Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic DOI Creative Commons
Jiaying Li,

Ye‐Xiao Cheng,

Chengyang Ji

et al.

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

Published: Oct. 24, 2023

Abstract The global prevalence of the XBB lineage presents a formidable challenge posed by recombinant SARS-CoV-2 virus. understanding SARS-CoV-2's recombination preference assumes utmost significance in predicting future variants and adequately preparing for subsequent pandemics. Thus, an urgent need arises to establish comprehensive landscape concerning recombinants worldwide elucidate their evolutionary mechanisms. However, initial step, involving detection potential from vast pool over ten million sequences, significant obstacle. In this study, we present CovRecomb, lightweight methodology specifically designed effectively identify dissect interlineage recombinants. Leveraging successfully detected 135,567 putative across entirety 14.5 accessed genomes. These could be classified into 1,451 distinct events, which 206 demonstrated transmission spanning multiple countries, continents, or globally. Hotspot regions were identified six specific areas, with particular prominence observed latter halves N-terminal domain receptor-binding within spike (S) gene. Epidemiological investigations revealed extensive events occurring among different (sub)lineages, independent frequencies.

Language: Английский

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

et al.

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

Published: April 17, 2024

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, an original data-driven method identification genomes, capable recognizing (or lineages) with one or two breakpoints high accuracy within reduced turn-around times. ReconbinHunt shows specificity sensitivity, compares favorably other state-of-the-art methods, confirms experts. RecombinHunt identifies viral from recent monkeypox epidemic concordance manually curated experts, suggesting that our approach robust can be applied to any epidemic/pandemic virus.

Language: Английский

Citations

8
RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: a design and retrospective evaluation study DOI Creative Commons

Neil Bray,

Will Sopwith,

Matt Edmunds

et al.

The Lancet Microbe, Journal Year: 2024, Volume and Issue: 5(2), P. e173 - e180

Published: Jan. 21, 2024

BackgroundWhole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, timeliness limit its use when large populations need rapidly assessing. We assessed potential of genotyping assays provide accurate timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March September, 2021, were used widely detection.MethodsWe chose a panel four RT-PCR detect circulating SARS-COV-2 developed decision algorithm assign probable samples using assay results. extracted data from UK Health Security Agency databases 115 934 SARS-CoV-2-positive (March 1–Sept 6, 2021) was available both WGS. By comparing WGS result, we calculated accuracy metrics (ie, sensitivity, specificity, positive predictive value [PPV]) time difference sample collection date availability information. number with assigned or WGS, both, over time.FindingsGenotyping an initial (April 10–May 11, 2021 data) key assignment: sensitivities PPVs 0·99 (95% CI 0·99–0·99) alpha, 1·00 (1·00–1·00) beta, 0·91 (0·80–1·00) gamma variants; specificities 0·97 (0·96–0·98), (1·00–1·00), respectively. A subsequent longer period (May 27–Sept remained 0·74–1·00) 0·98 (0·98–0·99) delta, 0·93 (0·81–1·00) 0·96 (0·96–0·97), respectively; 0·83 (0·62–1·00), 0·78 (0·59–0·97), Genotyping produced median 3 days (IQR 2–4) after date, which faster than (9 [8–11]). The flexibility enabled nine-times increase quantity tested this method (from 5000 45 000).InterpretationRT-PCR are suitable high-throughput could complement enabling larger testing known timelier results, important implications effective public health responses disease control globally, especially settings low capacity. However, choice panels highly dependent on database generated new spreading rapidly.FundingUK National Institute Research Protection Unit Emergency Preparedness Response.

Language: Английский

Citations

7
Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community – A multi-site evaluation DOI Creative Commons
Majid Khan, Lin Li, Laura Haak

et al.

One Health, Journal Year: 2023, Volume and Issue: 16, P. 100536 - 100536

Published: April 6, 2023

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends virus prevalence within community. The surveillance also provides precise and early detection any new circulating variants, which aids response outbreaks. Site-specific monitoring SARS-CoV-2 variants valuable information on or emerging We sequenced genomic RNA viruses present samples analyzed as well other a period one year account seasonal variations. were collected from Reno-Sparks metropolitan area weekly basis between November 2021 2022. Samples detect levels copies identification. This study confirmed that can used community supports wastewater-based epidemiology (WBE) complement clinical testing healthcare effort. Our showed persistence throughout compared presence viruses, implicating SARS-CoV-2's broad genetic diversity strength persist infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes same found WBE feasible tool AMR monitoring.

Language: Английский

Citations

13
Anti-interferon armamentarium of human coronaviruses DOI Creative Commons
Oyahida Khatun, Sumandeep Kaur, Shashank Tripathi

et al.

Cellular and Molecular Life Sciences, Journal Year: 2025, Volume and Issue: 82(1)

Published: March 13, 2025

Abstract Cellular innate immune pathways are formidable barriers against viral invasion, creating an environment unfavorable for virus replication. Interferons (IFNs) play a crucial role in driving and regulating these cell-intrinsic antiviral mechanisms through the action of interferon-stimulated genes (ISGs). The host IFN response obstructs replication at every stage, prompting viruses to evolve various strategies counteract or evade this response. Understanding interplay between proteins IFN-mediated is essential developing anti-inflammatory strategies. Human coronaviruses (HCoVs), including SARS-CoV-2, MERS-CoV, SARS-CoV, seasonal coronaviruses, encode range that, shared distinct mechanisms, inhibit responses. Compounding issue, dysregulated early can lead hyper-inflammatory reaction later infection, resulting severe disease. This review provides brief overview HCoV detailed account its interaction with cellular regulated by IFN.

Language: Английский

Citations

0
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

Citations

9
Impact of mutations defining SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 on Spike function and neutralization DOI Creative Commons
Chiara Pastorio, Sabrina Noettger, Rayhane Nchioua

et al.

iScience, Journal Year: 2023, Volume and Issue: 26(11), P. 108299 - 108299

Published: Oct. 27, 2023

Additional mutations in the viral Spike protein helped BA.2.12.1 and BA.4/5 SARS-CoV-2 Omicron subvariants to outcompete parental BA.2 subvariant. Here, we determined functional impact of that newly emerged (L452Q, S704L) (Δ69-70, L452R, F486V, R493Q) proteins. Our results show mutation L452Q/R or F486V typically increases R493Q S704L impair Spike-mediated infection. In combination, changes Δ69-70, contribute higher infectiousness fusogenicity Spike. L452R/Q are mainly responsible for reduced sensitivity neutralizing antibodies. However, combined required full infectivity, TMPRSS2 dependency, immune escape Thus, it is specific combination allows increased functionality evasion, which helps explain temporary dominance pathogenicity these subvariants.

Language: Английский

Citations

9
Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic DOI Creative Commons

J S Li,

Haoyang Wang,

Ye‐Xiao Cheng

et al.

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

Abstract The global prevalence of the XBB lineage presents a formidable challenge posed by recombinant SARS-CoV-2 virus. understanding SARS-CoV-2’s recombination preference assumes utmost significance in predicting future variants and adequately preparing for subsequent pandemics. Thus, an urgent need arises to establish comprehensive landscape concerning recombinants worldwide elucidate their evolutionary mechanisms. However, initial step, involving detection potential from vast pool over 10 million sequences, significant obstacle. In this study, we present CovRecomb, lightweight methodology specifically designed effectively identify dissect interlineage recombinants. Leveraging successfully detected 135,567 putative across entirety 14.5 accessed genomes. These could be classified into 1451 distinct events, which 206 demonstrated transmission spanning multiple countries, continents, or globally. Hotspot regions were identified six specific areas, with prominence observed latter halves N-terminal domain receptor-binding within spike (S) gene. Epidemiological investigations revealed extensive events occurring among different (sub)lineages, independent frequencies.

Language: Английский

Citations

2
Emergence of a second SARS‐CoV‐2 variant with a tremendous genetic leap from its ancestors DOI
Philippe Colson, Bernard La Scola,

Mamadou Beye

et al.

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(10)

Published: Oct. 1, 2023

The on-going emergence of the Omicron BA.2.86 variant is one major events in SARS-CoV-2 genetic evolution that remain enigmatic regarding overall virus mutation rate, together with initial variant, BA.1. Indeed, genomes lineage, an offspring second subvariant, BA.2, harbor 39 additional mutations spike compared to this ancestor. Here we comment on phylogeny BA.2.86, positions, and frequencies other SARS-CoV-2, its spike, structural model protein concentrates most mutations.

Language: Английский

Citations

5
Structural basis of main proteases of coronavirus bound to Bofutrelvir DOI
Weiwei Wang,

Pei Zeng,

Tongchao Liu

et al.

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: 436(22), P. 168784 - 168784

Published: Sept. 6, 2024

Language: Английский

Citations

1
Systematic analysis of SARS-CoV-2 Omicron subvariants’ impact on B and T cell epitopes DOI Creative Commons
Ruba Al Khalaf, Anna Bernasconi, Pietro Pinoli

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(9), P. e0307873 - e0307873

Published: Sept. 19, 2024

Introduction Epitopes are specific structures in antigens that recognized by the immune system. They widely used context of immunology-related applications, such as vaccine development, drug design, and diagnosis / treatment prevention disease. The SARS-CoV-2 virus has represented main point interest within viral genomic surveillance community last four years. Its ability to mutate acquire new characteristics while it reorganizes into variants been analyzed from many perspectives. Understanding how epitopes impacted mutations accumulate on protein level cannot be underrated. Methods With a focus Omicron-named lineages, including WHO-designated Variants Interest, we propose workflow for data retrieval, integration, analysis pipeline conducting database-wide study impact lineages’ characterizing all T cell B linear collected Immune Epitope Database (IEDB) SARS-CoV-2. Results Our allows us showcase novel qualitative quantitative results 1) coverage proteins deposited epitopes; 2) distribution mutated across Omicron variants; 3) epitopes. discussed based type epitope, response frequency assays, sample size. proposed can reproduced at any time, given updated variant characterizations IEDB, thereby guaranteeing observe landscape mutations’ demand. Conclusion A big data-driven one provided here inform next policies combatting future epidemic viruses.

Language: Английский

Citations

1