Data-driven recombination detection in viral genomes

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Апрель 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.

Язык: Английский

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Neutralization of the SARS-CoV-2 Deltacron and BA.3 Variants

New England Journal of Medicine, Год журнала: 2022, Номер 386(24), С. 2340 - 2342

Опубликована: Май 18, 2022

Язык: Английский

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Projecting the SARS-CoV-2 transition from pandemicity to endemicity: Epidemiological and immunological considerations

PLoS Pathogens, Год журнала: 2022, Номер 18(6), С. e1010591 - e1010591

Опубликована: Июнь 30, 2022

In this review, we discuss the epidemiological dynamics of different viral infections to project how transition from a pandemic endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing theories disease invasion and transmission dynamics, waning immunity in face evolution antigenic drift, empirical data influenza, dengue, seasonal coronaviruses, putative periodicity, severity, age SARS-CoV-2 as it becomes endemic. We review recent studies on epidemiology, immunology, that are particularly useful projecting endemicity highlight gaps warrant further research.

Язык: Английский

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Analysis of SARS-CoV-2 Recombinant Lineages XBC and XBC.1 in the Philippines and Evidence for Delta-Omicron Co-infection as a Potential Origin

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

Опубликована: Апрель 12, 2023

Abstract We report the sequencing and analysis of 60 XBC 114 XBC.1 SARS-CoV-2 lineages detected in Philippines from August to September 2022, which are regarded as recombinant BA.2 Omicron B.1.617.2 Delta (21I Clade) variants. The sequences described here place country with earliest highest number cases within included period. Majority were sampled adjacent Davao Soccskargen regions southern Philippines, but have also been observed at lower proportions other country. Time-scaled phylogenetic global samples GISAID reaffirms supposed root XBC-like Philippines. Furthermore, apparent clustering some foreign separate those collected suggests several occurrences cross-border transmissions resulting spread among countries. consensus mutation profile shows harboring mutations specific either or lineages, supporting nature XBC. Finally, alternative allele fraction pattern intrahost revealed that a relatively early case March 2022 is likely be an active co-infection event. This was already occurring facilitating generation recombinants may further evolved gained additional enabling its across certain local populations later time. Author summary More recently, various virus, causative agent COVID-19 pandemic, form expanding ways by virus can evolve adapt human interventions. Therefore, large part biosurveillance efforts dedicated detecting observing new including recombinants, for effective control. In this paper, we present 174 between contextualize these reported hybrid lineage. show when compared countries similar time, lineage Additionally, reclassified following update Pangolin, tool assigning samples, found two interest pointing potential origin via events 2022.

Язык: Английский

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Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage

The Science of The Total Environment, Год журнала: 2022, Номер 866, С. 161101 - 161101

Опубликована: Дек. 27, 2022

Язык: Английский

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The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Июль 25, 2023

Over three years’ pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and subvariants have emerged successively, outcompeted earlier become predominant. The sequential emergence reflects the evolutionary process mutation-selection-adaption severe acute respiratory syndrome 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in spike protein causes altered viral antigenicity, transmissibility, pathogenicity SARS-CoV-2. Early pandemic, D614G mutation conferred virus with advantages over previous increased it also laid a conservative background for subsequent substantial mutations. role genomic recombination evolution SARS-CoV-2 raised increasing concern occurrence recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, XBB.1.16 late phase pandemic. Co-circulation different co-infection immunocompromised patients accelerate recombinants. Surveillance variations, particularly recombination, is essential to identify ongoing changes genome antigenic epitopes thus leads development new vaccine strategies interventions.

Язык: Английский

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Deltacron: Apprehending a new phase of the COVID-19 pandemic

International Journal of Surgery, Год журнала: 2022, Номер 102, С. 106654 - 106654

Опубликована: Май 8, 2022

Язык: Английский

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Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA

The Science of The Total Environment, Год журнала: 2023, Номер 877, С. 162862 - 162862

Опубликована: Март 16, 2023

Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of pathogen within community. WBE has been adopted as one methods to monitor population dynamics SARS-CoV-2 virus, but significant challenges remain in bioinformatic analysis WBE-derived data. Here, we have developed new distance metric, CoVdist, an associated tool that facilitates application ordination data identification viral changes based on nucleotide variants. We applied these approaches large-scale dataset from 18 cities nine states USA using wastewater collected July 2021 June 2022. found trends shift between Delta Omicron lineages were largely consistent with what was seen clinical data, offered added benefit revealing differences at state, city, even neighborhood scales. also able observe early variants concern presence recombinant during transitions variants, both which are challenging analyze clinically-derived genomes. The outlined here will be beneficial future applications SARS-CoV-2, particularly becomes less prevalent. Additionally, generalizable, allowing them outbreaks.

Язык: Английский

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Delta-Omicron recombinant escapes therapeutic antibody neutralization

iScience, Год журнала: 2023, Номер 26(2), С. 106075 - 106075

Опубликована: Фев. 1, 2023

The emergence of recombinant viruses is a threat to public health, as recombination may integrate variant-specific features that together result in escape from treatment or immunity. selective advantages SARS-CoV-2 isolates over their parental lineages remain unknown. We identified Delta-Omicron (AY.45-BA.1) an immunosuppressed transplant recipient treated with monoclonal antibody Sotrovimab. single breakpoint located the spike N-terminal domain adjacent Sotrovimab binding site. While Delta and BA.1 are sensitive neutralization, highly resistant. To our knowledge, this first described instance between circulating variants functional mechanism resistance immune escape.

Язык: Английский

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A panel of multivalent nanobodies broadly neutralizing Omicron subvariants and recombinant

Journal of Medical Virology, Год журнала: 2024, Номер 96(3)

Опубликована: Март 1, 2024

Abstract The emerging Omicron subvariants have a remarkable ability to spread and escape nearly all current monoclonal antibody (mAb) treatments. Although the virulence of SARS‐CoV‐2 has now diminished, it remains significant threat public health due its high transmissibility susceptibility mutation. Therefore, is urgent develop broad‐acting potent therapeutics targeting variants. Here, we identified panel BA.1 spike receptor‐binding domain (RBD)‐targeted nanobodies (Nbs) from naive alpaca VHH library. This Nbs exhibited binding affinity RBD wild‐type, Alpha B.1.1.7, Beta B.1.351, Delta plus, BA.1, BA.2. Through multivalent Nb construction, obtained subpanel ultrapotent neutralizing against BA.2, BF.7 even XBB.1.5, XBB.1.16 pseudoviruses. Protein structure prediction docking analysis showed that trimer 2F2E5 targets two independent epitopes, thus minimizing viral escape. Taken together, broad BF.7, XBB.1.16. These hold great promise for treatment infection could possess superwide breadth novel omicron mutants or recombinants.

Язык: Английский

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