ABSTRACT
The current global epidemiology of COVID-19 is now characterized by the emergence and rapid spread of the SARS-CoV-2 Omicron variant on a global scale 1,2 . Despite the variant’s prompt predominance, there remain knowledge gaps in its origin and evolution history 3–6 . Here, we show that Omicron lineage SARS-CoV-2 is characterized by the feature of chimera. It was generated by genomic recombination of two early PANGO lineages of SARS-CoV-2. In the recombination event, strains with medium or high circulating intensity like SARS-CoV-2/human/USA/COR-21-434196/2021 belonging to PANGO lineage BA.1 provided the fundamental genome and served as the major parents, while the rare lineage strains like SARS-CoV-2/human/IRN/Ir-3/2019 belonging to B.35, as the minor parents, hybridized their genomic fractions into the major genomes at position 21593-23118nt. This recombination event results in 22 amino acid residue substitutions for the variant of Omicron, including 16 in the pivotal RBD of the spike protein. These substitutions have led to some subtle variations in the spatial structure and the affinity to hACE2 receptor of the spike protein 7,8 , thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics 9–12 . The global spread and explosive growth of the SARS-CoV-2 in human population increase opportunities for future recombination 13–15 .
Subject(s)
COVID-19ABSTRACT
Background: COVID-19 developed into a global pandemic in 2020 and poses challenges regarding the prevention and control capabilities of countries. A large number of inbound travelers from other regions could lead to a renewed outbreak of COVID-19 in the local regions. Globally, as a result of the imbalance in the control of the epidemic, all countries are facing the risk of a renewed COVID-19 outbreak brought about by travelers from epidemic areas. Therefore, studies on a proper management of the inbound travelers are urgent. Methods: We collected a total of 4,733,414 inbound travelers and 174 COVID-19 diagnosed patients in Yunnan province from 21 January 2020 to 20 February 2020. Data on place of origin, travel history, age, and gender, as well as whether they had suspected clinical manifestations for inbound travelers in Yunnan were collected. The impact of inbound travelers on the local epidemic was analyzed with a collinear statistical analysis and the effect of the control measures on the epidemic was evaluated with a sophisticated modeling approach. Results: Of the 174 COVID-19 patients, 60.9% were not from Yunnan, and 76.4% had a history of travel in Hubei. The amount of new daily cases in Yunnan was significant correlated with the number of inbound travelers from Hubei and suspected cases among them. Using Susceptible-Exposed-Infectious-Recovered (SEIR) model analysis, we found that the prevention and control measures dropped the local R0 down to 1.07 in Yunnan province. Conclusions: Our preliminary analysis showed that the proper management of inbound travelers from outbreak areas has a significantly positive effect on the prevention and control of the virus. In the process of resettlement, some effective measures taken by Yunnan province may provide an important reference for preventing the renewed COVID-19 outbreak in other regions.