Until recently, the use of pathogen sequencing to track emerging epidemics was mainly the domain of university research and public health laboratories in high-income countries. The SARS-CoV-2 pandemic has been pivotal in the expansion of real-time genomic epidemiology globally. Okeke and Ihekweazu1 recently discussed the historical reticence regarding implementation of molecular diagnostics in low-resource settings. For many countries, this reticence is dissipating following the expanded use of such diagnostics in the SARS-CoV-2 pandemic1. This has been similarly reflected in the implementation and repurposing of genomic sequencing pipelines in countries across the globe2,3,4,5. The Global Initiative on Sharing Avian Influenza Data (GISAID) database has become a repository for global sharing of SARS-CoV-2 genomes. Many low-and-middle-income countries (LMICs) have incorporated genomic sequencing into their public health response for the first time, which is reflected in GISAID submissions. In Bangladesh, MinION or Illumina sequencers that had previously been used for other diseases were repurposed to support SARS-CoV-2 sequencing3,4. This resulted in early generation of Bangladeshi SARS-CoV-2 genomes4 that contributed to investigation of the local reproductive number in Bangladesh among other descriptive epidemiological studies and reports4,6,7. Furthermore, the role played by mass population migration in SARS-CoV-2 dispersal across Bangladesh in 2020 was underscored by combining genomes sequenced in Bangladesh with detailed human population migration data4. This demonstrated spatiotemporal overlaps between lineage expansions and holiday-associated human movement. In addition, this paper also recognized the dominance of Alpha and Beta variants in early 2021, influencing policy decisions3.
https://www.nature.com/articles/s41579-021-00664-y
SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs
