Genomic Surveillance for SARS-CoV-2—China,September 26,2022 to January 29,2023

Introduction:The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has generated 2,431 variants over the course of its global transmission over the past 3 years.To better evaluate the genomic variation of SARS-CoV-2 before and after the optimization of coronavirus disease 2019(COVID-19)prevention and control strategies,we analyzed the genetic evolution branch composition and genomic variation of SARS-CoV-2 in both domestic and imported cases in China(the data from Hong Kong and Macao Special Administrative Regions and Taiwan,China were not included)from September 26,2022 to January 29,2023.Methods:Analysis of the number of genome sequences,sampling time,dynamic changes of evolutionary branches,origin,and clinical typing of SARS-CoV-2 variants submitted by 31 provincial-level administrative divisions(PLADs)and Xinjiang Production and Construction Corps(XPCC)was conducted to assess the accuracy and timeliness of SARS-CoV-2 variant surveillance.Results:From September 26,2022 to January 29,2023,20,013 valid genome sequences of domestic cases were reported in China,with 72 evolutionary branches.Additionally,1,978 valid genome sequences of imported cases were reported,with 169 evolutionary branches.The prevalence of the Omicron variants of SARS-CoV-2 in both domestic and imported cases was consistent with that of international epidemic variants.Conclusions:This study provides an overview of the prevalence of Omicron variants of SARS-CoV-2 in China.After optimizing COVID-19 prevention and control strategies,no novel Omicron variants of SARSCoV-2 with altered biological characteristics or public health significance have been identified since December 1,2022.

Surveillance and Analysis of SARS-CoV-2 Variant Importation—China,January–June 2022

Introduction:The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)Omicron variant is the dominant circulating strain worldwide.To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic,the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019(COVID-19)cases in the mainland of China during the first half of 2022 were analyzed.Methods:Sequences submitted from January to July 2022,with a collection date before June 30,2022,were incorporated.The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed.Results:4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions(PLADs),and the median submission interval was within 1 month after collection.In 3,851 Omicron sequences with good quality,1 recombinant(XU)and 4 subvariants under monitoring(BA.4,BA.5,BA.2.12.1,and BA.2.13)were recorded,and 3 of them(BA.4,BA.5,and BA.2.12.1)caused local transmissions in the mainland of China later than that recorded in the surveillance.Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5.The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data(GISAID).The imported cases from Hong Kong Special Administrative Region,China,accounted for 32.30%of Omicron cases sampled,and 98.71%of them were BA.2.Conclusions:The Omicron variant showed the intra-Omicron evolution in the first half of 2022,and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.

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 SARSCoV-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.