Data-driven recombination detection in viral genomes DOI Creative Commons
Tommaso Alfonsi, Anna Bernasconi, Matteo Chiara

et al.

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

Published: June 7, 2023

Abstract Recombination is a key molecular mechanism for the evolution and adaptation of viruses. The first recombinant SARS-CoV-2 genomes were recognized in 2021; as today, more than ninety lineages are designated recombinant. In wake COVID-19 pandemic, several methods detecting recombination have been proposed; however, none could faithfully confirm manual analyses by experts field. We hereby present RecombinHunt, novel, automated method identification recombinant/mosaic purely based on data-driven approach. RecombinHunt compares favorably with other state-of-the-art recognizes (or lineages) one or two breakpoints high accuracy, within reduced turn-around times small discrepancies respect to expert manually-curated standard nomenclature. Strikingly, applied complete collection viral sequences from recent monkeypox epidemic, identifies concordance manually curated experts, suggesting that our approach robust can be any epidemic/pandemic virus. conclusion, represents breakthrough detection pandemic/epidemic scenarios substantially improve/advance community-based approaches phylogenetic analyses.

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

768
Duration of immune protection of SARS-CoV-2 natural infection against reinfection DOI Creative Commons
Hiam Chemaitelly, Nico Nagelkerke, Houssein H. Ayoub

et al.

Journal of Travel Medicine, Journal Year: 2022, Volume and Issue: 29(8)

Published: Sept. 30, 2022

Abstract Background The future of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic hinges on virus evolution and duration immune protection natural infection against reinfection. We investigated afforded by infection, effect viral evasion reinfection, in Qatar, between 28 February 2020 5 June 2022. Methods Three national, matched, retrospective cohort studies were conducted to compare incidence SARS-CoV-2 disease 2019 (COVID-19) severity among unvaccinated persons with a documented primary those infection-naïve unvaccinated. Associations estimated using Cox proportional hazard regression models. Results Effectiveness pre-Omicron reinfection was 85.5% [95% confidence interval (CI): 84.8–86.2%]. peaked at 90.5% (95% CI: 88.4–92.3%) 7th month after but waned ~ 70% 16th month. Extrapolating this waning trend Gompertz curve suggested an effectiveness 50% 22nd < 10% 32nd Omicron 38.1% 36.3–39.8%) declined time since infection. A 15th severe, critical or fatal COVID-19 97.3% 94.9–98.6%), irrespective variant no evidence for waning. Similar results found sub-group analyses ≥50 years age. Conclusions Protection wanes may diminish within few years. Viral accelerates remains very strong, waning, variant, over 14 months

Language: Английский

Citations

93
Differential protection against SARS-CoV-2 reinfection pre- and post-Omicron DOI Creative Commons
Hiam Chemaitelly, Houssein H. Ayoub, Peter Coyle

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 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.

Language: Английский

Citations

7
Progress and challenges in infectious disease surveillance and early warning DOI Creative Commons
Ying Shen, Youngjoon Hong, Thomas Krafft

et al.

Medicine Plus, Journal Year: 2025, Volume and Issue: unknown, P. 100071 - 100071

Published: Jan. 1, 2025

Language: Английский

Citations

3
When to update COVID-19 vaccine composition DOI Open Access
Rebecca Grant, Jilian A. Sacks, Priya Abraham

et al.

Nature Medicine, Journal Year: 2023, Volume and Issue: 29(4), P. 776 - 780

Published: Feb. 20, 2023

Language: Английский

Citations

38
Fitness, growth and transmissibility of SARS-CoV-2 genetic variants DOI
Erik Volz

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(10), P. 724 - 734

Published: June 16, 2023

Language: Английский

Citations

37
Early computational detection of potential high-risk SARS-CoV-2 variants DOI Creative Commons
Karim Beguir, Marcin J. Skwark, Yunguan Fu

et al.

Computers in Biology and Medicine, Journal Year: 2023, Volume and Issue: 155, P. 106618 - 106618

Published: Feb. 2, 2023

The ongoing COVID-19 pandemic is leading to the discovery of hundreds novel SARS-CoV-2 variants daily. While most do not impact course pandemic, some pose an increased risk when acquired mutations allow better evasion antibody neutralisation or transmissibility. Early detection such high-risk (HRVs) paramount for proper management pandemic. However, experimental assays determine immune and transmissibility characteristics new are resource-intensive time-consuming, potentially delays in appropriate responses by decision makers. Presented herein a silico approach combining spike (S) protein structure modelling large transformer language models on S sequences accurately rank escape fitness potential. Both metrics were experimentally validated using vitro pseudovirus-based test binding subsequently combined explore changing landscape create automated Warning System (EWS) capable evaluating minutes risk-monitoring variant lineages near real-time. system pinpoints putatively dangerous selecting average less than 0.3% each week. EWS flagged all 16 designated World Health Organization (WHO) as interest (VOIs) if applicable concern (VOCs) otherwise with lead time more one half months ahead their designation such.

Language: Английский

Citations

32
COVID-19 infection, reinfection, and the transition to endemicity DOI Open Access
Cheryl Cohen, Juliet R. C. Pulliam

The Lancet, Journal Year: 2023, Volume and Issue: 401(10379), P. 798 - 800

Published: Feb. 16, 2023

Language: Английский

Citations

27
Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device DOI
Ying Liu, Yang Yang, Guanghui Wang

et al.

Nature Biomedical Engineering, Journal Year: 2023, Volume and Issue: 7(12), P. 1636 - 1648

Published: Sept. 21, 2023

Language: Английский

Citations

27
Early Detection and Surveillance of the SARS-CoV-2 Variant BA.2.86 — Worldwide, July–October 2023 DOI Open Access
Anastasia S. Lambrou,

Erin South,

Eliza S. Ballou

et al.

MMWR Morbidity and Mortality Weekly Report, Journal Year: 2023, Volume and Issue: 72(43), P. 1162 - 1167

Published: Oct. 26, 2023

Early detection of emerging SARS-CoV-2 variants is critical to guiding rapid risk assessments, providing clear and timely communication messages, coordinating public health action. CDC identifies monitors novel through diverse surveillance approaches, including genomic, wastewater, traveler-based, digital (e.g., global data repositories, news, social media). The variant BA.2.86 was first sequenced in Israel reported on August 13, 2023. U.S. COVID-19 case caused by this 17, 2023, after a patient received testing for at care facility 3. In the following month, eight additional states detected across various systems, specimens from settings, wastewater surveillance, traveler-based genomic surveillance. As October 23, sequences have been least 32 countries. Continued tracking further evidence are needed evaluate full impact BA.2.86. Timely sequence submissions databases aided early despite decline number being during past year. This report describes how multicomponent sequencing were used real time track emergence transmission variant. approach provides valuable information regarding implementing sustaining comprehensive not only but also future pathogen threats.

Language: Английский

Citations

23