Nicole Brock, Joanna A. Pulit-Penaloza, Jessica A. Belser, Claudia Pappas, Xiangjie Sun, Troy J. Kieran, Hui Zeng, Juan A. De La Cruz, Yasuko Hatta, Han Di, C. Todd Davis, Terrence M. Tumpey, Taronna R. Maines
{"title":"Avian Influenza A(H5N1) Isolated from Dairy Farm Worker, Michigan","authors":"Nicole Brock, Joanna A. Pulit-Penaloza, Jessica A. Belser, Claudia Pappas, Xiangjie Sun, Troy J. Kieran, Hui Zeng, Juan A. De La Cruz, Yasuko Hatta, Han Di, C. Todd Davis, Terrence M. Tumpey, Taronna R. Maines","doi":"10.3201/eid3106.250386","DOIUrl":"https://doi.org/10.3201/eid3106.250386","url":null,"abstract":"<p>Influenza A(H5N1) viruses have been detected in US dairy cow herds since 2024. We assessed the pathogenesis, transmission, and airborne release of A/Michigan/90/2024, an H5N1 isolate from a dairy farm worker in Michigan, in the ferret model. Results show this virus caused airborne transmission with moderate pathogenicity, including limited extrapulmonary spread, without lethality.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"44 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dorian J. Feistel, Rory Welsh, Jeffrey Mercante, Miguella Mark-Carew, Jason Caravas, Arun Boddapati, Samantha Sevilla, Matthew H. Seabolt, Dhwani Batra, Suchitra Chavan, Shatavia Morrison, Jesse Yoder, Hannah Long, Satvik Mishra, Benjamin Lorentz, Andi Dhroso, Iryna V. Goraichuk, Seonghye Jeon, Daniel M. Cornforth
{"title":"Detection and Tracking of SARS-CoV-2 Lineages through National Wastewater Surveillance System Pathogen Genomics","authors":"Dorian J. Feistel, Rory Welsh, Jeffrey Mercante, Miguella Mark-Carew, Jason Caravas, Arun Boddapati, Samantha Sevilla, Matthew H. Seabolt, Dhwani Batra, Suchitra Chavan, Shatavia Morrison, Jesse Yoder, Hannah Long, Satvik Mishra, Benjamin Lorentz, Andi Dhroso, Iryna V. Goraichuk, Seonghye Jeon, Daniel M. Cornforth","doi":"10.3201/eid3113.241411","DOIUrl":"https://doi.org/10.3201/eid3113.241411","url":null,"abstract":"<p>We conducted retrospective analysis of the emergence of the SARS-CoV-2 JN.1 variant in US wastewater during November 2023–July 2024 using Aquascope, a bioinformatics pipeline for the National Wastewater Surveillance System. This study highlights the value of open-source bioinformatics tools in tracking pathogen variants for public health monitoring.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"26 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jessica N. Ricaldi, J. Todd Parker, Nathelia Barnes, Hannah Turner, Scott Santibañez
{"title":"An Advanced Molecular Detection Roadmap for Nonlaboratorians","authors":"Jessica N. Ricaldi, J. Todd Parker, Nathelia Barnes, Hannah Turner, Scott Santibañez","doi":"10.3201/eid3113.241506","DOIUrl":"https://doi.org/10.3201/eid3113.241506","url":null,"abstract":"<p>This article, aimed at nonlaboratorians such as healthcare providers, public health professionals, and policymakers, provides basic concepts and terminology to enable better understanding of other manuscripts in this advanced molecular detection journal supplement. This article focuses on 3 aspects of advanced molecular detection: pathogen genomics, bioinformatics, and public health application, while providing additional resources for understanding.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"44 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elie Ishara-Nshombo, Anushri Somasundaran, Alessandra Romero-Ramirez, Konstantina Kontogianni, Daniel Mukadi-Bamuleka, Marithé Mukoka-Ntumba, Emile Muhindo-Milonde, Hugues Mirimo-Nguee, Jacob Parkes, Yusra Hussain, Susan Gould, Christopher T. Williams, Dominic Wooding, Juvenal Nkeramahame, Mikaela Watson, Hayley E. Hardwick, Malcolm G. Semple, John Kenneth Baillie, Jake Dunning, Thomas E. Fletcher, Thomas Edwards, Devy M. Emperador, Hugo Kavunga-Membo, Ana Isabel Cubas-Atienzar
{"title":"Diagnostic Accuracy of 3 Mpox Lateral Flow Assays for Antigen Detection, Democratic Republic of the Congo and United Kingdom","authors":"Elie Ishara-Nshombo, Anushri Somasundaran, Alessandra Romero-Ramirez, Konstantina Kontogianni, Daniel Mukadi-Bamuleka, Marithé Mukoka-Ntumba, Emile Muhindo-Milonde, Hugues Mirimo-Nguee, Jacob Parkes, Yusra Hussain, Susan Gould, Christopher T. Williams, Dominic Wooding, Juvenal Nkeramahame, Mikaela Watson, Hayley E. Hardwick, Malcolm G. Semple, John Kenneth Baillie, Jake Dunning, Thomas E. Fletcher, Thomas Edwards, Devy M. Emperador, Hugo Kavunga-Membo, Ana Isabel Cubas-Atienzar","doi":"10.3201/eid3106.250166","DOIUrl":"https://doi.org/10.3201/eid3106.250166","url":null,"abstract":"<p>The ongoing outbreaks of mpox highlight the urgent need for a rapid and low-cost diagnostic test to accurately detect and control this emerging disease. We estimated the analytical sensitivity using viral culture of the monkeypox virus clade IIb lineage and clinical diagnostic performance of 3 antigen detection rapid diagnostic tests (Ag-RDT) by using skin swab samples and upper-respiratory swab samples from mpox patients in the Democratic Republic of the Congo and the United Kingdom. The analytical limit of detection was 1.0 × 10<sup>4</sup> plaque-forming units/mL, fulfilling World Health Organization recommendations. Specificity of the 3 Ag-RDTs was 100%, but sensitivity was estimated at 0.00%–15.79% using skin samples and 0.00% using respiratory samples. None of the 3 Ag-RDTs reached the World Health Organization’s target clinical sensitivity, and we do not recommend them as diagnostic or screening tools for suspected mpox cases. Accurate Ag-RDTs for mpox diagnosis remain urgently needed.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"35 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isla E. Emmen, William C. Vuyk, Andrew J. Lail, Sydney Wolf, Eli J. O’Connor, Rhea Dalvie, Maansi Bhasin, Aanya Virdi, Caroline White, Nura R. Hassan, Alex Richardson, Grace VanSleet, Andrea Weiler, Savannah Rounds-Dunn, Kenneth Van Horn, Marc Gartler, Jane Jorgenson, Michael Spelman, Sean Ottosen, Nicholas R. Minor, Nancy Wilson, Thomas C. Friedrich, David H. O’Connor
{"title":"SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA","authors":"Isla E. Emmen, William C. Vuyk, Andrew J. Lail, Sydney Wolf, Eli J. O’Connor, Rhea Dalvie, Maansi Bhasin, Aanya Virdi, Caroline White, Nura R. Hassan, Alex Richardson, Grace VanSleet, Andrea Weiler, Savannah Rounds-Dunn, Kenneth Van Horn, Marc Gartler, Jane Jorgenson, Michael Spelman, Sean Ottosen, Nicholas R. Minor, Nancy Wilson, Thomas C. Friedrich, David H. O’Connor","doi":"10.3201/eid3113.241192","DOIUrl":"https://doi.org/10.3201/eid3113.241192","url":null,"abstract":"<p>In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification–based tests. However, use of those tests waned after the end of the COVID-19 Public Health Emergency on May 11, 2023. In Dane County, Wisconsin, we partnered with local- and state-level public health agencies and the South Central Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). During August 15, 2023–February 29, 2024, we received 227 RAT samples, from which we generated 127 sequences with >10× depth of coverage for <span>></span>90% of the SARS-CoV-2 genome. In a subset of tests, lower cycle threshold values correlated with sequence success. Our results demonstrated that collecting and sequencing results from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"18 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kien Pham, Chrispin Chaguza, Rafael Lopes, Ted Cohen, Emma Taylor-Salmon, Melanie Wilkinson, Volha Katebi, Nathan D. Grubaugh, Verity Hill
{"title":"Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States","authors":"Kien Pham, Chrispin Chaguza, Rafael Lopes, Ted Cohen, Emma Taylor-Salmon, Melanie Wilkinson, Volha Katebi, Nathan D. Grubaugh, Verity Hill","doi":"10.3201/eid3113.240981","DOIUrl":"https://doi.org/10.3201/eid3113.240981","url":null,"abstract":"<p>The COVID-19 pandemic has been marked by continuous emergence of novel SARS-CoV-2 variants. Questions remain about the mechanisms with which those variants establish themselves in new geographic areas. We performed a discrete phylogeographic analysis on 18,529 sequences of the SARS-CoV-2 Omicron BA.5 sublineage sampled during February–June 2022 to elucidate emergence of that sublineage in different regions of the United States. The earliest BA.5 sublineage introductions came from Africa, the putative variant origin, but most were from Europe, matching a high volume of air travelers. In addition, we discovered extensive domestic transmission between different US regions, driven by population size and cross-country transmission between key hotspots. We found most BA.5 virus transmission within the United States occurred between 3 regions in the southwestern, southeastern, and northeastern parts of the country. Our results form a framework for analyzing emergence of novel SARS-CoV-2 variants and other pathogens in the United States. </p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"43 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emmanuela Jules, Charlie Decker, Brianna Jeanne Bixler, Alaa Ahmed, Zijing Carol Zhou, Itika Arora, Henok Tafesse, Hannah Dakanay, Andrei Bombin, Ethan Wang, Jessica Ingersoll, Kathy Bifulco, Jennifer K Frediani, Richard Parsons, Julie Sullivan, Morgan Greenleaf, Jesse J Waggoner, Greg S Martin, Wilbur A Lam, Anne Piantadosi
{"title":"Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests.","authors":"Emmanuela Jules, Charlie Decker, Brianna Jeanne Bixler, Alaa Ahmed, Zijing Carol Zhou, Itika Arora, Henok Tafesse, Hannah Dakanay, Andrei Bombin, Ethan Wang, Jessica Ingersoll, Kathy Bifulco, Jennifer K Frediani, Richard Parsons, Julie Sullivan, Morgan Greenleaf, Jesse J Waggoner, Greg S Martin, Wilbur A Lam, Anne Piantadosi","doi":"10.3201/eid3113.241191","DOIUrl":"10.3201/eid3113.241191","url":null,"abstract":"<p><p>Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"31 13","pages":"39-44"},"PeriodicalIF":7.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143970106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
W Tanner Porter, David M Engelthaler, Crystal M Hepp
{"title":"Genomic Epidemiology for Estimating Pathogen Burden in a Population.","authors":"W Tanner Porter, David M Engelthaler, Crystal M Hepp","doi":"10.3201/eid3113.241203","DOIUrl":"10.3201/eid3113.241203","url":null,"abstract":"<p><p>The role of genomics in outbreak response and pathogen surveillance has expanded and ushered in the age of pathogen intelligence. Genomic surveillance enables detection and monitoring of novel pathogens; case clusters; and markers of virulence, antimicrobial resistance, and immune escape. We can leverage pathogen genomic diversity to estimate total pathogen burden in populations and environments, which was previously challenging because of unreliable data. Pathogen genomics might allow pathogen burdens to be estimated by sequencing even a small percentage of cases. Deeper genomic epidemiology analyses require multidisciplinary collaboration to ensure accurate and actionable real-time pathogen intelligence.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"31 13","pages":"22-24"},"PeriodicalIF":7.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hannah Padda, Claire Y-H Huang, Kacie Grimm, Brad J Biggerstaff, Jeremy P Ledermann, Janae Raetz, Karen Boroughs, Eric C Mossel, Stacey W Martin, Jennifer A Lehman, Rebecca L Townsend, David Krysztof, Paula Saá, Emily T N Dinh, Mary Grace Stobierski, Brenda Esponda-Morrison, Karen Ann A Wolujewicz, Matthew Osborne, Catherine M Brown, Brandi Hopkins, Elizabeth K Schiffman, Alex Garvin, Xia Lee, Rebecca A Osborn, Ryan J Wozniak, Aaron C Brault, Sridhar V Basavaraju, Susan L Stramer, J Erin Staples, Carolyn V Gould
{"title":"Powassan and Eastern Equine Encephalitis Virus Seroprevalence in Endemic Areas, United States, 2019-2020.","authors":"Hannah Padda, Claire Y-H Huang, Kacie Grimm, Brad J Biggerstaff, Jeremy P Ledermann, Janae Raetz, Karen Boroughs, Eric C Mossel, Stacey W Martin, Jennifer A Lehman, Rebecca L Townsend, David Krysztof, Paula Saá, Emily T N Dinh, Mary Grace Stobierski, Brenda Esponda-Morrison, Karen Ann A Wolujewicz, Matthew Osborne, Catherine M Brown, Brandi Hopkins, Elizabeth K Schiffman, Alex Garvin, Xia Lee, Rebecca A Osborn, Ryan J Wozniak, Aaron C Brault, Sridhar V Basavaraju, Susan L Stramer, J Erin Staples, Carolyn V Gould","doi":"10.3201/eid3105.240893","DOIUrl":"https://doi.org/10.3201/eid3105.240893","url":null,"abstract":"<p><p>Powassan virus (POWV) and Eastern equine encephalitis virus (EEEV) are regionally endemic arboviruses in the United States that can cause neuroinvasive disease and death. Recent identification of EEEV transmission through organ transplantation and POWV transmission through blood transfusion have increased concerns about infection risk. After historically high numbers of cases of both viruses were reported in 2019, we conducted a seroprevalence survey using blood donation samples from selected endemic counties. Specimens were screened for virus-specific neutralizing antibodies, and population seroprevalence was estimated using weights calibrated to county population census data. For POWV, median county seroprevalence in 4 states was 0.84%, ranging from 0% (95% CI 0%-2.28%) to 11.5% (95% CI 0.82%-40.9%). EEEV infection was identified in a single county (estimated seroprevalence 1.62% [95% CI 0.04%-8.75%]). Although seroprevalence estimates in sampled areas were generally low, additional investigation of higher-prevalence areas could inform risk for transmission from asymptomatic blood and organ donors.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"31 5","pages":"929-936"},"PeriodicalIF":7.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12044248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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