NGS Expansion and Capacity Building in Kenya for COVID-19 and Beyond
By Eugene Yeboah , MSc , senior specialist , Global Health ; Noah C . Hull , PhD , MPH , manager , Global Health ; and Lucy Maryogo-Robinson , MPH , director , Global Health
On March 12 , 2020 , the Kenya Ministry of Health confirmed its first case of COVID-19 in Nairobi . As of March 27 , 2022 , the ministry had reported 323,374 total confirmed COVID-19 cases and 5,647 cumulative fatalities . In addition , GISAID
— a global science initiative that provides open access to genomic data of influenza viruses and the coronavirus — has published 8,239 coronavirus specimens as of March 28 , 2022 , accounting for 8.4 % of all submitted submissions specimens in Africa .
“ No country can securely eliminate COVID-19 , or its devastating economic domino effects , if the disease becomes rampant across a continent of 1.3 billion people ,” said John Nkengasong , director of Africa CDC
. “ For Africa to get ahead of the pandemic , we need to scale up testing fast .” Increasing quality diagnostic testing as well as sequencing for monitoring new variants are key strategies Kenya is implementing in the fight against COVID-19 .
To support laboratory capacity building in Kenya , APHL worked with the US Centers for Disease Control and Prevention
( CDC ) Global Disease Detection ( GDD ) program within the Division of Global Health Protection in Kenya
( DGHP-Kenya ) to provide next-generation sequencing ( NGS ) support and training to CDC-Kenya Medical Research Institute
( KEMRI ) laboratories and the National Public Health Laboratory ( NPHL ) under the Department of Laboratory Services of the Kenyan Ministry of Health and Population ( MoHP ). Trainings were conducted over the course of three weeks at the KEMRI CDC Diagnostics and Laboratory System Programs ( DLSPs ) in Nairobi and Kisumu , and at MoHP-NPHL in Nairobi .
NPHL NGS trainees take a break after loading the Oxford Nanopore Sequencer . Photo : NPHL
CDC DLSP KEMRI Nairobi
Ten laboratory staff were trained on NGS using Illumina COVIDSeq protocol on the Illumina MiSeq™ . In addition , nine staff members were trained in genomic characterization and epidemiology using the Terra . bio platform and data repository submission to GISAID and the National Center for Biotechnology Information
( NCBI ). Training and guidance were provided on primer design and protocol optimization using ARTIC protocols to sequence Chikungunya virus , Dengue ( serotypes 1-4 ), Rift Valley Fever virus and Yellow Fever virus .
CDC DLSP KEMRI Kisumu
Eight laboratory staff were trained on NGS using Illumina COVIDSeq protocol on the Illumina iSeq™ 100 . All 23 positive samples passed . The iSeq™ 100 was a new instrument , and it was the first NGS run at the CDC DLSP KEMRI Kisumu laboratory . Twelve staff members were trained in genomic characterization , genomic epidemiology , using the Terra . bio platform , and data upload to GISAID and NCBI . As a result , the laboratory staff was able to take nucleic acid extracts from SARS-CoV-2 positive specimens and obtain consensus genomes to upload to GISAID in a matter of four business days . This work was supported by a generous donation made by Illumina to provide iSeq™ 100 sequencing flow cells and cartridges .
MoHP – NPHL
Four laboratory staff were trained on NGS using Oxford Nanopore ( ONT ) SARS-CoV-2 Midnight protocol on the ONT Mk1b instrument . Four staff members were trained in genomic characterization , genomic epidemiology , using the Terra . bio platform , and data upload to GISAID and NCBI . Support for this training was possible with a generous donation from Oxford Nanopore of sequencing reagents , flow cells and a Mk1b sequencer .
Sequences analyzed during these trainings and submitted to GISAID were some of the first to be submitted by the CDC-DLSP-KEMRI laboratories and the MoPH-NPHL laboratories . This capability of NGS and successful training conducted in these laboratories will increase the genomic surveillance for SARS-CoV-2 and have built genomic capacity for pandemic preparedness . The average turnaround time in the country ( extraction to upload ) was averaging 4-6 weeks . However , during this training , demonstrated turnaround time was down to less than a week .
Kenya is set to become one of the leading fronts in genomic surveillance with the expertise and capabilities acquired through NGS training and expansion . These training courses have also paved the way and provided the technical know-how to optimize existing wholegenome sequencing technologies and protocols for current and future pathogens and outbreaks of unknown origin . n