Omicron lineage spike proteins use ACE2 receptors extra effectively
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A latest research posted to the bioRxiv* preprint server demonstrated varied traits, together with the entry pathways and sensitivity to vaccination-elicited antibody responses by the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants.

Study: Characterization of entry pathways, species-specific ACE2 residues figuring out entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants. Image Credit: NIAID


Several SARS-CoV-2 variants of concern (VOCs) with improved immune evasion traits, angiotensin-converting enzyme 2 (ACE2) binding affinity, and transmissibility have emerged for the reason that begin of the CoV illness 2019 (COVID-19) pandemic, reminiscent of the latest Omicron VOCs. The Omicron variants of SARS-CoV-2 had been found first in Botswana in late November 2021, and varied Omicron lineages have since arisen, together with BA.2, BA.1, BA.4, BA.3, and BA.5. 

When Omicron BA.1 emerged, it shortly changed the dominant SARS-CoV-2 Delta VOC. Furthermore, the Omicron BA.1 variant grew to become globally prevalent due to its capacity to flee antibody neutralization and enhanced transmissibility. Therefore, a number of scientific teams are engaged on elucidating the processes of SARS-CoV-2 Omicron an infection and their sensitivity to neutralizing antibodies elicited by COVID-19 vaccination.

About the research

In the present work, the researchers utilizing pseudoviruses assessed the transmembrane serine protease 2 (TMPRSS2) influence on SARS-CoV-2 Omicron BA.1.1, BA.1, BA.3, and BA.2 variants’ an infection versus the SARS-CoV-2 ancestral D614G pressure. 

The crew analyzed how delicate Omicron variants had been to suppression by the endosomal inhibitor chloroquine and soluble ACE2 (sACE2) relative to D614G. They examined the affect of temperature on the soundness of spike (S) glycoprotein and therefore infectivity on the 293T cell line by incubating Omicron and D614G variant pseudoviruses at 25°C (room temperature/RT), 4°C, 37°C, 32°C, 50°C, and 42°C for an hour or 50°C for various timeframes. 

Omicron lineage substitutions in spike. Omicron substitutions are proven in a major construction of the SARS-CoV-2 spike protein, with varied domains and cleavage websites indicated. SP, sign peptide; NTD, N-terminal area; RBD, receptor binding area; RBM, receptor binding motif; C, C area; D, area D; S1/S2, furin cleavage junction of S1/S2 subunits; UH, upstream helix; FP, fusion peptide; HR1/2, heptad repeat 1/2; CH, central helix; BH, beta hairpin; CD, connector area; SH, stem helix; TM, transmembrane area. Substitutions frequent to Omicron (BA) VOCs are proven in black. Substitutions distinctive to BA.1 VOC are proven in purple. R346K substitution moreover current in BA.1.1 is proven in mild blue. Substitutions distinctive to BA.2 VOC are proven in inexperienced. Substitutions in BA.1 and BA.2 shared by BA.3 VOC are proven as residues marked with an asterisk.

The scientists examined how Omicron BA.2, BA.1, BA.1.1, and BA.3 variants used ACE2 orthologs from 10 totally different host species, together with the Chinese rufous horseshoe bat, African inexperienced monkey, Chinese hamster, ferret, mouse, white-tailed deer, Syrian golden hamster, bovine, Malayan pangolin, and swine. 293T cells transiently transfected with every species’ ACE2 receptors had been contaminated utilizing pseudoviruses expressing Omicron and D614G variants’ S proteins.

Further, the authors evaluated the residues in Omicron and D614G Ss that block or enable an infection of mouse and horseshoe bat ACE2-expressing cells. They assessed if the Q498R and Q493R substitutions in Omicron S’s receptor-binding motif (RBM) assist or stop the doorway of pseudoviruses of Omicron to cells exhibiting mouse and horseshoe bat ACE2, respectively.

Furthermore, the crew analyzed the serum neutralizing capacity in vaccinated individuals who had obtained three doses of the COVID-19 Pfizer/BNT162b2 messenger ribonucleic acid (mRNA) vaccine (two-dose major vaccination collection plus a 3rd booster dose). They additionally evaluated recovered sera from 5 vaccinated individuals who had a breakthrough an infection after the booster between December 2021 and January 2022, when BA.1.1 or BA.1 strains had been the commonest.


The research outcomes demonstrated that relative to the SARS-CoV-2 ancestral D614G pressure, the an infection by the Omicron BA.2, BA.1, BA.1.1, and BA.3 variants had been much less impacted by TMPRSS2, indicating that Omicron variants had been extra susceptible to endosomal entrance inhibition. The SARS-CoV-2 Omicron variants had increased sensitivity to sACE2 and chloroquine relative to the ancestral D614G sequence. 

The Omicron mutants additionally utilized ACE2 receptors extra successfully in 9 out of 10 animal species evaluated. Besides, because of the Q498R and Q493R S substitutions, Omicron employed mouse ACE2 for entrance distinction to the D614G kind. Nevertheless, the Q493R substitution prohibits the Omicron mutants from utilizing ACE2 of the Chinese rufous horseshoe bat.

Ultimately, sera from fully vaccinated individuals (three doses of the SARS-CoV-2 Pfizer/BNT162b2 vaccine) and absolutely vaccinated contributors with an Omicron breakthrough an infection successfully neutralize pseudoviruses containing S proteins of Omicron and D614G variants. The three-dose vaccinated topics had an identical levels of neutralization in opposition to the Omicron BA.2, BA.1, BA.1.1, and BA.3 sublineages. On the opposite hand, neutralization of the Omicron variants by antibodies generated by three BNT162b2 vaccine doses was seven to eight instances much less efficient than the D614G, with the Omicron variants but evading neutralization extra successfully.

Omicron lineage pseudovirus entry into cells expressing ACE2 from totally different species. Infectivity of D614G (A), BA.1 (B) BA.2 (C) BA.3 (D) BA.1.1 (E), Q493R (F), Q498R (G), S373P (H), and Y453F (I) pseudoviruses on 293T cells transiently transfected with ACE2 orthologs of indicated species. The ACE2 of African inexperienced monkey is denoted as ‘AGM’. 293T cells expressing ACE2 of indicated species, in addition to management 293T.ACE2 cells stably expressing human ACE2, had been concurrently contaminated with 106 RLU/ml of indicated pseudoviruses. Luciferase actions had been decided 48 hours publish an infection. Note: ‘ns’ denotes not important. Significant variations in infectivity between every species ACE2 in comparison with pcDNA3.1 management for pseudoviruses are denoted by asterisks, *: p ≤ 0.05; **:p ≤ 0.01; ***:p ≤ 0.0005; ****:p ≤ 0.0001. Dotted line signifies background degree an infection. Results proven are consultant of three impartial experiments with eight intraassay replicates. The SARS-CoV-2 Omicron RBD-ACE2 interface (PDB: 7WBP) is proven with contacting residues as sticks on the RBD-ACE2 interface (J-M). The SARS-CoV-2 Omicron RBD and ACE2 are coloured in gray and cyan respectively. Positions in RBD (blue) that contact ACE2 (purple) residues are highlighted. Residue positions are indicated by arrows. The SARS-CoV-2 RBD/ACE2 interactions between 493R/E35 (J), R493/K35 (Okay), Q493/K35 (L), and R498/D38-H353 (M) are proven.


The research findings had been per the prior reviews stating increased utilization of the endosomal entry route by SARS-CoV-2 Omicron variants in cells harboring solely ACE2. However, the crew found that the coexpression of TMPRSS2 augmented an infection. The authors reported that the Omicron BA.2, BA.1, and BA.1.1 variants had been extra and equally delicate to inhibition by the sACE2 monomer (three-fold versus D614G), whereas D614G and BA.3 had been comparatively much less delicate.

The current findings additionally reveal that Omicron lineage S proteins use ACE2 receptors from quite a few animal species extra successfully for entrance. The S alterations within the Omicron BA.2, BA.1, BA.1.1, and BA.3 mutants enable for strong utilization of a wide range of ACE2 orthologues for entrance, doubtlessly growing the prospect of the Omicron variants infecting animal species and spreading again to people.

The findings from the evaluation of three-dose vaccinees had been suitable with quite a few latest research underlining that three-dose mRNA vaccine-triggered antibody responses in opposition to Omicron VOCs had been stronger and broad. According to the present findings and knowledge from others, breakthrough infections elevated preexisting immunity established by three COVID-19 Pfizer/BNT162b2 vaccine doses, evoking antibodies that neutralize SARS-CoV-2 ancestral strains, Omicron, Beta, Delta, and Alpha variants.

*Important discover

bioRxiv publishes preliminary scientific reviews that aren’t peer-reviewed and, subsequently, shouldn’t be thought to be conclusive, information scientific follow/health-related conduct, or handled as established data.

Journal reference:

  • Characterization of entry pathways, species-specific ACE2 residues figuring out entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants; Sabari Nath Neerukonda, Richard Wang, Russell Vassell, Haseebullah Baha, Sabrina Lusvarghi, Shufeng Liu, Tony Wang, Carol D. Weiss, Wei Wang. bioRxiv preprint 2022. DOI:, material/10.1101/2022.06.01.494385v1

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