Genomic Surveillance for SARS-CoV-2 Variants of Concern from Imported COVID-19 Cases - the Mainland of China, 2021

Introduction: After the epidemic in Wuhan City was brought under control in 2020, local outbreaks of coronavirus disease 2019 (COVID-19) in the mainland of China were mainly due to imported COVID-19 cases. The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to generate new variants. Some have been designated as variants of concern (VOCs) by the World Health Organization (WHO). To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021, the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed. Methods: The analyses included the number of sequence submissions, time of sequence deposition, and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance. The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data (GISAID). Results: A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions, with differences in the number of sequence submissions and median time of sequence deposition. A total of 2,388 sequences with more than 90% genomic coverage were used for lineage analysis. The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID. In addition, VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks. Conclusions: The global distribution of SARS-CoV-2 VOCs changed rapidly in 2021. Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), is constantly mutating under the different circumstances of global transmission (1). The emerging SARS-CoV-2 variants may have potential adverse impacts on epidemic traits and severity. To some extent, it is also capable of escaping natural and vaccine-induced immunity (2-3). Some of them were designated as variants of concern (VOCs) by the World Health Organization (WHO) (4). Therefore, robust surveillance is essential to assess the evolution of viruses in real time. After the epidemic in Wuhan City was brought under control in 2020, several COVID-19 outbreaks in the mainland of China have been proven to relate to SARS-CoV-2 contaminated cold-chain products (5-7), while most were caused by transmission through imported cases on flights, at isolation facilities, or in designated hospitals (8-9). Therefore, genomic surveillance for SARS-CoV-2 from imported cases is of great significance for monitoring the risk of different variants that were imported into the mainland of China, assessing the risk of importation-associated domestic spread, and helping guide public health interventions. On March 17, 2020, the China CDC released a notice and launched genomic surveillance for SARS-CoV-2 from imported COVID-19 cases nationwide. The laboratories of provincial CDCs were required to conduct SARS-CoV-2 whole-genome sequencing for samples from imported cases and submit the genomic sequences to the China CDC in time. This study includes the analysis of genomic surveillance data of imported SARS-CoV-2 cases of 2021 from the mainland of China.