LI Yi, XU Yingchun. A New Chapter in the COVID-19 Pandemic: the Characteristics of Omicron Variant and A New Step for Scientific Epidemic Prevention and Control[J]. Medical Journal of Peking Union Medical College Hospital, 2023, 14(1): 9-17. DOI: 10.12290/xhyxzz.2022-0697
Citation: LI Yi, XU Yingchun. A New Chapter in the COVID-19 Pandemic: the Characteristics of Omicron Variant and A New Step for Scientific Epidemic Prevention and Control[J]. Medical Journal of Peking Union Medical College Hospital, 2023, 14(1): 9-17. DOI: 10.12290/xhyxzz.2022-0697

A New Chapter in the COVID-19 Pandemic: the Characteristics of Omicron Variant and A New Step for Scientific Epidemic Prevention and Control

Funds: 

National High Level Hospital Clinical Research Funding 2022-PUMCH-B-074

Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences 2021-I2M-1-038

Beijing Key Clinical Specialty for Laboratory Medicine -Excellent Project 2K201000

More Information
  • Corresponding author:

    XU Yingchun, E-mail: xycpumch@139.com

  • Received Date: December 05, 2022
  • Accepted Date: December 19, 2022
  • Available Online: December 25, 2022
  • Issue Publish Date: January 29, 2023
  • Since the outbreak of COVID-19, SARS-CoV-2 has continued to evolve. As the fifth variants of concern (VOCs) announced by the World Health Organization, Omicron has significantly changed from previous VOCs in terms of genome, biological and epidemiological characteristics. Although the severe illness and mortality caused by Omicron infection are significantly lower than those caused by the previous VOCs, Omicron's strong transmission ability has continued to break through the epidemic prevention barrier and human immunity barrier established by prior infections and vaccines. Omicron has opened a new chapter in the COVID-19 pandemic. In this paper, we review the changes in genome and biological characteristics of Omicron and its subspecies as well as the differences in epidemiological characteristics between Omicron and influenza viruses in order to provide scientific basis for the optimization of epidemic prevention and control.
  • [1]
    World Health Organization. SARS-CoV-2 variants of concern and variants of interest[EB/OL]. [2022-12-06]. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/.
    [2]
    Berkhout B, Herrera-Carrillo E. SARS-CoV-2 Evolution: On the Sudden Appearance of the Omicron Variant[J]. J Virol, 2022, 96: e0009022. DOI: 10.1128/jvi.00090-22
    [3]
    Dejnirattisai W, Huo J, Zhou D, et al. SARS-CoV-2 Omicron-B. 1.1.529 leads to widespread escape from neutralizing antibody responses[J]. Cell, 2022, 185: 467-484. e15. DOI: 10.1016/j.cell.2021.12.046
    [4]
    Chen J, Wang R, Gilby NB, et al. Omicron Variant (B. 1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance[J]. J Chem Inf Model, 2022, 62: 412-422. DOI: 10.1021/acs.jcim.1c01451
    [5]
    Mannar D, Saville JW, Zhu X, et al. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex[J]. Science, 2022, 375: 760-764. DOI: 10.1126/science.abn7760
    [6]
    Tegally H, Moir M, Everatt J, et al. Emergence of SARS-CoV-2 Omicron lineages BA. 4 and BA. 5 in South Africa[J]. Nat Med, 2022, 28: 1785-1790. DOI: 10.1038/s41591-022-01911-2
    [7]
    World Health Organization. Weekly epidemiological update on Covid-19-23 November 2022[EB/OL]. (2022-11-23)[2022-12-06] https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19-23-nove-mber-2022.
    [8]
    Hadfield J, Megill C, Bell SM, et al. Nextstrain: real-time tracking of pathogen evolution[J]. Bioinformatics, 2018, 34: 4121-4123. DOI: 10.1093/bioinformatics/bty407
    [9]
    Planas D, Saunders N, Maes P, et al. Considerable escape of SARS-CoV-2 Omicron to antibody neutralization[J]. Nature, 2022, 602: 671-675. DOI: 10.1038/s41586-021-04389-z
    [10]
    Simon-Loriere E, Schwartz O. Towards SARS-CoV-2 serotypes?[J]. Nat Rev Microbiol, 2022, 20: 187-188. DOI: 10.1038/s41579-022-00708-x
    [11]
    Wilks SH, Mühlemann B, Shen X, et al. Mapping SARS-CoV-2 antigenic relationships and serological responses[J]. bioRxiv, 2022. doi: 10.1101/2022.01.28.477987.
    [12]
    Thakur V, Ratho RK. OMICRON (B. 1.1.529): A new SARS-CoV-2 variant of concern mounting worldwide fear[J]. J Med Virol, 2022, 94: 1821-1824. DOI: 10.1002/jmv.27541
    [13]
    Menni C, Valdes AM, Polidori L, et al. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observa-tional study from the ZOE COVID Study[J]. Lancet, 2022, 399: 1618-1624. DOI: 10.1016/S0140-6736(22)00327-0
    [14]
    Kim MK, Lee B, Choi YY, et al. Clinical Characteristics of 40 Patients Infected With the SARS-CoV-2 Omicron Variant in Korea[J]. J Korean Med Sci, 2022, 37: e31. DOI: 10.3346/jkms.2022.37.e31
    [15]
    Wolter N, Jassat W, Walaza S, et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study[J]. Lancet, 2022, 399: 437-446. DOI: 10.1016/S0140-6736(22)00017-4
    [16]
    Lewnard JA, Hong VX, Patel MM, et al. Clinical outcomes associated with SARS-CoV-2 Omicron (B. 1.1.529) variant and BA. 1/BA. 1.1 or BA. 2 subvariant infection in Southern California[J]. Nat Med, 2022, 28: 1933-1943. DOI: 10.1038/s41591-022-01887-z
    [17]
    Jassat W, Abdool Karim SS, Mudara C, et al. Clinical severity of COVID-19 in patients admitted to hospital during the omicron wave in South Africa: a retrospective observational study[J]. Lancet Glob Health, 2022, 10: e961-e969. DOI: 10.1016/S2214-109X(22)00114-0
    [18]
    World Health Organization. Severity of disease associated with Omicron variant as compared with Delta variant in hospitalized patients with suspected or confirmed SARS-CoV-2 infection[EB/OL]. (2022-06-07)[2022-12-06]. https://www.who.int/publications/i/item/9789240051829.
    [19]
    Ulloa AC, Buchan SA, Daneman N, et al. Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada[J]. JAMA, 2022, 327: 1286-1288. DOI: 10.1001/jama.2022.2274
    [20]
    Strasser ZH, Greifer N, Hadavand A, et al. Estimates of SARS-CoV-2 Omicron BA. 2 Subvariant Severity in New England[J]. JAMA Netw Open, 2022, 5: e2238354. DOI: 10.1001/jamanetworkopen.2022.38354
    [21]
    Davies MA, Morden E, Rosseau P, et al. Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA. 4 and BA. 5 compared with previous waves in the Western Cape Province, South Africa[J]. Int J Infect Dis, 2022. doi: 10.1101/2022.06.28.22276983.
    [22]
    Callaway E. What Omicron's BA. 4 and BA. 5 variants mean for the pandemic[J]. Nature, 2022, 606: 848-849. DOI: 10.1038/d41586-022-01730-y
    [23]
    Bentley EG, Kirby A, Sharma P, et al. SARS-CoV-2 Omicron-B. 1.1.529 Variant leads to less severe disease than Pango B and Delta variants strains in a mouse model of severe COVID-19[J]. bioRxiv, 2021. doi: https://doi.org/10.1101/2021.12.26.474085.
    [24]
    Hui KPY, Ho JCW, Cheung MC, et al. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo[J]. Nature, 2022, 603: 715-720. DOI: 10.1038/s41586-022-04479-6
    [25]
    Brüssow H. COVID-19: Omicron-the latest, the least virulent, but probably not the last variant of concern of SARS-CoV-2[J]. Microb Biotechnol, 2022, 15: 1927-1939. DOI: 10.1111/1751-7915.14064
    [26]
    Peacock TP, Brown JC, Zhou J, et al. The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein[J]. bioRxiv, 2022: 2021.12.31.474653.
    [27]
    Meng B, Abdullahi A, Ferreira I, et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity[J]. Nature, 2022, 603: 706-714. DOI: 10.1038/s41586-022-04474-x
    [28]
    Goga A, Bekker LG, Garrett N, et al. Breakthrough Covid-19 infections during periods of circulating Beta, Delta and Omicron variants of concern, among health care workers in the Sisonke Ad26. COV2. S vaccine trial, South Africa[J]. medRxiv, 2021: 2021.12.21.21268171.
    [29]
    Altarawneh HN, Chemaitelly H, Hasan MR, et al. Protection against the Omicron Variant from Previous SARS-CoV-2 Infection[J]. N Engl J Med, 2022, 386: 1288-1290. DOI: 10.1056/NEJMc2200133
    [30]
    Khan K, Karim F, Ganga Y, et al. Omicron BA. 4/BA. 5 escape neutralizing immunity elicited by BA. 1 infection[J]. Nat Commun, 2022, 13: 4686. DOI: 10.1038/s41467-022-32396-9
    [31]
    Ohashi H, Hishiki T, Akazawa D, et al. Different efficacies of neutralizing antibodies and antiviral drugs on SARS-CoV-2 Omicron subvariants, BA. 1 and BA. 2[J]. Antiviral Res, 2022, 205: 105372. DOI: 10.1016/j.antiviral.2022.105372
    [32]
    Takashita E, Kinoshita N, Yamayoshi S, et al. Efficacy of Antiviral Agents against the SARS-CoV-2 Omicron Subvariant BA. 2[J]. N Engl J Med, 2022, 386: 1475-1477. DOI: 10.1056/NEJMc2201933
    [33]
    Wang Q, Guo Y, Iketani S, et al. Antibody evasion by SARS-CoV-2 Omicron subvariants BA. 2.12.1, BA. 4 and BA. 5[J]. Nature, 2022, 608: 603-608.
    [34]
    Yu J, Collier AY, Rowe M, et al. Neutralization of the SARS-CoV-2 Omicron BA. 1 and BA. 2 Variants[J]. N Engl J Med, 2022, 386: 1579-1580. DOI: 10.1056/NEJMc2201849
    [35]
    Kurhade C, Zou J, Xia H, et al. Neutralization of Omicron BA. 1, BA. 2, and BA. 3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine[J]. Nat Commun, 2022, 13: 3602. DOI: 10.1038/s41467-022-30681-1
    [36]
    Chemaitelly H, Abu-Raddad LJ. Waning effectiveness of COVID-19 vaccines[J]. Lancet, 2022, 399: 771-773. DOI: 10.1016/S0140-6736(22)00277-X
    [37]
    Hachmann NP, Miller J, Collier AY, et al. Neutralization Escape by SARS-CoV-2 Omicron Subvariants BA. 2.12.1, BA. 4, and BA. 5[J]. N Engl J Med, 2022, 387: 86-88. DOI: 10.1056/NEJMc2206576
    [38]
    Tuekprakhon A, Nutalai R, Dijokaite-Guraliuc A, et al. Antibody escape of SARS-CoV-2 Omicron BA. 4 and BA. 5 from vaccine and BA. 1 serum[J]. Cell, 2022, 185: 2422-2433. e13. DOI: 10.1016/j.cell.2022.06.005
    [39]
    Karim SSA, Karim QA. Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic[J]. Lancet, 2021, 398: 2126-2128. DOI: 10.1016/S0140-6736(21)02758-6
    [40]
    Redd AD, Nardin A, Kared H, et al. Minimal Crossover between Mutations Associated with Omicron Variant of SARS-CoV-2 and CD8(+) T-Cell Epitopes Identified in COVID-19 Convalescent Individuals[J]. mBio, 2022, 13: e0361721. DOI: 10.1128/mbio.03617-21
    [41]
    Liao M, Liu Y, Yuan J, et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19[J]. Nat Med, 2020, 26: 842-844. DOI: 10.1038/s41591-020-0901-9
    [42]
    Liu J, Chandrashekar A, Sellers D, et al. Vaccines elicit highly conserved cellular immunity to SARS-CoV-2 Omicron[J]. Nature, 2022, 603: 493-496. DOI: 10.1038/s41586-022-04465-y
    [43]
    Tarke A, Coelho CH, Zhang Z, et al. SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron[J]. Cell, 2022, 185: 847-859. e11. DOI: 10.1016/j.cell.2022.01.015
    [44]
    Kirsebom FCM, Andrews N, Stowe J, et al. COVID-19 vaccine effectiveness against the omicron (BA. 2) variant in England[J]. Lancet Infect Dis, 2022, 22: 931-933. DOI: 10.1016/S1473-3099(22)00309-7
    [45]
    Cheung PH, Chan CP, Jin DY. Lessons learned from the fifth wave of COVID-19 in Hong Kong in early 2022[J]. Emerg Microbes Infect, 2022, 11: 1072-1078. DOI: 10.1080/22221751.2022.2060137
    [46]
    Ministry of Health, Singapore. COVID-19 Statistics[EB/OL]. [2022-12-06]. https://www.moh.gov.sg/COVID-19/statistics.
    [47]
    McMenamin ME, Nealon J, Lin Y, et al. Vaccine effectiveness of one, two, and three doses of BNT162b2 and CoronaVac against COVID-19 in Hong Kong: a population-based observational study[J]. Lancet Infect Dis, 2022, 22: 1435-1443. DOI: 10.1016/S1473-3099(22)00345-0
    [48]
    Xu H, Li H, You H, et al. Effectiveness of inactivated COVID-19 vaccines against mild disease, pneumonia, and severe disease among persons infected with SARS-CoV-2 Omicron variant: Real-world study in Jilin Province, China[J]. Emerg Microbes Infect, 2022: 1-30.
    [49]
    Zhang X, Zhang W, Chen S. Shanghai's life-saving efforts against the current omicron wave of the COVID-19 pandemic[J]. Lancet, 2022, 399: 2011-2012. DOI: 10.1016/S0140-6736(22)00838-8
    [50]
    Domingo FR, Waddell LA, Cheung AM, et al. Prevalence of long-term effects in individuals diagnosed with COVID-19: an updated living systematic review[J]. medRxiv, 2021: 2021.06.03.21258317.
    [51]
    Wulf Hanson S, Abbafati C, Aerts JG, et al. Estimated Global Proportions of Individuals With Persistent Fatigue, Cognitive, and Respiratory Symptom Clusters Following Symptomatic COVID-19 in 2020 and 2021[J]. JAMA, 2022, 328: 1604-1615. DOI: 10.1001/jama.2022.18931
    [52]
    Hastie CE, Lowe DJ, McAuley A, et al. Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study[J]. Nat Commun, 2022, 13: 5663. DOI: 10.1038/s41467-022-33415-5
    [53]
    Antonelli M, Penfold RS, Merino J, et al. Risk factors and disease profile of post-vaccination SARS-CoV-2 infection in UK users of the COVID Symptom Study app: a prospective, community-based, nested, case-control study[J]. Lancet Infect Dis, 2022, 22: 43-55. DOI: 10.1016/S1473-3099(21)00460-6
    [54]
    Ayoubkhani D, Bermingham C, Pouwels KB, et al. Trajectory of long covid symptoms after COVID-19 vaccination: community based cohort study[J]. Bmj, 2022, 377: e069676.
    [55]
    Antonelli M, Pujol JC, Spector TD, et al. Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2[J]. Lancet, 2022, 399: 2263-2264. DOI: 10.1016/S0140-6736(22)00941-2
    [56]
    Faust JS, Del Rio C. Assessment of Deaths From COVID-19 and From Seasonal Influenza[J]. JAMA Intern Med, 2020, 180: 1045-1046. DOI: 10.1001/jamainternmed.2020.2306
    [57]
    Ludwig M, Jacob J, Basedow F, et al. Clinical outcomes and characteristics of patients hospitalized for Influenza or COVID-19 in Germany[J]. Int J Infect Dis, 2021, 103: 316-322. DOI: 10.1016/j.ijid.2020.11.204
    [58]
    Xue L, Jing S, Zhang K, et al. Infectivity versus fatality of SARS-CoV-2 mutations and influenza[J]. Int J Infect Dis, 2022, 121: 195-202. DOI: 10.1016/j.ijid.2022.05.031
    [59]
    Jay Hilotin, Vijith Pulikkal. COVID-19: Omicron now less deadly than flu?[EB/OL]. (2022-3-11)[2022-12-06]. https://gulfnews.com/special-reports/COVID-19-omicron-now-less-deadly-than-flu-1.1647011926766.
    [60]
    Bilinski A, Thompson K, Emanuel E. COVID-19 and Excess All-Cause Mortality in the US and 20 Comparison Countries, June 2021-March 2022[J]. JAMA, 2022. doi: 10.1001/jama.2022.21795.
    [61]
    Ministry of Health (Singapore). COVID-19 Situation at a Glance[EB/OL]. [2022-12-06] https://www.moh.gov.sg/.
    [62]
    Iuliano AD, Roguski KM, Chang HH, et al. Estimates of global seasonal influenza-associated respiratory mortality: a modelling study[J]. Lancet, 2018, 391: 1285-1300. DOI: 10.1016/S0140-6736(17)33293-2
    [63]
    Li ZJ, Yu LJ, Zhang HY, et al. Broad Impacts of Coronavirus Disease 2019(COVID-19) Pandemic on Acute Respiratory Infections in China: An Observational Study[J]. Clin Infect Dis, 2022, 75: e1054-e1062. DOI: 10.1093/cid/ciab942
    [64]
    Huang WJ, Cheng YH, Tan MJ, et al. Epidemiological and virological surveillance of influenza viruses in China during 2020-2021[J]. Infect Dis Poverty, 2022, 11: 74. DOI: 10.1186/s40249-022-01002-x
    [65]
    Cohen R, Ashman M, Taha MK, et al. Pediatric Infectious Disease Group (GPIP) position paper on the immune debt of the COVID-19 pandemic in childhood, how can we fill the immunity gap?[J]. Infect Dis Now, 2021, 51: 418-423. DOI: 10.1016/j.idnow.2021.05.004
    [66]
    Cai J, Deng X, Yang J, et al. Modeling transmission of SARS-CoV-2 Omicron in China[J]. Nat Med, 2022, 28: 1468-1475. DOI: 10.1038/s41591-022-01855-7
    [67]
    Mallapaty S. Can China avoid a wave of deaths if it lifts strict zero COVID policy?[J]. Nature, 2022, 612: 203. DOI: 10.1038/d41586-022-04235-w
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