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

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 sites that can become fixed as single nucleotide polymorphisms (SNPs), iSNVs cluster within the phylogenetic tree, with branches supporting the same variants as SNPs. This observation suggests that iSNVs likely serve as reservoirs for SNPs. Additionally, the BA.1.1 samples carried iSNVs identical to the characteristic mutations of BA.2 and BA.2.3. These findings provide important insights into the evolution and transmission inference of SARS-CoV-2.

Understanding the mechanisms behind viral evolution and transmission is crucial, as novel SARS-CoV-2 variants continue to emerge and spread worldwide. Viral evolution is driven not only by variants that circulate globally but also by mutations arising within individual hosts, resulting in the emergence of iSNVs. The role of iSNVs in shaping SARS-CoV-2 evolution and transmission remains poorly characterized. Our results showed a significant enrichment of shared iSNVs in high-density genomic regions, potentially contributing to the formation of co-mutation patterns. However, the presence of shared iSNVs in samples lacking epidemiological links indicates that they alone are insufficient for accurately reconstructing transmission routes. Instead, iSNVs may act as a reservoir for the emergence of single nucleotide polymorphisms. Our study offers new insights into the evolution of SARS-CoV-2 and the interpretation of transmission from sequencing data.