Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.

ABSTRACT: Investigating the intra-host diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for understanding its transmission and the emergence of new variants. However, there is limited insight into SARS-CoV-2 intra-host diversity and the extent to which shared intra-host single nucleotide variants (iSNVs) occur among samples without epidemiological links. To characterize intra-host diversity, we analyzed sequencing data from 803 samples across four Omicron transmission clusters. The potential co-mutation patterns formed by shared iSNVs contributed to regions in the genome with elevated iSNV density. Most samples did not share iSNVs. Even among the sample pairs that did share at least one iSNV, 24.4% originated from different transmission clusters. For shared iSNV

SUBMITTER: Wei X 

PROVIDER: S-EPMC12570505 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature