Abstract

Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing capacity and bioinformatics access remain scarce. To demonstrate 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 System (GPAS). The GPAS bioinformatics pipeline performs sequence assembly, lineage identification and relatedness measures. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,436 (89.8%) had a lineage identified. Omicron lineages dominated this sample group, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences recovered from globally disparate sites. A cloud- based analysis platform can address bioinformatics bottlenecks and enhance collaboration in pathogen surveillance, enhancing pandemic preparedness.