KENYA – Genome sequencing at the laboratory in the Kenya Medical Research Institute (KEMRI) in Kilifi town has advanced its pathogen surveillance to effectively monitor, detect and respond to COVID-19 variants in Africa.

The pathogen genomic surveillance also allows KEMRI scientists to investigate COVID-19 outbreaks to better understand the transmission, validate diagnostics and develop therapeutics.

The Kilifi laboratory is well equipped with human resource such as laboratory technicians along with proper air conditioning, glinting LED screens, test tubes and pore through spreadsheets to help propel Africa’s efforts in boosting pandemic response.

Genome sequencing allows governments and health authorities to make informed public health decisions such as measures to bolster preparedness for potential surges due to more infectious variants or stepping up vaccination, diagnostics and treatment.

World Health Organization (WHO) recommends that countries ship at least 5% of their COVID-19 samples to reference sequencing laboratory or continuously produce sequencing data if they have the capacity.

From a sequence we learn about the history of the virus which helps us understand transmission patterns and how to keep COVID-19 from spreading,” explained Dr George Githinji, Team Lead of Genomic Surveillance at the KEMRI in Kilifi.

The Kenyan laboratory is part of the continent-wide 12 laboratory network established to ramp up the African region’s pathogen surveillance through genome sequencing.

Additionally, it has produced more than 8000 sequences since April 2020 from samples sent by Comoros, Eswatini, Ethiopia, Seychelles, Sudan as well as from within Kenya.

The more sequences the better because the virus is always changing thus it’s crucial that samples from all over the continent are sequenced regularly so we can understand SARS-CoV-2 as it evolves,” revealed Dr Nicksy Gumede-Moeletsi, Regional Virologist at WHO Regional Office for Africa.

Dr Nicksy Gumede-Moeletsi pointed out that sequencing is a detailed process that can be costly especially when samples are sent from abroad as well as time consuming to fully process samples sent from other countries and provide complete analysis.

WHO acts as a broker in collaboration with governments and labs to facilitate agreements, navigate customs, manage paperwork and organize logistics to speed up the administrative processes so that samples can arrive cold and intact.

The health organization has also provided more than US$ 6.5 million to help African countries to either increase existing sequencing capabilities or build new expertise for example Eswatini now sequences its own COVID-19 samples after receiving WHO training.

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