1
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Shafer MM, Bobholz MJ, Vuyk WC, Gregory DA, Roguet A, Haddock Soto LA, Rushford C, Janssen KH, Emmen IE, Ries HJ, Pilch HE, Mullen PA, Fahney RB, Wei W, Lambert M, Wenzel J, Halfmann P, Kawaoka Y, Wilson NA, Friedrich TC, Pray IW, Westergaard R, O'Connor DH, Johnson MC. Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage. Lancet Microbe 2024; 5:e335-e344. [PMID: 38484748 PMCID: PMC11049544 DOI: 10.1016/s2666-5247(23)00372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 04/08/2024]
Abstract
BACKGROUND The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time. METHODS We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage. FINDINGS We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7 × 109 genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13 consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants. INTERPRETATION We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread. FUNDING The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.
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Affiliation(s)
- Martin M Shafer
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Max J Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Devon A Gregory
- School of Medicine, University of Missouri, Columbia, MO, USA
| | - Adelaide Roguet
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Luis A Haddock Soto
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Kayley H Janssen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Isla E Emmen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Hunter J Ries
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hannah E Pilch
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Paige A Mullen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Rebecca B Fahney
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew Lambert
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - Jeff Wenzel
- Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy A Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian W Pray
- Wisconsin Department of Health Services, Madison, WI, USA
| | - Ryan Westergaard
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- School of Medicine, University of Missouri, Columbia, MO, USA.
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2
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Singh T, Miller IG, Venkatayogi S, Webster H, Heimsath HJ, Eudailey JA, Dudley DM, Kumar A, Mangan RJ, Thein A, Aliota MT, Newman CM, Mohns MS, Breitbach ME, Berry M, Friedrich TC, Wiehe K, O'Connor DH, Permar SR. Prior dengue virus serotype 3 infection modulates subsequent plasmablast responses to Zika virus infection in rhesus macaques. mBio 2024; 15:e0316023. [PMID: 38349142 PMCID: PMC10936420 DOI: 10.1128/mbio.03160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/17/2024] [Indexed: 03/14/2024] Open
Abstract
Immunodominant and highly conserved flavivirus envelope proteins can trigger cross-reactive IgG antibodies against related flaviviruses, which shapes subsequent protection or disease severity. This study examined how prior dengue serotype 3 (DENV-3) infection affects subsequent Zika virus (ZIKV) plasmablast responses in rhesus macaques (n = 4). We found that prior DENV-3 infection was not associated with diminished ZIKV-neutralizing antibodies or magnitude of plasmablast activation. Rather, characterization of 363 plasmablasts and their derivative 177 monoclonal antibody supernatants from acute ZIKV infection revealed that prior DENV-3 infection was associated with a differential isotype distribution toward IgG, lower somatic hypermutation, and lesser B cell receptor variable gene diversity as compared with repeat ZIKV challenge. We did not find long-lasting DENV-3 cross-reactive IgG after a ZIKV infection but did find persistent ZIKV-binding cross-reactive IgG after a DENV-3 infection, suggesting non-reciprocal cross-reactive immunity. Infection with ZIKV after DENV-3 boosted pre-existing DENV-3-neutralizing antibodies by two- to threefold, demonstrating immune imprinting. These findings suggest that the order of DENV and ZIKV infections has impact on the quality of early B cell immunity which has implications for optimal immunization strategies. IMPORTANCE The Zika virus epidemic of 2015-2016 in the Americas revealed that this mosquito-transmitted virus could be congenitally transmitted during pregnancy and cause birth defects in newborns. Currently, there are no interventions to mitigate this disease and Zika virus is likely to re-emerge. Understanding how protective antibody responses are generated against Zika virus can help in the development of a safe and effective vaccine. One main challenge is that Zika virus co-circulates with related viruses like dengue, such that prior exposure to one can generate cross-reactive antibodies against the other which may enhance infection and disease from the second virus. In this study, we sought to understand how prior dengue virus infection impacts subsequent immunity to Zika virus by single-cell sequencing of antibody producing cells in a second Zika virus infection. Identifying specific qualities of Zika virus immunity that are modulated by prior dengue virus immunity will enable optimal immunization strategies.
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Affiliation(s)
- Tulika Singh
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | | | - Sravani Venkatayogi
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Helen Webster
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Holly J. Heimsath
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Josh A. Eudailey
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amit Kumar
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Riley J. Mangan
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Amelia Thein
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mariel S. Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Madison Berry
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Wiehe
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sallie R. Permar
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
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3
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Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. Lancet Infect Dis 2024:S1473-3099(23)00815-0. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
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Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Grunst MW, Gil HM, Grandea AG, Snow BJ, Andrabi R, Nedellec R, Burton I, Clark NM, Janaka SK, Keles NK, Moriarty RV, Weiler AM, Capuano S, Fennessey CM, Friedrich TC, O’Connor SL, O’Connor DH, Broman AT, Keele BF, Lifson JD, Hangartner L, Burton DR, Evans DT. Potent antibody-dependent cellular cytotoxicity of a V2-specific antibody is not sufficient for protection of macaques against SIV challenge. PLoS Pathog 2024; 20:e1011819. [PMID: 38252675 PMCID: PMC10833561 DOI: 10.1371/journal.ppat.1011819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/01/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Fc-mediated antibody effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), can contribute to the containment HIV-1 replication but whether such activities are sufficient for protection is unclear. We previously identified an antibody to the variable 2 (V2) apex of the HIV-1 Env trimer (PGT145) that potently directs the lysis of SIV-infected cells by NK cells but poorly neutralizes SIV infectivity. To determine if ADCC is sufficient for protection, separate groups of six rhesus macaques were treated with PGT145 or a control antibody (DEN3) by intravenous infusion followed five days later by intrarectal challenge with SIVmac239. Despite high concentrations of PGT145 and potent ADCC activity in plasma on the day of challenge, all animals became infected and viral loads did not differ between the PGT145- and DEN3-treated animals. To determine if PGT145 can protect against a neutralization-sensitive virus, two additional groups of six macaques were treated with PGT145 and DEN3 and challenged with an SIVmac239 variant with a single amino acid change in Env (K180S) that increases PGT145 binding and renders the virus susceptible to neutralization by this antibody. Although there was no difference in virus acquisition, peak and chronic phase viral loads were significantly lower and time to peak viremia was significantly delayed in the PGT145-treated animals compared to the DEN3-treated control animals. Env changes were also selected in the PGT145-treated animals that confer resistance to both neutralization and ADCC. These results show that ADCC is not sufficient for protection by this V2-specific antibody. However, protection may be achieved by increasing the affinity of antibody binding to Env above the threshold required for neutralization.
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Affiliation(s)
- Michael W. Grunst
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Hwi Min Gil
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andres G. Grandea
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian J. Snow
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Iszac Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Natasha M. Clark
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nida K. Keles
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aimee T. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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5
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Wang H, Solomon J, Reza SMS, Yang HJ, Chu WT, Crozier I, Sayre PJ, Lee BY, Mani V, Friedrich TC, O’Connor DH, Worwa G, Kuhn JH, Calcagno C, Castro MA. Repeatability of computed tomography liver radiomic features in a nonhuman primate model of diet-induced steatosis. J Med Imaging (Bellingham) 2023; 10:066004. [PMID: 38090646 PMCID: PMC10711681 DOI: 10.1117/1.jmi.10.6.066004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Purpose We describe a method to identify repeatable liver computed tomography (CT) radiomic features, suitable for detection of steatosis, in nonhuman primates. Criteria used for feature selection exclude nonrepeatable features and may be useful to improve the performance and robustness of radiomics-based predictive models. Approach Six crab-eating macaques were equally assigned to two experimental groups, fed regular chow or an atherogenic diet. High-resolution CT images were acquired over several days for each macaque. First-order and second-order radiomic features were extracted from six regions in the liver parenchyma, either with or without liver-to-spleen intensity normalization from images reconstructed using either a standard (B-filter) or a bone-enhanced (D-filter) kernel. Intrasubject repeatability of each feature was assessed using a paired t -test for all scans and the minimum p -value was identified for each macaque. Repeatable features were defined as having a minimum p -value among all macaques above the significance level after Bonferroni's correction. Features showing a significant difference with respect to diet group were identified using a two-sample t -test. Results A list of repeatable features was generated for each type of image. The largest number of repeatable features was achieved from spleen-normalized D-filtered images, which also produced the largest number of second-order radiomic features that were repeatable and different between diet groups. Conclusions Repeatability depends on reconstruction kernel and normalization. Features were quantified and ranked based on their repeatability. Features to be excluded for more robust models were identified. Features that were repeatable but different between diet groups were also identified.
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Affiliation(s)
- Hui Wang
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Jeffrey Solomon
- Frederick National Laboratory for Cancer Research, Clinical Monitoring Research Program Directorate, Frederick, Maryland, United States
| | - Syed M. S. Reza
- National Institutes of Health, Center for Infectious Disease Imaging, Radiology and Imaging Sciences, Clinical Center, Bethesda, Maryland, United States
| | - Hee-Jeong Yang
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Winston T. Chu
- National Institutes of Health, Center for Infectious Disease Imaging, Radiology and Imaging Sciences, Clinical Center, Bethesda, Maryland, United States
| | - Ian Crozier
- Frederick National Laboratory for Cancer Research, Clinical Monitoring Research Program Directorate, Frederick, Maryland, United States
| | - Philip J. Sayre
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Byeong Y. Lee
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Venkatesh Mani
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Thomas C. Friedrich
- University of Wisconsin–Madison, Department of Pathobiological Sciences, School of Veterinary Medicine, Madison, Wisconsin, United States
| | - David H. O’Connor
- University of Wisconsin–Madison, Department of Pathology and Laboratory Medicine, Madison, Wisconsin, United States
| | - Gabriella Worwa
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Jens H. Kuhn
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Claudia Calcagno
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
| | - Marcelo A. Castro
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Fort Detrick, Frederick, Maryland, United States
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6
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Jaeger AS, Marano J, Riemersma KK, Castaneda D, Pritchard EM, Pritchard JC, Bohm EK, Baczenas JJ, O'Connor SL, Weger-Lucarelli J, Friedrich TC, Aliota MT. Gain without pain: adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector. J Virol 2023; 97:e0116223. [PMID: 37800949 PMCID: PMC10653995 DOI: 10.1128/jvi.01162-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
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Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kasen K. Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David Castaneda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Elise M. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
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7
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Boehm EC, Jaeger AS, Ries HJ, Castañeda D, Weiler AM, Valencia CC, Weger-Lucarelli J, Ebel GD, O’Connor SL, Friedrich TC, Zamanian M, Aliota MT. Wolbachia-mediated resistance to Zika virus infection in Aedes aegypti is dominated by diverse transcriptional regulation and weak evolutionary pressures. PLoS Negl Trop Dis 2023; 17:e0011674. [PMID: 37782672 PMCID: PMC10569609 DOI: 10.1371/journal.pntd.0011674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/12/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023] Open
Abstract
A promising candidate for arbovirus control and prevention relies on replacing arbovirus-susceptible Aedes aegypti populations with mosquitoes that have been colonized by the intracellular bacterium Wolbachia and thus have a reduced capacity to transmit arboviruses. This reduced capacity to transmit arboviruses is mediated through a phenomenon referred to as pathogen blocking. Pathogen blocking has primarily been proposed as a tool to control dengue virus (DENV) transmission, however it works against a range of viruses, including Zika virus (ZIKV). Despite years of research, the molecular mechanisms underlying pathogen blocking still need to be better understood. Here, we used RNA-seq to characterize mosquito gene transcription dynamics in Ae. aegypti infected with the wMel strain of Wolbachia that are being released by the World Mosquito Program in Medellín, Colombia. Comparative analyses using ZIKV-infected, uninfected tissues, and mosquitoes without Wolbachia revealed that the influence of wMel on mosquito gene transcription is multifactorial. Importantly, because Wolbachia limits, but does not completely prevent, replication of ZIKV and other viruses in coinfected mosquitoes, there is a possibility that these viruses could evolve resistance to pathogen blocking. Therefore, to understand the influence of Wolbachia on within-host ZIKV evolution, we characterized the genetic diversity of molecularly barcoded ZIKV virus populations replicating in Wolbachia-infected mosquitoes and found that within-host ZIKV evolution was subject to weak purifying selection and, unexpectedly, loose anatomical bottlenecks in the presence and absence of Wolbachia. Together, these findings suggest that there is no clear transcriptional profile associated with Wolbachia-mediated ZIKV restriction, and that there is no evidence for ZIKV escape from this restriction in our system.
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Affiliation(s)
- Emma C. Boehm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Hunter J. Ries
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - David Castañeda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Corina C. Valencia
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - James Weger-Lucarelli
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Gregory D. Ebel
- Colorado State University, Fort Collins, Colorado, United States of America
| | - Shelby L. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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8
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Krabbe NP, Razo E, Abraham HJ, Spanton RV, Shi Y, Bhattacharya S, Bohm EK, Pritchard JC, Weiler AM, Mitzey AM, Eickhoff JC, Sullivan E, Tan JC, Aliota MT, Friedrich TC, O’Connor DH, Golos TG, Mohr EL. Control of maternal Zika virus infection during pregnancy is associated with lower antibody titers in a macaque model. Front Immunol 2023; 14:1267638. [PMID: 37809089 PMCID: PMC10556460 DOI: 10.3389/fimmu.2023.1267638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Zika virus (ZIKV) infection during pregnancy results in a spectrum of birth defects and neurodevelopmental deficits in prenatally exposed infants, with no clear understanding of why some pregnancies are more severely affected. Differential control of maternal ZIKV infection may explain the spectrum of adverse outcomes. Methods Here, we investigated whether the magnitude and breadth of the maternal ZIKV-specific antibody response is associated with better virologic control using a rhesus macaque model of prenatal ZIKV infection. We inoculated 18 dams with an Asian-lineage ZIKV isolate (PRVABC59) at 30-45 gestational days. Plasma vRNA and infectious virus kinetics were determined over the course of pregnancy, as well as vRNA burden in the maternal-fetal interface (MFI) at delivery. Binding and neutralizing antibody assays were performed to determine the magnitude of the ZIKV-specific IgM and IgG antibody responses throughout pregnancy, along with peptide microarray assays to define the breadth of linear ZIKV epitopes recognized. Results Dams with better virologic control (n= 9) cleared detectable infectious virus and vRNA from the plasma by 7 days post-infection (DPI) and had a lower vRNA burden in the MFI at delivery. In comparison, dams with worse virologic control (n= 9) still cleared detectable infectious virus from the plasma by 7 DPI but had vRNA that persisted longer, and had higher vRNA burden in the MFI at delivery. The magnitudes of the ZIKV-specific antibody responses were significantly lower in the dams with better virologic control, suggesting that higher antibody titers are not associated with better control of ZIKV infection. Additionally, the breadth of the ZIKV linear epitopes recognized did not differ between the dams with better and worse control of ZIKV infection. Discussion Thus, the magnitude and breadth of the maternal antibody responses do not seem to impact maternal virologic control. This may be because control of maternal infection is determined in the first 7 DPI, when detectable infectious virus is present and before robust antibody responses are generated. However, the presence of higher ZIKV-specific antibody titers in dams with worse virologic control suggests that these could be used as a biomarker of poor maternal control of infection and should be explored further.
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Affiliation(s)
- Nicholas P. Krabbe
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Elaina Razo
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Hunter J. Abraham
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Rachel V. Spanton
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Yujia Shi
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Saswati Bhattacharya
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Ann M. Mitzey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Jens C. Eickhoff
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Healthy, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric Sullivan
- Nimble Therapeutics, Inc, Madison, WI, United States
| | - John C. Tan
- Nimble Therapeutics, Inc, Madison, WI, United States
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Emma L. Mohr
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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9
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O’Connor DH, Lang JD, Reynolds MR, O’Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV replication in M3+ Mauritian cynomolgus macaques initiated on ART two weeks post-infection. PLoS Pathog 2023; 19:e1011676. [PMID: 37747933 PMCID: PMC10553806 DOI: 10.1371/journal.ppat.1011676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/05/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). None of the MCMs possessed MHC haplotypes previously associated with SIV control. For six months after ART withdrawal, we observed undetectable or transient viremia in seven of the eight MCMs, despite detecting replication competent SIV using quantitative viral outgrowth assays. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the observed PTC was mediated, at least in part, by CD8α+ cells. With intact proviral DNA assays, we found that MCMs had significantly smaller viral reservoirs two wpi than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. We found a similarly small viral reservoir among six additional SIV+ MCMs in which ART was initiated at eight wpi, some of whom exhibited viral rebound. These results suggest that an unusually small viral reservoir is a hallmark among SIV+ MCMs. By evaluating immunological differences between MCMs that did and did not rebound, we identified that PTC was associated with a reduced frequency of CD4+ and CD8+ lymphocyte subsets expressing exhaustion markers. Together, these results suggest a combination of small reservoirs and immune-mediated virus suppression contribute to PTC in MCMs. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E. Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lea M. Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexis J. Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Abigail J. Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amy L. Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Lee C. Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Courtney V. Fletcher
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Jessica D. Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew R. Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
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10
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Koenig MR, Mitzey AM, Zeng X, Reyes L, Simmons HA, Morgan TK, Bohm EK, Pritchard JC, Schmidt JA, Ren E, Leyva Jaimes FB, Winston E, Basu P, Weiler AM, Friedrich TC, Aliota MT, Mohr EL, Golos TG. Vertical transmission of African-lineage Zika virus through the fetal membranes in a rhesus macaque (Macaca mulatta) model. PLoS Pathog 2023; 19:e1011274. [PMID: 37549143 PMCID: PMC10434957 DOI: 10.1371/journal.ppat.1011274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/17/2023] [Accepted: 07/14/2023] [Indexed: 08/09/2023] Open
Abstract
Zika virus (ZIKV) can be transmitted vertically from mother to fetus during pregnancy, resulting in a range of outcomes including severe birth defects and fetal/infant death. Potential pathways of vertical transmission in utero have been proposed but remain undefined. Identifying the timing and routes of vertical transmission of ZIKV may help us identify when interventions would be most effective. Furthermore, understanding what barriers ZIKV overcomes to effect vertical transmission may help improve models for evaluating infection by other pathogens during pregnancy. To determine the pathways of vertical transmission, we inoculated 12 pregnant rhesus macaques with an African-lineage ZIKV at gestational day 30 (term is 165 days). Eight pregnancies were surgically terminated at either seven or 14 days post-maternal infection. Maternal-fetal interface and fetal tissues and fluids were collected and evaluated for ZIKV using RT-qPCR, in situ hybridization, immunohistochemistry, and plaque assays. Four additional pregnant macaques were inoculated and terminally perfused with 4% paraformaldehyde at three, six, nine, or ten days post-maternal inoculation. For these four cases, the entire fixed pregnant uterus was evaluated with in situ hybridization for ZIKV RNA. We determined that ZIKV can reach the MFI by six days after infection and infect the fetus by ten days. Infection of the chorionic membrane and the extraembryonic coelomic fluid preceded infection of the fetus and the mesenchymal tissue of the placental villi. We did not find evidence to support a transplacental route of ZIKV vertical transmission via infection of syncytiotrophoblasts or villous cytotrophoblasts. The pattern of infection observed in the maternal-fetal interface provides evidence of paraplacental vertical ZIKV transmission through the chorionic membrane, the outer layer of the fetal membranes.
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Affiliation(s)
- Michelle R. Koenig
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ann M. Mitzey
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Leticia Reyes
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Terry K. Morgan
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Jenna A. Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emily Ren
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Fernanda B. Leyva Jaimes
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eva Winston
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Puja Basu
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thaddeus G. Golos
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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11
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Jaeger AS, Crooks CM, Weiler AM, Bliss MI, Rybarczyk S, Richardson A, Einwalter M, Peterson E, Capuano S, Barkhymer A, Becker JT, Greene JT, Freedman TS, Langlois RA, Friedrich TC, Aliota MT. Primary infection with Zika virus provides one-way heterologous protection against Spondweni virus infection in rhesus macaques. Sci Adv 2023; 9:eadg3444. [PMID: 37390207 PMCID: PMC10313173 DOI: 10.1126/sciadv.adg3444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/30/2023] [Indexed: 07/02/2023]
Abstract
Spondweni virus (SPONV) is the closest known relative of Zika virus (ZIKV). SPONV pathogenesis resembles that of ZIKV in pregnant mice, and both viruses are transmitted by Aedes aegypti mosquitoes. We aimed to develop a translational model to further understand SPONV transmission and pathogenesis. We found that cynomolgus macaques (Macaca fascicularis) inoculated with ZIKV or SPONV were susceptible to ZIKV but resistant to SPONV infection. In contrast, rhesus macaques (Macaca mulatta) supported productive infection with both ZIKV and SPONV and developed robust neutralizing antibody responses. Crossover serial challenge in rhesus macaques revealed that SPONV immunity did not protect against ZIKV infection, whereas ZIKV immunity was fully protective against SPONV infection. These findings establish a viable model for future investigation into SPONV pathogenesis and suggest that the risk of SPONV emergence is low in areas with high ZIKV seroprevalence due to one-way cross-protection between ZIKV and SPONV.
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Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Saint Paul, Minnesota, USA
| | - Chelsea M. Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mason I. Bliss
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sierra Rybarczyk
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alex Richardson
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Morgan Einwalter
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric Peterson
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alison Barkhymer
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Jordan T. Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Joseph T. Greene
- Department of Pharmacology, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Tanya S. Freedman
- Department of Pharmacology, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
- Center for Immunology, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Saint Paul, Minnesota, USA
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12
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Boehm EC, Jaeger AS, Ries HJ, Castañeda D, Weiler AM, Valencia CC, Weger-Lucarelli J, Ebel GD, O’Connor SL, Friedrich TC, Zamanian M, Aliota MT. Wolbachia -mediated resistance to Zika virus infection in Aedes aegypti is dominated by diverse transcriptional regulation and weak evolutionary pressures. bioRxiv 2023:2023.06.26.546271. [PMID: 37425681 PMCID: PMC10327090 DOI: 10.1101/2023.06.26.546271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
A promising candidate for arbovirus control and prevention relies on replacing arbovirus-susceptible Aedes aegypti populations with mosquitoes that have been colonized by the intracellular bacterium Wolbachia and thus have a reduced capacity to transmit arboviruses. This reduced capacity to transmit arboviruses is mediated through a phenomenon referred to as pathogen blocking. Pathogen blocking has primarily been proposed as a tool to control dengue virus (DENV) transmission, however it works against a range of viruses, including Zika virus (ZIKV). Despite years of research, the molecular mechanisms underlying pathogen blocking still need to be better understood. Here, we used RNA-seq to characterize mosquito gene transcription dynamics in Ae. aegypti infected with the w Mel strain of Wolbachia that are being released by the World Mosquito Program in Medellín, Colombia. Comparative analyses using ZIKV-infected, uninfected tissues, and mosquitoes without Wolbachia revealed that the influence of w Mel on mosquito gene transcription is multifactorial. Importantly, because Wolbachia limits, but does not completely prevent, replication of ZIKV and other viruses in coinfected mosquitoes, there is a possibility that these viruses could evolve resistance to pathogen blocking. Therefore, to understand the influence of Wolbachia on within-host ZIKV evolution, we characterized the genetic diversity of molecularly barcoded ZIKV virus populations replicating in Wolbachia -infected mosquitoes and found that within-host ZIKV evolution was subject to weak purifying selection and, unexpectedly, loose anatomical bottlenecks in the presence and absence of Wolbachia . Together, these findings suggest that there is no clear transcriptional profile associated with Wolbachia -mediated ZIKV restriction, and that there is no evidence for ZIKV escape from this restriction in our system. Author Summary When Wolbachia bacteria infect Aedes aegypti mosquitoes, they dramatically reduce the mosquitoes' susceptibility to infection with a range of arthropod-borne viruses, including Zika virus (ZIKV). Although this pathogen-blocking effect has been widely recognized, its mechanisms remain unclear. Furthermore, because Wolbachia limits, but does not completely prevent, replication of ZIKV and other viruses in coinfected mosquitoes, there is a possibility that these viruses could evolve resistance to Wolbachia -mediated blocking. Here, we use host transcriptomics and viral genome sequencing to examine the mechanisms of ZIKV pathogen blocking by Wolbachia and viral evolutionary dynamics in Ae. aegypti mosquitoes. We find complex transcriptome patterns that do not suggest a single clear mechanism for pathogen blocking. We also find no evidence that Wolbachia exerts detectable selective pressures on ZIKV in coinfected mosquitoes. Together our data suggest that it may be difficult for ZIKV to evolve Wolbachia resistance, perhaps due to the complexity of the pathogen blockade mechanism.
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Affiliation(s)
- Emma C. Boehm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Hunter J. Ries
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - David Castañeda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Corina C. Valencia
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | | | | | - Shelby L. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, United States
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
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13
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Koenig MR, Mitzey AM, Morgan TK, Zeng X, Simmons HA, Mejia A, Leyva Jaimes F, Keding LT, Crooks CM, Weiler AM, Bohm EK, Aliota MT, Friedrich TC, Mohr EL, Golos TG. Infection of the maternal-fetal interface and vertical transmission following low-dose inoculation of pregnant rhesus macaques (Macaca mulatta) with an African-lineage Zika virus. PLoS One 2023; 18:e0284964. [PMID: 37141276 PMCID: PMC10159132 DOI: 10.1371/journal.pone.0284964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/13/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Congenital Zika virus (ZIKV) infection can result in birth defects, including malformations in the fetal brain and visual system. There are two distinct genetic lineages of ZIKV: African and Asian. Asian-lineage ZIKVs have been associated with adverse pregnancy outcomes in humans; however, recent evidence from experimental models suggests that African-lineage viruses can also be vertically transmitted and cause fetal harm. METHODOLOGY/PRINCIPAL FINDINGS To evaluate the pathway of vertical transmission of African-lineage ZIKV, we inoculated nine pregnant rhesus macaques (Macaca mulatta) subcutaneously with 44 plaque-forming units of a ZIKV strain from Senegal, (ZIKV-DAK). Dams were inoculated either at gestational day 30 or 45. Following maternal inoculation, pregnancies were surgically terminated seven or 14 days later and fetal and maternal-fetal interface tissues were collected and evaluated. Infection in the dams was evaluated via plasma viremia and neutralizing antibody titers pre- and post- ZIKV inoculation. All dams became productively infected and developed strong neutralizing antibody responses. ZIKV RNA was detected in maternal-fetal interface tissues (placenta, decidua, and fetal membranes) by RT-qPCR and in situ hybridization. In situ hybridization detected ZIKV predominantly in the decidua and revealed that the fetal membranes may play a role in ZIKV vertical transmission. Infectious ZIKV was detected in the amniotic fluid of three pregnancies and one fetus had ZIKV RNA detected in multiple tissues. No significant pathology was observed in any fetus; and ZIKV did not have a substantial effect on the placenta. CONCLUSIONS/SIGNIFICANCE This study demonstrates that a very low dose of African-lineage ZIKV can be vertically transmitted to the macaque fetus during pregnancy. The low inoculating dose used in this study suggests a low minimal infectious dose for rhesus macaques. Vertical transmission with a low dose in macaques further supports the high epidemic potential of African ZIKV strains.
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Affiliation(s)
- Michelle R. Koenig
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ann M. Mitzey
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Terry K. Morgan
- Department of Pathology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Fernanda Leyva Jaimes
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Logan T. Keding
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chelsea M. Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thaddeus G. Golos
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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14
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Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Wilson N, Bobholz M, Vuyk WC, Wei W, Ries H, O'Connor DH, Friedrich TC, Sordillo EM, van Bakel H, Simon V, Kawaoka Y. Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2. J Med Virol 2023; 95:e28788. [PMID: 37212288 DOI: 10.1002/jmv.28788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 05/23/2023]
Abstract
Diagnosis by rapid antigen tests (RATs) is useful for early initiation of antiviral treatment. Because RATs are easy to use, they can be adapted for self-testing. Several kinds of RATs approved for such use by the Japanese regulatory authority are available from drug stores and websites. Most RATs for COVID-19 are based on antibody detection of the SARS-CoV-2 N protein. Since Omicron and its subvariants have accumulated several amino acid substitutions in the N protein, such amino acid changes might affect the sensitivity of RATs. Here, we investigated the sensitivity of seven RATs available in Japan, six of which are approved for public use and one of which is approved for clinical use, for the detection of BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1, as well as the delta variant (B.1.627.2). All tested RATs detected the delta variant with a detection level between 7500 and 75 000 pfu per test, and all tested RATs showed similar sensitivity to the Omicron variant and its subvariants (BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1). Human saliva did not reduce the sensitivity of the RATs tested. Espline SARS-CoV-2 N showed the highest sensitivity followed by Inspecter KOWA SARS-CoV-2 and V Trust SARS-CoV-2 Ag. Since the RATs failed to detect low levels of infectious virus, individuals whose specimens contained less infectious virus than the detection limit would be considered negative. Therefore, it is important to note that RATs may miss individuals shedding low levels of infectious virus.
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Affiliation(s)
- Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hunter Ries
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Infection and Advanced Research Center, The University of Tokyo Pandemic Preparedness, Tokyo, Japan
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15
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Jaeger AS, Marano J, Riemersma K, Castañeda D, Pritchard E, Pritchard J, Bohm EK, Baczenas JJ, O’Connor SL, Weger-Lucarelli J, Friedrich TC, Aliota MT. Gain without pain: Adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector. bioRxiv 2023:2023.03.20.533515. [PMID: 36993525 PMCID: PMC10055270 DOI: 10.1101/2023.03.20.533515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses also have enhanced transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased neurotropism and distinct innate immune signaling patterns in the brain. None of the substitutions contributed to changes in transmission potential in mosquitoes. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex.
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Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University
| | - Kasen Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison
| | - David Castañeda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Elise Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Julia Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
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16
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O'Connor DH, Lang JD, Reynolds MR, O'Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV in Mauritian cynomolgus macaques. bioRxiv 2023:2023.03.01.530655. [PMID: 36909458 PMCID: PMC10002716 DOI: 10.1101/2023.03.01.530655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). For six months after ART withdrawal, we observed undetectable or transient viremia in seven of eight MCMs. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the PTC was mediated, at least in part, by CD8α+ cells. We found that MCMs had smaller acute viral reservoirs than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. The mechanisms by which unusually small viral reservoirs and CD8α+ cell-mediated virus suppression enable PTC can be investigated using this MHC-haplomatched MCM model. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Lea M Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
| | - Ryan V Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Alexis J Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Abigail J Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Amy L Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Lee C Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | | | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Jessica D Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Matthew R Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
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17
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Rosinski JR, Raasch LE, Barros Tiburcio P, Breitbach ME, Shepherd PM, Yamamoto K, Razo E, Krabbe NP, Bliss MI, Richardson AD, Einwalter MA, Weiler AM, Sneed EL, Fuchs KB, Zeng X, Noguchi KK, Morgan TK, Alberts AJ, Antony KM, Kabakov S, Ausderau KK, Bohm EK, Pritchard JC, Spanton RV, Ver Hoove JN, Kim CBY, Nork TM, Katz AW, Rasmussen CA, Hartman A, Mejia A, Basu P, Simmons HA, Eickhoff JC, Friedrich TC, Aliota MT, Mohr EL, Dudley DM, O’Connor DH, Newman CM. Frequent first-trimester pregnancy loss in rhesus macaques infected with African-lineage Zika virus. PLoS Pathog 2023; 19:e1011282. [PMID: 36976812 PMCID: PMC10081769 DOI: 10.1371/journal.ppat.1011282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/07/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
In the 2016 Zika virus (ZIKV) pandemic, a previously unrecognized risk of birth defects surfaced in babies whose mothers were infected with Asian-lineage ZIKV during pregnancy. Less is known about the impacts of gestational African-lineage ZIKV infections. Given high human immunodeficiency virus (HIV) burdens in regions where African-lineage ZIKV circulates, we evaluated whether pregnant rhesus macaques infected with simian immunodeficiency virus (SIV) have a higher risk of African-lineage ZIKV-associated birth defects. Remarkably, in both SIV+ and SIV- animals, ZIKV infection early in the first trimester caused a high incidence (78%) of spontaneous pregnancy loss within 20 days. These findings suggest a significant risk for early pregnancy loss associated with African-lineage ZIKV infection and provide the first consistent ZIKV-associated phenotype in macaques for testing medical countermeasures.
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Affiliation(s)
- Jenna R. Rosinski
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Lauren E. Raasch
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Patrick Barros Tiburcio
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Phoenix M. Shepherd
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Keisuke Yamamoto
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Elaina Razo
- Department of Pediatrics, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Nicholas P. Krabbe
- Department of Pediatrics, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Mason I. Bliss
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Alexander D. Richardson
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Morgan A. Einwalter
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Emily L. Sneed
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Kerri B. Fuchs
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases; Fort Detrick, Maryland, Unites States of America
| | - Kevin K. Noguchi
- Department of Psychiatry, Washington University School of Medicine; St. Louis, Washington, Unites States of America
| | - Terry K. Morgan
- Department of Pathology, Oregon Health and Science University; Portland, Oregon, Unites States of America
- Department of Obstetrics and Gynecology, Oregon Health and Science University; Portland, Oregon, Unites States of America
| | - Alexandra J. Alberts
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Kathleen M. Antony
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Sabrina Kabakov
- Department of Kinesiology, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Karla K. Ausderau
- Department of Kinesiology, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
- Waisman Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Science, University of Minnesota; St. Paul, Minnesota, Unites States of America
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Science, University of Minnesota; St. Paul, Minnesota, Unites States of America
| | - Rachel V. Spanton
- Department of Kinesiology, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - James N. Ver Hoove
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Charlene B. Y. Kim
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - T. Michael Nork
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Alex W. Katz
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Carol A. Rasmussen
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Amy Hartman
- Department of Communication Sciences and Disorders, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Puja Basu
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Jens C. Eickhoff
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Science, University of Minnesota; St. Paul, Minnesota, Unites States of America
| | - Emma L. Mohr
- Department of Pediatrics, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, Wisconsin, Unites States of America
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18
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Braun KM, Haddock III LA, Crooks CM, Barry GL, Lalli J, Neumann G, Watanabe T, Imai M, Yamayoshi S, Ito M, Moncla LH, Koelle K, Kawaoka Y, Friedrich TC. Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals. Virus Evol 2023; 9:vead004. [PMID: 36814938 PMCID: PMC9939568 DOI: 10.1093/ve/vead004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
H7N9 avian influenza viruses (AIVs) have caused over 1,500 documented human infections since emerging in 2013. Although wild-type H7N9 AIVs can be transmitted by respiratory droplets in ferrets, they have not yet caused widespread outbreaks in humans. Previous studies have revealed molecular determinants of H7N9 AIV host switching, but little is known about potential evolutionary constraints on this process. Here, we compare patterns of sequence evolution for H7N9 AIV and mammalian H1N1 viruses during replication and transmission in ferrets. We show that three main factors-purifying selection, stochasticity, and very narrow transmission bottlenecks-combine to severely constrain the ability of H7N9 AIV to effectively adapt to mammalian hosts in isolated, acute spillover events. We find rare evidence of natural selection favoring new, potentially mammal-adapting mutations within ferrets but no evidence of natural selection acting during transmission. We conclude that human-adapted H7N9 viruses are unlikely to emerge during typical spillover infections. Our findings are instead consistent with a model in which the emergence of a human-transmissible virus would be a rare and unpredictable, though highly consequential, 'jackpot' event. Strategies to control the total number of spillover infections will limit opportunities for the virus to win this evolutionary lottery.
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Affiliation(s)
| | | | - Chelsea M Crooks
- AIDS Vaccine Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 585 Science Dr. Madison, WI 53711, USA
| | - Gabrielle L Barry
- AIDS Vaccine Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 585 Science Dr. Madison, WI 53711, USA
| | - Joseph Lalli
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall Madison, WI 53706, US
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 575 Science Dr. Madison, WI 53711, USA
| | - Tokiko Watanabe
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka Suita City, Osaka 565-0871, Japan,Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-8 Yamadaoka Suita City, Osaka 565-0871, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1 Chome-21-1 Toyama Shinjuku City, Tokyo 162-8655, Japan
| | | | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan
| | | | | | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 575 Science Dr. Madison, WI 53711, USA,Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1 Chome-21-1 Toyama Shinjuku City, Tokyo 162-8655, Japan
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19
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Takashita E, Yamayoshi S, Halfmann P, Wilson N, Ries H, Richardson A, Bobholz M, Vuyk W, Maddox R, Baker DA, Friedrich TC, O'Connor DH, Uraki R, Ito M, Sakai-Tagawa Y, Adachi E, Saito M, Koga M, Tsutsumi T, Iwatsuki-Horimoto K, Kiso M, Yotsuyanagi H, Watanabe S, Hasegawa H, Imai M, Kawaoka Y. In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6. N Engl J Med 2022; 387:2094-2097. [PMID: 36383452 PMCID: PMC9730936 DOI: 10.1056/nejmc2211845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | - Hunter Ries
- University of Wisconsin-Madison, Madison, WI
| | | | - Max Bobholz
- University of Wisconsin-Madison, Madison, WI
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20
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Amjadi MF, Adyniec RR, Gupta S, Bashar SJ, Mergaert AM, Braun KM, Moreno GK, O’Connor DH, Friedrich TC, Safdar N, McCoy SS, Shelef MA. Anti-membrane Antibodies Persist at Least One Year and Discriminate Between Past Coronavirus Disease 2019 Infection and Vaccination. J Infect Dis 2022; 226:1897-1902. [PMID: 35758987 PMCID: PMC9278254 DOI: 10.1093/infdis/jiac263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The consequences of past coronavirus disease 2019 (COVID-19) infection for personal and population health are emerging, but accurately identifying distant infection is a challenge. Anti-spike antibodies rise after both vaccination and infection and anti-nucleocapsid antibodies rapidly decline. METHODS We evaluated anti-membrane antibodies in COVID-19 naive, vaccinated, and convalescent subjects to determine if they persist and accurately detect distant infection. RESULTS We found that anti-membrane antibodies persist for at least 1 year and are a sensitive and specific marker of past COVID-19 infection. CONCLUSIONS Thus, anti-membrane and anti-spike antibodies together can differentiate between COVID-19 convalescent, vaccinated, and naive states to advance public health and research.
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Affiliation(s)
- Maya F Amjadi
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - Ryan R Adyniec
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - Srishti Gupta
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - S Janna Bashar
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - Aisha M Mergaert
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
- Department of Pathology and Laboratory Medicine, UW-Madison, Madison, 53705USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, UW-Madison, Madison, 53705USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, UW-Madison, Madison, 53705USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, UW-Madison, Madison, 53705USA
| | | | - Nasia Safdar
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - Sara S McCoy
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin (UW)-Madison, Madison, 53705USA
- William S. Middleton Memorial Veterans Hospital, Madison, 53705USA
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21
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Halfmann PJ, Minor NR, Haddock III LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O’Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol 2022; 9:veac104. [PMID: 37692895 PMCID: PMC10491860 DOI: 10.1093/ve/veac104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 09/12/2023] Open
Abstract
Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Luis A Haddock III
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Robert Maddox
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kasen K Riemersa
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Ankur Prasad
- Division of Allergy, Pulmonary and Critical Care Medicine, School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705-2281, USA
| | - Kirsten J Alman
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Matthew C Lambert
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Ryan Westergaard
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Nasia Safdar
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - David R Andes
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Madiha Fida
- Division of Infectious Diseases, Mayo Clinic, 200 First St. SW, Rochester, Rochester, Minnesota 55905, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
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22
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Castro MA, Reza S, Chu WT, Bradley D, Lee JH, Crozier I, Sayre PJ, Lee BY, Mani V, Friedrich TC, O’Connor DH, Finch CL, Worwa G, Feuerstein IM, Kuhn JH, Solomon J. Toward the determination of sensitive and reliable whole-lung computed tomography features for robust standard radiomics and delta-radiomics analysis in a nonhuman primate model of coronavirus disease 2019. J Med Imaging (Bellingham) 2022; 9:066003. [PMID: 36506838 PMCID: PMC9731356 DOI: 10.1117/1.jmi.9.6.066003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose We propose a method to identify sensitive and reliable whole-lung radiomic features from computed tomography (CT) images in a nonhuman primate model of coronavirus disease 2019 (COVID-19). Criteria used for feature selection in this method may improve the performance and robustness of predictive models. Approach Fourteen crab-eating macaques were assigned to two experimental groups and exposed to either severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or a mock inoculum. High-resolution CT scans were acquired before exposure and on several post-exposure days. Lung volumes were segmented using a deep-learning methodology, and radiomic features were extracted from the original image. The reliability of each feature was assessed by the intraclass correlation coefficient (ICC) using the mock-exposed group data. The sensitivity of each feature was assessed using the virus-exposed group data by defining a factor R that estimates the excess of variation above the maximum normal variation computed in the mock-exposed group. R and ICC were used to rank features and identify non-sensitive and unstable features. Results Out of 111 radiomic features, 43% had excellent reliability ( ICC > 0.90 ), and 55% had either good ( ICC > 0.75 ) or moderate ( ICC > 0.50 ) reliability. Nineteen features were not sensitive to the radiological manifestations of SARS-CoV-2 exposure. The sensitivity of features showed patterns that suggested a correlation with the radiological manifestations. Conclusions Features were quantified and ranked based on their sensitivity and reliability. Features to be excluded to create more robust models were identified. Applicability to similar viral pneumonia studies is also possible.
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Affiliation(s)
- Marcelo A. Castro
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States,Address all correspondence to Marcelo A. Castro,
| | - Syed Reza
- National Institutes of Health, Clinical Center, Radiology and Imaging Sciences, Center for Infectious Disease Imaging, Bethesda, Maryland, United States
| | - Winston T. Chu
- National Institutes of Health, Clinical Center, Radiology and Imaging Sciences, Center for Infectious Disease Imaging, Bethesda, Maryland, United States
| | - Dara Bradley
- National Institutes of Health, Clinical Center, Radiology and Imaging Sciences, Center for Infectious Disease Imaging, Bethesda, Maryland, United States
| | - Ji Hyun Lee
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Ian Crozier
- Frederick National Laboratory for Cancer Research, Clinical Monitoring Research Program Directorate, Frederick, Maryland, United States
| | - Philip J. Sayre
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Byeong Y. Lee
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Venkatesh Mani
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Thomas C. Friedrich
- University of Wisconsin–Madison, School of Veterinary Medicine, Department of Pathobiological Sciences, Madison, Wisconsin, United States
| | - David H. O’Connor
- University of Wisconsin–Madison, Department of Pathology and Laboratory Medicine, Madison, Wisconsin, United States
| | - Courtney L. Finch
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Gabriella Worwa
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Irwin M. Feuerstein
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Jens H. Kuhn
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, Maryland, United States
| | - Jeffrey Solomon
- Frederick National Laboratory for Cancer Research, Clinical Monitoring Research Program Directorate, Frederick, Maryland, United States
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23
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Halfmann PJ, Kuroda M, Armbrust T, Theiler J, Balaram A, Moreno GK, Accola MA, Iwatsuki-Horimoto K, Valdez R, Stoneman E, Braun K, Yamayoshi S, Somsen E, Baczenas JJ, Mitamura K, Hagihara M, Adachi E, Koga M, McLaughlin M, Rehrauer W, Imai M, Yamamoto S, Tsutsumi T, Saito M, Friedrich TC, O’Connor SL, O’Connor DH, Gordon A, Korber B, Kawaoka Y. Characterization of the SARS-CoV-2 B.1.621 (Mu) variant. Sci Transl Med 2022; 14:eabm4908. [PMID: 35579540 PMCID: PMC9392899 DOI: 10.1126/scitranslmed.abm4908] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 B.1.621 (Mu) variant emerged in January 2021 and was categorized as a variant of interest by the World Health Organization in August 2021. This designation prompted us to study the sensitivity of this variant to antibody neutralization. In a live virus neutralization assay with serum samples from individuals vaccinated with the Pfizer/BioNTech or Moderna mRNA vaccines, we measured neutralization antibody titers against B.1.621, an early isolate (spike 614D), and a variant of concern (B.1.351, Beta variant). We observed reduced neutralizing antibody titers against the B.1.621 variant (3.4- to 7-fold reduction, depending on the serum sample and time after the second vaccination) compared to the early isolate and a similar reduction when compared to B.1.351. Likewise, convalescent serum from hamsters previously infected with an early isolate neutralized B.1.621 to a lower degree. Despite this antibody titer reduction, hamsters could not be efficiently rechallenged with the B.1.621 variant, suggesting that the immune response to the first infection is adequate to provide protection against a subsequent infection with the B.1.621 variant.
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Affiliation(s)
- Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Corresponding authors: (Y.K.); (P.H.)
| | - Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Tammy Armbrust
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - James Theiler
- Los Alamos National Laboratory, Space Data Science and Systems, Los Alamos, NM 87545
| | - Ariane Balaram
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - Molly A. Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Emily Stoneman
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109
| | - Katarina Braun
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Elizabeth Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, 110-8645, Tokyo, Japan
| | - Masao Hagihara
- Department of Hematology, Eiju General Hospital, 110-8645, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Matthew McLaughlin
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - William Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Masaki Imai
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Shinya Yamamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM 87545.,The New Mexico Consortium, Los Alamos, NM 87545
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan.,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.,Corresponding authors: (Y.K.); (P.H.)
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24
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Raasch LE, Yamamoto K, Newman CM, Rosinski JR, Shepherd PM, Razo E, Crooks CM, Bliss MI, Breitbach ME, Sneed EL, Weiler AM, Zeng X, Noguchi KK, Morgan TK, Fuhler NA, Bohm EK, Alberts AJ, Havlicek SJ, Kabakov S, Mitzey AM, Antony KM, Ausderau KK, Mejia A, Basu P, Simmons HA, Eickhoff JC, Aliota MT, Mohr EL, Friedrich TC, Golos TG, O’Connor DH, Dudley DM. Fetal loss in pregnant rhesus macaques infected with high-dose African-lineage Zika virus. PLoS Negl Trop Dis 2022; 16:e0010623. [PMID: 35926066 PMCID: PMC9380952 DOI: 10.1371/journal.pntd.0010623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/16/2022] [Accepted: 06/29/2022] [Indexed: 11/29/2022] Open
Abstract
Countermeasures against Zika virus (ZIKV), including vaccines, are frequently tested in nonhuman primates (NHP). Macaque models are important for understanding how ZIKV infections impact human pregnancy due to similarities in placental development. The lack of consistent adverse pregnancy outcomes in ZIKV-affected pregnancies poses a challenge in macaque studies where group sizes are often small (4-8 animals). Studies in small animal models suggest that African-lineage Zika viruses can cause more frequent and severe fetal outcomes. No adverse outcomes were observed in macaques exposed to 1x104 PFU (low dose) of African-lineage ZIKV at gestational day (GD) 45. Here, we exposed eight pregnant rhesus macaques to 1x108 PFU (high dose) of African-lineage ZIKV at GD 45 to test the hypothesis that adverse pregnancy outcomes are dose-dependent. Three of eight pregnancies ended prematurely with fetal death. ZIKV was detected in both fetal and placental tissues from all cases of early fetal loss. Further refinements of this exposure system (e.g., varying the dose and timing of infection) could lead to an even more consistent, unambiguous fetal loss phenotype for assessing ZIKV countermeasures in pregnancy. These data demonstrate that high-dose exposure to African-lineage ZIKV causes pregnancy loss in macaques and also suggest that ZIKV-induced first trimester pregnancy loss could be strain-specific.
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Affiliation(s)
- Lauren E. Raasch
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Keisuke Yamamoto
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Jenna R. Rosinski
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Phoenix M. Shepherd
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Elaina Razo
- Department of Pediatrics, UW Madison, Madison, Wisconsin, United States of America
| | - Chelsea M. Crooks
- Department of Pathobiological Sciences, UW Madison, Madison, Wisconsin, United States of America
| | - Mason I. Bliss
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Emily L. Sneed
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Kevin K. Noguchi
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Terry K. Morgan
- Department of Pathology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Nicole A. Fuhler
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alexandra J. Alberts
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Samantha J. Havlicek
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
| | - Sabrina Kabakov
- Department of Kinesiology Occupational Therapy Program, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Ann M. Mitzey
- Department of Comparative Biosciences, UW Madison, Madison, Wisconsin, United States of America
| | - Kathleen M. Antony
- Department of Obstetrics and Gynecology, UW Madison, Madison, Wisconsin, United States of America
| | - Karla K. Ausderau
- Department of Kinesiology Occupational Therapy Program, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Waisman Center, UW Madison, Madison, Wisconsin, United States of America
| | - Andres Mejia
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Puja Basu
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Jens C. Eickhoff
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, UW Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, UW Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Kinesiology Occupational Therapy Program, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, UW Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, UW Madison, Madison, Wisconsin, United States of America
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25
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Dudley DM, Koenig MR, Stewart LM, Semler MR, Newman CM, Shepherd PM, Yamamoto K, Breitbach ME, Schotzko M, Kohn S, Antony KM, Qiu H, Tunga P, Anderson DM, Guo W, Dennis M, Singh T, Rybarczyk S, Weiler AM, Razo E, Mitzey A, Zeng X, Eickhoff JC, Mohr EL, Simmons HA, Fritsch MK, Mejia A, Aliota MT, Friedrich TC, Golos TG, Kodihalli S, Permar SR, O’Connor DH. Human immune globulin treatment controls Zika viremia in pregnant rhesus macaques. PLoS One 2022; 17:e0266664. [PMID: 35834540 PMCID: PMC9282477 DOI: 10.1371/journal.pone.0266664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
There are currently no approved drugs to treat Zika virus (ZIKV) infection during pregnancy. Hyperimmune globulin products such as VARIZIG and WinRho are FDA-approved to treat conditions during pregnancy such as Varicella Zoster virus infection and Rh-incompatibility. We administered ZIKV-specific human immune globulin as a treatment in pregnant rhesus macaques one day after subcutaneous ZIKV infection. All animals controlled ZIKV viremia following the treatment and generated robust levels of anti-Zika virus antibodies in their blood. No adverse fetal or infant outcomes were identified in the treated animals, yet the placebo control treated animals also did not have signs related to congenital Zika syndrome (CZS). Human immune globulin may be a viable prophylaxis and treatment option for ZIKV infection during pregnancy, however, more studies are required to fully assess the impact of this treatment to prevent CZS.
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Affiliation(s)
- Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michelle R. Koenig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Laurel M. Stewart
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew R. Semler
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Phoenix M. Shepherd
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Keisuke Yamamoto
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michele Schotzko
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Sarah Kohn
- Department of Radiology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kathleen M. Antony
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Hongyu Qiu
- Emergent BioSolutions, Canada Inc., Winnipeg, MB, Canada
| | | | | | - Wendi Guo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States of America
| | - Maria Dennis
- Department of Pediatrics and Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Tulika Singh
- Department of Pediatrics and Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Sierra Rybarczyk
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Elaina Razo
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ann Mitzey
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States of America
| | - Jens C. Eickhoff
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael K. Fritsch
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thaddeus G. Golos
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States of America
| | | | - Sallie R. Permar
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States of America
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- * E-mail:
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Amato KA, Haddock LA, Braun KM, Meliopoulos V, Livingston B, Honce R, Schaack GA, Boehm E, Higgins CA, Barry GL, Koelle K, Schultz-Cherry S, Friedrich TC, Mehle A. Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks. Nat Commun 2022; 13:3416. [PMID: 35701424 PMCID: PMC9197827 DOI: 10.1038/s41467-022-31147-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation. Transmission of influenza A viruses (IAV) between hosts and replication within host impose genetic bottlenecks, constraining viral diversity and adaptation. Here, Amato et al. perform site-specific inoculation of barcoded IAV of ferrets and track viral diversity as infection spreads to the lower respiratory tract and conclude that narrow population bottlenecks are an important feature of the within-host infection dynamics.
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Affiliation(s)
- Katherine A Amato
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Luis A Haddock
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Victoria Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Grace A Schaack
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emma Boehm
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Christina A Higgins
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gabrielle L Barry
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Ramuta MD, Newman CM, Brakefield SF, Stauss MR, Wiseman RW, Kita-Yarbro A, O'Connor EJ, Dahal N, Lim A, Poulsen KP, Safdar N, Marx JA, Accola MA, Rehrauer WM, Zimmer JA, Khubbar M, Beversdorf LJ, Boehm EC, Castañeda D, Rushford C, Gregory DA, Yao JD, Bhattacharyya S, Johnson MC, Aliota MT, Friedrich TC, O'Connor DH, O'Connor SL. SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. medRxiv 2022. [PMID: 35378751 PMCID: PMC8978944 DOI: 10.1101/2022.03.29.22272716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.
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Moriarty RV, Golfinos AE, Gellerup DD, Schweigert H, Mathiaparanam J, Balgeman AJ, Weiler AM, Friedrich TC, Keele BF, Davenport MP, Venturi V, O’Connor SL. The mucosal barrier and anti-viral immune responses can eliminate portions of the viral population during transmission and early viral growth. PLoS One 2021; 16:e0260010. [PMID: 34855793 PMCID: PMC8639003 DOI: 10.1371/journal.pone.0260010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Little is known about how specific individual viral lineages replicating systemically during acute Human Immunodeficiency Virus or Simian Immunodeficiency Virus (HIV/SIV) infection persist into chronic infection. In this study, we use molecularly barcoded SIV (SIVmac239M) to track distinct viral lineages for 12 weeks after intravenous (IV) or intrarectal (IR) challenge in macaques. Two Mafa-A1*063+ cynomolgus macaques (Macaca fascicularis, CM) were challenged IV, and two Mamu-A1*001+ rhesus macaques (Macaca mulatta, RM) were challenged IR with 200,000 Infectious Units (IU) of SIVmac239M. We sequenced the molecular barcode of SIVmac239M from all animals over the 12 weeks of the study to characterize the diversity and persistence of virus lineages. During the first three weeks post-infection, we found ~70–560 times more unique viral lineages circulating in the animals challenged IV compared to those challenged IR, which is consistent with the hypothesis that the challenge route is the primary driver restricting the transmission of individual viral lineages. We also characterized the sequences of T cell epitopes targeted during acute SIV infection, and found that the emergence of escape variants in acutely targeted epitopes can occur on multiple virus templates simultaneously, but that elimination of some of these templates is likely a consequence of additional host factors. These data imply that virus lineages present during acute infection can still be eliminated from the systemic virus population even after initial selection.
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Affiliation(s)
- Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Athena E. Golfinos
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dane D. Gellerup
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Hannah Schweigert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jaffna Mathiaparanam
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexis J. Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- * E-mail:
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29
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Amjadi MF, Adyniec RR, Gupta S, Bashar SJ, Mergaert AM, Braun KM, Moreno GK, O'Connor DH, Friedrich TC, Safdar N, McCoy SS, Shelef MA. Anti-membrane and anti-spike antibodies are long-lasting and together discriminate between past COVID-19 infection and vaccination. medRxiv 2021:2021.11.02.21265750. [PMID: 34790984 PMCID: PMC8597887 DOI: 10.1101/2021.11.02.21265750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The consequences of past COVID-19 infection for personal health and long-term population immunity are only starting to be revealed. Unfortunately, detecting past infection is currently a challenge, limiting clinical and research endeavors. Widely available anti-SARS-CoV-2 antibody tests cannot differentiate between past infection and vaccination given vaccine-induced anti-spike antibodies and the rapid loss of infection-induced anti-nucleocapsid antibodies. Anti-membrane antibodies develop after COVID-19, but their long-term persistence is unknown. Here, we demonstrate that anti-membrane IgG is a sensitive and specific marker of past COVID-19 infection and persists at least one year. We also confirm that anti-receptor binding domain (RBD) Ig is a long-lasting, sensitive, and specific marker of past infection and vaccination, while anti-nucleocapsid IgG lacks specificity and quickly declines after COVID-19. Thus, a combination of anti-membrane and anti-RBD antibodies can accurately differentiate between distant COVID-19 infection, vaccination, and naïve states to advance public health, individual healthcare, and research goals.
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Valesano AL, Fitzsimmons WJ, Blair CN, Woods RJ, Gilbert J, Rudnik D, Mortenson L, Friedrich TC, O’Connor DH, MacCannell DR, Petrie JG, Martin ET, Lauring AS. SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community. Open Forum Infect Dis 2021; 8:ofab518. [PMID: 34805437 PMCID: PMC8600169 DOI: 10.1093/ofid/ofab518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has had high incidence rates at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are poorly understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearby communities. METHODS We implemented high-density prospective genomic surveillance to investigate these dynamics at the University of Michigan and the surrounding community during the Fall 2020 semester (August 16-November 24). We sequenced complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 1659 individuals, including 468 students, representing 20% of cases in students and 25% of total cases in Washtenaw County over the study interval. RESULTS Phylogenetic analysis identified >200 introductions into the student population, most of which were not related to other student cases. There were 2 prolonged student transmission clusters, of 115 and 73 individuals, that spanned multiple on-campus residences. Remarkably, <5% of nonstudent genomes were descended from student clusters, and viral descendants of student cases were rare during a subsequent wave of infections in the community. CONCLUSIONS The largest outbreaks among students at the University of Michigan did not significantly contribute to the rise in community cases in Fall 2020. These results provide valuable insights into SARS-CoV-2 transmission dynamics at the regional level.
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Affiliation(s)
- Andrew L Valesano
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher N Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Julie Gilbert
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dawn Rudnik
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Lindsey Mortenson
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Joshua G Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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31
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Currie DW, Moreno GK, Delahoy MJ, Pray IW, Jovaag A, Braun KM, Cole D, Shechter T, Fajardo GC, Griggs C, Yandell BS, Goldstein S, Bushman D, Segaloff HE, Kelly GP, Pitts C, Lee C, Grande KM, Kita-Yarbro A, Grogan B, Mader S, Baggott J, Bateman AC, Westergaard RP, Tate JE, Friedrich TC, Kirking HL, O'Connor DH, Killerby ME. Interventions to Disrupt Coronavirus Disease Transmission at a University, Wisconsin, USA, August-October 2020. Emerg Infect Dis 2021; 27:2776-2785. [PMID: 34586058 PMCID: PMC8544969 DOI: 10.3201/eid2711.211306] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
University settings have demonstrated potential for coronavirus disease (COVID-19) outbreaks; they combine congregate living, substantial social activity, and a young population predisposed to mild illness. Using genomic and epidemiologic data, we describe a COVID-19 outbreak at the University of Wisconsin-Madison, Madison, Wisconsin, USA. During August-October 2020, a total of 3,485 students, including 856/6,162 students living in dormitories, tested positive. Case counts began rising during move-in week, August 25-31, 2020, then rose rapidly during September 1-11, 2020. The university initiated multiple prevention efforts, including quarantining 2 dormitories; a subsequent decline in cases was observed. Genomic surveillance of cases from Dane County, in which the university is located, did not find evidence of transmission from a large cluster of cases in the 2 quarantined dorms during the outbreak. Coordinated implementation of prevention measures can reduce COVID-19 spread in university settings and may limit spillover to the surrounding community.
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32
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Temte JL, Barlow S, Temte E, Goss M, Florek K, Braun KM, Friedrich TC, Reisdorf E, Bateman AC, Uzicanin A. Evidence of Early Household Transmission of SARS-CoV-2 Involving a School-aged Child. WMJ 2021; 120:233-236. [PMID: 34710308 PMCID: PMC8721881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Little is known about the role of school-aged children and household transmission at the start of the SARS-CoV-2 pandemic. To evaluate for SARS-CoV-2 in school-aged children and assess household transmission, we performed reverse transcription polymerase chain reaction on 670 archived specimens that were collected between September 1, 2019 and June 30, 2020 as part of a community-based study. CASE PRESENTATION A single SARS-CoV-2 case was detected in an 11-year-old girl on March 18, 2020, resulting in very low prevalence (0.15% [95% CI, 0.03-0.84]) in this population. This case was associated with SARS-CoV-2 detection in all other household members. Symptoms were reported as mild to moderate. Whole genome sequencing supported household transmission of near-identical viruses within the 19B clade. DISCUSSION This case represents the earliest known household cluster of SARS-CoV2 in Wisconsin. CONCLUSION This case suggests that household transmission associated with school-aged children may have contributed to wide seeding across populations.
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Affiliation(s)
- Jonathan L Temte
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin,
| | - Shari Barlow
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Emily Temte
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Maureen Goss
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin
| | - Katarina M Braun
- University of Wisconsin School of Veterinary Medicine, Department of Pathobiological Sciences, Madison, Wisconsin
| | - Thomas C Friedrich
- University of Wisconsin School of Veterinary Medicine, Department of Pathobiological Sciences, Madison, Wisconsin
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin
| | | | - Amra Uzicanin
- US Centers for Disease Control and Prevention, Atlanta, Georgia
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Braun KM, Moreno GK, Buys A, Somsen ED, Bobholz M, Accola MA, Anderson L, Rehrauer WM, Baker DA, Safdar N, Lepak AJ, O’Connor DH, Friedrich TC. Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel. Clin Infect Dis 2021; 73:e1329-e1336. [PMID: 33857303 PMCID: PMC8083259 DOI: 10.1093/cid/ciab281] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting. METHODS In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP. RESULTS We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source. CONCLUSIONS Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ashley Buys
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Elizabeth D Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Laura Anderson
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Alexander J Lepak
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O'Connor SL, O'Connor DH. Initial Evaluation of a Mobile SARS-CoV-2 RT-LAMP Testing Strategy. J Biomol Tech 2021; 32:137-147. [PMID: 35035293 PMCID: PMC8730517 DOI: 10.7171/jbt.21-32-03-009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16, 2020, to November 19, 2020, surveillance samples (n = 4704) were collected from volunteers and tested for SARS-CoV-2 at 5 sites. Twenty-one samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, whereas 8 tested negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the false-negative rate of the RT-LAMP assay only from July 16, 2020, to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or fewer and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP-negative pools (2493 total samples) testing positive in the more-sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and that can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robert J Maddox
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Mason I Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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35
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Braun KM, Moreno GK, Wagner C, Accola MA, Rehrauer WM, Baker DA, Koelle K, O’Connor DH, Bedford T, Friedrich TC, Moncla LH. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks. PLoS Pathog 2021; 17:e1009849. [PMID: 34424945 PMCID: PMC8412271 DOI: 10.1371/journal.ppat.1009849] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/02/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Molly A. Accola
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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36
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Moreno GK, Braun KM, Pray IW, Segaloff HE, Lim A, Poulsen K, Meiman J, Borcher J, Westergaard RP, Moll MK, Friedrich TC, O'Connor DH. Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in Intercollegiate Athletics Not Fully Mitigated With Daily Antigen Testing. Clin Infect Dis 2021; 73:S45-S53. [PMID: 33977295 PMCID: PMC8136076 DOI: 10.1093/cid/ciab343] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background High-frequency, rapid-turnaround severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, 2 SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester, despite mandatory directly observed daily antigen testing. Methods During the fall 2020 semester, athletes and staff in both programs were tested daily using Quidel’s Sofia SARS Antigen Fluorescent Immunoassay, with positive antigen results requiring confirmatory testing with real-time reverse-transcription polymerase chain reaction. We used genomic sequencing to investigate transmission dynamics in these 2 outbreaks. Results In the first outbreak, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious, despite a negative antigen test on the day of the meeting. Among isolates sequenced from that outbreak, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In the second outbreak, 12 confirmed cases occurred among athletes from 2 university programs that faced each other in an athletic competition, despite receipt of negative antigen test results on the day of the competition. Sequences from both teams were closely related and distinct from viruses circulating in the community for team 1, suggesting transmission during intercollegiate competition in the community for team 2. Conclusions These findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and they highlight the importance of vaccination to prevent SARS-CoV-2 outbreak in congregate settings.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ian W Pray
- Wisconsin Department of Health Services, Madison, Wisconsin, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hannah E Segaloff
- Wisconsin Department of Health Services, Madison, Wisconsin, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ailam Lim
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Keith Poulsen
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonathan Meiman
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | - James Borcher
- Department of Family Medicine, Division of Sports Medicine, Ohio State University, Columbus Ohio, USA
| | - Ryan P Westergaard
- Wisconsin Department of Health Services, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael K Moll
- Athletic Department, University of Wisconsin-Madison, Madison, Wisconsin USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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37
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Juang DS, Juang TD, Dudley DM, Newman CM, Accola MA, Rehrauer WM, Friedrich TC, O'Connor DH, Beebe DJ. Oil immersed lossless total analysis system for integrated RNA extraction and detection of SARS-CoV-2. Nat Commun 2021; 12:4317. [PMID: 34262053 PMCID: PMC8280165 DOI: 10.1038/s41467-021-24463-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing. Bottlenecks in qPCR-based COVID-19 diagnostics include the lengthy multistep process and reagent shortages. Here the authors report OIL-TAS which integrates RNA extraction and detection into a single device.
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Affiliation(s)
- Duane S Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Terry D Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Christina M Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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38
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Hangartner L, Beauparlant D, Rakasz E, Nedellec R, Hozé N, McKenney K, Martins MA, Seabright GE, Allen JD, Weiler AM, Friedrich TC, Regoes RR, Crispin M, Burton DR. Effector function does not contribute to protection from virus challenge by a highly potent HIV broadly neutralizing antibody in nonhuman primates. Sci Transl Med 2021; 13:13/585/eabe3349. [PMID: 33731434 DOI: 10.1126/scitranslmed.abe3349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Accepted: 02/03/2021] [Indexed: 01/11/2023]
Abstract
Protection from immunodeficiency virus challenge in nonhuman primates (NHPs) by a first-generation HIV broadly neutralizing antibody (bnAb) b12 has previously been shown to benefit from interaction between the bnAb and Fcγ receptors (FcγRs) on immune cells. To investigate the mechanism of protection for a more potent second-generation bnAb currently in clinical trials, PGT121, we carried out a series of NHP studies. These studies included treating with PGT121 at a concentration at which only half of the animals were protected to avoid potential masking of FcγR effector function benefits by dominant neutralization and using a new variant that more completely eliminated all rhesus FcγR binding than earlier variants. In contrast to b12, which required FcγR binding for optimal protection, we concluded that PGT121-mediated protection is not augmented by FcγR interaction. Thus, for HIV-passive antibody prophylaxis, these results, together with existing literature, emphasize the importance of neutralization potency for clinical antibodies, with effector function requiring evaluation for individual antibodies.
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Affiliation(s)
- Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Beauparlant
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eva Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nathanaël Hozé
- Institute of Integrative Biology (IBZ), ETH Zurich, ETH Zentrum, CHN H76.2, Universitätstrasse 16, 8092 Zurich, Switzerland.,Theoretical Biology, ETH Zurich, ETH Zentrum, CHN K12.2, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mauricio A Martins
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Roland R Regoes
- Institute of Integrative Biology (IBZ), ETH Zurich, ETH Zentrum, CHN H76.2, Universitätstrasse 16, 8092 Zurich, Switzerland.,Theoretical Biology, ETH Zurich, ETH Zentrum, CHN K12.2, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
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39
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Crooks CM, Weiler AM, Rybarczyk SL, Bliss MI, Jaeger AS, Murphy ME, Simmons HA, Mejia A, Fritsch MK, Hayes JM, Eickhoff JC, Mitzey AM, Razo E, Braun KM, Brown EA, Yamamoto K, Shepherd PM, Possell A, Weaver K, Antony KM, Morgan TK, Newman CM, Dudley DM, Schultz-Darken N, Peterson E, Katzelnick LC, Balmaseda A, Harris E, O’Connor DH, Mohr EL, Golos TG, Friedrich TC, Aliota MT. Previous exposure to dengue virus is associated with increased Zika virus burden at the maternal-fetal interface in rhesus macaques. PLoS Negl Trop Dis 2021; 15:e0009641. [PMID: 34329306 PMCID: PMC8357128 DOI: 10.1371/journal.pntd.0009641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/11/2021] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
Concerns have arisen that pre-existing immunity to dengue virus (DENV) could enhance Zika virus (ZIKV) disease, due to the homology between ZIKV and DENV and the observation of antibody-dependent enhancement (ADE) among DENV serotypes. To date, no study has examined the impact of pre-existing DENV immunity on ZIKV pathogenesis during pregnancy in a translational non-human primate model. Here we show that macaques with a prior DENV-2 exposure had a higher burden of ZIKV vRNA in maternal-fetal interface tissues as compared to DENV-naive macaques. However, pre-existing DENV immunity had no detectable impact on ZIKV replication kinetics in maternal plasma, and all pregnancies progressed to term without adverse outcomes or gross fetal abnormalities detectable at delivery. Understanding the risks of ADE to pregnant women worldwide is critical as vaccines against DENV and ZIKV are developed and licensed and as DENV and ZIKV continue to circulate.
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Affiliation(s)
- Chelsea M. Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sierra L. Rybarczyk
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mason I. Bliss
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Megan E. Murphy
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael K. Fritsch
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer M. Hayes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jens C. Eickhoff
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ann M. Mitzey
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elaina Razo
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elizabeth A. Brown
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Keisuke Yamamoto
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Phoenix M. Shepherd
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amber Possell
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kara Weaver
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kathleen M. Antony
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Terry K. Morgan
- Department of Pathology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nancy Schultz-Darken
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eric Peterson
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Leah C. Katzelnick
- Division of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, California, United States of America
| | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, California, United States of America
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
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40
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Newman CM, Tarantal AF, Martinez ML, Simmons HA, Morgan TK, Zeng X, Rosinski JR, Bliss MI, Bohm EK, Dudley DM, Aliota MT, Friedrich TC, Miller CJ, O’Connor DH. Early Embryonic Loss Following Intravaginal Zika Virus Challenge in Rhesus Macaques. Front Immunol 2021; 12:686437. [PMID: 34079560 PMCID: PMC8165274 DOI: 10.3389/fimmu.2021.686437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/04/2021] [Indexed: 01/25/2023] Open
Abstract
Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) and is primarily transmitted by Aedes species mosquitoes; however, ZIKV can also be sexually transmitted. During the initial epidemic and in places where ZIKV is now considered endemic, it is difficult to disentangle the risks and contributions of sexual versus vector-borne transmission to adverse pregnancy outcomes. To examine the potential impact of sexual transmission of ZIKV on pregnancy outcome, we challenged three rhesus macaques (Macaca mulatta) three times intravaginally with 1 x 107 PFU of a low passage, African lineage ZIKV isolate (ZIKV-DAK) in the first trimester (~30 days gestational age). Samples were collected from all animals initially on days 3 through 10 post challenge, followed by twice, and then once weekly sample collection; ultrasound examinations were performed every 3-4 days then weekly as pregnancies progressed. All three dams had ZIKV RNA detectable in plasma on day 3 post-ZIKV challenge. At approximately 45 days gestation (17-18 days post-challenge), two of the three dams were found with nonviable embryos by ultrasound. Viral RNA was detected in recovered tissues and at the maternal-fetal interface (MFI) in both cases. The remaining viable pregnancy proceeded to near term (~155 days gestational age) and ZIKV RNA was detected at the MFI but not in fetal tissues. These results suggest that sexual transmission of ZIKV may represent an underappreciated risk of pregnancy loss during early gestation.
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Affiliation(s)
- Christina M. Newman
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Alice F. Tarantal
- Pediatrics, Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA, United States
- California National Primate Research Center, University of California, Davis, CA, United States
| | - Michele L. Martinez
- Pediatrics, Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA, United States
- California National Primate Research Center, University of California, Davis, CA, United States
| | - Heather A. Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Terry K. Morgan
- Pathology, Oregon Health and Sciences University, Portland, OR, United States
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Jenna R. Rosinski
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mason I. Bliss
- Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Ellie K. Bohm
- Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Dawn M. Dudley
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Matthew T. Aliota
- Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Thomas C. Friedrich
- Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Christopher J. Miller
- California National Primate Research Center, University of California, Davis, CA, United States
- Pathology, Microbiology, and Immunology, School of Veterinary Medicine, Center for Immunology and Infectious Diseases, University of California, Davis, CA, United States
| | - David H. O’Connor
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
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Cai Y, Yu S, Fang Y, Bollinger L, Li Y, Lauck M, Postnikova EN, Mazur S, Johnson RF, Finch CL, Radoshitzky SR, Palacios G, Friedrich TC, Goldberg TL, O’Connor DH, Jahrling PB, Kuhn JH. Development and Characterization of a cDNA-Launch Recombinant Simian Hemorrhagic Fever Virus Expressing Enhanced Green Fluorescent Protein: ORF 2b' Is Not Required for In Vitro Virus Replication. Viruses 2021; 13:v13040632. [PMID: 33917085 PMCID: PMC8067702 DOI: 10.3390/v13040632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Simian hemorrhagic fever virus (SHFV) causes acute, lethal disease in macaques. We developed a single-plasmid cDNA-launch infectious clone of SHFV (rSHFV) and modified the clone to rescue an enhanced green fluorescent protein-expressing rSHFV-eGFP that can be used for rapid and quantitative detection of infection. SHFV has a narrow cell tropism in vitro, with only the grivet MA-104 cell line and a few other grivet cell lines being susceptible to virion entry and permissive to infection. Using rSHFV-eGFP, we demonstrate that one cricetid rodent cell line and three ape cell lines also fully support SHFV replication, whereas 55 human cell lines, 11 bat cell lines, and three rodent cells do not. Interestingly, some human and other mammalian cell lines apparently resistant to SHFV infection are permissive after transfection with the rSHFV-eGFP cDNA-launch plasmid. To further demonstrate the investigative potential of the infectious clone system, we introduced stop codons into eight viral open reading frames (ORFs). This approach suggested that at least one ORF, ORF 2b’, is dispensable for SHFV in vitro replication. Our proof-of-principle experiments indicated that rSHFV-eGFP is a useful tool for illuminating the understudied molecular biology of SHFV.
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Affiliation(s)
- Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Shuiqing Yu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Ying Fang
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (Y.F.); (Y.L.)
| | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Yanhua Li
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (Y.F.); (Y.L.)
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
| | - Elena N. Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Steven Mazur
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Reed F. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA; (S.R.R.); (G.P.)
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA; (S.R.R.); (G.P.)
| | - Thomas C. Friedrich
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI 53706, USA;
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA; (M.L.); (T.C.F.); (D.H.O.)
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI 53715, USA
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Emerging Infectious Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA; (Y.C.); (S.Y.); (L.B.); (E.N.P.); (S.M.); (R.F.J.); (C.L.F.); (P.B.J.)
- Correspondence: ; Tel.: +1-301-631-7245
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Moreno GK, Braun KM, Pray IW, Segaloff HE, Lim A, Poulson K, Meiman J, Borcher J, Westergaard RP, Moll MK, Friedrich TC, O'Connor DH. SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing. medRxiv 2021. [PMID: 33688665 PMCID: PMC7941640 DOI: 10.1101/2021.03.03.21252838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing. Methods During the fall 2020 semester, athletes and staff in both programs were tested daily using Quidel's Sofia SARS Antigen Fluorescent Immunoassay (FIA), with positive antigen results requiring confirmatory testing with real-time reverse transcription polymerase chain reaction (RT-PCR). We used genomic sequencing to investigate transmission dynamics in these two outbreaks. Results In Outbreak 1, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious despite a negative antigen test on the day of the meeting. Among isolates sequenced from Outbreak 1, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In Outbreak 2, 12 confirmed cases occurred among athletes from two university programs that faced each other in an athletic competition despite receiving negative antigen test results on the day of the competition. Sequences from both teams were closely related and unique from strains circulating in the community, suggesting transmission during intercollegiate competition. Conclusions These findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and highlights the importance of supplementing serial antigen testing with appropriate mitigation strategies to prevent SARS-CoV-2 outbreak in congregate settings. Summary High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, here we describe two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison USA 53711
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison USA 53711
| | - Ian W Pray
- Wisconsin Department of Health Services, USA 53703.,Epidemic Intelligence Service, Centers for Disease Control and Prevention USA 30333
| | - Hannah E Segaloff
- Wisconsin Department of Health Services, USA 53703.,Epidemic Intelligence Service, Centers for Disease Control and Prevention USA 30333
| | - Ailam Lim
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison USA 53711
| | - Keith Poulson
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison USA 53711
| | | | - James Borcher
- Department of Family Medicine, Division of Sports Medicine, Ohio State University USA 43210
| | - Ryan P Westergaard
- Wisconsin Department of Health Services, USA 53703.,Department of Medicine, University of Wisconsin-Madison, USA 53711
| | - Michael K Moll
- Athletic Department, University of Wisconsin-Madison USA 53711
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison USA 53711
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison USA 53711
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O’Connor SL, O’Connor DH. Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy. medRxiv 2021:2020.07.28.20164038. [PMID: 33655260 PMCID: PMC7924282 DOI: 10.1101/2020.07.28.20164038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16 to November 19, 2020, 4,704 surveillance samples were collected from volunteers and tested for SARS-CoV-2 at 5 sites. A total of 21 samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, while 8 were negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the RT-LAMP assay's false-negative rate from July 16 to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or less and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP negative pools (2,493 samples) testing positive in the more sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M. Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D. Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T. McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W. Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A. Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M. Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Mason I. Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A. Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G. Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K. Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S. Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E. Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R. Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E. Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V. Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M. Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M. Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M. Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K. Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D. Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B. Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L. Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M. Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C. Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O’Connor DH, Friedrich TC. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. PLoS Pathog 2021; 17:e1009373. [PMID: 33635912 PMCID: PMC7946358 DOI: 10.1371/journal.ppat.1009373] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/10/2021] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma B. Hodcroft
- Institute of Social and Preventative Medicine, University of Bern, Bern, Switzerland
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma C. Boehm
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amelia K. Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Masato Hatta
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shiho Chiba
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tadashi Maemura
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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45
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Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. bioRxiv 2021:2020.11.16.384917. [PMID: 33236011 PMCID: PMC7685321 DOI: 10.1101/2020.11.16.384917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Emma B Hodcroft
- Institute of Social and Preventative Medicine, University of Bern, Bern, Switzerland
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma C Boehm
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Masato Hatta
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Shiho Chiba
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Tadashi Maemura
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
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46
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Dudley DM, Newman CM, Weiler AM, Ramuta MD, Shortreed CG, Heffron AS, Accola MA, Rehrauer WM, Friedrich TC, O’Connor DH. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples. PLoS One 2020; 15:e0244882. [PMID: 33382861 PMCID: PMC7775089 DOI: 10.1371/journal.pone.0244882] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Frequent surveillance of individuals attending work or school is currently unavailable to most people but will likely be necessary to reduce the ~50% of transmission that occurs when individuals are nonsymptomatic. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed primary samples with a limit of detection (LOD) of ~625 copies/μl, approximately 100-fold lower sensitivity than qRT-PCR. While less sensitive than extraction-based molecular methods, RT-LAMP without RNA extraction is fast and inexpensive. Here we also demonstrate that adding a lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 surveillance programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.
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Affiliation(s)
- Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mitchell D. Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cecilia G. Shortreed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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47
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Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nat Commun 2020; 11:5558. [PMID: 33144575 PMCID: PMC7609670 DOI: 10.1038/s41467-020-19346-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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48
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Safdar N, Moreno GK, Braun KM, Friedrich TC, O'Connor DH. Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker. Emerg Infect Dis 2020; 26:2489-2491. [PMID: 32758345 PMCID: PMC7510721 DOI: 10.3201/eid2610.202322] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Whether a healthcare worker's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for 2 SARS-CoV-2-infected patients was probably community acquired. Appropriate personal protective equipment may have protected against hospital-acquired infection.
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49
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Schmidt JK, Mean KD, Puntney RC, Alexander ES, Sullivan R, Simmons HA, Zeng X, Weiler AM, Friedrich TC, Golos TG. Zika virus in rhesus macaque semen and reproductive tract tissues: a pilot study of acute infection†. Biol Reprod 2020; 103:1030-1042. [PMID: 32761051 DOI: 10.1093/biolre/ioaa137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/09/2019] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Although sexual transmission of Zika virus (ZIKV) is well-documented, the viral reservoir(s) in the male reproductive tract remains uncertain in humans and immune-intact animal models. We evaluated the presence of ZIKV in a rhesus macaque pilot study to determine persistence in semen, assess the impact of infection on sperm functional characteristics, and define the viral reservoir in the male reproductive tract. Five adult male rhesus monkeys were inoculated with 105 PFU of Asian-lineage ZIKV isolate PRVABC59, and two males were inoculated with the same dose of African-lineage ZIKV DAKAR41524. Viremia and viral RNA (vRNA) shedding in semen were monitored, and a cohort of animals were necropsied for tissue collection to assess tissue vRNA burden and histopathology. All animals exhibited viremia for limited periods (1-11 days); duration of shedding did not differ significantly between viral isolates. There were sporadic low levels of vRNA in the semen from some, but not all animals. Viral RNA levels in reproductive tract tissues were also modest and present in the epididymis in three of five cases, one case in the vas deferens, but not detected in testis, seminal vesicles or prostate. ZIKV infection did not impact semen motility parameters as assessed by computer-assisted sperm analysis. Despite some evidence of prolonged ZIKV RNA shedding in human semen and high tropism of ZIKV for male reproductive tract tissues in mice deficient in Type 1 interferon signaling, in the rhesus macaques assessed in this pilot study, we did not consistently find ZIKV RNA in the male reproductive tract.
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Affiliation(s)
- Jenna K Schmidt
- Wisconsin National Primate Research Center, Madison, WI, USA
| | | | - Riley C Puntney
- Wisconsin National Primate Research Center, Madison, WI, USA
| | | | - Ruth Sullivan
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, Madison, WI, USA.,Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, Madison, WI, USA.,Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA.,Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
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50
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Pomplun NL, Vosler L, Weisgrau KL, Furlott J, Weiler AM, Abdelaal HM, Evans DT, Watkins DI, Matano T, Skinner PJ, Friedrich TC, Rakasz EG. Immunophenotyping of Rhesus CMV-Specific CD8 T-Cell Populations. Cytometry A 2020; 99:278-288. [PMID: 32713108 PMCID: PMC7855655 DOI: 10.1002/cyto.a.24197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 01/06/2023]
Abstract
A vaccine to ameliorate cytomegalovirus (CMV)-related pathogenicity in transplantation patients is considered a top priority. A therapeutic vaccine must include components that elicit both neutralizing antibodies, and highly effective CD8 T-cell responses. The most important translational model of vaccine development is the captive-bred rhesus macaque (Macaca mulatta) of Indian origin. There is a dearth of information on rhesus cytomegalovirus (rhCMV)-specific CD8 T cells due to the absence of well-defined CD8 T-cell epitopes presented by classical MHC-I molecules. In the current study, we defined two CD8 T-cell epitopes restricted by high-frequency Mamu alleles: the Mamu-A1*002:01 restricted VY9 (VTTLGMALY aa291-299) epitope of protein IE-1, and the Mamu-A1*008:01 restricted NP8 (NPTDRPIP aa96-103) epitope of protein phosphoprotein 65-2. We developed tetramers and determined the level, phenotype, and functional capability of the two epitope-specific T-cell populations in circulation and various tissues. We demonstrated the value of these tetramers for in situ tetramer staining. Here, we first provided critical reagents and established a flow cytometric staining strategy to study rhCMV-specific T-cell responses in up to 40% of captive-bred rhesus macaques. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Nicholas L Pomplun
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Logan Vosler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kim L Weisgrau
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jessica Furlott
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hadia M Abdelaal
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - David T Evans
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David I Watkins
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Pamela J Skinner
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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