Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing DOI Creative Commons
Wiep van der Toorn, Patrick Bohn, Wang Liu-Wei

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 21, 2025

Abstract Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast highly adapter-barcoding demultiplexing approach for dRNA-seq with SQK-RNA002 SQK-RNA004 chemistries. WarpDemuX enhances speed accuracy fast processing raw nanopore signal, use a light-weight machine-learning algorithm design optimized barcode sets. We demonstrate its utility performing rapid phenotypic profiling different SARS-CoV-2 viruses through multiplexed longitudinal samples on single flowcell, identifying systematic differences in transcript abundance poly(A) tail lengths during infection. Additionally, integrating control software real-time enrichment target molecules barcode-specific adaptive sampling, which enriching low viral RNA. In summary, represents broadly applicable, high-performance, economical multiplexing solution dRNA-seq, facilitating advanced (epi-) transcriptomic research.

Язык: Английский

VirusWarn: A Mutation-Based Early Warning System to Prioritize Concerning SARS-CoV-2 and Influenza Virus Variants from Sequencing Data DOI Creative Commons

C. Kirschbaum,

Kunaphas Kongkitimanon, Sarah Lanferini Frank

и другие.

Computational and Structural Biotechnology Journal, Год журнала: 2025, Номер 27, С. 1081 - 1088

Опубликована: Янв. 1, 2025

The rapid evolution of respiratory viruses is characterized by the emergence variants with concerning phenotypes that are efficient in antibody escape or show high transmissibility. This necessitates timely identification such surveillance networks to assist public health interventions. Here, we introduce VirusWarn, a comprehensive system designed for detecting, prioritizing, and warning emerging virus from large genomic datasets. VirusWarn uses both manually-curated rules machine-learning (ML) classifiers generate rank pathogen sequences based on mutations concern regions interest. Validation results SARS-CoV-2 showed successfully identifies assessments, manual- ML-derived criteria positive selection analyses. Although initially developed SARS-CoV-2, was adapted Influenza their dynamics, provides robust performance, integrating scheme accounts fixed past seasons. HTML reports provide detailed searchable tables visualizations, including mutation plots heatmaps. Because written Nextflow, it can be easily other pathogens, demonstrating its flexibility scalability efforts.

Язык: Английский

Процитировано

0
Spike Protein–Fibrinogen Interaction: A Novel Immune Evasion Strategy of SARS-CoV-2? DOI Creative Commons
Saroj Kumar Panda, Shashi Bala Singh, Parth Sarthi Sen Gupta

и другие.

ACS Pharmacology & Translational Science, Год журнала: 2025, Номер 8(4), С. 1182 - 1184

Опубликована: Март 19, 2025

The host protein fibrinogen has been found to interact with the N-terminal domain (NTD) of spike in SARS-CoV-2. However, evolutionary benefit this binding virus still remains unclear. Herein, we put forward rationale and supporting evidence that its more conserved NTD is an immune evasion strategy adopted by outsmart targeted neutralizing antibodies.

Язык: Английский

Процитировано

0
Deciphering SARS-CoV-2 evolution under antibody immune pressure DOI
Fanchong Jian, Yunlong Cao

Trends in Immunology, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing DOI Creative Commons
Wiep van der Toorn, Patrick Bohn, Wang Liu-Wei

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 21, 2025

Abstract Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast highly adapter-barcoding demultiplexing approach for dRNA-seq with SQK-RNA002 SQK-RNA004 chemistries. WarpDemuX enhances speed accuracy fast processing raw nanopore signal, use a light-weight machine-learning algorithm design optimized barcode sets. We demonstrate its utility performing rapid phenotypic profiling different SARS-CoV-2 viruses through multiplexed longitudinal samples on single flowcell, identifying systematic differences in transcript abundance poly(A) tail lengths during infection. Additionally, integrating control software real-time enrichment target molecules barcode-specific adaptive sampling, which enriching low viral RNA. In summary, represents broadly applicable, high-performance, economical multiplexing solution dRNA-seq, facilitating advanced (epi-) transcriptomic research.

Язык: Английский

Процитировано

0