SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021 DOI Creative Commons
Andrew D. Marques, Scott Sherrill-Mix, J.K. Everett

et al.

mBio, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 8, 2022

The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of global outbreak COVID-19. Evidence suggests that virus evolving to allow efficient spread through human population, including vaccinated individuals. Here, we report a study viral variants from surveillance Delaware Valley, city Philadelphia, and infecting subjects. We sequenced analyzed complete genomes 2621 samples March 2020 September 2021 compared them genome sequences 159 vaccine breakthroughs. In early spring 2020, all detected were B.1 closely related lineages. A mixture lineages followed, notably B.1.243 followed by B.1.1.7 (alpha), with other present at lower levels. Later isolations dominated B.1.617.2 (delta) delta lineages; was exclusive variant last time sampled. To investigate whether any appeared preferentially in breakthroughs, devised model based on Bayesian autoregressive moving average logistic multinomial regression rigorous comparison. This revealed showed 3-fold enrichment breakthrough cases (odds ratio 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated N501Y substitution found alpha, beta gamma 2.04; of1.25-3.18). thus overviews evolution breakthroughs Valley introduces statistical approach interrogating against changing background.

Language: Английский

The evolution of SARS-CoV-2 DOI Open Access
Peter V. Markov, Mahan Ghafari, Martin Beer

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(6), P. 361 - 379

Published: April 5, 2023

Language: Английский

Citations

791
Drivers of adaptive evolution during chronic SARS-CoV-2 infections DOI Creative Commons
Sheri Harari,

Maayan Tahor,

Natalie Rutsinsky

et al.

Nature Medicine, Journal Year: 2022, Volume and Issue: 28(7), P. 1501 - 1508

Published: June 20, 2022

Abstract In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in infections are lineage-defining mutations variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from infections. this study, we searched for drivers VOC-like emergence by consolidating sequencing results a set 27 Most reflected VOC mutations; however, subset associated successful global transmission was absent We further tested ability associate antibody evasion patient-specific and virus-specific features viral rebound is strongly correlated evasion. evidence dynamic polymorphic populations most patients, suggesting compromised immune system selects particular niches patient’s body. suggest tradeoff exists between transmissibility extensive monitoring necessary understanding emergence.

Language: Английский

Citations

131
SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines DOI Creative Commons
John E. Bowen, Young‐Jun Park, Cameron Stewart

et al.

Science Immunology, Journal Year: 2022, Volume and Issue: 7(78)

Published: Nov. 10, 2022

Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies engineering strategies. We show here containing prefusion-stabilizing S mutations elicit antibody responses in humans with enhanced recognition of the

Language: Английский

Citations

72
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy DOI Creative Commons
Allison J. Greaney, Tyler N. Starr, Rachel Eguia

et al.

PLoS Pathogens, Journal Year: 2022, Volume and Issue: 18(2), P. e1010248 - e1010248

Published: Feb. 8, 2022

Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited infection with these target the same or different regions of viral spike as earlier isolates. Here we compare specificities polyclonal produced humans infected early 2020 isolates versus B.1.351 variant concern (also known Beta 20H/501Y.V2), which contains in multiple epitopes. The serum neutralizing activity both viruses and heavily focused on receptor-binding domain (RBD). within RBD, B.1.351-elicited are more "class 3" epitope spanning 443 to 452, neutralization notably less affected residue 484. Our results show that can elicit immunodominance hierarchies.

Language: Английский

Citations

67
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution DOI
Richard A. Neher

Virus Evolution, Journal Year: 2022, Volume and Issue: 8(2)

Published: July 1, 2022

Abstract Continued evolution and adaptation of SARS-CoV-2 has led to more transmissible immune-evasive variants with profound impacts on the course pandemic. Here I analyze virus over 2.5 years since its emergence estimate rates for synonymous non-synonymous changes separately within clades—well-defined monophyletic groups gradual evolution—and pandemic overall. The rate mutation is found be around 6 per year. Synonymous vary little from variant are compatible overall 7 year (or $7.5 \times 10^{-4}$ codon). In contrast, at which accumulate amino acid (non-synonymous mutations) was initially 12-16 year, but in 2021 2022 it dropped 6-9 evolution, that across variants, estimated about 26 $2.7 10^{-3}$ This strong acceleration compared clade indicates evolutionary process gave rise different qualitatively typical transmission chains likely dominated by adaptive evolution. further quantify spectrum mutations purifying selection proteins show massive global sampling sufficient site-specific fitness costs entire genome. Many accessory evolve under limited constraints short-term selection. About half other strongly deleterious.

Language: Английский

Citations

54
Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic DOI Open Access
Luis Daniel González-Vázquez, Miguel Arenas

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 407 - 407

Published: Feb. 4, 2023

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well resistance to monoclonal antibodies polyclonal sera, among other treatments. In order understand causes consequences observed SARS-CoV-2 diversity, a variety studies investigated evolution this virus humans. general, evolves with moderate rate evolution, 10

Language: Английский

Citations

29
An atlas of continuous adaptive evolution in endemic human viruses DOI Creative Commons
Kathryn E. Kistler, Trevor Bedford

Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 31(11), P. 1898 - 1909.e3

Published: Oct. 25, 2023

Through antigenic evolution, viruses such as seasonal influenza evade recognition by neutralizing antibodies. This means that a person with antibodies well tuned to an initial infection will not be protected against the same virus years later and vaccine-mediated protection decay. To expand our understanding of which endemic human evolve in this fashion, we assess adaptive evolution across genome 28 spanning wide range viral families transmission modes. Surface proteins consistently show highest rates adaptation, ten panel are estimated undergo selectively fix mutations enable escape prior immunity. Thus, antibody evasion is uncommon evolutionary strategy among viruses, monitoring inform future vaccine efforts. Additionally, comparing overall amino acid substitution rates, SARS-CoV-2 accumulating protein-coding changes at substantially faster than viruses.

Language: Английский

Citations

29
Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge DOI Creative Commons
Ching‐Lin Hsieh, Sarah R. Leist, Emily Happy Miller

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 20, 2024

Abstract Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers greater breadth protection against current future VOCs would eliminate need to reformulate COVID-19 Here, we rationally engineer sequence-conserved S2 subunit spike protein characterize resulting S2-only antigens. Structural studies demonstrate introduction interprotomer disulfide bonds can lock in prefusion trimers, although apex samples continuum conformations between open closed states. Immunization with prefusion-stabilized constructs elicits broadly neutralizing responses several sarbecoviruses protects female BALB/c mice from mouse-adapted lethal challenge partially SARS-CoV challenge. These engineering immunogenicity results should inform development next-generation pan-coronavirus therapeutics

Language: Английский

Citations

16
Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation DOI Creative Commons
Farina Karim, Catherine Riou, Mallory Bernstein

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 15, 2024

Abstract SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which responses associate with long-term infection HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort infected people South Africa ( n = 994) including participants advanced HIV disease characterized by due to cell depletion. Fifty-four percent had prolonged (>1 month). In five vaccinated tested, associates emergence not specific CD8 cells, while CD4 were determined low numbers. Further, complete suppression required for clearance, although it necessary an effective vaccine response. Persistent led evolution, virus extensive neutralization escape Delta variant participant. The results provide evidence that are recovery, ART curtail evolution co-infecting pathogens reduce individual health consequences as well public risk linked generation mutants.

Language: Английский

Citations

15
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections DOI Creative Commons
Sheri Harari, Danielle Miller,

Shay Fleishon

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 20, 2024

Language: Английский

Citations

13