SARS-CoV-2 Omicron variant: Characteristics and prevention.

Received: 5 December 2021 Revised: 7 December 2021 Accepted: 7 December 2021 DOI: 10.1002/mco2.110 PERSPECTIVE SARS-CoV-2 Omicron variant: Characteristics and prevention Xuemei He1 Weiqi Hong1 1 Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China 2 West China Hospital Emergency Xiangyu Pan1 Guangwen Lu2 Xiawei Wei1 Abstract Coronavirus disease 2019 (COVID-19) has brought about a great threat to global public health. Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.529 has been reported in South Africa and induced a rapid increase in COVID-19 cases. On November 24, 2021, B.1.1.529 named Omi- Department, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China cron was designated as a variant under monitoring (VUM) by World Health Organization (WHO). Two days later, the Omicron variant was classified as a variant of concern (VOC). This variant harbors a high number of mutations, including 15 Correspondence Guangwen Lu, West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China. Email: Xiawei Wei, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China. Email: mutations in the receptor-binding domain (RBD) of spike. The Omicron variant also shares several mutations with the previous VOC Alpha, Beta, and Gamma variants, which immediately raised global concerns about viral transmissibility, pathogenicity, and immune evasion. Here we described the discovery and characteristics of the Omicron variant, compared the mutations of the spike in the five VOCs, and further raised possible strategies to prevent and overcome the prevalence of the Omicron variant. Xuemei He and Weiqi Hong contributed equally to this work. Funding information National Science Foundation for Excellent Young Scholars, Grant/Award Number: 32122052; National Natural Science Foundation Regional Innovation and Development, Grant/Award Number: U19A2003; National Natural Science Foundation of China, Grant/Award Number: 81800421 1 INTRODUCTION The Coronavirus disease 2019 (COVID-19) pandemic has been surging for almost two years. More than 260 million confirmed cases have been reported according to the statistics of the World Health Organization (WHO), including over five million deaths.1 The original severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2021 The Authors. MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd. 838 wileyonlinelibrary.com/journal/mco2 MedComm. 2021;2:838–845. HE et al. 839 was identified at the end of 2019 had evolved and a variety of variants emerged. In order to prioritize monitoring and research of these variants, WHO has classified them into three categories: variants of concern (VOCs), variants of interest (VOIs), and variants under monitoring (VUMs). The previous four VOCs include Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2).2 They all resulted in a new wave of pandemic and thousands of deaths in more than one country and area, and even across the whole world. On November 26, 2021, a new variant named Omicron (B.1.1.529) was designated as the fifth VOC by WHO, which immediately raised global concerns. Where and how the Omicron variant evolved remains to be investigated. The analysis of sequences of SARS-CoV2 variants reveals that Omicron is a lot different from the other SARS-CoV-2 variants such that it is difficult to identify its closest relative.9 The results of phylogenetic studies indicate that the Omicron variant likely has diverged early from other SARS-CoV-2 variants rather than being developed from one of the previous VOCs.9 It is speculated that the Omicron variant might have been gestated in immunocompromised individuals (e.g., HIV patients co-infected by SARS-CoV-2) for a certain period of time, or it might have evolved in a nonhuman species and is just recently spilled back into human beings.10 2 EMERGENCE OF OMICRON VARIANT 3 CHARACTERISTICS OF OMICRON VARIANT According to the WHO reports, the first known confirmed infection by Omicron could be traced back to a specimen collected on November 9, 2021.3 The first Omicron sequence available, however, was from a specimen collected on November 11, 2021, in Botswana. Ever since the identification of Omicron, the variant appears to rapidly spread. A recent genomic-sequence analysis on 77 virus samples collected in Gauteng province of South Africa from November 12 to 20 showed that all the analyzed variants were actually B.1.1.529,4 indicating that Omicron was becoming dominant in Gauteng. Furthermore, the identification of Omicron coincides with the recent sharp increase in the number of confirmed COVID-19 cases in South Africa. The mean number of COVID-19 cases per day increased from 280 to 800 after the Omicron variant was verified.5 This number exceeded 2000 on November 26, 2021, and broke through 10,000 on December 3, 2021.6 In addition, tracing the source of COVID-19 cases revealed that B.1.1.529 had probably spread in western Europe before the first cases were detected in southern Africa.7 B.1.1.529 variant was first reported to WHO on November 24, 2021. On the day after receiving the report, WHO designated it as VUM and named it as Omicron variant (B.1.1.529). Only 2 days later, WHO categorized the Omicron variant as VOC, which recorded the shortest interval period of reclassifying a variant from VUM to VOC and subsequently brought about great public concerns. A few days after the identification of Omicron in Africa, the variant has emerged in the other continents. At the time of this writing, Omicron has been reported in 34 countries and areas, including Botswana, Hong Kong, South Africa, Israel, Belgium, Italy, and the USA.8 Apparently, the variant has not stopped spreading to other countries and regions. Since early 2020, three big waves of COVID-19 outbreaks have been recorded in South Africa (Figure 1A). Among them, two are caused by the Beta and Delta variants respectively (Figure 1B). The epidemiological data showed that the percentage of infections associated with the Beta variant increased to ∼50% of the total daily infections within approximately 100 days since its outbreak (Figure 2). The infection percentage of the Delta variant, however, raised to ∼80% during the same period of tim (...truncated)