § ILRI’s investment in COVID-19 testing reflects its full commitment to demonstrating how the One Health approach translates to practice Re-purposing ILRI labs to support national COVID-19 testing in Kenya ILRI-COVID Diagnostic Group International Livestock Research Institute Edward Okoth: e.okoth@cigar.org Samuel Oyola: s.oyola@cgiar.org Context • The COVID-19 pandemic has had a negative impact on human life and the global economy. • Timely diagnostic tests to identify infected individuals play a major role in controlling spread of the SARS-CoV-2 virus. • At the onset of increased virus transmission in Kenya, the Kenyan Ministry of Health requested ILRI to support its national COVID-19 diagnostic effort. • Leveraging our molecular diagnosis and infectious disease research experience and expertise, part of our facilities were repurposed for COVID-19 testing. • Supported by the Ministry for Economic Cooperation and Federal Development (BMZ) under the ILRI-led One Health Research, Education and Outreach Centre for Africa (OHRECA), and the Government of Kenya, COVID-19 testing was launched on 1st June 2020. ANIMAL & HUMAN HEALTH Results/Impact • Several diagnostic kits, sample work-flows and process were optimized and validated prior to starting the service. • Samples received from Kenyan government institutions & labs are deactivated and processed in a BSL-3 lab prior to PCR testing in a clean BSL-2 room. This ensures high safety and quality standards are maintained. • Results are returned to Ministry of Health within 24hrs: o Data is used at an individual level to identify positive cases and guide control measures, e.g. quarantine. o Nationally the data helps estimate the rate of virus spread to set national policies for public health. Fig.1. Graphical data outputs of PCR testing for COVID-19 Partners Future steps • Develop in-house reagents to support COVID-19 testing and reduce costs. • Leverage ILRI’s whole genome sequencing and genomic platforms to support COVID-19 research: virus surveillance, evolution, vaccine and drug development • Extend the diagnostic capacity to investigate pathogens at the wildlife-livestock-human-environment interface to help prevent spill-over events. • Help develop capacity for diagnostics and rapid response for surveillance. We acknowledge with thanks the loan of a PCR machine to this effort by CIFOR-ICRAF (World Agroforestry) and KEMRI-Wellcome Trust labs for sharing information and materials Our innovative approach 6. Waste management • Autoclave & Incinerate –solid waste • Effluent treatment – Liquid waste 4. Results review and Reporting • Amplification profile • Baseline setting • Status determination 2. Sample Processing • Sample aliquoting • RNA extraction • RT-PCR reaction set-up 1. Sample reception • Sample quality & safety checks • Metadata entry 3. Real Time PCR • cDNA generation • qPCR 5. Sample Archiving • Aliquoting & storage • Nasal/Oral sawbs in VTM: Liquid Nitrogen • RNA extracts: – 80 0 C ultra low freezer