Publications by authors named "Emory Hufbauer"
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions.
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- The global scientific community has sequenced over 11 million SARS-CoV-2 genomes by May 2022, allowing real-time tracking of virus evolution.
- Outbreak.info is a platform that monitors over 40 million variants and mutations across 7,000 locations, providing valuable insights for researchers and public health officials.
- The platform features user-friendly visualizations and robust infrastructure for data ingestion and dissemination, supporting genomic surveillance and hypothesis generation regarding the pandemic.
Outbreak.info Research Library is a standardized, searchable interface of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) publications, clinical trials, datasets, protocols and other resources, built with a reusable framework. We developed a rigorous schema to enforce consistency across different sources and resource types and linked related resources.
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- Effective detection of SARS-CoV-2 variants through wastewater analysis can complement existing clinical testing methods, especially in resource-limited areas where traditional testing may be biased.* -
- The study implemented improved virus concentration techniques and software to enhance the sequencing of multiple virus strains from wastewater, resulting in high-resolution data over 295 days at a university and its surrounding county.* -
- Wastewater surveillance identified emerging variants up to 14 days earlier than clinical methods and revealed instances of virus spread that clinical testing missed, highlighting its potential for public health monitoring.*
The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time.
View Article and Find Full Text PDFAs SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing.
View Article and Find Full Text PDFTo combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within the first year. To address the challenge in tracking the vast amount of new research located in separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface of COVID-19 and SARS-CoV-2 resources.
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