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

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          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.

          Highlights

          • Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron variant is a heavily mutated virus and designated as a variant of concern.

          • This variant may evade vaccine‐induced immunity.

          • There might have increased risk of SARS‐CoV‐2 reinfection by the Omicron variant.

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          Most cited references28

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          mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant

          Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured the neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild-type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that received their primary series recently (<3 months), distantly (6–12 months), or an additional “booster” dose, while accounting for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinees. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron, only 4–6-fold lower than wild type, suggesting enhanced cross-reactivity of neutralizing antibody responses. In addition, we find that Omicron pseudovirus infects more efficiently than other variants tested. Overall, this study highlights the importance of additional mRNA doses to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants. SARS-CoV-2 Omicron variant pseudovirus exhibits escape from vaccine-induced humoral immunity. However, a third dose of COVID-19 mRNA vaccine elicited humoral immunity capable of cross-neutralizing this strain. In addition, pseudovirus produced with the Omicron spike exhibited more efficient transduction of ACE2-expressing target cells than other variants.
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            Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

            SARS-CoV-2 has undergone progressive change with variants conferring advantage rapidly becoming dominant lineages e.g. B.1.617. With apparent increased transmissibility variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the UK. Here we study the ability of monoclonal antibodies, convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2 and complement this with structural analyses of Fab/RBD complexes and map the antigenic space of current variants. Neutralization of both viruses is reduced when compared with ancestral Wuhan related strains but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2 suggesting that individuals previously infected by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insight for immunisation policy with future variant vaccines in non-immune populations. The B.1.617 lineage of SARS-CoV-2, especially the delta strain that is B.1.617.2 has contributed to the wave of infection in the Indian subcontinent. Structural and serological analyses show no evidence of antibody escape but individuals previously infected with either the B.1.351 (beta) and P.1 (gamma) variants are likely more susceptible to reinfection by the delta strain. Vaccines based on B.1.1.7 (alpha) are likely to provide the broadest protection against current variants.
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              The Omicron variant is highly resistant against antibody-mediated neutralization – implications for control of the COVID-19 pandemic

              The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike-protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by Sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent or BNT162b2-vaccinated individuals with 10- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1/BNT162b2-vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant. The SARS-CoV-2 Omicron variant is rapidy spreading worldwide and a public health concern. Experiments show that this variant resistant against several therapeutic antibodies for COVID-19 and efficiently evades antibodies induced upon infection or double BNT162b2 vaccination, however not triple BNT162b2 or ChAdOx1/BNT162b2 vaccination.
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                Author and article information

                Contributors
                zheng.alan@hotmail.com
                mghossain@bau.edu.bd
                Journal
                J Med Virol
                J Med Virol
                10.1002/(ISSN)1096-9071
                JMV
                Journal of Medical Virology
                John Wiley and Sons Inc. (Hoboken )
                0146-6615
                1096-9071
                23 January 2022
                May 2022
                23 January 2022
                : 94
                : 5 , Special Issue on New Coronavirus (2019‐nCoV or SARS‐CoV‐2) and the Outbreak of the Respiratory Illness (COVID‐19): Part‐XX ( doiID: 10.1002/jmv.v94.5 )
                : 1825-1832
                Affiliations
                [ 1 ] Department of Immunology, School of Basic Medical Sciences Fujian Medical University Fuzhou China
                [ 2 ] Department of Genetic Engineering and Biotechnology, School of Life Sciences Shahjalal University of Science and Technology Sylhet Bangladesh
                [ 3 ] Department of Mathematics and Natural Sciences, Biotechnology Program, School of Data and Sciences BRAC University Dhaka Bangladesh
                [ 4 ] State Key Laboratory of Veterinary Biotechnology Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences Harbin China
                [ 5 ] Department of Genetic Engineering and Biotechnology East‐West University Dhaka Bangladesh
                [ 6 ] Department of Microbiology, Immunology and Infectious Diseases University of Calgary Calgary Alberta Canada
                [ 7 ] Department of Microbiology and Hygiene Bangladesh Agricultural University Mymensingh Bangladesh
                Author notes
                [*] [* ] Correspondence Chunfu Zheng, Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.

                Email: zheng.alan@ 123456hotmail.com

                Md. Golzar Hossain, Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.

                Email: mghossain@ 123456bau.edu.bd

                Author information
                http://orcid.org/0000-0002-0144-5875
                https://orcid.org/0000-0001-8920-4218
                https://orcid.org/0000-0002-5690-2690
                https://orcid.org/0000-0003-1490-4724
                https://orcid.org/0000-0002-9726-1009
                http://orcid.org/0000-0002-8797-1322
                https://orcid.org/0000-0002-1487-5444
                Article
                JMV27588
                10.1002/jmv.27588
                9015557
                35023191
                42fedace-29a5-4716-b5be-207d95aa0834
                © 2022 Wiley Periodicals LLC

                This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.

                History
                : 01 January 2022
                : 22 December 2021
                : 10 January 2022
                Page count
                Figures: 2, Tables: 0, Pages: 8, Words: 5666
                Categories
                Review
                Reviews
                Custom metadata
                2.0
                May 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.4 mode:remove_FC converted:18.04.2022

                Microbiology & Virology
                coronavirus,disease control,immune responses,sars coronavirus,vaccines/vaccine strains,virus classification

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