Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves

Focosi, Daniele; Quiroga, Rodrigo; McConnell, Scott A.; Johnson, Marc C.; Casadevall, Arturo

doi:10.1101/2022.12.05.518843

Cited by 11 publications

(21 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The copyright holder for this preprint this version posted February 7, 2023. ; https://doi.org/10.1101/2023.02.06.527236 doi: bioRxiv preprint in the recent Omicron subvariants of BA.5, which is consistent with the recent observation that a large number of immune evasive mutations were found in Omicron subvariants 15 . This tendency is likely owing to the imprinted humoral immunity, which resulted in reduced diversity of neutralizing antibodies and thus exerted more concentrated immunological pressure on recent variants 14,31 .…”

Section: Discussionsupporting

confidence: 85%

“…The copyright holder for this preprint this version posted February 7, 2023. ; https://doi.org/10.1101/2023.02.06.527236 doi: bioRxiv preprint SARS-CoV-2 evolution 14,15 . However, previous studies mainly focused on a few fast-growing variants and mutations that were known to have a great impact on immune evasion, and thus may suffer from survival bias, i.e., the findings may not be applicable to other variants that account for a large fraction of the data.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinity

Jian

et al. 2023

Preprint

View full text Add to dashboard Cite

The evolution of SARS-CoV-2 is characterized by the emergence of new variants with a sheer number of mutations compared to their predecessors, which conferred resistance to pre-existing antibodies and/or increased transmissibility. The recently emerged Omicron subvariants also exhibit a strong tendency for immune evasion, suggesting adaptive evolution. However, previous studies have been limited to specific lineages or subsets of mutations, the overall evolutionary trajectory of SARS-CoV-2 and the underlying driving forces are still not fully understood. In this study, we analyzed the mutations present in all open-access SARS-CoV-2 genomes (until November 2022) and correlated the mutation's incidence and fitness change with its impact on immune evasion and ACE2 binding affinity. Our results showed that the Omicron lineage had an accelerated mutation rate in the RBD region, while the mutation incidence in other genomic regions did not change dramatically over time. Moreover, mutations in the RBD region (but not in any other genomic regions) exhibited a lineage-specific pattern and tended to become more aggregated over time, and the mutation incidence was positively correlated with the strength of antibody pressure on the specific position. Additionally, the incidence of mutation was also positively correlated with changes in ACE2 binding affinity, but with a lower correlation coefficient than with immune evasion. In contrast, the mutation's effect on fitness was more closely correlated with changes in ACE2 binding affinity than immune evasion. In conclusion, our results suggest that immune evasion and ACE2 binding affinity play significant and diverse roles in the evolution of SARS-CoV-2.

show abstract

Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinity

Jian

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…1 ). As of December 2022, recently emerging Omicron subvariants are under convergent evolution: recently emerging variants acquired substitutions at the same residues of the spike (S) protein, such as R346, K444, L452, N460, and F486 2, 3 . For instance, Omicron BQ.1.1 variant, which is a descendant of Omicron BA.5 and is currently becoming predominant in the Western countries 1 , possesses all convergent substitutions, such as R346T, K444T, L452R, N460K, and F486V.…”

Section: Introductionmentioning

confidence: 99%

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Tamura

Ito

Uriu

et al. 2022

Preprint

159

View full text Add to dashboard Cite

In late 2022, the SARS-CoV-2 Omicron subvariants have highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged by recombination of two co-circulating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022 around India. In vitro experiments revealed that XBB is the most profoundly resistant variant to BA.2/5 breakthrough infection sera ever and is more fusogenic than BA.2.75. Notably, the recombination breakpoint is located in the receptor-binding domain of spike, and each region of recombined spike conferred immune evasion and augmented fusogenicity to the XBB spike. Finally, the intrinsic pathogenicity of XBB in hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provided evidence suggesting that XBB is the first documented SARS-CoV-2 variant increasing its fitness through recombination rather than single mutations.

show abstract

“…Although BA.5 is still circulating with high frequency at recent time, a diverse array of Omicron sub-lineages has arisen, including BA.2.75, BN.1, BF.7, BQ.1, BQ.1.1, XBB, and more recently, XBB.1.5 (Figure 1B). The unprecedented diversity of the so-called ''variant soup'' makes it harder to predict coming waves of infection (Callaway, 2022;Focosi et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China

Wang

Jiang

et al. 2023

Preprint

View full text Add to dashboard Cite

SARS-CoV-2 is continuing to evolve and diversify, with an array of various Omicron sub-lineages, including BA.5, BA.2.75, BN.1, BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5, now circulating globally at recent time. In this study, we evaluated the neutralization sensitivity of a comprehensive panel of Omicron subvariants to sera from different clinical cohorts, including individuals who received homologous or heterologous booster vaccinations, vaccinated people who had Delta or BA.2 breakthrough infection in previous waves, and patients who had BA.5 or BF.7 breakthrough infection in the current wave in China. All the Omicron subvariants exhibited substantial neutralization evasion, with BQ.1, BQ.1.1, XBB.1, and XBB.1.5 being the strongest escaped subvariants. Sera from Omicron breakthrough infection, especially the recent BA.5 or BF.7 breakthrough infection, exhibited higher neutralizing activity against all Omicron sub-lineages, indicating the chance of BA.5 and BF.7 being entirely replaced by BQ or XBB subvariants in China in a short-term might be low. We also demonstrated that the BQ and XBB subvariants were the most resistant viruses to monoclonal antibodies. Continuing to monitor the immune escape of SARS-CoV-2 emerging variants and developing novel broad-spectrum vaccines and antibodies are still crucial.

show abstract

Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves

Cited by 11 publications

References 60 publications

Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinity

Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinity

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China

Contact Info

Product

Resources

About