Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis

Abstract

Background: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic.

Methods: We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study.

Findings: We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022.

Interpretation: The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility.

Funding: National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences.

Translation: For the Chinese translation of the abstract see Supplementary Materials section.

Figure 1

Temporal dynamics of local and imported SARS-CoV-2 cases in Beijing in 2022 (A) Number of reported SARS-CoV-2 cases in Beijing, identified by local and imported cases. An asterisk is used to indicate the uncertainty on the number of infected cases since Nov 30, the start of the current COVID-19 surge in Beijing. (B) Number of SARS-CoV-2 cases caused by major variants in Beijing.

Figure 2

Phylogeny and statistics of SARS-CoV-2 variants circulating in Beijing during the whole year 2022 (A) The phylogenetic tree of complete high-quality SARS-CoV-2 genomes generated in this study. The phylogenetic tree was visualised by the Auspice online tool. Tips with a circle indicate the genomic sequences generated in this study. Others are reference sequences. The colour of the circle corresponds to different clades. (B) The phylogenetic tree of complete high-quality SARS-CoV-2 genomes generated in this study. The phylogenetic tree was visualised by the Auspice online tool. Tips with a circle indicate the genomic sequences generated in this study. Others are reference sequences. The colour of the circle corresponds to local or imported cases. (C) The composition of SARS-CoV-2 variants circulating in Beijing during the whole year 2022. The inner doughnut represents the composition of clades. The outer doughnut represents the detailed Pango lineage within each clade. (D) The composition of SARS-CoV-2 variants circulating in Beijing after Nov 14, 2022. The inner doughnut represents the composition of clades. The outer doughnut represents the detailed Pango lineage within each clade.

Figure 3

Sampling and distribution of omicron subvariants in local cases and imported cases since Nov 14, 2022 (A) The sampling distribution of local cases (outpatient and inpatient cases) and imported cases from Nov 14 to Dec 20. (B) The distribution of omicron subvariants in 350 local cases.

Figure 4

Temporal population dynamics of BA.5.2 and BF.7 in Beijing after Nov 14, 2022 (A) The dated phylogeny (top) and corresponding estimation of effective population size, Ne (bottom) during the same period for BA.5.2 in Beijing. These two plots share the same timeline axis. (B) The dated phylogeny (top) and corresponding estimation of effective population size, Ne (bottom) during the same period for BF.7 in Beijing. These two plots share the same timeline axis. (C) The distribution of local subvariants identified in Beijing over time from Nov 14 to Dec 20.