Coordinated SARS-CoV-2 genomic surveillance across six continents using cloud informatics
Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain imbalanced. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly, lineage assignment and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites submitted sequencing reads for a total of 5,346 clinical samples, of which 4,799/5,346 (89.8%) were assigned lineages. Omicron lineages dominated, with the vast majority being BA.5, BA.4, and BA.2, commensurate withal contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based platform like GPAS addresses bioinformatic bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic/pandemic preparedness.