Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.
Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.
Nat Commun. 2022 May 18;13(1):2745. doi: 10.1038/s41467-022-30518-x.
Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data.
SARS-CoV-2 不同变体的合并感染是重组事件的关键前提，这些事件可能推动 SARS-CoV-2 的进化。需要快速识别此类合并感染，以确定其在社区中的频率，特别是在已经被确定为 COVID-19 严重风险人群中的频率，这些人群已被认为是突变速率进化事件的孵化器。然而，目前可用于检测和描述与已知关注变体相关的 SARS-CoV-2 合并感染的有限数据和工具。在这里，我们描述了两名患有慢性肾病需要维持性血液透析的成年患者中与 SARS-CoV-2 关注变体奥密克戎和德尔塔的合并感染。在检测时，两种变体都在社区中同时传播。基于扩增子和探针测序的基因组监测使用短读长和长读长技术，在呼吸道样本中鉴定和定量了德尔塔和奥密克戎病毒的亚群。这些发现强调了在脆弱人群中进行综合基因组监测的重要性，并提供了使用基因组数据识别 SARS-CoV-2 合并感染的诊断途径。
