SARS-Cov2 seasonality and adaptation are driven by solar activity. DOI Creative Commons
Octavio Gonzalez-Lugo

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 22, 2023

Abstract Since its isolation, SARS-Cov2 showed a high mutation rate hindering the ability to properly characterize it. Also as consequence of size, traditional sequence analysis methods are computationally constrained. Nonetheless, machine learning technologies and particularly deep offer viable scalable solution analysis. Applying variational autoencoders (VAEs), special kind neural network used for unsupervised learning, custom genomic representations cluster genomes by similarity. The resulting learned representation sorts sunshine duration (SD) change (SDRC) other solar-derived features. transition between clusters is characterized changes in viral genome size. Different deletions can be found throughout genome. Deletions might behave an internal clock inside Or adaptation mechanism seasonal variations solar radiation. As follows SDRC COVID-19 cases could also follow same pattern. However, spherical geometry our planet adds confounding variable Spherical correction dynamic fractional differentiation SD synchronizes into single period. This results general coordinate system that shows seasonality disease allows us analyze impact environmental Atmospheric affect radiation such ozone column cloudiness gradients correlation with cases. Analyzing composition (amount each specific nucleotide) time series displays attractor-like behavior under different scales. Oscillations explain efficacy antiviral treatments through pandemic. To further expand prediction capability model set features added targets supervised task. Allowing correlate composition. Genome sorting obtained two-dimensional appears only one dimension encodes temporal variable. show interaction host or particular tissue virus. VAE modified fit predator-prey using observations model. Retrieved dynamics transitory phase similar incubation time. characterization needed accurately interpret those results. Under system, mutations adaptations regular deterministic If result means copy codon usage bias(CUB) it likely expression compositionally genes. Selection highly transcripts isolation genes whose dysregulation matches some symptoms reported post-acute sequelae long Covid. Also, regulate circadian rhythm expressed at periods prevalence. Copying optimizing towards host's CUB will increase probability virus significant fragment protein leading autoimmunity. Dysregulation solar-based regulation variability random-like post acute phase. Further development techniques help better understand pathogenic organisms.

Language: Английский

The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: present status and prospects DOI Creative Commons

Wanchen Song,

Zhongbiao Fang, Feike Ma

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 14, 2023

Despite many countries rapidly revising their strategies to prevent contagions, the number of people infected with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues surge. The emergent variants that can evade immune response significantly affect effectiveness mainstream vaccines and diagnostic products based on original spike protein. Therefore, it is essential focus highly conserved nature nucleocapsid protein as a potential target in field diagnostics. In this regard, our review initially discusses structure, function, mechanism action N Based discussion, we summarize relevant research in-depth development application methods protein, such serology nucleic acid detection. Such valuable information aid designing more efficient vaccine tools could help end SARS-CoV-2 pandemic.

Language: Английский

Citations

18
Trivalent SARS-CoV-2 S1 Subunit Protein Vaccination Induces Broad Humoral Responses in BALB/c Mice DOI Creative Commons
Muhammad S. Khan, Eun Sun Kim, Shaohua Huang

et al.

Vaccines, Journal Year: 2023, Volume and Issue: 11(2), P. 314 - 314

Published: Jan. 31, 2023

This paper presents a novel approach for improving the efficacy of COVID-19 vaccines against emergent SARS-CoV-2 variants. We have evaluated immunogenicity unadjuvanted wild-type (WU S1-RS09cg) and variant-specific (Delta S1-RS09cg OM S1 subunit protein delivered either as monovalent or trivalent antigen in BALB/c mice. Our results show that induced broader humoral response with more coverage antigenically distinct variants, especially when compared to Omicron-specific S1. was also found increased equivalent ACE2 binding inhibition, IgG endpoint titer at early timepoints, spike variants Wuhan, Delta, Omicron demonstrate utility provide insights into impact vaccine approaches on immune current variant landscape. Particularly, our study provides insight effects further increasing valency currently approved vaccines, promising protection curtail emerging viral

Language: Английский

Citations

11
SARS-CoV-2 S1 Subunit Booster Vaccination Elicits Robust Humoral Immune Responses in Aged Mice DOI Creative Commons
Eun Kim, Muhammad S. Khan, Alessandro Ferrari

et al.

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(3)

Published: May 10, 2023

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concerns about reduced vaccine effectiveness and the increased risk infection, while repeated homologous booster shots are recommended for elderly immunocompromised individuals, they cannot completely protect against breakthrough infections. In our previous study, we assessed immunogenicity an adenovirus-based expressing SARS-CoV-2 S1 (Ad5.S1) in mice, which induced robust humoral cellular immune responses (E. Kim, F. J. Weisel, S. C. Balmert, M. Khan, et al., Eur J Immunol 51:1774-1784, 2021, https://doi.org/10.1002/eji.202149167). this follow-up found that mice had high titers anti-S1 antibodies 1 year after vaccination, one dose nonadjuvanted rS1Beta (recombinant protein Beta [B.1.351]) subunit was effective at stimulating strong long-lived S1-specific inducing significantly neutralizing Wuhan, Beta, Delta strains, with 3.6- to 19.5-fold increases. Importantly, also elicited cross-reactive antibodies, resulting angiotensin-converting enzyme (ACE2) binding inhibition spikes SARS-CoV-2, including Omicron variants, persisting >28 weeks vaccination. Interestingly, levels were correlated not only level IgG but ACE2 inhibition. Our findings suggest candidate as a potential offer cross-neutralization broad important implications control newly emerging individuals primed vaccines like AZD1222 Ad26.COV2.S.

Language: Английский

Citations

10
Intranasal delivery of a recombinant adenovirus vaccine encoding the PEDV COE elicits potent mucosal and systemic antibody responses in mice DOI Creative Commons
Shijie Yan, Yi Luo,

Ningjia Zhan

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(10)

Published: Aug. 15, 2024

ABSTRACT Porcine epidemic diarrhea virus (PEDV) is an enteropathogenic coronavirus that causes substantial economic loss to the global pig industry. The emergence of PEDV variants has increased need for new vaccines, as commercial vaccines confer inferior protection against currently circulating strains. It well established induction mucosal immunity crucial provide better infection. In this study, we constructed a recombinant adenovirus expressing core neutralization epitope (COE) G2b based on human serotype 5 (Ad5). We evaluated effects different administration routes and doses vaccine immunogenicity in Balb/c mice. Both intramuscular (IM) intranasal (IN) elicited significant humoral responses, including COE-specific IgG serum secretions, along with serum-neutralizing antibodies. Moreover, IN delivery was more potent than IM stimulating IgA samples dampening immune response Ad5 vector. stronger after high versus low dose injection, whereas no difference observed between doses. summary, our findings important insights developing novel vaccines. IMPORTANCE (PED) highly contagious disease severe implications pork Developing effective remains necessity. Here, generated express COE protein (rAd5-PEDV-COE) systematically adenovirus-vectored using (intramuscular intranasal) mouse model. Our results show rAd5-PEDV-COE induced systemic regardless or immunization route. Notably, superior induce peripheral antibodies compared injection. data valuable into designing

Language: Английский

Citations

3
Durable CD8 T Cell Memory against SARS-CoV-2 by Prime/Boost and Multi-Dose Vaccination: Considerations on Inter-Dose Time Intervals DOI Open Access
Ambra Natalini, Sonia Simonetti,

Carmel Sher

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(22), P. 14367 - 14367

Published: Nov. 19, 2022

Facing the COVID-19 pandemic, anti-SARS-CoV-2 vaccines were developed at unprecedented pace, productively exploiting contemporary fundamental research and prior art. Large-scale use of has greatly limited severe morbidity mortality. Protection been correlated with high serum titres neutralizing antibodies capable blocking interaction between viral surface protein spike host SARS-CoV-2 receptor, ACE-2. Yet, vaccine-induced protection subsides over time, breakthrough infections are commonly observed, mostly reflecting decay emergence variant viruses mutant proteins. Memory CD8 T cells a potent weapon against viruses, as they tumour cells. Anti-SARS-CoV-2 memory induced by either natural infection or vaccination can be potentially exploited spike-mutated viruses. We offer here an overview current about induction vaccination, in context knowledge on mechanisms immunological memory. focus particularly how two doses (prime/boost) more (boosters) promotes differentiation cells, time-length inter-dose intervals may influence magnitude persistence cell

Language: Английский

Citations

9
Tetravalent SARS-CoV-2 S1 subunit protein vaccination elicits robust humoral and cellular immune responses in SIV-infected rhesus macaque controllers DOI Creative Commons
Muhammad S. Khan, Eun Kim, Quentin Le Hingrat

et al.

mBio, Journal Year: 2023, Volume and Issue: 14(5)

Published: Oct. 13, 2023

ABSTRACT The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for safe and effective vaccines to be rapidly developed distributed worldwide, especially considering emergence of new severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Protein subunit have emerged as a promising approach due their proven safety record ability elicit robust immune responses. In this study, we evaluated immunogenicity efficacy an adjuvanted tetravalent S1 protein COVID-19 vaccine candidate composed Wuhan, B.1.1.7 variant, B.1.351 P.1 variant spike proteins in nonhuman primate model with controlled SIVsab infection. induced both humoral cellular responses, T B cell responses mainly peaking post boost immunization. also elicited neutralizing cross-reactive antibodies, angiotensin-converting enzyme (ACE2)-blocking including spike-specific CD4 + cells. Importantly, was able generate Omicron spike-binding ACE2-blocking antibodies without specifically vaccinating Omicron, suggesting potential broad protection against emerging composition significant implications development implementation, providing antibody numerous SARS-CoV-2 IMPORTANCE study provides important insights into (SARS-CoV-2). primates SIVagm infection variant-specific Omicron. These findings suggest that could provide multiple variants while minimizing risk escape Additionally, use rhesus macaques may better represent humans chronic viral diseases, highlighting importance preclinical animal models development. Overall, valuable information implementation vaccines, particularly achieving global equity addressing

Language: Английский

Citations

2
Optimization and validation of analytical affinity chromatography for the in-process monitoring and quantification of peptides containing a C-tag DOI

Carolin A. Lappöhn,

Lea Maerz,

Robin Stei

et al.

Journal of Chromatography B, Journal Year: 2023, Volume and Issue: 1229, P. 123899 - 123899

Published: Sept. 1, 2023

Language: Английский

Citations

1
Tetravalent SARS-CoV-2 S1 Subunit Protein Vaccination Elicits Robust Humoral and Cellular Immune Responses in SIV-Infected Rhesus Macaque Controllers DOI Creative Commons
Muhammad S. Khan, Eun Kim, Quentin Le Hingrat

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 16, 2023

The COVID-19 pandemic has highlighted the need for safe and effective vaccines to be rapidly developed distributed worldwide, especially considering emergence of new SARS-CoV-2 variants. Protein subunit have emerged as a promising approach due their proven safety record ability elicit robust immune responses. In this study, we evaluated immunogenicity efficacy an adjuvanted tetravalent S1 protein vaccine candidate composed Wuhan, B.1.1.7 variant, B.1.351 P.1 variant spike proteins in nonhuman primate model with controlled SIVsab infection. induced both humoral cellular responses, T- B cell responses mainly peaking post-boost immunization. also elicited neutralizing cross-reactive antibodies, ACE2 blocking T-cell including specific CD4+ T cells. Importantly, was able generate Omicron binding antibodies without specifically vaccinating Omicron, suggesting potential broad protection against emerging composition significant implications development implementation, providing antibody numerous

Language: Английский

Citations

0
SARS-Cov2 seasonality and adaptation are driven by solar activity. DOI Creative Commons
Octavio Gonzalez-Lugo

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: April 11, 2023

Abstract Since its isolation in Wuhan SARS-Cov2 showed a high mutation rate hindering the ability to properly characterize. Also as consequence of size, traditional sequence analysis methods were computationally constrained. However, applying variational autoencoders (VAEs) custom representation results series clusters sorted by sunshine duration (SD) change (SDRC). The transition between is characterized changes viral genome apparent deletions can be found throughout genome. This might behave an internal clock inside Using SD-derived features time scale synchronizing COVID-19 cases into single period. Both and solar correlate with cases, except for wavelengths at SWIR band, pointing towards solar-dependent seasonality. Further development techniques will help us better understand seasonality adaptation pathogenic organisms.

Language: Английский

Citations

0
SARS-Cov2 seasonality and adaptation are driven by solar activity. DOI Creative Commons
Octavio Gonzalez-Lugo

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: June 26, 2023

Abstract Since its isolation in Wuhan SARS-Cov2 showed a high mutation rate hindering the ability to properly characterize. Also as consequence of size, traditional sequence analysis methods were computationally constrained. However, applying variational autoencoders (VAEs) custom representations results series clusters sorted by sunshine duration (SD) change (SDRC) and other solar-derived features. The transition between is characterized changes viral genome apparent deletions can be found throughout genome. This might behave an internal clock inside SDRC-derived features synchronize COVID-19 cases into single period. Both solar correlate with pointing towards solar-dependent seasonality. Atmospheric that affect radiation also correlation cases. Analyzing composition time displays attractor-like behavior under different scales. While clustering them environmental conditions shows similar pattern one VAE models. Further development techniques will help us better understand seasonality adaptation pathogenic organisms.

Language: Английский

Citations

0