NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges DOI Creative Commons

Aileen C. Tartanian,

Nicole Mulroney,

Kelly Poselenzny

et al.

Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11

Published: April 20, 2023

Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits institutions with an expectation high informational upside little insight in regards practicality implementation execution such complexity testing the midst a pandemic. This article details our institution's experience implementing using Next Generation Sequencing (NGS) monitor northern Chicagoland area throughout To date, we have sequenced nearly 7,000 previously known positive samples from various patient populations (e.g., outpatient, inpatient, outreach sites) reduce bias sampling. As result, hospital was guided while making crucial decisions about staffing, masking, other infection control measures during While beneficial, establishing this NGS procedure challenging, countless considerations at every stage assay development validation. Reduced staffing prompted transition manual automated throughput workflow, requiring further validation, lab space, instrumentation. Data management IT security were additional that delayed dictated bioinformatic capabilities. Taken together, highlights obstacles triumphs sequencing.

Language: Английский

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology DOI Creative Commons
Irene Bianconi,

Richard Aschbacher,

Elisabetta Pagani

et al.

Antibiotics, Journal Year: 2023, Volume and Issue: 12(11), P. 1580 - 1580

Published: Oct. 30, 2023

Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.

Language: Английский

Citations

29
ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance DOI Creative Commons
Alexandre Freitas da Silva, Antônio Marinho da Silva Neto, Cleber Furtado Aksenen

et al.

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(2)

Published: April 4, 2024

Abstract ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned into general-purpose reference-based genome assembler all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. runs on broad range of infrastructures, from laptop computers high-performance computing (HPC) environments, generates standard well-formatted outputs suited both public health reporting scientific problem-solving. at: https://viralflow.github.io/index-en.html.

Language: Английский

Citations

12
Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia DOI Creative Commons
Sukma Oktavianthi, Aksar Chair Lages,

Rinaldy Kusuma

et al.

Pathogens, Journal Year: 2024, Volume and Issue: 13(4), P. 279 - 279

Published: March 25, 2024

The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 isolates collected from selected regions Indonesia between January October 2021 was performed to identify distribution common in Indonesia. During January–April 2021, Indonesian lineages B.1.466.2 B.1.470 dominated, but May Delta’s AY.23 lineage outcompeted them. An analysis 7515 published sequences June 2022 revealed decline Delta November followed by emergence Omicron December 2021. We identified C241T (5′UTR), P314L (NSP12b), F106F (NSP3), D614G (Spike) all sequences. other substitutions included P681R (76.4%) T478K (60%) Spike, D377Y Nucleocapsid (61%), I82T Membrane proteins. Breakthrough prolonged viral shedding cases were associated carrying Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, V1264L mutations. dynamic highlights importance continuous genomic surveillance monitoring identifying potential strains leading disease outbreaks.

Language: Английский

Citations

7
Increasing evolution, prevalence, and outbreaks for rift valley fever virus in the process of breaking geographical barriers DOI
Zekun Wang,

Shaojun Pei,

Run‐Ze Ye

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 917, P. 170302 - 170302

Published: Jan. 24, 2024

Language: Английский

Citations

4
Monitoring and Early Warning System: Regional Monitoring Strategy in Lombardy Region DOI Creative Commons

Sarah Cataldi,

Elena Maria Ticozzi,

Federica Morani

et al.

Epidemiologia, Journal Year: 2025, Volume and Issue: 6(1), P. 7 - 7

Published: Feb. 11, 2025

This article examines the infectious disease surveillance system in Lombardy region of Italy, with a focus on its response mechanisms to respiratory syndromes. study aims describe alert and organizational procedures place, assessing their effectiveness managing health crises. is based analysis Lombardy's regional resolution No. 1125, developed by public experts. Surveillance levels were categorized incidence thresholds healthcare impacts, establishing specific indicators activation protocols. Information flows are managed through real-time data portals, enabling monitoring COVID-19, influenza, other diseases. A multi-level was established, ranging from ordinary regimes critical epidemic activation. Each level includes actions, such as resource reallocation, emergency department support, suspension elective procedures. The use technological tools, electronic records, streamlined reporting processes, flow management, has strengthened region's capabilities. underscores value structured, for showing that unified approach improves crisis efficiency. It suggests sharing protocols within scientific community can help harmonize national international responses future pandemics. system, while effective current context, may require adaptation challenges.

Language: Английский

Citations

0
Microbial genomics and genome sequencing approaches DOI
Subhasish Chatterjee

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 3 - 20

Published: Jan. 1, 2025

Language: Английский

Citations

0
Instant Diagnosis Using Raman Spectroscopy and Generative Adversarial Networks: A Blood‐Based Study on Seasonal Flu, COVID‐19, and Dengue DOI

Rekha Puthenkaleekkal Thankappan,

Dhanya Reghu,

Dipak Kumbhar

et al.

Journal of Biophotonics, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Rapid detection of infectious diseases like COVID-19, flu, and dengue is crucial for healthcare professionals preparing contagious outbreaks. Given the constant mutations in viruses recurring emergence threats Nipah Zika, there an urgent demand a technology capable distinguishing between infections that share similar symptoms. In this paper, we utilize laser-based Raman scattered signals from drop dried blood plasma, combined with generative artificial intelligence, to provide rapid precise diagnosis. Our optimized model exhibits exceptional performance, yielding high predictive scores 96%, 98%, 100% dengue, respectively. The proposed spectroscopic analysis, turnaround time, can ensure near-accurate diagnosis proper quarantining highly cases. Furthermore, potential extension our method include other viral offers alternative challenge developing different diagnostic kits each disease.

Language: Английский

Citations

0
SARS-CoV-2 genomic surveillance using self-collected saliva specimens during occupational testing programs DOI Creative Commons

Andrew T Schnaubelt,

David M. Brett-Major,

John Williamson

et al.

Frontiers in Public Health, Journal Year: 2025, Volume and Issue: 13

Published: April 8, 2025

Continually emerging SARS-CoV-2 variants pose challenges to clinical and public health interventions, necessitating sustainable approaches real-time variant monitoring. This case study describes an innovative screening surveillance program that demonstrates the utility of sequencing-based monitoring using self-collected saliva specimens. We conducted saliva-based in occupational settings Omaha, Nebraska from December 2021 through November 2022. 8,372 specimens collected 1,480 participants were tested for RNA by extraction-free PCR, with 334 positive samples referred whole-genome sequencing analysis. Program utilization, quality metrics, outputs compared across sites. Specimen was high settings, demonstrating suitability PCR genomic testing. Virus successfully determined strain 83 67% SARS-CoV-2-positive two successful integration determination into programs qRT-PCR testing method. further demonstrate sensitivity efficiency analysis is dependent on cycle threshold (Ct) cutoff diagnostic assay virus gene target. Use optimized Ct value referral recommended. Community-based can be utilized enhance monitoring, could considered risk identification other respiratory infections. approach offers advantages a non-invasive specimen collection, no need supervised collection healthcare worker, supply chain resiliency, distributable access, scalability.

Language: Английский

Citations

0
Integrating patient metadata and pathogen genomic data: advancing pandemic preparedness with a multi-parametric simulator DOI Creative Commons

Bonjean Maxime,

Jérôme Ambroise, Francisco Orchard

et al.

BMC Research Notes, Journal Year: 2025, Volume and Issue: 18(1)

Published: April 15, 2025

Stakeholder training is essential for handling unexpected crises swiftly, safely, and effectively. Functional tabletop exercises simulate potential public health using complex scenarios with realistic data. These are designed by integrating datasets that represent populations exposed to a pandemic pathogen, combining pathogen genomic data generated through high-throughput sequencing (HTS) together patient epidemiological, clinical, demographic information. However, sharing between EU member states faces challenges due disparities in collection practices, standardisation, legal frameworks, privacy, security regulations, resource allocation. In the Horizon 2020 PANDEM-2 project, we developed multi-parametric tool links metadata, enabling managers enhance customise more accurate simulations. The available as an R package: https://github.com/maous1/Pandem2simulator Shiny application: https://uclouvain-ctma.Shinyapps.io/Multi-parametricSimulator/ , facilitating rapid scenario A structured procedure, complete video tutorials exercises, was shown be effective user-friendly during session twenty participants. conclusion, this enhances pandemics preparedness contextual metadata into increased realism of these significantly improves emergency responder readiness, regardless biological incident's nature, whether natural, accidental, or intentional.

Language: Английский

Citations

0
AI in the development of vaccines for emerging and re-emerging diseases DOI
Rita Elizabeth Velastegui-Hernández, Verónica Gabriela Salinas Velasteguí, Diana Catalina Velasteguí Hernández

et al.

Salud Ciencia y Tecnología, Journal Year: 2025, Volume and Issue: 4

Published: Jan. 15, 2025

Introduction: The integration of artificial intelligence (AI) into vaccine development has revolutionized traditional methodologies, significantly enhancing the speed, precision, and scalability immunological research. Emerging re-emerging infectious diseases, driven by zoonotic spillovers, antimicrobial resistance, global environmental changes, pose substantial challenges. Addressing these requires innovative approaches, with AI playing a pivotal role in advancing solutions.Development: applications vaccinology include antigen detection, adjuvant optimization, immune response simulation. Deep learning algorithms streamline identification immunogenic targets conserved antigens, enabling for highly mutable pathogens such as SARS-CoV-2, HIV, influenza. Case studies demonstrate AI's transformative impact, including its rapid creation mRNA vaccines COVID-19, promising antigens malaria, enhanced efficacy influenza through predictive modeling. However, challenges unequal access to technology, biases data models, ethical concerns regarding genomic privacy persist. Recommendations address barriers increasing diversity, strengthening frameworks, investing infrastructure democratize AI-driven innovations.Conclusions: ability reduce time cost, improve enable personalized immunization strategies positions it cornerstone modern vaccinology. With continued advancements equitable implementation, holds potential reshape development, pandemic preparedness, longstanding public health disparities globally.

Language: Английский

Citations

0