CoChat
Sign Up
Cited by 862SARS-CoV-2 and COVID-19 ResearchCOVID-19 Clinical Research StudiesCOVID-19 epidemiological studies

Omicron variant of SARS‐CoV‐2: Genomics, transmissibility, and responses to current COVID‐19 vaccines

Open access
Araf, Yusha, Akter, Fariya, Tang, Yan‐dong, Fatemi, Rabeya, Parvez, Md. Sorwer Alam, Zheng, Chunfu, Hossain, Md. Golzar·2022·Journal of Medical Virology
DOI 10.1002/jmv.27588PMC PMC9015557
Open this paper in CoChat — free account

Abstract

Currently, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has spread worldwide as an Omicron variant. This variant is a heavily mutated virus and designated as a variant of concern by the World Health Organization (WHO). WHO cautioned that the Omicron variant of SARS‐CoV‐2 held a very high risk of infection, reigniting anxieties about the economy's recovery from the 2‐year pandemic. The extensively mutated Omicron variant is likely to spread internationally, posing a high risk of infection surges with serious repercussions in some areas. According to preliminary data, the Omicron variant of SARS‐CoV‐2 has a higher risk of reinfection. On the other hand, whether the current COVID‐19 vaccines could effectively resist the new strain is still under investigation. However, there is very limited information on the current situation of the Omicron variant, such as genomics, transmissibility, efficacy of vaccines, treatment, and management. This review focused on the genomics, transmission, and effectiveness of vaccines against the Omicron variant, which will be helpful for further investigation of a new variant of SARS‐CoV‐2.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1002/jmv.27588

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 31 · Cited by 862

Research works printed but not linked: 37

  1. [3]3. Gao SJ, Guo H, Luo G. Omicron variant (B.1.1.529) of SARS‐CoV‐2, a global urgent public health alert!. J Med Virol. Published online November 30, 2021. [DOI] [PMC free article] [PubMed]
  2. [4]4. Torjesen I. COVID‐19: Omicron may be more transmissible than other variants and partly resistant to existing vaccines, scientists fear. BMJ. 2021;375:n2943. [DOI] [PubMed] [Google Scholar]
  3. [7]7. Zhang X, Wu S, Wu B, et al. SARS‐CoV‐2 Omicron strain exhibits potent capabilities for immune evasion and viral entrance. Signal Transduct Target Ther. 2021;6(1):430. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. [11]11. Bansal K, Kumar S. Mutational cascade of SARS‐CoV‐2 leading to evolution and emergence of omicron variant. bioRxiv. 2021. 2021;2012(2006):471389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. [12]12. Daria S, Bhuiyan MA, Islam MR. Detection of highly muted coronavirus variant Omicron (B.1.1.529) is triggering the alarm for South Asian countries: Associated risk factors and preventive actions. J Med Virol. Published online December 4, 2021. [DOI] [PMC free article] [PubMed]
  6. [13]13. Garcia‐Beltran WF St., Denis KJ, Hoelzemer A, et al. mRNA‐based COVID‐19 vaccine boosters induce neutralizing immunity against SARS‐CoV‐2 Omicron variant. Cell. Published online January 6, 2022. [DOI] [PMC free article] [PubMed]
  7. [14]14. Hoffmann M, Krüger N, Schulz S, et al. The Omicron variant is highly resistant against antibody‐mediated neutralization – implications for control of the COVID‐19 pandemic. Cell. Published online December 24, 2021. [DOI] [PMC free article] [PubMed]
  8. [16]16. Liu C, Ginn HM, Dejnirattisai W, et al. Reduced neutralization of SARS‐CoV‐2 B.1.617 by vaccine and convalescent serum. Cell. 2021;184(16):4220‐4236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. [18]18. Quarleri J, Galvan V, Delpino MV. Omicron variant of the SARS‐CoV‐2: a quest to define the consequences of its high mutational load. GeroScience. Published online December 18, 2021. [DOI] [PMC free article] [PubMed]
  10. [19]19. Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and Delta variant of SARS‐CoV‐2: A comparative computational study of spike protein. J Med Virol. Published online December 15, 2021. [DOI] [PubMed]
  11. [20]20. Kandeel M, Mohamed MEM, Abd El‐Lateef HM, Venugopala KN, El‐Beltagi HS. Omicron variant genome evolution and phylogenetics. J Med Virol. Published online December 10, 2021. [DOI] [PMC free article] [PubMed]
  12. [21]21. Wang L, Cheng G. Sequence analysis of the emerging Sars‐CoV‐2 variant omicron in South Africa. J Med Virol. Published online December 12, 2021. [DOI] [PubMed]
  13. [23]23. Shanmugaraj B, Malla A, Khorattanakulchai N, Phoolcharoen W. SARS‐CoV‐2 omicron variant: could it be another threat? J Med Virol. Published online December 19, 2021. [DOI] [PMC free article] [PubMed]
  14. [24]24. Dyer O. COVID‐19: South Africa's surge in cases deepens alarm over omicron variant. BMJ. 2021;375:n3013. [DOI] [PubMed] [Google Scholar]
  15. [25]25. Callaway E. Heavily mutated Omicron variant puts scientists on alert. Nature News. Accessed December 16, 2021. https://www.nature.com/articles/d41586-021-03552-w [DOI] [PubMed]
  16. [27]27. Hossain G, Tang Y‐d, Akter S, Zheng C. Roles of the polybasic furin cleavage site of spike protein in SARS‐CoV‐2 replication, pathogenesis, and host immune responses and vaccination. J Med Virol. Published online December 22, 2021. [DOI] [PubMed]
  17. [28]28. Peacock TP, Goldhill DH, Zhou J, et al. The furin cleavage site in the SARS‐CoV‐2 spike protein is required for transmission in ferrets. Nat Microbiol. 2021;6(7):899‐909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. [29]29. Wu L, Zhou L, Mo M, et al. The effect of the multiple mutations in Omicron RBD on its binding to human ACE2 receptor and immune evasion: an investigation of molecular dynamics simulations. ChemRxiv. 2021.
  19. [30]30. Pascarella S, Ciccozzi M, Zella D, et al. SARS‐CoV‐2 B.1.617 Indian variants: are electrostatic potential changes responsible for a higher transmission rate? J Med Virol. 2021;93(12):6551‐6556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. [31]31. Pascarella S, Ciccozzi M, Bianchi M, Benvenuto D, Cauda R, Cassone A. The electrostatic potential of the omicron variant spike is higher than in delta and delta‐plus variants: a hint to higher transmissibility? J Med Virol. Published online December 16, 2021. [DOI] [PubMed]
  21. [32]32. Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and Delta variant of SARS‐CoV‐2: a comparative computational study of spike protein. J Med Virol. Published online December 15, 2021. [DOI] [PubMed]
  22. [33]33. Meng B, Ferreira IATM, Abdullahi A, et al. SARS‐CoV‐2 Omicron spike mediated immune escape, infectivity and cell‐cell fusion. bioRxiv. 2021;2012(2017):473248. [Google Scholar]
  23. [34]34. Li X. Omicron: call for updated vaccines. J Med Virol. Published online December 20, 2021. [DOI] [PubMed]
  24. [35]35. Saxena SK, Kumar S, Ansari S, et al. Characterization of the novel SARS‐CoV‐2 Omicron (B.1.1.529) Variant of Concern and its global perspective. J Med Virol. Published online December 14, 2021. [DOI] [PubMed]
  25. [36]36. Shah M, Woo HG. Omicron: A heavily mutated SARS‐CoV‐2 variant exhibits stronger binding to ACE2 and potently escape approved COVID‐19 therapeutic antibodies. bioRxiv. 2021;2012(2004):471200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. [37]37. Schmidt F, Muecksch F, Weisblum Y, et al. Plasma neutralization properties of the SARS‐CoV‐2 Omicron variant. medRxiv. Published online December 13, 2021.
  27. [38]38. Greaney AJ, Starr TN, Bloom JD. An antibody‐escape calculator for mutations to the SARS‐CoV‐2 receptor‐binding domain. bioRxiv. Published online December 21, 2021.
  28. [39]39. Krause PR, Fleming TR, Longini IM, et al. SARS‐CoV‐2 Variants and Vaccines. N Engl J Med. 2021;385(2):179‐186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. [40]40. Kemp SA, Collier DA, Datir R, et al. Neutralising antibodies in Spike mediated SARS‐CoV‐2 adaptation. medRxiv. Published online December 11, 2020.
  30. [42]42. Siddle KJ, Krasilnikova LA, Moreno GK, et al. Transmission from vaccinated individuals in a large SARS‐CoV‐2 Delta variant outbreak. Cell. Published online December 23, 2021. [DOI] [PMC free article] [PubMed]
  31. [43]43. Lu L, Mok BW‐Y, Chen L, et al. Neutralization of SARS‐CoV‐2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients medRxiv. Published online December 14, 2021.
  32. [44]44. Mudd PA, Minervina AA, Pogorelyy MV, et al. SARS‐CoV‐2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans. Cell. Published online December 23, 2021. [DOI] [PMC free article] [PubMed]
  33. [45]45. Pfizer . Pfizer and BioNTech Provide Update on Omicron Variant. Accessed December 16, 2021. https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-provide-update-omicron-variant
  34. [46]46. Mahase E. COVID‐19: Omicron and the need for boosters. BMJ. 2021;375:n3079. [DOI] [PubMed] [Google Scholar]
  35. [51]51. WHO . 2021. https://www.afro.who.int/news/africa-steps-omicron-variant-detection-covid-19-cases-rise-southern-africa [Google Scholar]
  36. [57]57. Christie B. Covid‐19: Early studies give hope omicron is milder than other variants. BMJ. 2021;375:n3144. [DOI] [PubMed] [Google Scholar]
  37. [65]65. Chitravanshi R. Separate isolation area for Omicron positive patients must: Health Ministry. Business Standard. Accessed December 16, 2021. https://www.business-standard.com/article/current-affairs/separate-isolation-area-for-omicron-positive-patients-must-health-ministry-121120800951_1.html Associated Data This section collects any data citations, data availability statements, or supplementary materials included in this article. Data Availability Statement The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. Articles from Journal of Medical Virology are provided here courtesy of Wiley

Authors
Araf, Y., Akter, F., Tang, Y., Fatemi, R., Parvez, M. S. A., Zheng, C., & Hossain, M. G.
Affiliations
  • Fujian Medical University (CN)
  • BRAC University (BD)
  • State Key Laboratory of Veterinary Biotechnology (CN)
  • East West University (BD)
  • Shahjalal University of Science and Technology (BD)
  • Bangladesh Agricultural University (BD)
ORCID
Venue
Journal of Medical Virology
Publisher
Wiley
Published
2022-01-23
Volume
94
Issue
5
Pages
1825-1832
ISSN
  • 0146-6615 (ISSN-L)
  • 1096-9071
DOI
10.1002/jmv.27588
PMC
PMC9015557
OpenAlex
W4205170082
Cited by
862
References
31
Citations by year
2026: 23 · 2025: 88 · 2024: 162 · 2023: 280 · 2022: 305 · 2021: 4
FWCI
32.26
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • Journal of Medical Virology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
  • Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
Keywords
Omicron variant, SARS-CoV-2, COVID-19 pandemic, viral genomics, transmissibility, vaccine efficacy, variants of concern, reinfection, viral mutations, COVID-19 vaccines
MeSH terms
COVID-19, SARS-CoV-2, COVID-19 Vaccines, Humans, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review