A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology

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Background Viral sequencing has made critical contributions to our understanding of and response to the COVID-19 pandemic, but sequencing capacity and bioinformatic expertise remain limited in many settings. This proof-of-principle study aimed to demonstrate the utility of a cloud-based sequencing analysis pipeline, the Tiled Amplicon Pipeline (TAP), for rapid and collaborative SARS-CoV-2 sequencing across seven globally distributed sites. Methods In this cross-sectional study from July to August 2022, seven international sites submitted all SARS-CoV-2 sequence data generated over a two-week period to our cloud platform. No patient identifying information was uploaded, and human reads were removed prior to upload to the cloud. Users could opt in to share sample information with collaborators via a tagging system. The pipeline performed sequence assembly, lineage identification and relatedness analysis. Results Seven sites contributed 5,432 sequences, of which 5,342 (98.3%) were from clinical samples and 90 (1.7%) were controls. 4,470/5,342 (83.7%) clinical samples had sufficient coverage for lineage assignment. Omicron lineages dominated, with BA.5, BA.4 and BA.2 comprising the vast majority, consistent with contemporary epidemiological observations at the time. Phylogenetic analysis demonstrated low diversity within lineages, and genotypically identical or highly similar sequences were recovered from globally disparate sites. Conclusions A cloud-based analysis platform like TAP addresses bioinformatic bottlenecks and facilitates international capacity building and collaboration in pathogen surveillance, enhancing global epidemic and pandemic preparedness.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.