S glycoprotein diversity of the Omicron variant

Sarkar, Rakesh; Lo, Mahadeb; Saha, Ritubrita; Chawla‐Sarkar, Mamta

doi:10.1101/2021.12.04.21267284

Cited by 33 publications

(33 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3B ) and may affect Spike affinity for ACE2 ( 69 – 72 ). A significant portion of mutations in the S1 subunit (ΔH69/V70, T95I, ΔY144, K417N, T478K, N501Y, D614G, H655Y, and P681H) has previously been observed in other VOCs ( 68 ). For some of them, phenotypic effects such as increased transmission and immune evasion have been reported.…”

Section: Alterations In the Omicron Spike Proteinmentioning

confidence: 82%

“…The Omicron 21K and 21L Spike proteins share 20 amino acid changes compared to the original Wuhan Hu-1 strain, with an additional 19 21K- and 14 21L-specific mutations, respectively ( Fig. 3A ), although even higher numbers of mutations might be found in some viral isolates ( 68 ). In comparison, the Delta VOC differs by only nine amino acid changes from the initial viral isolate, two of which (E478K and D614G) are shared by the Omicron VOC ( Fig.…”

Section: Alterations In the Omicron Spike Proteinmentioning

confidence: 99%

See 1 more Smart Citation

Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?

Jung

Kmieć

Koepke

et al. 2022

J Virol

178

140

View full text Add to dashboard Cite

Emerging strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, that show increased transmission fitness and/or immune evasion are classified as “variants of concern” (VOCs). Recently, a SARS-CoV-2 variant first identified in November 2021 in South Africa has been recognized as a fifth VOC, termed “Omicron”. What makes this VOC so alarming is the high number of changes, especially in the viral Spike protein, and accumulating evidence for increased transmission efficiency and escape from neutralizing antibodies. In an amazingly short time, the Omicron VOC has outcompeted the previously dominating Delta VOC. However, it seems that the Omicron VOC is overall less pathogenic compared to other SARS-CoV-2 VOCs. Here, we provide an overview of the mutations in the Omicron genome and the resulting changes in viral proteins compared to other SARS-CoV-2 strains and discuss their potential functional consequences.

show abstract

Section: Alterations In the Omicron Spike Proteinmentioning

confidence: 82%

Section: Alterations In the Omicron Spike Proteinmentioning

confidence: 99%

Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?

Jung

Kmieć

Koepke

et al. 2022

J Virol

178

140

View full text Add to dashboard Cite

show abstract

“…These mutations are located within the heptad repeat 1 (HR1) region that acts in the process of fusion with the host cell. Thus these mutations may affect transmissibility and infectivity [86,87]. Located in the transmembrane domain, this mutation can affect the configuration of E protein and provides a stronger anchoring to the viral membrane [88,89].…”

Section: Y145dmentioning

confidence: 99%

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

Abbas

Kusakin

Sharrouf

et al. 2022

Preprint

View full text Add to dashboard Cite

Aided by extensive protein mutations, the SARS-CoV-2 Omicron (B.1.1.529) variant overtook the previously dominant Delta variant and rapidly spread around the world. It was shown to exhibit significant resistance to current vaccines and evasion from neutralizing antibodies. It is therefore critical to investigate the Omicron mutations trajectories. In this study, a literature search of published articles and SARS-CoV-2 databases was conducted, We explored the full list of mutations in Omicron BA.1, BA.1.1, BA.2, and BA.3 lineages. We described in detail the prevalence and occurrence of the mutations across variants, and how Omicron differs from them. We used GISAID as our primary data source, which provides open access to genomics data of the SARS-CoV-2 virus, in addition to epidemiological and geographical data. We examined how these mutations interact with each other, their co-occurrence and clustering. Our study offers for the first time a comprehensive description of all mutations with a focus on non-spike mutations and demonstrated that mutations in regions other than the Spike (S) genes are worth investigating further. Our research established that the Omicron variant has retained some mutations reported in other SARS-CoV-2 variants, yet many of its mutations are extremely rare in other variants and unique to Omicron. Some of these mutations have been linked to the transmissibility and immune escape of the virus, and indicate a significant shift in SARS-CoV-2 evolution. The most likely theories for the evolution of the Omicron variant were also discussed.

show abstract

“…Beta possesses these key mutations in the S RBD, in addition to the K417N and E484K mutations which are not directly implicated in altered viral transmission and hACE2 binding ( 16 , 17 ). In December 2020, the VoC, B.1.617.2 (Delta) of SARS-CoV-2 first appeared in India, becoming quickly the global predominant circulating variant; however, this distinction could be soon displaced by the novel Omicron variant ( 18 – 20 ). The most common Delta variant has two important mutations on the viral S RBD, L452R and T478K, allowing for increased infectivity, transmissibility, as well as its ability of escaping neutralizing antibodies ( 21 – 23 ).…”

Section: Introductionmentioning

confidence: 99%

Evaluating Antibody Mediated Protection against Alpha, Beta, and Delta SARS-CoV-2 Variants of Concern in K18-hACE2 Transgenic Mice

Wong

Horspool

Russ

et al. 2022

J Virol

View full text Add to dashboard Cite

SARS-CoV-2 variants of concern (VoC) are impacting responses to the COVID-19 pandemic. Here, we utilized passive immunization using human convalescent plasma (HCP) obtained from a critically ill COVID-19 patient in the early pandemic to study the efficacy of polyclonal antibodies generated to ancestral SARS-CoV-2 against the Alpha, Beta, and Delta VoC in the K18 human angiotensin converting enzyme 2 (hACE2) transgenic mouse model. HCP protected mice from challenge with the original WA-1 SARS-CoV-2 strain; however, only partially protected mice challenged with the Alpha VoC (60% survival) and failed to save Beta challenged mice from succumbing to disease. HCP treatment groups had elevated receptor binding domain (RBD) and nucleocapsid IgG titers in the serum; however, Beta VoC viral burden in the lung and brain was not decreased due to HCP treatment. While mice could be protected from WA-1 or Alpha challenge with a single dose of HCP, six doses of HCP could not decrease mortality of Delta challenged mice. Overall, these data demonstrate that VoC have enhanced immune evasion and this work underscores the need for in vivo models to evaluate future emerging strains. IMPORTANCE Emerging SARS-CoV-2 VoC are posing new problems regarding vaccine and monoclonal antibody efficacy. To better understand immune evasion tactics of the VoC, we utilized passive immunization to study the effect of early-pandemic SARS-CoV-2 HCP against, Alpha, Beta, and Delta VoC. We observed that HCP from a human infected with the original SARS-CoV-2 was unable to control lethality of Alpha, Beta, or Delta VoC in the K18-hACE2 transgenic mouse model of SARS-CoV-2 infection. Our findings demonstrate that passive immunization can be used as a model to evaluate immune evasion of emerging VoC strains.

show abstract

S glycoprotein diversity of the Omicron variant

Cited by 33 publications

References 43 publications

Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?

Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

Evaluating Antibody Mediated Protection against Alpha, Beta, and Delta SARS-CoV-2 Variants of Concern in K18-hACE2 Transgenic Mice

Contact Info

Product

Resources

About