One-pot synthesized Au@Pt nanostars-based lateral flow immunoassay for colorimetric and photothermal dual-mode detection of SARS-CoV-2 nucleocapsid antibody

Analytica Chimica Acta, Год журнала: 2024, Номер 1292, С. 342241 - 342241

Опубликована: Янв. 11, 2024

Язык: Английский

---

Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules

PLoS Computational Biology, Год журнала: 2024, Номер 20(1), С. e1011795 - e1011795

Опубликована: Янв. 25, 2024

The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped viral, individual human and population factors. SARS-CoV-2 variants are defined their unique combinations of mutations there a clear adaptation to more efficient infection since the emergence this new coronavirus in late 2019. Here, we use machine learning models identify shared signatures, i.e., common underlying mutational processes link these subset that define concern (VOCs). First, examined global genomes associated metadata determine how viral properties public health measures have influenced magnitude waves, as measured number cases, different geographic locations using regression models. This analysis showed that, expected, both virus were with regional reported numbers impact varies geographically. We attribute intrinsic differences such vaccine coverage, testing sequencing capacity effectiveness government stringency. To assess evolutionary change, used non-negative matrix factorisation observed three distinct substitution patterns exposures from genomes. Signatures 1, 2 3 biased C→T, T→C/A→G G→T point mutations. hypothesise assignments signatures host antiviral molecules APOBEC, ADAR ROS respectively. observe shift amidst relative signature activity predominantly Signature 1 changes an increasingly high proportion consistent 2. could represent immune response interact indicates may continue generate variation future. Linkage detected VOC-defining amino acids substitutions majority SARS-CoV-2’s is likely be action rather than replication errors.

Язык: Английский

---

Differential protection against SARS-CoV-2 reinfection pre- and post-Omicron

Nature, Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved over short timescales, leading to the emergence of more transmissible variants such as Alpha and Delta 1–3 . arrival Omicron variant marked a major shift, introducing numerous extra mutations in spike gene compared with earlier 1,2 These evolutionary changes have raised concerns regarding their potential impact on immune evasion, disease severity effectiveness vaccines treatments 1,3 In this epidemiological study, we identified two distinct patterns protective effect natural infection against reinfection versus pre-Omicron eras. Before Omicron, provided strong durable protection reinfection, minimal waning time. However, during era, was robust only for those recently infected, declining time diminishing within year. results demonstrate that SARS-CoV-2 is shaped by dynamic interaction between host immunity viral evolution, contrasting before after Omicron’s first wave. This shift suggests change pressures, intrinsic transmissibility driving adaptation escape becoming dominant post-Omicron, underscoring need periodic vaccine updates sustain immunity.

Язык: Английский

---

SARS-CoV-2 evolution on a dynamic immune landscape

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 29, 2025

Abstract Since the onset of pandemic, many SARS-CoV-2 variants have emerged, exhibiting substantial evolution in virus’ spike protein 1 , main target neutralizing antibodies 2 . A plausible hypothesis proposes that virus evolves to evade antibody-mediated neutralization (vaccine- or infection-induced) maximize its ability infect an immunologically experienced population 1,3 Because viral infection induces antibodies, may thus navigate on a dynamic immune landscape is shaped by local history. Here we developed comprehensive mechanistic model, incorporating deep mutational scanning data 4,5 antibody pharmacokinetics and regional genomic surveillance data, predict variant-specific relative number susceptible individuals over time. We show this quantity precisely matched historical variant dynamics, predicted future dynamics explained global differences dynamics. Our work strongly suggests ongoing pandemic continues shape immunity, which determines variant’s transmit, defining fitness. The model can be applied any region utilizing allows contextualizing risk assessment provides information for vaccine design.

Язык: Английский

---

A unified evolution-driven deep learning framework for virus variation driver prediction

Nature Machine Intelligence, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

Язык: Английский

---

Implications of diversity in sperm size and function for sperm competition and fertility

The International Journal of Developmental Biology, Год журнала: 2008, Номер 52(5-6), С. 439 - 447

Опубликована: Янв. 1, 2008

Sperm competition is now recognised as a potent selective force shaping many male reproductive traits. While the influence of sperm on number widely accepted, its effects upon size remain controversial. It had been traditionally assumed that there trade-off between and size, so an increase in would result decrease under conditions competition. Contrary to this prediction, we proposed some time ago favours because longer swim faster are more likely win race fertilize ova. Comparative studies species show taxa such relationship exists, but consequences may vary depending environment which spermatozoa have compete. We present new evidence showing mammals at higher speeds. also mean swimming speed highly correlated with maximum speed, even if fastest fertilize, both measures informative. When individuals same compared, ratios dimensions different components, well shape head, seem better explaining velocity. Finally, determine fertility. Other shown competitive contexts, males fertilization success. conclude available supports our original hypothesis.

Язык: Английский

---

B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity

Cellular and Molecular Immunology, Год журнала: 2023, Номер 21(2), С. 144 - 158

Опубликована: Ноя. 10, 2023

Abstract The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- vaccine-induced immune responses the context this pathogen. B-cell antibody are at center these investigations, as neutralizing antibodies (nAbs) an important correlate protection (COP) from infection primary target SARS-CoV-2 vaccine modalities. In addition absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype subtype composition, presence mucosal sites have become topics for scientists health policy makers. recent pandemic was still is a unique setting which study de novo memory (MBC) dynamic interplay immunity. It also provided opportunity explore new platforms, such mRNA or adenoviral vector vaccines, unprecedented cohort sizes. Combined with technological advances years, situation has detailed mechanistic insights into development but revealed some unexpected findings. review, we summarize key findings last 2.5 years regarding immunity, believe significant value not only future vaccination approaches endemic settings.

Язык: Английский

---

Fitness effects of mutations to SARS-CoV-2 proteins

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 31, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino-acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

Язык: Английский

---

COVID-19 annual update: a narrative review

Human Genomics, Год журнала: 2023, Номер 17(1)

Опубликована: Июль 24, 2023

Abstract Three and a half years after the pandemic outbreak, now that WHO has formally declared emergency is over, COVID-19 still significant global issue. Here, we focus on recent developments in genetic genomic research COVID-19, give an outlook state-of-the-art therapeutical approaches, as gradually transitioning to endemic situation. The sequencing characterization of rare alleles different populations made it possible identify numerous genes affect either susceptibility or severity disease. These findings provide beginning new avenues pan-ethnic therapeutic well potential screening protocols. causative virus, SARS-CoV-2, spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance further warranted. We also note emphatically prevent future pandemics other world-wide health crises, imperative capitalize what have learnt from COVID-19: specifically, regarding its origins, world’s response, insufficient preparedness. This requires unprecedented international collaboration timely data sharing for coordination effective response rapid implementation containment measures.

Язык: Английский

---

Vaccines’ New Era-RNA Vaccine

Viruses, Год журнала: 2023, Номер 15(8), С. 1760 - 1760

Опубликована: Авг. 18, 2023

RNA vaccines, including conventional messenger (mRNA) circular (circRNA) and self-amplifying (saRNA) have ushered in a promising future revolutionized vaccine development. The success of mRNA vaccines combating the COVID-19 pandemic caused by SARS-CoV-2 virus that emerged 2019 has highlighted potential vaccines. These possess several advantages, such as high efficacy, adaptability, simplicity antigen design, ability to induce both humoral cellular immunity. They also offer rapid cost-effective manufacturing, flexibility target emerging or mutant pathogens approach for clearing immunotolerant microbes targeting bacterial parasitic survival mechanisms. self-adjuvant effect mRNA-lipid nanoparticle (LNP) formulations further enhances However, some challenges need be addressed. include technology’s immaturity, research expenses, limited duration antibody response, instability, low efficiency circRNA cyclization, production double-stranded side product. factors hinder widespread adoption utilization particularly developing countries. This review provides comprehensive overview mRNA, circRNA, saRNA infectious diseases while discussing their development, current applications, challenges.

Язык: Английский

---