Explanipedia

Genomic epidemiology uncovers the origin of the mpox epidemic in Sierra Leone Open

Allan Campbell, John Demby Sandi, Ifeanyi F. Omah, Martin Faye, Edyth Parker , et al. · 2025

In January 2025, Sierra Leone reported its first mpox case in eight years, followed by a rapid nationwide surge that made it the epicenter of the continental mpox virus (MPXV) Clade IIb A.2.2 outbreak, with more than 5,000 confirmed cases …

Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics Open

Rob Knight, M. Omar Din, Rodolfo A. Salido, Gillian Wright, Caitriona Brennan , et al. · 2025

Widespread interest in the development of population-wide pathogen and antimicrobial resistance (AMR) monitoring has revealed wastewater’s microbial footprint as a marker of public health. Near-source wastewater remains a difficult sample …

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Open

Joshua I. Levy, Praneeth Gangavarapu, Dylan Pilz, Maryam Ahmadi Jesvaghane, Allison Steedman , et al. · 2025

Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasingly been used for population-scale mon…

Fixing the plumbing: Building interoperability between wastewater genomic surveillance datasets and systems using the PHA4GE contextual data specification Open

Jillian S. Paull, Charlotte Barclay, Rhiannon Cameron, Damion Dooley, Ivan Gill , et al. · 2025

The evolution of wastewater genomic surveillance (WWGS) has led to the development of many new methodologies, allowing for the broad application of WWGS for detection and monitoring of diverse pathogens and genetic markers. Variability in …

Wastewater-integrated pathogen surveillance dashboards enable real-time, transparent, and interpretable public health risk assessment and dissemination Open

Nosihle S Msomi, Joshua I. Levy, Nathaniel L. Matteson, Nkosenhle Ndlovu, Phindile Ntuli , et al. · 2025

Timely pathogen surveillance and reporting is essential for effective public health guidance. Web dashboards have become a key tool for communicating public health information to stakeholders, health care workers, and the broader community…

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic Open

Alexander Crits‐Christoph, Joshua I. Levy, Jonathan E. Pekar, Stephen A. Goldstein, Reema Singh , et al. · 2024

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open

Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen, Jennifer J. Knapp, Alyssa K. Overton , et al. · 2024

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open

Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen, Jennifer J. Knapp, Alyssa K. Overton , et al. · 2023

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…

Rapid threat assessment in the<i>Drosophila</i>thermosensory system Open

Genevieve C. Jouandet, Michael H. Alpert, José Miguel Simões, Richard Suhendra, Dominic D. Frank , et al. · 2023

SUMMARY Neurons that participate in sensory processing often display “ON” responses, i.e. fire transiently at the onset of a stimulus. ON transients are widespread, perhaps universal to sensory coding, yet their function is not always well…

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic Open

Alexander Crits‐Christoph, Joshua I. Levy, Jonathan E. Pekar, Stephen A. Goldstein, Reema Singh , et al. · 2023

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in th…

Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. Open

Kayla G. Barnes, Joshua I. Levy, Kristian G. Andersen, Jillian Gauld, Jonathan Rigby , et al. · 2023

The COVID-19 pandemic continues to impact health systems globally and robust surveillance is critical for pandemic control, however not all countries can sustain community surveillance programs. Wastewater surveillance has proven valuable …

Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control Open

Alex Crits-Christoph, Karthik Gangavarapu, Jonathan E. Pekar, Niema Moshiri, Reema Singh , et al. · 2023

Report: Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics Open

Nathaniel L. Matteson, Gabriel W. Hassler, Ezra Kurzban, Madison Schwab, Sarah A. Perkins , et al. · 2023

Summary 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 epidemic…

Wastewater surveillance for public health Open

Joshua I. Levy, Kristian G. Andersen, Rob Knight, Smruthi Karthikeyan · 2023

Wastewater contains information on pathogen spread, evolution, and outbreak risk

Molecular identification of SARS-CoV-2 variants of concern at urban wastewater treatment plants across South Africa Open

Mukhlid Yousif, R. Saïd, Setshaba Taukobong, Nkosenhle Ndlovu, Chinwe Juliana Iwu , et al. · 2022

The use of wastewater for SARS-CoV-2 surveillance is a useful complementary tool to clinical surveillance. The aims of this study were to characterize SARS-CoV-2 from wastewater samples, and to identify variants of concern present in sampl…

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 Open

Jonathan E. Pekar, Andrew F. Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich , et al. · 2022

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pa…

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic Open

Michael Worobey, Joshua I. Levy, Lorena M. Malpica Serrano, Alexander Crits‐Christoph, Jonathan E. Pekar , et al. · 2022

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, w…

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission Open

Smruthi Karthikeyan, Joshua I. Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham , et al. · 2022

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations Open

Laura D. Hughes, Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny , et al. · 2022

SARS-CoV-2 emergence very likely resulted from at least two zoonotic events Open

Jonathan E. Pekar, Andrew F. Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich , et al. · 2022

Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversit…

SARS-CoV-2 emergence very likely resulted from at least two zoonotic events Open

Jonathan E. Pekar, Andrew F. Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich , et al. · 2022

<p>Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic…

The Huanan market was the epicenter of SARS-CoV-2 emergence Open

Michael Worobey, Joshua I. Levy, Lorena M. Malpica Serrano, Alexander Crits‐Christoph, Jonathan E. Pekar , et al. · 2022

<p>Geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-…

SARS-CoV-2 emergence very likely resulted from at least two zoonotic events Open

Jonathan E. Pekar, Andrew F. Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich , et al. · 2022

Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversit…

The Huanan market was the epicenter of SARS-CoV-2 emergence Open

Michael Worobey, Joshua I. Levy, Lorena M. Malpica Serrano, Alexander Crits‐Christoph, Jonathan E. Pekar , et al. · 2022

Geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-19 pandem…

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations Open

Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer , et al. · 2022

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, h…

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission Open

Smruthi Karthikeyan, Joshua I. Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham , et al. · 2021

Summary As 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 …

Robustness and plasticity in Drosophila heat avoidance Open

José Miguel Simões, Joshua I. Levy, Emanuela E. Zaharieva, Leah T. Vinson, Peixiong Zhao , et al. · 2021

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