Challenges of SARS-CoV-2 Omicron Variant and appropriate countermeasures

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Abstract

The Omicron (B.1.1.529) variant was first reported in South Africa and rapidly spread worldwide in early November 2021. This caused panic in various countries, so it is necessary to understand Omicron Variant. This paper summarizes omicron variant-related research achievements. Studies have shown that Omicron Variant contains many mutations that make it more infectious and transmissible. At the same time, immune escape is also caused, resulting in reduced efficacy of existing vaccines, increased risk of reinfection, treatment failure or reduction of monoclonal antibody therapies, and detection failure. However, current data indicate that Omicron Variant causes mild clinical symptoms and few severe cases and deaths. Omicron Variant is valid for a range of nonpharmaceutical interventions against SARS-CoV-2. Improving diagnostic accuracy and enabling timely isolation and treatment of diagnosed cases is also critical to interrupting the spread of omicron variants. COVID-19 vaccine boosters could undoubtedly help control Omicron spread and infection. However, developing a vaccine specific to Omicron Variant is also imminent.

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Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Jun Lan, Jiwan Ge, Jinfang Yu … (2020)

A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2, SARS-CoV-2) caused an outbreak in Wuhan city, Hubei province, China, starting from December 2019 that quickly spread nationwide and to other countries around the world1-3. Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor4. Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses1-3,5. The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.

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Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Renhong Yan, Yuanyuan Zhang, Yaning Li … (2020)

How SARS-CoV-2 binds to human cells Scientists are racing to learn the secrets of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2), which is the cause of the pandemic disease COVID-19. The first step in viral entry is the binding of the viral trimeric spike protein to the human receptor angiotensin-converting enzyme 2 (ACE2). Yan et al. present the structure of human ACE2 in complex with a membrane protein that it chaperones, B0AT1. In the context of this complex, ACE2 is a dimer. A further structure shows how the receptor binding domain of SARS-CoV-2 interacts with ACE2 and suggests that it is possible that two trimeric spike proteins bind to an ACE2 dimer. The structures provide a basis for the development of therapeutics targeting this crucial interaction. Science, this issue p. 1444

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Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

B Korber, W.M. Fischer, S. Gnanakaran … (2020)

Summary A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to the introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to higher titer as pseudotyped virions. In infected individuals G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, although not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus, and support continuing surveillance of Spike mutations to aid in the development of immunological interventions.

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Author and article information

Journal

Journal ID (nlm-ta): J Microbiol Immunol Infect

Journal ID (iso-abbrev): J Microbiol Immunol Infect

Title: Journal of Microbiology, Immunology, and Infection

Publisher: Taiwan Society of Microbiology. Published by Elsevier Taiwan LLC.

ISSN (Print): 1684-1182

ISSN (Electronic): 1995-9133

Publication date PMC-release: 26 April 2022

Publication date (Electronic): 26 April 2022

Affiliations

[1]Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China

Author notes

[∗ ]Corresponding author. Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, No.261, Huansha Road, Hangzhou, PR China.

[∗∗ ]Corresponding author.

[1]

These authors have contributed equally to this work.

Article

Publisher Item ID: S1684-1182(22)00054-8

DOI: 10.1016/j.jmii.2022.03.007

PMC ID: 9040366

PubMed ID: 35501267

SO-VID: d2d01a2c-4c0a-4a8e-ab68-899671f9a7c6

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Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

Challenges of SARS-CoV-2 Omicron Variant and appropriate countermeasures

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Novel Coronavirus Disease COVID-19

Most cited references 45

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

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