From microscopy to sequencing and metagenomic analysis.Soon after the introduction of SARS-CoV-2 in Ethiopia, AHRI has been putting effort to sequence and analyse samples from COVID-19 patients. Although reagent delay has been a great challenge, through the support of partners we managed to secure reagents and consumables and successfully performed the first SARS-CoV-2 whole genome sequencing (WGS) and analysis; a great milestone as an Institute and as a country!
We started our journey of WGS on 5 isolates of M. tuberculosis in mid 2020 where the analysis was relatively simple compared to SARS-CoV2 RNA sequencing using metagenomics approach in which swab samples can potentially contain any additional bacteria, fungi or virus as well as human cells found in the sample. As a consequence, any nucleic acid (RNA/DNA) can be sequenced. Accordingly, sample processing/preparation, sequencing and sequence analysis is challenging. Yet, staff at AHRI has developed skills of sample processing, preparing libraries, sequencing and performing metagenomics analysis.
The findings from SARS-CoV-2 sequencing and analysis will soon be deposited in GISAID and GenBank and published for the public but the capacity built and the experience gained so far will help tracking and monitoring of potential new strains introduced or emerged which, when possible, at least 10% of samples need to be tested by WGS to identify potential new variants as new variants may affect available diagnostics and vaccines and impact transmissibility, diseases severity and reinfection. This however, requires a well-organized surveillance team to collect representative samples using a geospatial approach and budget with ultimate goal of supporting the Federal MoH in its epidemic response plan. To do so, a simpler-low cost, and high throughput sequencing platform is recommended.
As always, we are grateful to FMoH, Norad and Sida for the contribution to this achievement.