Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft

•Scientific question: What are the dynamic characteristics of intra-host single nucleotide variations (iSNVs) and single nucleotide polymorphisms (SNPs) during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission?•Evidence before this study: SARS-CoV-2 replication can generate a large amount of quasispecies that carried iSNVs within infected individuals. These iSNVs and SNPs provide much more viral intra-host genetic diversities in individuals, which may be helpful to SARS-CoV-2 evolution and evade both host and vaccine immunity.•New findings: The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. The intra-host diversity of SARS-CoV-2 increased gradually with time, and new mutations can occur directly in vivo without travelling through a transmission bottleneck. The generational relationship of SARS-CoV-2 cannot be determined from the mutation site changes alone.•Significance of the study: This study informs that the intra-host diversity of SARS-CoV-2-infected individuals increased rapidly with time. Mutation site changes alone are insufficient to determine a generational relationship. We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3–31 days later. All 47 nasopharyngeal swabs were deep-sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n = 31), Beta (n = 1), and C.1.2 (n = 1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95% CI]: 2.77–10.22) than did the first samples (T1; median: 2; 95% CI: 1.63–3.74; Wilcoxon test, P = 0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited ra