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 |
[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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