“Is Omicron mild”? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies

Rajpal, Vijay Rani; Sharma, Shashi; Kumar, Akhilesh; Chand, Shweta; Joshi, Lata; Chandra, Atika; Babbar, Sadhna; Goel, Shailendra; Raina, S. N.; Shiran, Behrouz

doi:10.1002/jmv.27749

Cited by 20 publications

(11 citation statements)

References 114 publications

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“…The Omicron (21 L, BA.2) spike protein contains 29 amino acid substitutions and one insertion (T19I, L24S, ins25PPA, D142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K) ( https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/sars-cov-2-genomic-surveillance-update/ ). There are 20 identical spike mutations (G142D, G339D, S373P, S375F, K417N, N440K, S477N, T478K, E484A, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K) in all five Omicron lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) and BA.1.1, BA.2.12.1 sublineage, 22 as shown in Figure 1 and Table 1 .…”

Section: Introductionmentioning

confidence: 99%

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Zhou

Zhi

Teng

2022

Journal of Medical Virology

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As of November 2021, several SARS‐CoV‐2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID‐19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) ( https://www.gisaid.org/ ). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild‐type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.

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Section: Introductionmentioning

confidence: 99%

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Zhou

Zhi

Teng

2022

Journal of Medical Virology

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“…In comparison to the ancestral Wuhan SARS-CoV-2 isolate, the omicron SARS-CoV-2 VOC has a total of 60 mutations, with 37 (6 deletions, 1 insertion, and 30 substitutions) located in the spike protein. 31 , 32 The omicron VOC has been reported to share 10 and 5 common mutations with alpha and beta variants, respectively, while seven mutations each were shared with the gamma and delta variants. Compared to the ancestral virus and delta VOC, the omicron spike protein is less efficiently cleaved and is less fusogenic, 33 indicating changed binding affinity and potential for enzymatic cleavage.…”

Section: Resultsmentioning

confidence: 99%

Surface Inactivation of Highly Mutated SARS-CoV-2 Variants of Concern: Alpha, Delta, and Omicron

et al. 2022

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Continued SARS-CoV-2 transmission among the human population has meant the evolution of the virus to produce variants of increased infectiousness and virulence, coined variants of concern (VOCs). The last wave of pandemic infections was driven predominantly by the delta VOC, but because of continued transmission and adaptive mutations, the more highly transmissible omicron variant emerged and is now dominant. However, due to waning immunity and emergence of new variants, vaccines alone cannot control the pandemic. The application of an antiviral coating to high-touch surfaces and physical barriers such as masks are an effective means to inactivate the virus and their spread. Here, we demonstrate an environmentally friendly water-borne polymer coating that can completely inactivate SARS-CoV-2 independent of the infectious variant. The polymer was designed to target the highly glycosylated spike protein on the virion surface and inactivate the virion by disruption of the viral membrane through a nano-mechanical process. Our findings show that, even with low amounts of coating on the surface (1 g/m 2 ), inactivation of alpha, delta, and omicron VOCs and degradation of their viral genome were complete. Furthermore, our data shows that the polymer induces little to no skin sensitization in mice and is non-toxic upon oral ingestion in rats. We anticipate that our transparent polymer coating can be applied to face masks and many other surfaces to capture and inactivate the virus, aiding in the reduction of SARS-CoV-2 transmission and evolution of new variants of concern.

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“…The evolution of SARS-CoV-2 has always been characterized by the emergence of sets of new mutations impacting the virus's main features. Therefore, the emergence and spread of the Omicron BA.2 lineage were enabled by its unique abilities: flexibility of transmission, replication advantage, and significant neutralization escape [66]. Moreover, this new surge has again demonstrated that a "one pill fits all" strategy does not exist for SARS-CoV-2 or, more specifically, for the Omicron variant [50].…”

Section: Discussionmentioning

confidence: 99%

Omicron BA.2 Lineage, the “Stealth” Variant: Is It Truly a Silent Epidemic? A Literature Review

Tiecco

Storti

Arsuffi

et al. 2022

IJMS

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The epidemic curve of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is silently rising again. Worldwide, the dominant SARS-CoV-2 variant of concern (VOC) is Omicron, and its virological characteristics, such as transmissibility, pathogenicity, and resistance to both vaccine- and infection-induced immunity as well as antiviral drugs, are an urgent public health concern. The Omicron variant has five major sub-lineages; as of February 2022, the BA.2 lineage has been detected in several European and Asian countries, becoming the predominant variant and the real antagonist of the ongoing surge. Hence, although global attention is currently focused on dramatic, historically significant events and the multi-country monkeypox outbreak, this new epidemic is unlikely to fade away in silence. Many aspects of this lineage are still unclear and controversial, but its apparent replication advantage and higher transmissibility, as well as its ability to escape neutralizing antibodies induced by vaccination and previous infection, are rising global concerns. Herein, we review the latest publications and the most recent available literature on the BA.2 lineage of the Omicron variant.

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“Is Omicron mild”? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies

Cited by 20 publications

References 114 publications

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Surface Inactivation of Highly Mutated SARS-CoV-2 Variants of Concern: Alpha, Delta, and Omicron

Omicron BA.2 Lineage, the “Stealth” Variant: Is It Truly a Silent Epidemic? A Literature Review

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