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Yaglom HD, Roth A, Alvarez C, Corbus E, Ghai RR, Ferguson S, Ritter JM, Hecht G, Rekant S, Engelthaler DM, Venkat H, Tygielski S. DETECTION OF SARS-COV-2 IN A SQUIRREL MONKEY ( SAIMIRI SCIUREUS): A ONE HEALTH INVESTIGATION AND RESPONSE. J Zoo Wildl Med 2024; 55:471-478. [PMID: 38875205 PMCID: PMC11247420 DOI: 10.1638/2023-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 06/16/2024] Open
Abstract
Through collaborative efforts, One Health partners have responded to outbreaks of COVID-19 among animals, including those in human care at zoos. Zoos have been faced with numerous challenges, including the susceptibility of many mammalian species, and therefore the need to heighten biosecurity measures rapidly. Robust One Health collaborations already exist in Arizona to address endemic and emerging zoonoses, but these have rarely included zoos. The pandemic shed light on this, and Arizona subsequently expanded its SARS-CoV-2 surveillance efforts to include zoo animals. Testing and epidemiologic support was provided to expedite the detection of and response to zoonotic SARS-CoV-2 infection in zoo animals, as well as to understand possible transmission events. Resulting from this program, SARS-CoV-2 was detected from a rectal swab collected from an 8-yr-old squirrel monkey (Saimiri sciureus) from a zoo in Southern Arizona. The animal had rapidly become ill with nonrespiratory symptoms and died in July 2022. Genomic sequencing from the swab revealed mutations consistent with the Omicron (BA.2) lineage. An epidemiologic investigation identified an animal caretaker in close proximity to the affected squirrel monkey who tested positive for COVID-19 the same day the squirrel monkey died. Critical One Health partners provided support to the zoo through engagement of local, state, and federal agencies. Necropsy and pathologic evaluation showed significant necrotizing colitis; the overall clinical and histopathological findings did not implicate SARS-CoV-2 infection alone as a causal or contributing factor in the squirrel monkey's illness and death. This report documents the first identification of SARS-CoV-2 in a squirrel monkey and highlights a successful and timely One Health investigation conducted through multisectoral collaboration.
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Affiliation(s)
- Hayley D Yaglom
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA,
| | | | | | | | - Ria R Ghai
- One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Sylvia Ferguson
- Veterinary Diagnostic Pathology Center, Midwestern University, Glendale, AZ 85308, USA
| | - Jana M Ritter
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Gavriella Hecht
- Arizona Department of Health Services, Office of Infectious Disease Control, Phoenix, AZ 85007, USA
| | - Steven Rekant
- Office of Interagency Coordination, United States Department of Agriculture, Animal and Plant Health Inspection Service, Riverdale, MD 20737, USA
| | - David M Engelthaler
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA
| | - Heather Venkat
- Arizona Department of Health Services, Office of Infectious Disease Control, Phoenix, AZ 85007, USA
- Center for Preparedness and Response, Career Epidemiology Field Officer Program, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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2
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Erickson DE, Simmons KM, Barrand ZA, Ridenour CL, Hawkinson PB, Lemke L, Sellner SP, Brock BN, Rivas AN, Sheridan K, Lemmer D, Yaglom HD, Porter WT, Belanger M, Torrey RM, Stills AJR, McCormack K, Black M, Holmes W, Rostain D, Mikus J, Sotelo K, Haq E, Neupane R, Weiss J, Johnson J, Collins C, Avalle S, White C, Howard BJ, Maltinsky SA, Whealy RN, Gordon NB, Sahl JW, Pearson T, Fofanov VY, Furstenau T, Driebe EM, Caporaso JG, Barber J, Terriquez J, Engelthaler DM, Hepp CM. Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.20.23297677. [PMID: 38562876 PMCID: PMC10984038 DOI: 10.1101/2023.11.20.23297677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Most seasonally circulating enteroviruses result in asymptomatic or mildly symptomatic infections. In rare cases, however, infection with some subtypes can result in paralysis or death. Of the 300 subtypes known, only poliovirus is reportable, limiting our understanding of the distribution of other enteroviruses that can cause clinical disease. Objective The overarching objectives of this study were to: 1) describe the distribution of enteroviruses in Arizona during the late summer and fall of 2022, the time of year when they are thought to be most abundant, and 2) demonstrate the utility of viral pan-assay approaches for semi-agnostic discovery that can be followed up by more targeted assays and phylogenomics. Methods This study utilizes pooled nasal samples collected from school-aged children and long-term care facility residents, and wastewater from multiple locations in Arizona during July-October of 2022. We used PCR to amplify and sequence a region common to all enteroviruses, followed by species-level bioinformatic characterization using the QIIME 2 platform. For Enterovirus-D68 (EV-D68), detection was carried out using RT-qPCR, followed by confirmation using near-complete whole EV-D68 genome sequencing using a newly designed tiled amplicon approach. Results In the late summer and early fall of 2022, multiple enterovirus species were identified in Arizona wastewater, with Coxsackievirus A6, EV-D68, and Coxsackievirus A19 composing 86% of the characterized reads sequenced. While EV-D68 was not identified in pooled human nasal samples, and the only reported acute flaccid myelitis case in Arizona did not test positive for the virus, an in-depth analysis of EV-D68 in wastewater revealed that the virus was circulating from August through mid-October. A phylogenetic analysis on this relatively limited dataset revealed just a few importations into the state, with a single clade indicating local circulation. Significance This study further supports the utility of wastewater-based epidemiology to identify potential public health threats. Our further investigations into EV-D68 shows how these data might help inform healthcare diagnoses for children presenting with concerning neurological symptoms.
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Affiliation(s)
- Daryn E Erickson
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kyle M Simmons
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Zachary A Barrand
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Chase L Ridenour
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Paige B Hawkinson
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Lacey Lemke
- Northern Arizona Healthcare, Flagstaff, AZ, USA
| | - Shayne P Sellner
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Breezy N Brock
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Alexis N Rivas
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Hayley D Yaglom
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - W Tanner Porter
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Rachel M Torrey
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | | | - Kiley McCormack
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | - Matt Black
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | - Wydale Holmes
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Drew Rostain
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Jeremy Mikus
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Kimberly Sotelo
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Emmen Haq
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | | | - Joli Weiss
- Arizona Department of Health Services, Phoenix, AZ, USA
| | | | | | - Sarah Avalle
- Arizona Department of Health Services, Phoenix, AZ, USA
| | - Chelsi White
- Maricopa County Department of Public Health, Phoenix, AZ, USA
| | | | - Sara A Maltinsky
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Ryann N Whealy
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nathaniel B Gordon
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Talima Pearson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Viacheslav Y Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Tara Furstenau
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | | | - J Gregory Caporaso
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jarrett Barber
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Crystal M Hepp
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Chan AP, Siddique A, Desplat Y, Choi Y, Ranganathan S, Choudhary KS, Khalid MF, Diaz J, Bezney J, DeAscanis D, George Z, Wong S, Selleck W, Bowers J, Zismann V, Reining L, Highlander S, Brown K, Armstrong JR, Hakak Y, Schork NJ. A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness. CELL REPORTS METHODS 2023; 3:100463. [PMID: 37323571 PMCID: PMC10110940 DOI: 10.1016/j.crmeth.2023.100463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/22/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first reported case, would be of significant value. Next-generation sequencing (NGS) has such capabilities; however, it has limited detection sensitivity for low-copy-number pathogens. Here, we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS work flow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.
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Affiliation(s)
- Agnes P. Chan
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | - Yongwook Choi
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | | | - Josh Diaz
- Jumpcode Genomics, San Diego, CA 92121, USA
| | - Jon Bezney
- Jumpcode Genomics, San Diego, CA 92121, USA
| | | | | | - Shukmei Wong
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - William Selleck
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Jolene Bowers
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Victoria Zismann
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Lauren Reining
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | - Sarah Highlander
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
| | | | | | | | - Nicholas J. Schork
- The Translational Genomics Research Institute (TGen), An Affiliate of the City of Hope National Medical Center, Phoenix, AZ 85004, USA
- The University of California, San Diego, San Diego, CA 92093, USA
- The Scripps Research Institute, San Diego, CA 92037, USA
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Yaglom HD, Maurer M, Collins B, Hojnacki J, Monroy-Nieto J, Bowers JR, Packard S, Erickson DE, Barrand ZA, Simmons KM, Brock BN, Lim ES, Smith S, Hepp CM, Engelthaler DM. One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021. PLoS One 2022; 17:e0272830. [PMID: 36315517 PMCID: PMC9621446 DOI: 10.1371/journal.pone.0272830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022] Open
Abstract
Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to SARS-CoV-2 genomes belonging to an outbreak of AY.25 identified through ongoing phylogenomic analyses. Continued phylogenetic analyses were conducted to further describe the AY.25 outbreak. Wastewater collected twice weekly from sites across campus was tested for SARS-CoV-2 by RT-qPCR, and subsequently sequenced to identify variants. The AY.25 outbreak was defined by a single mutation (C18804T) and comprised 379 genomes from SARS-CoV-2 positive cases associated with the university and community. Several undergraduate student gatherings and congregate living settings on campus likely contributed to the rapid spread of COVID-19 across the university with secondary transmission into the community. The clade defining mutation was also found in wastewater samples collected from around student dormitories a week before the semester began, and 9 days before cases were identified. Genomic, epidemiologic, and wastewater surveillance provided evidence that an AY.25 clone was likely imported into the university setting just prior to the onset of the Fall 2021 semester, rapidly spread through a subset of the student population, and then subsequent spillover occurred in the surrounding community. The university and local public health department worked closely together to facilitate timely reporting of cases, identification of close contacts, and other necessary response and mitigation strategies. The emergence of new SARS-CoV-2 variants and potential threat of other infectious disease outbreaks on university campuses presents an opportunity for future comprehensive One Health genomic data driven, targeted interventions.
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Affiliation(s)
- Hayley D. Yaglom
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Matthew Maurer
- Coconino County Health and Human Services, Flagstaff, Arizona, United States of America
| | - Brooke Collins
- Coconino County Health and Human Services, Flagstaff, Arizona, United States of America
| | - Jacob Hojnacki
- Coconino County Health and Human Services, Flagstaff, Arizona, United States of America
| | - Juan Monroy-Nieto
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jolene R. Bowers
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Samuel Packard
- Coconino County Health and Human Services, Flagstaff, Arizona, United States of America
| | - Daryn E. Erickson
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Zachary A. Barrand
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kyle M. Simmons
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Breezy N. Brock
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Efrem S. Lim
- Arizona State University, Tempe, Arizona, United States of America
| | - Sandra Smith
- Campus Health Services, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
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