SARS-CoV-2 genomic epidemiology: data and sequencing infrastructure.

ABSTRACT

Background: Genomic surveillance of SARS-CoV-2 is critical in monitoring viral lineages. Available data reveal a significant gap between low- and middle-income countries and the rest of the world. Methods: The SARS-CoV-2 sequencing costs using the Oxford Nanopore MinION device and hardware prices for data computation in Lebanon were estimated and compared with those in developed countries. SARS-CoV-2 genomes deposited on the Global Initiative on Sharing All Influenza Data per 1000 COVID-19 cases were determined per country. Results: Sequencing costs in Lebanon were significantly higher compared with those in developed countries. Low- and middle-income countries showed limited sequencing capabilities linked to the lack of support, high prices, long delivery delays and limited availability of trained personnel. Conclusion: The authors recommend the mobilization of funds to develop whole-genome sequencing-based surveillance platforms and the implementation of genomic epidemiology to better identify and track outbreaks, leading to appropriate and mindful interventions.

Lebanon and other low- and middle-income countries have limited sequencing capabilities. Sequencing costs using MinION in Lebanon were higher than the approximate sequencing costs in developed countries. The challenges faced by low- and middle-income countries include lack of support, few established sequencing facilities, high prices, long delivery delays and the limited availability of trained personnel. There is a need to focus on the development of whole-genome sequencing-based surveillance platforms and the implementation of genomic epidemiology to improve sequencing efforts in many resource-limited settings and to contain and prevent future pandemic-level outbreaks.