Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 19, 2024

Abstract Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods analyzing data are not designed to detect novel variants that have been characterized in humans. Here, we present unsupervised learning approach clusters co-varying time-evolving mutation patterns leading the identification of To build our model, sequenced 3,659 samples collected over a span more than two years urban rural locations Southern Nevada. We then developed multivariate independent component analysis (ICA)-based pipeline transform frequencies into sources with compared variant predictions >5,000 clinical genomes isolated Nevadans. Using source data-driven reference “barcodes”, demonstrated model’s accuracy by successfully detecting Delta late 2021, Omicron 2022, emerging recombinant XBB 2023. Our revealed spatial temporal dynamics both regions; achieved earlier detection most other computational tools; uncovered unique associated any known variant. The nature boosts statistical power can support early This feature offers opportunity pathogen detection, even absence testing.

Language: Английский

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The PHA4GE Microbial Data-Sharing Accord: establishing baseline consensus microbial data-sharing norms to facilitate cross-sectoral collaboration

BMJ Global Health, Journal Year: 2024, Volume and Issue: 9(10), P. e016474 - e016474

Published: Oct. 1, 2024

Microbial data sharing underlies evidence-based microbial research, as well pathogen surveillance and analysis essential to public health. While the need for was highlighted during SARS-CoV-2 pandemic, some concerns regarding secondary use have also surfaced. Although general guidelines are available sharing, we note absence of a set established, universal, unambiguous accessible principles guide data. Here, propose Public Health Alliance Genomic Epidemiology (PHA4GE) Data-Sharing Accord consolidate consensus norms accepted practices The provides seven simple, baseline address key that may arise researchers providing datasets responsible by users. By clear rules data, can increase confidence in providers protect against mis-use analyses.

Language: Английский

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The Crosstalk Between HIV-TB Co-Infection and Associated Resistance in the Indian Population

Venereology, Journal Year: 2024, Volume and Issue: 3(4), P. 183 - 198

Published: Nov. 6, 2024

Extensive research on tuberculosis (TB) and HIV co-infection reveals the diverse prevalence co-epidemic patterns across populations, necessitating tailored public health strategies. Co-infection is bidirectional; individuals with are more susceptible to TB, vice versa. Antiretroviral therapy (ART) antituberculosis treatment (ATT) critical for managing these conditions, but pose risks due drug–pathogen drug–drug interactions, potentially leading immune reconstitution inflammatory syndrome (IRIS) in patients HIV/AIDS. IRIS, often triggered by highly active antiretroviral (HAART), can exacerbate progression, increase drug resistance, deteriorate patients’ quality of life. Approximately one-third global population also infected extensive drug-resistant (XDR) multidrug-resistant (MDR) strains posing significant challenges. Latent TB infection (LTBI) further complicates scenario, as it progress particularly both conditions. The Indian mortality rates TB-HIV remain high, emphasizing need new Additionally, unreported cases inadequate post-treatment monitoring contribute high rate, among LTBI. complexity HIV-TB co-infection, especially LTBI, underscores urgency addressing challenges improve outcomes affected populations.

Language: Английский

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Wastewater-Based Epidemiology of SARS-CoV-2 and Other Respiratory Viruses: Bibliometric Tracking of the Last Decade and Emerging Research Directions

Water, Journal Year: 2023, Volume and Issue: 15(19), P. 3460 - 3460

Published: Sept. 30, 2023

The COVID-19 pandemic has prompted an overwhelming surge in research investigating different aspects of the disease and its causative agent. In this study, we aim to discern themes trends field wastewater-based epidemiology (WBE) SARS-CoV-2 other respiratory viruses over past decade. We examined 904 papers authored by researchers from 87 countries. Despite low reported incidence 2023, are still interested application WBE SARS-CoV-2. Based on network visualization mapping 189 keyword co-occurrences, method optimization, source, transmission, survival, surveillance or early-warning detection systems, variants concern wastewater were found be topics greatest interest among researchers. A trend toward evaluations utility new technologies such as digital PCR for viruses, particularly influenza, was observed. USA emerged leading country terms publications, citations, international collaborations. Additionally, Science Total Environment stood out journal with highest number publications citations. study highlighted areas further research, including data normalization biosensor-based collection, emphasized need collaboration standardized methodology future directions.

Language: Английский

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

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

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