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.

病毒测序在新型冠状病毒肺炎（COVID-19）疫情应对中发挥了关键作用，但测序与生物信息学能力仍存在不均衡性。为评估基于云的测序分析平台在严重急性呼吸综合征冠状病毒2（SARS-CoV-2）测序中的应用价值，我们于2022年7月开展了一项覆盖7个国家的横断面研究。各研究站点在两周内陆续向全球病原体分析服务（Global Pathogen Analysis Service, GPAS）提交SARS-CoV-2序列数据。GPAS生物信息学云平台可完成序列组装、谱系分型及相关样本识别。用户可与合作者共享研究信息，同时保留数据所有权。本次研究共有7个站点提交了总计5346份临床样本的测序读段，其中4799/5346（89.8%）完成了谱系分型。奥密克戎（Omicron）谱系占据主导，绝大多数为BA.5、BA.4及BA.2，与同期基因组流行病学观测结果一致。系统发育分析显示，各谱系内多样性较低，且全球不同站点间存在高度相似的序列。像GPAS这类基于云的平台可解决生物信息学瓶颈问题，助力病原体监测领域的协作，提升疫情及大流行防范能力。