Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes

Cell Reports Medicine, Год журнала: 2024, Номер 5(1), С. 101361 - 101361

Опубликована: Янв. 1, 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the disease 2019 (COVID-19) pandemic, but impact of these on severity has remained unclear. In this single-center, retrospective cohort study, we examined association between SARS-CoV-2 clade patient outcome over a two-year period in Chicago, Illinois. Between March 2020 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients outpatients alongside linked clinical demographic metadata, which 2,114 processed for viral whole-genome sequencing. When controlling demographics vaccination status, several clades associated risk hospitalization, was negated by inclusion population-level confounders, including case count, sampling bias, shifting standards care. These data highlight importance integrating non-virological factors into models accurate assessment risk.

Язык: Английский

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Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Viruses, Год журнала: 2024, Номер 16(3), С. 430 - 430

Опубликована: Март 11, 2024

Genomic sequencing of clinical samples to identify emerging variants SARS-CoV-2 has been a key public health tool for curbing the spread virus. As result, an unprecedented number genomes were sequenced during COVID-19 pandemic, which allowed rapid identification genetic variants, enabling timely design and testing therapies deployment new vaccine formulations combat variants. However, despite technological advances deep sequencing, analysis raw sequence data generated globally is neither standardized nor consistent, leading vastly disparate sequences that may impact Here, we show both Illumina Oxford Nanopore platforms, downstream bioinformatic protocols used by industry, government, academic groups resulted in different virus from same sample. These workflows produced consensus with differences single nucleotide polymorphisms, inclusion exclusion insertions, and/or deletions, using as input datasets. compared characterized such discrepancies propose specific suite parameters should be adopted across field. Consistent results are fundamental future pathogen surveillance efforts, including pandemic preparation, allow data-driven response.

Язык: Английский

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

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 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.

Язык: 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, Год журнала: 2024, Номер 9(10), С. e016474 - e016474

Опубликована: Окт. 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.

Язык: 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, Год журнала: 2023, Номер 15(19), С. 3460 - 3460

Опубликована: Сен. 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.

Язык: Английский

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