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

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. 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. 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. 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.