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Lisius G, Duttagupta R, Ahmed AA, Hensley M, Al-Yousif N, Lu M, Bain W, Shah F, Blauwkamp TA, Bercovici S, Schaefer C, Qin S, Wang X, Zhang Y, Mitchell KJ, Hughes EK, Jacobs JL, Naqvi A, Haidar G, Mellors JW, Methé B, McVerry BJ, Morris A, Kitsios GD. Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA. iScience 2023; 26:108093. [PMID: 37965142 PMCID: PMC10641743 DOI: 10.1016/j.isci.2023.108093] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 11/16/2023] Open
Abstract
Secondary infection (SI) diagnosis in severe COVID-19 remains challenging. We correlated metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) with clinical SI assessment, immune response, and outcomes. We classified 42 COVID-19 inpatients as microbiologically confirmed-SI (Micro-SI, n = 8), clinically diagnosed-SI (Clinical-SI, n = 13, i.e., empiric antimicrobials), or no-clinical-suspicion-for-SI (No-Suspected-SI, n = 21). McfDNA-Seq was successful in 73% of samples. McfDNA detection was higher in Micro-SI (94%) compared to Clinical-SI (57%, p = 0.03), and unexpectedly high in No-Suspected-SI (83%), similar to Micro-SI. We detected culture-concordant mcfDNA species in 81% of Micro-SI samples. McfDNA correlated with LRT 16S rRNA bacterial burden (r = 0.74, p = 0.02), and biomarkers (white blood cell count, IL-6, IL-8, SPD, all p < 0.05). McfDNA levels were predictive of worse 90-day survival (hazard ratio 1.30 [1.02-1.64] for each log10 mcfDNA, p = 0.03). High mcfDNA levels in COVID-19 patients without clinical SI suspicion may suggest SI under-diagnosis. McfDNA-Seq offers a non-invasive diagnostic tool for pathogen identification, with prognostic value on clinical outcomes.
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Affiliation(s)
- Grace Lisius
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | | | - Matthew Hensley
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nameer Al-Yousif
- Division of Pulmonary, Critical Care, and Sleep Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Michael Lu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Veterans Affairs Pittsburgh Health System, Pittsburgh, PA 15240, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Veterans Affairs Pittsburgh Health System, Pittsburgh, PA 15240, USA
| | | | | | - Caitlin Schaefer
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | - Ellen K. Hughes
- Computer Vision Group, VeyTel LLC, Pittsburgh, PA 15217, USA
| | - Jana L. Jacobs
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA 15213, USA
| | - Asma Naqvi
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA 15213, USA
| | - Ghady Haidar
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA 15213, USA
| | - John W. Mellors
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA 15213, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
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2
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Haidar G, Hodges JC, Bilderback A, Lukanski A, Linstrum K, Postol B, Troyan R, Wisniewski MK, Coughenour L, Heaps A, Jacobs JL, Hughes Kramer K, Klamar-Blain C, Kohl J, Liang W, Morris B, Macatangay BJC, Parikh UM, Sobolewksi MD, Musgrove C, Crandall MD, Mahon J, Mulvey K, Collins K, King AC, Wells A, Zapf R, Agha M, Minnier T, Angus DC, Mellors JW. Prospective assessment of humoral and cellular immune responses to a 3rd COVID-19 mRNA vaccine dose among immunocompromised individuals. J Infect Dis 2023:jiad511. [PMID: 37972260 DOI: 10.1093/infdis/jiad511] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Improved COVID-19 prevention is needed for immunocompromised individuals. METHODS Prospective study of healthcare workers (HCW) and immunocompromised participants with baseline serology following 2 mRNA vaccines and who were retested after dose 3 (D3); multivariable regression was used to identify predictors of serological responses. IFNγ/TNFα T-cell responses were assessed in a subset. RESULTS 536 participants were included: 492 immunocompromised [(206 solid organ transplant (SOT), 128 autoimmune, 80 hematologic malignancy (HM), 48 solid tumor, 25 HIV], 44 HCW. D3 significantly increased Spike IgG levels among all, but SOT and HM participants had the lowest median antibody levels post-D3 (increase from 0.09 to 0.83 and 0.27 to 1.92, respectively), versus HCW and persons with HIV, autoimmune conditions, and solid tumors (increases from 4.44 to 19.79, 2.9 to 15.75, 3.82 to 16.32, and 4.1 to 25.54, respectively). Seropositivity post-D3 was lowest for SOT (49.0%) and HM (57.8%), versus others (>90% seropositive). Neutralization post-D3 was lowest among SOT and HM. Predictors of lower antibody levels included low baseline levels and shorter intervals between vaccines. T-cell responses against Spike increased significantly among HCW and non-significantly among immunocompromised individuals. CONCLUSIONS D3 significantly improves serological but not T-cell responses among immunocompromised individuals. SOT and HM patients have suboptimal responses to D3.
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Affiliation(s)
- Ghady Haidar
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jacob C Hodges
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Andrew Bilderback
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Amy Lukanski
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kelsey Linstrum
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Barbara Postol
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rachel Troyan
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mary K Wisniewski
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lindsay Coughenour
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amy Heaps
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kailey Hughes Kramer
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua Kohl
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Wendy Liang
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Benjamin Morris
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michele D Sobolewksi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christopher Musgrove
- Internal Medicine Residency Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Melissa D Crandall
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John Mahon
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Katie Mulvey
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kevin Collins
- Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Adam C King
- Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Alan Wells
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rachel Zapf
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mounzer Agha
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, US
| | - Tami Minnier
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Derek C Angus
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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3
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Nieves-Rosado HM, Jacobs JL, Naqvi A, Mellors JW, Macatangay BJC, Kane LP. TIM-3 signaling contributes to the suppressive capacity of Tregs from people with HIV on antiretroviral therapy. J Leukoc Biol 2023; 114:368-372. [PMID: 37350502 PMCID: PMC10882646 DOI: 10.1093/jleuko/qiad068] [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: 11/12/2022] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
TIM-3 expression is increased on peripheral regulatory T cells (Tregs) of virally suppressed persons with HIV-1 on antiretroviral therapy (PWH-ART). However, the relevance of TIM-3 expression in this setting is unclear. We used flow cytometry to evaluate the suppressive phenotype and signaling pathways in peripheral TIM-3- vs TIM-3+ Tregs in PWH-ART. TIM-3+ Tregs showed increased expression of IL-10 compared with persons without HIV-1. In addition, TIM-3+ Tregs displayed elevated signaling and activation, relative to TIM-3- Tregs from the same PWH-ART. Dramatically, TIM-3 blockade restrained the in vitro suppressive capacity of peripheral Tregs. Therefore, our data demonstrate not only that TIM-3 expression by Tregs is associated with an immunosuppressive response among PWH-ART, but also that TIM-3 contributes directly to the enhanced suppressive activity of Tregs in this setting.
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Affiliation(s)
- Hector M Nieves-Rosado
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Jana L Jacobs
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Asma Naqvi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Bernard J C Macatangay
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Lawrence P Kane
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
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4
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Haidar G, Jacobs JL, Kramer KH, Naqvi A, Heaps A, Parikh U, McCormick KD, Sobolewski MD, Agha M, Bogdanovich T, Bushunow V, Farah R, Hensley M, Hsu YMS, Johnson B, Klamar-Blain C, Kozar J, Lendermon E, Macatangay BJC, Marino CC, Raptis A, Salese E, Silveira FP, Leen AM, Marshall WL, Miller M, Patel B, Atillasoy E, Mellors JW. Therapy With Allogeneic Severe Acute Respiratory Syndrome Coronavirus-2-Specific T Cells for Persistent Coronavirus Disease 2019 in Immunocompromised Patients. Clin Infect Dis 2023; 77:696-702. [PMID: 37078720 PMCID: PMC10495124 DOI: 10.1093/cid/ciad233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
We administered severe acute respiratory syndrome coronavirus-2 viral-specific T cells (VSTs) under emergency investigational new drug applications to 6 immunocompromised patients with persistent coronavirus disease 2019 (COVID-19) and characterized clinical and virologic responses. Three patients had partial responses after failing other therapies but then died. Two patients completely recovered, but the role of VSTs in recovery was unclear due to concomitant use of other antivirals. One patient had not responded to 2 courses of remdesivir and experienced sustained recovery after VST administration. The use of VSTs in immunocompromised patients with persistent COVID-19 requires further study.
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Affiliation(s)
- Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jana L Jacobs
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kailey Hughes Kramer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvi Parikh
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin D McCormick
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michele D Sobolewski
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mounzer Agha
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Tatiana Bogdanovich
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vasilii Bushunow
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Rafic Farah
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Matthew Hensley
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Yen-Michael S Hsu
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Bruce Johnson
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer Kozar
- Department of Pharmacy, Investigational Drug Services, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Elizabeth Lendermon
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher C Marino
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Anastasios Raptis
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Erin Salese
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Fernanda P Silveira
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ann M Leen
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | | | | | | | | | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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5
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Jacobs JL, Haidar G, Naqvi A, McCormick KD, Sobolewski M, Treat BR, Heaps AL, Simpson J, Kramer KH, McCreary E, Bariola JR, Klamar-Blain C, Macatangay BJC, Dimitrov D, Li W, Marino CC, Raptis A, Sethi R, Chandran U, Barratt-Boyes S, Parikh UM, Mellors JW. Rapid Emergence of Potentially Transmissible Severe Acute Respiratory Syndrome Coronavirus 2 With Resistance to Combination Monoclonal Antibody Therapy. Open Forum Infect Dis 2023; 10:ofad278. [PMID: 37265667 PMCID: PMC10230564 DOI: 10.1093/ofid/ofad278] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Prolonged coronavirus disease 2019 may generate new viral variants. We report an immunocompromised patient treated with monoclonal antibodies who experienced rebound of viral RNA and emergence of an antibody-resistant (>1000-fold) variant containing 5 mutations in the spike gene. The mutant virus was isolated from respiratory secretions, suggesting the potential for secondary transmission.
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Affiliation(s)
- Jana L Jacobs
- Correspondence: Jana Jacobs, PhD, Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace St, Scaife Hall, Suite A807.1, Pittsburgh, PA 15261 (); John W. Mellors, MD, Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace St, Scaife Hall, Suite 818, Pittsburgh, PA 15261 ()
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michele Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Benjamin R Treat
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Amy L Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jordan Simpson
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kailey Hughes Kramer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Erin McCreary
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - J Ryan Bariola
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter Dimitrov
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher C Marino
- Department of Medicine, Division of Hematology and Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anastasios Raptis
- Department of Medicine, Division of Hematology and Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rahil Sethi
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Correspondence: Jana Jacobs, PhD, Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace St, Scaife Hall, Suite A807.1, Pittsburgh, PA 15261 (); John W. Mellors, MD, Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace St, Scaife Hall, Suite 818, Pittsburgh, PA 15261 ()
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6
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Abstract
The COVID-19 pandemic has been accompanied by SARS-CoV-2 evolution and emergence of viral variants that have far exceeded initial expectations. Five major variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) have emerged, each having both unique and overlapping amino acid substitutions that have affected transmissibility, disease severity, and susceptibility to natural or vaccine-induced immune responses and monoclonal antibodies. Several of the more recent variants appear to have evolved properties of immune evasion, particularly in cases of prolonged infection. Tracking of existing variants and surveillance for new variants are critical for an effective pandemic response.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
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7
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Jacobs JL, Naqvi A, Shah FA, Boltz VF, Kearney MF, McVerry BJ, Ray P, Schaefer C, Fitzpatrick M, Methé B, Lee JS, Morris A, Mellors JW, Kitsios GD, Bain W. Plasma SARS-CoV-2 RNA Levels as a Biomarker of Lower Respiratory Tract SARS-CoV-2 Infection in Critically Ill Patients With COVID-19. J Infect Dis 2022; 226:2089-2094. [PMID: 35511031 PMCID: PMC10205612 DOI: 10.1093/infdis/jiac157] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/26/2022] [Indexed: 01/04/2023] Open
Abstract
Plasma SARS-CoV-2 viral RNA (vRNA) levels are predictive of COVID-19 outcomes in hospitalized patients, but whether plasma vRNA reflects lower respiratory tract (LRT) vRNA levels is unclear. We compared plasma and LRT vRNA levels in serially collected samples from mechanically ventilated patients with COVID-19. LRT and plasma vRNA levels were strongly correlated at first sampling (n = 33, r = 0.83, P < 10-9) and then declined in parallel in available serial samples except in nonsurvivors who exhibited delayed vRNA clearance in LRT samples. Plasma vRNA measurement may offer a practical surrogate of LRT vRNA burden in critically ill patients, especially early after ICU admission.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Faraaz A Shah
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Valerie F Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Meghan Fitzpatrick
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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8
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Castanha PMS, Tuttle DJ, Kitsios GD, Jacobs JL, Braga-Neto U, Duespohl M, Rathod S, Marti MM, Wheeler S, Naqvi A, Staines B, Mellors J, Morris A, McVerry BJ, Shah F, Schaefer C, Macatangay BJC, Methe B, Fernandez CA, Barratt-Boyes SM, Burke D, Marques ETA. Contribution of Coronavirus-Specific Immunoglobulin G Responses to Complement Overactivation in Patients with Severe Coronavirus Disease 2019. J Infect Dis 2022; 226:766-777. [PMID: 35267024 PMCID: PMC8992249 DOI: 10.1093/infdis/jiac091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 01/06/2022] [Accepted: 03/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Excessive complement activation has been implicated in the pathogenesis of coronavirus disease 2019 (COVID-19), but the mechanisms leading to this response remain unclear. METHODS We measured plasma levels of key complement markers, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and antibodies against SARS-CoV-2 and seasonal human common cold coronaviruses (CCCs) in hospitalized patients with COVID-19 of moderate (n = 18) and critical severity (n = 37) and in healthy controls (n = 10). RESULTS We confirmed that complement activation is systemically increased in patients with COVID-19 and is associated with a worse disease outcome. We showed that plasma levels of C1q and circulating immune complexes were markedly increased in patients with severe COVID-19 and correlated with higher immunoglobulin (Ig) G titers, greater complement activation, and higher disease severity score. Additional analyses showed that the classical pathway was the main arm responsible for augmented complement activation in severe patients. In addition, we demonstrated that a rapid IgG response to SARS-CoV-2 and an anamnestic IgG response to the nucleoprotein of the CCCs were strongly correlated with circulating immune complex levels, complement activation, and disease severity. CONCLUSIONS These findings indicate that early, nonneutralizing IgG responses may play a key role in complement overactivation in severe COVID-19. Our work underscores the urgent need to develop therapeutic strategies to modify complement overactivation in patients with COVID-19.
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Affiliation(s)
- Priscila M S Castanha
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dylan J Tuttle
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ulisses Braga-Neto
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Matthew Duespohl
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sanjay Rathod
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michelle M Marti
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sarah Wheeler
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Faraaz Shah
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian A Fernandez
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon M Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Donald Burke
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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9
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Haidar G, Agha M, Bilderback A, Lukanski A, Linstrum K, Troyan R, Rothenberger S, McMahon DK, Crandall MD, Sobolewksi MD, Nathan Enick P, Jacobs JL, Collins K, Klamar-Blain C, Macatangay BJC, Parikh UM, Heaps A, Coughenour L, Schwartz MB, Dueker JM, Silveira FP, Keebler ME, Humar A, Luketich JD, Morrell MR, Pilewski JM, McDyer JF, Pappu B, Ferris RL, Marks SM, Mahon J, Mulvey K, Hariharan S, Updike GM, Brock L, Edwards R, Beigi RH, Kip PL, Wells A, Minnier T, Angus DC, Mellors JW. Prospective Evaluation of Coronavirus Disease 2019 (COVID-19) Vaccine Responses Across a Broad Spectrum of Immunocompromising Conditions: the COVID-19 Vaccination in the Immunocompromised Study (COVICS). Clin Infect Dis 2022; 75:e630-e644. [PMID: 35179197 PMCID: PMC8903515 DOI: 10.1093/cid/ciac103] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [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: 10/31/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND We studied humoral responses after coronavirus disease 2019 (COVID-19) vaccination across varying causes of immunodeficiency. METHODS Prospective study of fully vaccinated immunocompromised adults (solid organ transplant [SOT], hematologic malignancy, solid cancers, autoimmune conditions, human immunodeficiency virus [HIV]) versus nonimmunocompromised healthcare workers (HCWs). The primary outcome was the proportion with a reactive test (seropositive) for immunoglobulin G to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain. Secondary outcomes were comparisons of antibody levels and their correlation with pseudovirus neutralization titers. Stepwise logistic regression was used to identify factors associated with seropositivity. RESULTS A total of 1271 participants enrolled: 1099 immunocompromised and 172 HCW. Compared with HCW (92.4% seropositive), seropositivity was lower among participants with SOT (30.7%), hematological malignancies (50.0%), autoimmune conditions (79.1%), solid tumors (78.7%), and HIV (79.8%) (P < .01). Factors associated with poor seropositivity included age, greater immunosuppression, time since vaccination, anti-CD20 monoclonal antibodies, and vaccination with BNT162b2 (Pfizer) or adenovirus vector vaccines versus messenger RNA (mRNA)-1273 (Moderna). mRNA-1273 was associated with higher antibody levels than BNT162b2 or adenovirus vector vaccines after adjusting for time since vaccination, age, and underlying condition. Antibody levels were strongly correlated with pseudovirus neutralization titers (Spearman r = 0.89, P < .0001), but in seropositive participants with intermediate antibody levels, neutralization titers were significantly lower in immunocompromised individuals versus HCW. CONCLUSIONS Antibody responses to COVID-19 vaccines were lowest among SOT and anti-CD20 monoclonal recipients, and recipients of vaccines other than mRNA-1273. Among those with intermediate antibody levels, pseudovirus neutralization titers were lower in immunocompromised patients than HCWs. Additional SARS-CoV-2 preventive approaches are needed for immunocompromised persons, which may need to be tailored to the cause of immunodeficiency.
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Affiliation(s)
- Ghady Haidar
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mounzer Agha
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Andrew Bilderback
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Amy Lukanski
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Kelsey Linstrum
- Health Care Innovation, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Rachel Troyan
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Scott Rothenberger
- Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Melissa D Crandall
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Michele D Sobolewksi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - P Nathan Enick
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin Collins
- Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lindsay Coughenour
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marc B Schwartz
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeffrey M Dueker
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Fernanda P Silveira
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary E Keebler
- Department of Cardiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abhinav Humar
- Division of Transplantation, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James D Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew R Morrell
- Division of Pulmonary and Critical Care, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Joseph M Pilewski
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John F McDyer
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bhanu Pappu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Robert L Ferris
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Stanley M Marks
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John Mahon
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Katie Mulvey
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Sundaram Hariharan
- Division of Transplantation, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Transplant Nephrology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Glenn M Updike
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USAand
| | - Lorraine Brock
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Robert Edwards
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USAand
| | - Richard H Beigi
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USAand
| | - Paula L Kip
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Alan Wells
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Tami Minnier
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Derek C Angus
- Health Care Innovation, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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10
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Chen C, Saville JW, Marti MM, Schäfer A, Cheng MH, Mannar D, Zhu X, Berezuk AM, Banerjee A, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Enick N, McCormick KD, Liu X, Adams C, Hines MG, Sun Z, Chen W, Jacobs JL, Barratt-Boyes SM, Mellors JW, Baric RS, Bahar I, Dimitrov DS, Subramaniam S, Martinez DR, Li W. Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains. bioRxiv 2022:2022.02.18.481058. [PMID: 35194603 PMCID: PMC8863138 DOI: 10.1101/2022.02.18.481058] [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] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics that are effective against a variety of strains of the virus. Herein, we characterize a human V H domain, F6, which we generated by sequentially panning large phage displayed V H libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized V H domain, resulted in a construct (F6-ab8-Fc) that neutralized Omicron pseudoviruses with a half-maximal neutralizing concentration (IC 50 ) of 4.8 nM in vitro . Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 VOCs - including the recently emerged Omicron variant - and highlight a vulnerable epitope within the spike protein RBD that may be exploited to achieve broad protection against circulating variants.
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Affiliation(s)
- Chuan Chen
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Michelle M. Marti
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michele D. Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Andrew Kim
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Benjamin R. Treat
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Priscila Mayrelle Da Silva Castanha
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan Enick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Xianglei Liu
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Cynthia Adams
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Margaret Grace Hines
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Zehua Sun
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | | | - Jana L. Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America,Abound Bio, Pittsburgh, PA, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Abound Bio, Pittsburgh, PA, USA,Correspondence: , , and
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3,Correspondence: , , and
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA,Correspondence: , , and
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Correspondence: , , and
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11
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Jacobs JL, Naqvi A, Shah FA, Boltz VF, Kearney MF, McVerry BJ, Ray P, Schaefer C, Fitzpatrick M, Methé B, Lee J, Morris A, Mellors JW, Kitsios GD, Bain W. Plasma SARS-CoV-2 RNA levels as a biomarker of lower respiratory tract SARS-CoV-2 infection in critically ill patients with COVID-19. medRxiv 2022:2022.01.10.22269018. [PMID: 35043122 PMCID: PMC8764731 DOI: 10.1101/2022.01.10.22269018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Plasma SARS-CoV-2 viral RNA (vRNA) levels are predictive of COVID-19 outcomes in hospitalized patients, but whether plasma vRNA reflects lower respiratory tract (LRT) vRNA levels is unclear. We compared plasma and LRT vRNA levels in simultaneously collected longitudinal samples from mechanically-ventilated patients with COVID-19. LRT and plasma vRNA levels were strongly correlated at first sampling (r=0.83, p<10 -8 ) and then declined in parallel except in non-survivors who exhibited delayed vRNA clearance in LRT samples. Plasma vRNA measurement may offer a practical surrogate of LRT vRNA burden in critically ill patients, especially early in severe disease.
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Affiliation(s)
- Jana L. Jacobs
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Asma Naqvi
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Valerie F. Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Meghan Fitzpatrick
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Janet Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John W. Mellors
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
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12
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Jacobs JL, Bain W, Naqvi A, Staines B, Castanha PMS, Yang H, Boltz VF, Barratt-Boyes S, Marques ETA, Mitchell SL, Methé B, Olonisakin TF, Haidar G, Burke TW, Petzold E, Denny T, Woods CW, McVerry BJ, Lee JS, Watkins SC, St Croix CM, Morris A, Kearney MF, Ladinsky MS, Bjorkman PJ, Kitsios GD, Mellors JW. Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes. Clin Infect Dis 2021; 74:1525-1533. [PMID: 34374761 PMCID: PMC9070832 DOI: 10.1093/cid/ciab686] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [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: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA) is detected in the bloodstream of some patients with coronavirus disease 2019 (COVID-19), but it is not clear whether this RNAemia reflects viremia (ie, virus particles) and how it relates to host immune responses and outcomes. METHODS SARS-CoV-2 vRNA was quantified in plasma samples from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non-intensive care unit [ICU]), and 23 ICU patients. vRNA levels were compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in plasma. RESULTS SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6%, and 11.1% of ICU, non-ICU, and outpatients, respectively. Virions were detected in plasma pellets using electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU > non-ICU > outpatients (P < .0001); for inpatients, plasma vRNA levels were strongly associated with higher World Health Organization (WHO) score at admission (P = .01), maximum WHO score (P = .002), and discharge disposition (P = .004). A plasma vRNA level >6000 copies/mL was strongly associated with mortality (hazard ratio, 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (P < .01) but not with plasma neutralizing antibody titers (P = .8). CONCLUSIONS Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers.
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Affiliation(s)
- Jana L Jacobs
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Priscila M S Castanha
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,School of Medicine, Tsinghua University, Beijing, China
| | - Valerie F Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Simon Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tolani F Olonisakin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Thomas Denny
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Chris W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Claudette M St Croix
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Correspondence: John W. Mellors, Division of Infectious Diseases, University of Pittsburgh, Scaife Hall, Suite 818, 3550 Terrace Street, Pittsburgh, PA 15261 USA ()
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Brandt LD, Guo S, Joseph KW, Jacobs JL, Naqvi A, Coffin JM, Kearney MF, Halvas EK, Wu X, Hughes SH, Mellors JW. Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR. Viruses 2021; 13:1235. [PMID: 34202310 PMCID: PMC8310066 DOI: 10.3390/v13071235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022] Open
Abstract
Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.
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Affiliation(s)
- Leah D. Brandt
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., 8560 Progress Drive, ATRF, Room C3004, Frederick, MD 21701, USA; (S.G.); (X.W.)
| | - Kevin W. Joseph
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Jana L. Jacobs
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Asma Naqvi
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, 145 Harrison Avenue, Jaharis 409, Boston, MA 02111, USA;
| | - Mary F. Kearney
- HIV-Dynamics and Replication Program, National Cancer Institute, 1050 Boyles Street, Building 535, Room 308, Frederick, MD 21702, USA; (M.F.K.); (S.H.H.)
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., 8560 Progress Drive, ATRF, Room C3004, Frederick, MD 21701, USA; (S.G.); (X.W.)
| | - Stephen H. Hughes
- HIV-Dynamics and Replication Program, National Cancer Institute, 1050 Boyles Street, Building 535, Room 308, Frederick, MD 21702, USA; (M.F.K.); (S.H.H.)
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
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14
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Nace DA, Kip KE, Mellors JW, Peck Palmer OM, Shurin MR, Mulvey K, Crandall M, Sobolewski MD, Enick PN, McCormick KD, Jacobs JL, Kane AL, Lukanski A, Kip PL, Wells A. Antibody Responses After mRNA-Based COVID-19 Vaccination in Residential Older Adults: Implications for Reopening. J Am Med Dir Assoc 2021; 22:1593-1598. [PMID: 34129831 PMCID: PMC8196346 DOI: 10.1016/j.jamda.2021.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 05/05/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023]
Abstract
Objective COVID-19 disproportionately impacts residents in long-term care facilities. Our objective was to quantify the presence and magnitude of antibody response in vaccinated, older adult residents at assisted living, personal care, and independent living communities. Design A cross-sectional quality improvement study was conducted March 15 – April 1, 2021 in the greater Pittsburgh region. Setting and Population Participants were older adult residents at assisted living, personal care, and independent living communities, who received mRNA-based COVID-19 vaccine. Conditions that impair immune responses were exclusionary criteria. Methods Sera were collected to measure IgG anti-SARS-CoV-2 antibody level with reflex to total anti-SARS-CoV-2 immunoglobulin levels, and blinded evaluation of SARS-CoV-2 pseudovirus neutralization titers. Descriptive statistics, Pearson correlation coefficients, and multiple linear regression analysis evaluated relationships between factors potentially associated with antibody levels. Spearman correlations were calculated between antibody levels and neutralization titers. Results All participants (N = 70) had received two rounds of vaccination and were found to have antibodies with wide variation in relative levels. Antibody levels trended lower in males, advanced age, current use of steroids, and longer length of time from vaccination. Pseudovirus neutralization titer levels were strongly correlated (P < .001) with Beckman Coulter antibody levels [D614 G NT50, rs = 0.91; B.1.1.7 (UK) NT50, rs = 0.91]. Conclusions and Implications Higher functioning, healthier, residential older adults mounted detectable antibody responses when vaccinated with mRNA-based COVID-19 vaccines. Data suggests some degree of immunity is present during the immediate period following vaccination. However, protective effects remain to be determined in larger studies as clinical protection is afforded by ongoing adaptive immunity, which is known to be decreased in older adults. This study provides important preliminary results on level of population risk in older adult residents at assisted living, personal care, and independent living communities to inform reopening strategies, but are not likely to be translatable for residents in nursing homes.
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Affiliation(s)
- David A Nace
- Division of Geriatric Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Kevin E Kip
- Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John W Mellors
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Michael R Shurin
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katie Mulvey
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Melissa Crandall
- Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michele D Sobolewski
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - P Nathan Enick
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D McCormick
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - April L Kane
- Senior Services, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Amy Lukanski
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Paula L Kip
- Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA; Clinical Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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15
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Affiliation(s)
- Kevin D McCormick
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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16
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Halvas EK, Joseph KW, Brandt LD, Guo S, Sobolewski MD, Jacobs JL, Tumiotto C, Bui JK, Cyktor JC, Keele BF, Morse GD, Bale MJ, Shao W, Kearney MF, Coffin JM, Rausch JW, Wu X, Hughes SH, Mellors JW. HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus. J Clin Invest 2021; 130:5847-5857. [PMID: 33016926 DOI: 10.1172/jci138099] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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: 03/13/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUNDHIV-1 viremia that is not suppressed by combination antiretroviral therapy (ART) is generally attributed to incomplete medication adherence and/or drug resistance. We evaluated individuals referred by clinicians for nonsuppressible viremia (plasma HIV-1 RNA above 40 copies/mL) despite reported adherence to ART and the absence of drug resistance to the current ART regimen.METHODSSamples were collected from at least 2 time points from 8 donors who had nonsuppressible viremia for more than 6 months. Single templates of HIV-1 RNA obtained from plasma and viral outgrowth of cultured cells and from proviral DNA were amplified by PCR and sequenced for evidence of clones of cells that produced infectious viruses. Clones were confirmed by host-proviral integration site analysis.RESULTSHIV-1 genomic RNA with identical sequences were identified in plasma samples from all 8 donors. The identical viral RNA sequences did not change over time and did not evolve resistance to the ART regimen. In 4 of the donors, viral RNA sequences obtained from plasma matched those sequences from viral outgrowth cultures, indicating that the viruses were replication competent. Integration sites for infectious proviruses from those 4 donors were mapped to the introns of the MATR3, ZNF268, ZNF721/ABCA11P, and ABCA11P genes. The sizes of the clones were estimated to be from 50 million to 350 million cells.CONCLUSIONThese findings show that clones of HIV-1-infected cells producing virus can cause failure of ART to suppress viremia. The mechanisms involved in clonal expansion and persistence need to be defined to effectively target viremia and the HIV-1 reservoir.FUNDINGNational Cancer Institute, NIH; Howard Hughes Medical Research Fellows Program, Howard Hughes Medical Institute; Bill and Melinda Gates Foundation; Office of AIDS Research; American Cancer Society; National Cancer Institute through a Leidos subcontract; National Institute for Allergy and Infectious Diseases, NIH, to the I4C Martin Delaney Collaboratory; University of Rochester Center for AIDS Research and University of Rochester HIV/AIDS Clinical Trials Unit.
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Affiliation(s)
- Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin W Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah D Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | | | - Jana L Jacobs
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Camille Tumiotto
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John K Bui
- New York-Presbyterian Hospital/Weill Cornell Medical Center, Weill Department of Medicine, New York, New York, USA
| | - Joshua C Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Gene D Morse
- NYS Center of Excellence in Bioinformatics and Life Sciences, Translational Pharmacology Research Core, University at Buffalo, Buffalo, New York, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Wei Shao
- Advanced Biomedical Computing Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - John W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Abstract
PURPOSE OF REVIEW In response to the HIV-AIDS pandemic, great strides have been made in developing molecular methods that accurately quantify nucleic acid products of HIV-1 at different stages of viral replication and to assess HIV-1 sequence diversity and its effect on susceptibility to small molecule inhibitors and neutralizing antibodies. Here, we review how knowledge gained from these approaches, including viral RNA quantification and sequence analyses, have been rapidly applied to study SARS-CoV-2 and the COVID-19 pandemic. RECENT FINDINGS Recent studies have shown detection of SARS-CoV-2 RNA in blood of infected individuals by reverse transcriptase PCR (RT-PCR); and, as in HIV-1 infection, there is growing evidence that the level of viral RNA in plasma may be related to COVID disease severity. Unlike HIV-1, SARS-CoV-2 sequences are highly conserved limiting SARS-CoV-2 sequencing applications to investigating interpatient genetic diversity for phylogenetic analysis. Sensitive sequencing technologies, originally developed for HIV-1, will be needed to investigate intrapatient SARS-CoV-2 genetic variation in response to antiviral therapeutics and vaccines. SUMMARY Methods used for HIV-1 have been rapidly applied to SARS-CoV-2/COVID-19 to understand pathogenesis and prognosis. Further application of such methods should improve precision of therapy and outcome.
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Affiliation(s)
- Kevin D McCormick
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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18
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Jacobs JL, Mellors JW. Detection of SARS-CoV-2 RNA in Blood of Patients with COVID-19: What Does It Mean? Clin Infect Dis 2020; 73:e2898-e2900. [PMID: 32898242 PMCID: PMC7499541 DOI: 10.1093/cid/ciaa1316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine
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19
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Roth MG, Jacobs JL, Napieralski S, Byrne AM, Stouffer-Hopkins A, Warner F, Chilvers MI. Fluopyram Suppresses Population Densities of Heterodera glycines in Field and Greenhouse Studies in Michigan. Plant Dis 2020; 104:1305-1311. [PMID: 32155114 DOI: 10.1094/pdis-04-19-0874-re] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, causes significant damage to soybean production annually. Fluopyram is a fungicide commonly used in soybean seed treatments intended to control soilborne fungal pathogens; however, recent studies have also suggested inhibitory effects on SCN. We examined the effects of a fluopyram seed treatment, ILeVO, on SCN reproduction, sudden death syndrome (SDS) development, and yield in a 3-year field study. Overall, fluopyram had a significant effect on yield (P = 0.046) and end-of-season SCN eggs and second-stage juveniles (Pf, P = 0.033) but no significant effect on SCN reproduction (Rf) or SDS disease index (P > 0.05). Post hoc tests indicated that fluopyram increased yield and suppressed SCN quantities. However, Rf was consistently greater than 1 whether or not the seed was treated with fluopyram, indicating that SCN populations were still increasing in the presence of fluopyram. A follow-up greenhouse study indicated that fluopyram reduced SCN relative to nontreated controls, as observed in the field, but only reduced SCN DNA within roots of a susceptible cultivar. These results indicate that fluopyram can suppress SCN quantities relative to nontreated seed but may not successfully reduce nematode populations without the use of additional management strategies.
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Affiliation(s)
- M G Roth
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, U.S.A
| | - J L Jacobs
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - S Napieralski
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - A M Byrne
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - A Stouffer-Hopkins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - F Warner
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - M I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, U.S.A
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20
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Jacobs JL, Halvas EK, Tosiano MA, Mellors JW. Persistent HIV-1 Viremia on Antiretroviral Therapy: Measurement and Mechanisms. Front Microbiol 2019; 10:2383. [PMID: 31681237 PMCID: PMC6804636 DOI: 10.3389/fmicb.2019.02383] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 07/13/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022] Open
Abstract
HIV-1 viremia persists at low-levels despite clinically effective antiretroviral therapy (ART). Here we review new methods to quantify and characterize persistent viremia at the single genome level, and discuss the mechanisms of persistence including clonal expansion of infected cells and tissue origins of viremia. A deeper understanding of how viremia persists on ART is critically important to the design of therapies to eliminate viremia and achieve a functional cure for HIV-1.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Elias K Halvas
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Melissa A Tosiano
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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21
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Spudich S, Robertson KR, Bosch RJ, Gandhi RT, Cyktor JC, Mar H, Macatangay BJ, Lalama CM, Rinaldo C, Collier AC, Godfrey C, Eron JJ, McMahon D, Jacobs JL, Koontz D, Hogg E, Vecchio A, Mellors JW. Persistent HIV-infected cells in cerebrospinal fluid are associated with poorer neurocognitive performance. J Clin Invest 2019; 129:3339-3346. [PMID: 31305262 DOI: 10.1172/jci127413] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 01/15/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUNDPersistence of HIV in sanctuary sites despite antiretroviral therapy (ART) presents a barrier to HIV remission and may affect neurocognitive function. We assessed HIV persistence in cerebrospinal fluid (CSF) and associations with inflammation and neurocognitive performance during long-term ART.METHODSParticipants enrolled in the AIDS Clinical Trials Group (ACTG) HIV Reservoirs Cohort Study (A5321) underwent concurrent lumbar puncture, phlebotomy, and neurocognitive assessment. Cell-associated HIV DNA and HIV RNA (CA-DNA, CA-RNA) were measured by quantitative PCR (qPCR). in peripheral blood mononuclear cells (PBMCs) and in cell pellets from CSF. In CSF supernatant and blood plasma, cell-free HIV RNA was quantified by qPCR with single copy sensitivity, and inflammatory biomarkers were measured by enzyme immunoassay.RESULTSSixty-nine participants (97% male, median age 50 years, CD4 696 cells/mm3, plasma HIV RNA <100 copies/mL) were assessed after a median 8.6 years of ART. In CSF, cell-free RNA was detected in 4%, CA-RNA in 9%, and CA-DNA in 48% of participants (median level 2.1 copies/103 cells). Detection of cell-free CSF HIV RNA was associated with higher plasma HIV RNA (P = 0.007). CSF inflammatory biomarkers did not correlate with HIV persistence measures. Detection of CSF CA-DNA HIV was associated with worse neurocognitive outcomes including global deficit score (P = 0.005), even after adjusting for age and nadir CD4 count.CONCLUSIONHIV-infected cells persist in CSF in almost half of individuals on long-term ART, and their detection is associated with poorer neurocognitive performance.FUNDINGThis observational study, AIDS Clinical Trials Group (ACTG) HIV Reservoirs Cohort Study (A5321), was supported by the National Institutes of Health (NIAID and NIMH).
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Affiliation(s)
| | - Kevin R Robertson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald J Bosch
- Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Hanna Mar
- Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | | | | | - Joseph J Eron
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Jana L Jacobs
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dianna Koontz
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Evelyn Hogg
- Social & Scientific Systems, Silver Spring, Maryland, USA
| | - Alyssa Vecchio
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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22
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Alvarez-Hess PS, Williams SRO, Jacobs JL, Hannah MC, Beauchemin KA, Eckard RJ, Wales WJ, Morris GL, Moate PJ. Effect of dietary fat supplementation on methane emissions from dairy cows fed wheat or corn. J Dairy Sci 2019; 102:2714-2723. [PMID: 30660414 DOI: 10.3168/jds.2018-14721] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 03/08/2018] [Accepted: 11/21/2018] [Indexed: 11/19/2022]
Abstract
Diets that contain high proportions of either wheat or supplementary fat have been individually reported to reduce enteric methane production. The objective of this research was to determine the effect of dietary fat supplementation on methane emissions and milk yield from cows fed diets containing either corn or wheat grains. It was hypothesized that cows fed a diet containing wheat would produce less methane and have lower methane yield (methane per kg of dry matter intake; MY) than cows fed a diet containing corn and that methane mitigation from fat supplementation would occur irrespective of the type of grain in the basal diet. The experiment involved 32 Holstein-Friesian dairy cows allocated to 1 of 4 treatment groups (n = 8) and individually fed different diets restricted to approximately 90% of their mean ad libitum intake measured during a covariate period. All animals were offered 11.5 kg of dry matter/d of alfalfa hay, 1.8 kg of dry matter/d of solvent-extracted canola meal, and 1 of 4 dietary supplements. Dietary supplements were 8 kg of dry matter/d of either corn or wheat, or these same treatments with the addition of 0.8 kg of canola oil. In this 5-wk experiment, d 1 to 7 served as the covariate period, d 8 to 14 as the transition period, d 15 to 28 as the adaptation period, and d 29 to 35 as the experimental period. Cows were fed their full treatment diets from d 15 to 35 during which time milk production and feed intake were measured daily. During d 29 to 35, methane production was measured for individual cows daily using the sulfur hexafluoride tracer method. The resulting averages for milk production and feed intake were analyzed by analysis of covariance with factorial grain by fat as treatment structure, animal as the unit within blocks, and the corresponding milk production or feed intake covariate averages as principal covariate. Data on milk fatty acids, ruminal fluid data on pH, ammonia, volatile fatty acids, protozoa, and methane were analyzed by ANOVA using the same treatment and blocking structures excluding the principal covariate. Cows fed a diet containing wheat had greater MY than cows fed a diet containing corn. Irrespective of the type of grain in the diet, increasing the fat concentration from 2 to 6% dry matter reduced MY. It is concluded that the grain component in the basal diet does not affect the mitigating effects of dietary fat supplements on MY.
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Affiliation(s)
- P S Alvarez-Hess
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia.
| | - S R O Williams
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
| | - J L Jacobs
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
| | - M C Hannah
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
| | - K A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada T1J 4B1
| | - R J Eckard
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - W J Wales
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
| | - G L Morris
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
| | - P J Moate
- Agriculture Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, Victoria 3821, Australia
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23
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Abstract
This review discusses the importance of red meat from ruminants as a source of omega-3 (n-3) fatty acids (FAs) for human life in the context of the contribution of animals to human welfare. Red meat is a valuable food commodity for human life because it is naturally rich in key nutrients such as protein, trace elements, vitamins and essential FAs. In developed countries and high socio-economic groups from developing countries, red meat intake is greater than that of oily fish, owing to availability, preference and affordability. Omega-3 FA concentration is higher in red meat (beef, lamb and mutton) than in white meat (pork, poultry and turkey), due to the fibre types present in muscle tissues and the specialised digestive systems of ruminants. There is mounting evidence that regular consumption of n-3 FAs is beneficial for growth and development as well as the health and welfare of humans of all ages. The dietary background of ruminants significantly influences the concentration of n-3 FAs in red meat. Meat from forage- or grassfed ruminants has a greater concentration of n-3 FAs than that from their feedlot or grain-fed counterparts and can also offer a favourable n-6:n-3 ratio in the meat. Scientific literature shows that the advantages of consuming n-3 FAs enriched meat (foods) outweigh the disadvantages.
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Ponnampalam EN, Kerr MG, Butler KL, Cottrell JJ, Dunshea FR, Jacobs JL. Filling the out of season gaps for lamb and hogget production: Diet and genetic influence on carcass yield, carcass composition and retail value of meat. Meat Sci 2018; 148:156-163. [PMID: 30388480 DOI: 10.1016/j.meatsci.2018.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/16/2018] [Revised: 08/31/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
This study investigated the use of camelina forage and meal supplementation to a finishing diet on carcass traits, composition and retail value of lamb and hoggets. The metabolisable energy and crude protein concentrations of all 3 diets were 10-11 MJ/kg DM and 14-15% CP. Thirty maternal Composite wether lambs (28-38 kg) and 30 Merino wether hoggets (37-43 kg) were used in a 3 × 2 factorial experiment. Animals were slaughtered after 10 weeks of feeding with carcasses classified as 'Heavy lamb' or 'Heavy hogget' (>22 kg carcass weight). Carcass traits, composition, meat mineral concentrations and retail colour were measured. Camelina diets increased liveweight (P < 0.02) and carcass weight (P < 0.002) for both sheep types. Carcass weight (P < 0.005) and dressing % (P < 0.01) were lower for Merino hoggets than Composite lambs. Mineral concentration and retail colour stability of fresh meat were unaffected by diet, with 72 h retail colour considered acceptable for consumers.
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Affiliation(s)
- E N Ponnampalam
- Animal Production Science, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC 3083, Australia.
| | - M G Kerr
- Animal Production Science, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC 3083, Australia
| | - K L Butler
- Biometrics Group, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Hamilton, VIC 3300, Australia
| | - J J Cottrell
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - F R Dunshea
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - J L Jacobs
- Animal Production Science, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Ellinbank, VIC 3821, Australia
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Hong F, Jacobs JL, Aga E, Cillo AR, Fyne E, Koontz DL, Zheng L, Mellors JW. Associations between HIV-1 DNA copy number, proviral transcriptional activity, and plasma viremia in individuals off or on suppressive antiretroviral therapy. Virology 2018; 521:51-57. [PMID: 29879542 DOI: 10.1016/j.virol.2018.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/13/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
The relationships between HIV-1 DNA copy number, proviral transcriptional activity, and residual plasma viremia in individuals off and on ART are not well defined. To address this, we performed a cross-sectional study of 12 viremic donors and 23 ART-treated virologically suppressed (plasma HIV-1 RNA<20 copies/ml) donors. We report a strong association between HIV-1 DNA copy number and HIV-1 transcriptional activity in blood that persists on suppressive ART, but not between transcriptional activity and the levels of persistent viremia on ART. The latter finding contrasts with that in viremic donors and suggests that most HIV transcription in donors on suppressive ART does not result in virion production. This uncoupling of proviral transcription and viremia warrants closer investigation.
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Affiliation(s)
- Feiyu Hong
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Jana L Jacobs
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Evgenia Aga
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Anthony R Cillo
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Elizabeth Fyne
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Dianna L Koontz
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Lu Zheng
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - John W Mellors
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States.
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Moate PJ, Jacobs JL, Hannah MC, Morris GL, Beauchemin KA, Alvarez Hess PS, Eckard RJ, Liu Z, Rochfort S, Wales WJ, Williams SRO. Adaptation responses in milk fat yield and methane emissions of dairy cows when wheat was included in their diet for 16 weeks. J Dairy Sci 2018; 101:7117-7132. [PMID: 29729908 DOI: 10.3168/jds.2017-14334] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022]
Abstract
Short-term studies have shown that feeding dairy cows diets containing a high proportion (>40%) of wheat may result in reduced milk fat concentration and reduced CH4 emissions (g of CH4/cow per d), but no long-term studies have been done on these responses. This study compared the milk production and CH4 responses when 24 dairy cows were fed diets containing high proportions of either wheat or corn over 16 wk. Cows were assigned to 2 groups and offered a diet (CRN) containing 10.0 kg of dry matter/d of crushed corn grain, 1.8 kg of dry matter/d of canola meal, 0.2 kg of dry matter/d of minerals, and 11.0 kg of dry matter/d of chopped alfalfa hay or a similar diet (WHT) in which wheat replaced the corn. Dry matter intake and milk yields of individual cows were measured daily. Methane emissions from individual cows were measured using controlled climate respiration chambers over 2 consecutive days during each of wk 4, 10, and 16. Milk composition was measured on the 2 d when cows were in chambers during wk 4, 10, and 16. Over the 16-wk experimental period, total dry matter intake remained relatively constant and similar for the 2 dietary treatment groups. At wk 4, CH4 emission, CH4 yield (g of CH4/kg of dry matter intake), milk fat yield, and milk fat concentration were substantially less in cows fed the WHT diet compared with the same metrics in cows fed the CRN diet; but these differences were not apparent at wk 10 and 16. The responses over time in these metrics were not similar in all cows. In 4 cows fed the WHT diet, CH4 yield, milk fat concentration, and milk fat yield remained relatively constant from wk 4 to 16, whereas for 5 fed the WHT diet, their CH4 emissions, milk fat yields, and milk fat concentrations almost doubled between wk 4 and 16. In the short term (4 wk), the inclusion of approximately 45% wheat instead of corn in the diet of cows resulted in reductions of 39% in CH4 yield, 35% in milk fat concentration, and 40% in milk fat yield. However, these reductions did not persist to wk 10 or beyond. Our data indicate that cows do not all respond in the same way with some "adaptive" cows showing a marked increase in CH4 yield, milk fat concentration, and milk fat yield after wk 4, whereas in other "nonadaptive" cows, these metrics were persistently inhibited to 16 wk. This research shows that short-term studies on dietary interventions to mitigate enteric CH4 emissions may not always predict the long-term effects of such interventions.
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Affiliation(s)
- P J Moate
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia.
| | - J L Jacobs
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia
| | - M C Hannah
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia
| | - G L Morris
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia
| | - K A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada T1J 4B1
| | - P S Alvarez Hess
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - R J Eckard
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Z Liu
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - S Rochfort
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, 5 Ring Road, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - W J Wales
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia
| | - S R O Williams
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Research Victoria, Ellinbank, Victoria 3821, Australia
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27
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Ponnampalam EN, Hopkins DL, Giri K, Jacobs JL, Plozza T, Lewandowski P, Bekhit A. The use of oxidative stress biomarkers in live animals (in vivo) to predict meat quality deterioration postmortem (in vitro) caused by changes in muscle biochemical components. J Anim Sci 2017; 95:3012-3024. [PMID: 28727089 DOI: 10.2527/jas.2016.0887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to determine whether circulating concentrations of blood isoprostanes can be used as an effective biomarker in lambs to predict degradation of color and/or lipid stability in meat. Lambs ( = 84) were fed diets of either lucerne pasture, annual ryegrass pasture, a commercial feedlot pellet, or a combination of annual ryegrass and feedlot pellet for 8 wk, including a 2-wk adaptation period. Blood isoprostane concentration at wk 0, 4, 6 or 8 of feeding was determined. Blood isoprostane concentration for each animal was then correlated with muscle biochemical components that impact color and/or lipid oxidative status during retail display. This included lipid oxidation levels in muscle assessed by thiobarbituric acid reactive substances and meat redness determined by a HunterLab colorimetric spectrometer. Lambs that consumed the commercial feedlot pellet had a lower muscle vitamin E level (< 0.01) and a greater level of -6 PUFA ( < 0.001) compared with lambs finished on annual ryegrass or lucerne. Lipid oxidation levels were greatest for lambs finished on the feedlot ration, lowest in lambs finished on the ryegrass diet, and intermediate for lambs finished on lucerne and ryegrass-feedlot combination ( < 0.01). After 8 wk of feeding, blood isoprostane concentration was positively correlated with lipid oxidation of meat displayed for 72 h in simulated retail conditions ( < 0.01). There was a negative linear relationship between isoprostane concentration and muscle vitamin E concentration ( = 0.07), lipid oxidation and muscle vitamin E concentration ( < 0.01) but a positive linear relationship between isoprostane concentration and muscle -6 PUFA ( < 0.001) or lipid oxidation and muscle -6 PUFA concentration ( < 0.001). Blood isoprostane concentration and lipid oxidation in meat were influenced by muscle vitamin E and -6 PUFA but not by -3 PUFA. There was no significant relationship observed between blood isoprostane concentration at 0, 4, 6 or 8 wk feeding vs. overall meat color (redness of meat) at 0 and 72 h of display, stored under simulated retail conditions. The results indicate that circulating blood isoprostane concentration can be a useful tool to predict the oxidative status of postmortem meat. Future work will examine the impact of this relationship on meat flavor/aroma deterioration post farm.
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Rossman DR, Rojas A, Jacobs JL, Mukankusi C, Kelly JD, Chilvers MI. Pathogenicity and Virulence of Soilborne Oomycetes on Phaseolus vulgaris. Plant Dis 2017; 101:1851-1859. [PMID: 30677317 DOI: 10.1094/pdis-02-17-0178-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dry bean (Phaseolus vulgaris L.) is a globally important leguminous food crop. Yields can be reduced by high incidence of soilborne oomycetes that cause seedling disease. Breeders have attempted to develop Pythium root rot-resistant bean varieties; however, relationships between dry bean and most soilborne oomycete species remain uncharacterized. Oomycete species (n = 28), including Pythium spp. and Phytopythium spp., were tested in a growth chamber seedling assay at 20°C and an in vitro seed assay at 20°C and 26°C to evaluate their pathogenicity and virulence on 'Red Hawk' dark red kidney bean and 'Zorro' black bean. Root size or disease severity was significantly impacted by 14 oomycete species, though results varied by bean variety, temperature, and assay. Of these 14 pathogenic oomycete species, 11 species exhibited significant differences in DSI due to temperature on at least one bean variety. Pythium aphanidermatum, P. myriotylum, P. ultimum, P. ultimum var. sporangiiferium, and P. ultimum var. ultimum were the most virulent species in both assays, causing seed rot and pre-emergence damping-off of dry bean. Oomycete species were clustered into three groups based on symptom development: seed rot pathogens, root rot pathogens, or nonpathogens. Intraspecific variability in virulence was observed for eight of the 14 pathogenic oomycete species. Improved understanding of Pythium and Phytopythium interactions with dry bean may enable breeders and pathologists to more effectively evaluate strategies for oomycete seedling disease management.
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Affiliation(s)
- D R Rossman
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - A Rojas
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - J L Jacobs
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - C Mukankusi
- International Center for Tropical Agriculture, Kawanda Agricultural Research Institute, Kampala, Uganda
| | - J D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - M I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
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Muir SK, Ward GN, Jacobs JL. Herbage intake and milk production of late-lactation dairy cows offered a second-year chicory crop during summer. J Dairy Sci 2015; 98:8825-35. [PMID: 26409973 DOI: 10.3168/jds.2014-9147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 08/03/2015] [Indexed: 12/16/2023]
Abstract
Chicory (Cichorum intybus L.) is a summer-active forage herb which has been proposed as an option to increase summer feed supply, increase dry matter intake, nutrient intake, and milk yield from nonirrigated dairy production systems in southern Australia. Dry matter intake, nutrient intake, milk yield, and yield of milk fat and protein of predominantly Holstein-Friesian dairy cows in late lactation consuming 3 herbage-based diets (4 replicates per treatment) were measured. The 3 grazed herbages were second-year chicory (CHIC) and perennial ryegrass (Lolium perenne L.; PRG) monocultures and a mixed sward (~50:50) of chicory and perennial ryegrass (MIX). All diets (CHIC, PRG, and MIX) were supplemented with alfalfa (Medicago sativa L.) hay (5.5kg of DM/cow per day) and an energy-based concentrate pellet (4.0kg of DM/cow per day). There were no significant differences in milk yield (12.0 to 12.6kg/d across the treatments) or the yield of milk fat (539 to 585g/d) and milk protein (433 to 447g/d) between the 3 herbage-based diets. No differences in DMI (17.9 to 19.2kg/d) or estimated metabolizable energy intake (173 to 185MJ/d) were noted between treatments. Estimated metabolizable energy concentrations in the forages on offer were lower in CHIC than PRG (7.6 vs. 8.2MJ/kg of dry matter), but the concentration in consumed herbage was not different (9.1 vs. 9.2MJ/kg of dry matter); as such, potential for increased milk yield in cows offered CHIC was limited. Increased concentration of polyunsaturated fatty acids was observed in chicory herbage compared with perennial ryegrass. This was associated with increased milk conjugated linoleic acid and milk polyunsaturated fatty acids when chicory formed part of the diet (CHIC compared to PRG and MIX). Chicory could be used as an alternative to perennial ryegrass in summer; however, the developmental stage of chicory will influence concentrations of metabolizable energy and neutral detergent fiber and, therefore, intake and milk production responses compared with perennial ryegrass.
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Affiliation(s)
- S K Muir
- Department of Economic Development, Jobs, Transport and Resources, Warrnambool, Vic 3280, Australia.
| | - G N Ward
- Department of Economic Development, Jobs, Transport and Resources, Warrnambool, Vic 3280, Australia
| | - J L Jacobs
- Department of Economic Development, Jobs, Transport and Resources, Warrnambool, Vic 3280, Australia
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Auldist MJ, Marett LC, Greenwood JS, Wright MM, Hannah M, Jacobs JL, Wales WJ. Milk production responses to different strategies for feeding supplements to grazing dairy cows. J Dairy Sci 2015; 99:657-71. [PMID: 26585473 DOI: 10.3168/jds.2015-9834] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 05/20/2015] [Accepted: 09/17/2015] [Indexed: 11/19/2022]
Abstract
Milk production responses of grazing cows offered supplements in different ways were measured. Holstein-Friesian cows, averaging 45 d in milk, were allocated into 8 groups of 24, with 2 groups randomly assigned to each of 4 feeding strategies. These were control: cows grazed a restricted allowance of perennial ryegrass pasture supplemented with milled wheat grain fed in the milking parlor and alfalfa hay offered in the paddock; FGM: same pasture and allowance as the control supplemented with a formulated grain mix containing wheat grain, corn grain, and canola meal fed in the parlor and alfalfa hay fed in the paddock; PMRL: same pasture and allowance as the control, supplemented with a PMR consisting of the same FGM but mixed with alfalfa hay and presented on a feed pad after each milking; and PMRH: same PMR fed in the same way as PMRL but with a higher pasture allowance. For all strategies, supplements provided the same metabolizable energy and grain:forage ratio [75:25, dry matter (DM) basis]. Each group of 24 cows was further allocated into 4 groups of 6, which were randomly assigned to receive 8, 12, 14, or 16 kg of DM supplement/cow per d. Thus, 2 replicated groups per supplement amount per dietary strategy were used. The experiment had a 14-d adaptation period and a 14-d measurement period. Pasture allowance, measured to ground level, was approximately 14 kg of DM/d for control, FGM, and PMRL cows, and 28 kg of DM/d for the PMRH cows, and was offered in addition to the supplement. Positive linear responses to increasing amounts of supplement were observed for yield of milk, energy-corrected milk, fat, and protein for cows on all 4 supplement feeding strategies. Production of energy-corrected milk was greatest for PMRH cows, intermediate for FGM and PMRL cows, and lowest for control cows. Some of these differences in milk production related to differences in intake of pasture and supplement. Milk fat concentration decreased with increasing amount of supplement for all feeding strategies, but the decline was most marked for the control cows. Milk protein concentration increased for all groups as the amount of supplement increased, but was greater for FGM, PMRL, and PMRH cows than control cows. It is concluded that when supplements are fed to grazing dairy cows, inclusion of corn grain and canola meal can increase milk production even at similar metabolizable energy intakes, and that it does not matter whether these supplements are fed as a PMR or in the parlor and paddock.
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Affiliation(s)
- M J Auldist
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia.
| | - L C Marett
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
| | - J S Greenwood
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
| | - M M Wright
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
| | - M Hannah
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
| | - J L Jacobs
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
| | - W J Wales
- Agriculture Research Division, Department of Economic Development, Jobs, Transport and Resources, Ellinbank VIC 3821, Australia
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Mollov D, Chilvers MI, Jacobs JL. First Report of Aster Yellows Phytoplasma in Soybean in Michigan. Plant Dis 2014; 98:1578. [PMID: 30699807 DOI: 10.1094/pdis-05-14-0451-pdn] [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] [Indexed: 06/09/2023]
Abstract
During the summer of 2012, soybean plants in a commercial field in Clinton County, Michigan, exhibited symptoms characteristic of phytoplasmal diseases (1,2). Symptoms included extensive top dieback, stunting, purple stem surfaces, internal necrosis, leaf vein discoloration, and bud proliferation. Approximately 80% of plants in a half hectare along the southern edge of the field were symptomatic, although the majority of plants in the 4-ha field appeared symptomless. Total genomic DNA was extracted from one symptomatic and one asymptomatic leaf sample using a Qiagen DNeasy Plant Mini Kit (Qiagen, Germantown, MD) according to manufacturer's instructions. The DNA was used as template in direct PCR primed by the phytoplasma-universal primers P1/P7 followed by nested PCR primed by P1/AYint (3). Reactions containing template DNA from the symptomatic plant yielded ribosomal RNA gene amplicons of 1.8 kbp (P1/P7-primed) and 1.6 kbp (P1/AYint-primed), respectively. Reactions containing template DNA from the asymptomatic plant or water did not yield amplicons. The products of PCRs primed by P1/P7 were purified using PureLink PCR Purification kit (Life Technologies, Carlsbad, CA) and cloned in a pGem T-Easy vector system (Promega, Madison, WI). Three separate clones were sequenced using the sequencing primers M13For, M13Rev, SAYF nt 755, (5'-AAAGCGTGGGGAGCAAACAG), and SAYR nt 1159, (5'-TTTGACGTCGTCCCCACCTT). The sequences of all three clones were identical. A consensus (Sequencher 4.1, Gene Codes Corporation, Ann Arbor, MI) nucleotide sequence of 1,830 bp was deposited in GenBank under the accession number KF528320. A BLASTn similarity search revealed that the sequence shared 100% identity to rDNA of aster yellows phytoplasma (AF222063). Additionally, analysis of the 16Sr group/subgroup classification, based on in silico RFLP analyses using iPhyClassifier (4), indicated that the soybean phytoplasma is a member of subgroup 16SrI-B aster yellows phytoplasma subgroup. In a phylogenic tree deduced using the neighbor joining algorithm, the phytoplasma consensus sequence obtained from soybean in Michigan clustered with other group 16SrI (aster yellows phytoplasma) strains. While aster yellows phytoplasma has been previously reported in soybean in Wisconsin (2), to our knowledge, this is the first report of aster yellows in soybean in Michigan. References: (1) C. R. Grau et al. Compendium of Soybean Diseases, 4th ed. G. L. Hartman et al., eds. American Phytopathological Society, St. Paul, MN, 1999. (2) M. E. Lee et al. Can. J. Plant Pathol. 24:125, 2002. (3) C. D. Smart et al. Appl. Env. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
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Affiliation(s)
| | - M I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
| | - J L Jacobs
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
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32
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Moate PJ, Williams SRO, Torok VA, Hannah MC, Ribaux BE, Tavendale MH, Eckard RJ, Jacobs JL, Auldist MJ, Wales WJ. Grape marc reduces methane emissions when fed to dairy cows. J Dairy Sci 2014; 97:5073-87. [PMID: 24952778 DOI: 10.3168/jds.2013-7588] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 10/10/2013] [Accepted: 05/05/2014] [Indexed: 11/19/2022]
Abstract
Grape marc (the skins, seeds, stalk, and stems remaining after grapes have been pressed to make wine) is currently a by-product used as a feed supplement by the dairy and beef industries. Grape marc contains condensed tannins and has high concentrations of crude fat; both these substances can reduce enteric methane (CH4) production when fed to ruminants. This experiment examined the effects of dietary supplementation with either dried, pelleted grape marc or ensiled grape marc on yield and composition of milk, enteric CH4 emissions, and ruminal microbiota in dairy cows. Thirty-two Holstein dairy cows in late lactation were offered 1 of 3 diets: a control (CON) diet; a diet containing dried, pelleted grape marc (DGM); and a diet containing ensiled grape marc (EGM). The diet offered to cows in the CON group contained 14.0kg of alfalfa hay dry matter (DM)/d and 4.3kg of concentrate mix DM/d. Diets offered to cows in the DGM and EGM groups contained 9.0kg of alfalfa hay DM/d, 4.3kg of concentrate mix DM/d, and 5.0kg of dried or ensiled grape marc DM/d, respectively. These diets were offered individually to cows for 18d. Individual cow feed intake and milk yield were measured daily and milk composition measured on 4d/wk. Individual cow CH4 emissions were measured by the SF6 tracer technique on 2d at the end of the experiment. Ruminal bacterial, archaeal, fungal, and protozoan communities were quantified on the last day of the experiment. Cows offered the CON, DGM, and EGM diets, ate 95, 98, and 96%, respectively, of the DM offered. The mean milk yield of cows fed the EGM diet was 12.8kg/cow per day and was less than that of cows fed either the CON diet (14.6kg/cow per day) or the DGM diet (15.4kg/cow per day). Feeding DGM and EGM diets was associated with decreased milk fat yields, lower concentrations of saturated fatty acids, and enhanced concentrations of mono- and polyunsaturated fatty acids, in particular cis-9,trans-11 linoleic acid. The mean CH4 emissions were 470, 375, and 389g of CH4/cow per day for cows fed the CON, DGM, and EGM diets, respectively. Methane yields were 26.1, 20.2, and 21.5g of CH4/kg of DMI for cows fed the CON, DGM, and EGM diets, respectively. The ruminal bacterial and archaeal communities were altered by dietary supplementation with grape marc, but ruminal fungal and protozoan communities were not. Decreases of approximately 20% in CH4 emissions and CH4 yield indicate that feeding DGM and EGM could play a role in CH4 abatement.
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Affiliation(s)
- P J Moate
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia.
| | - S R O Williams
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia
| | - V A Torok
- South Australian Research and Development Institute, Soil Biology and Diagnostics, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - M C Hannah
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia
| | - B E Ribaux
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia
| | | | - R J Eckard
- Melbourne School of Land and Environment, The University of Melbourne, Victoria 3010, Australia
| | - J L Jacobs
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Warrnambool, Victoria 3280, Australia
| | - M J Auldist
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia
| | - W J Wales
- Future Farming Systems Research Division, Department of Environment and Primary Industries, Ellinbank, Victoria 3821, Australia
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Jesche A, McCallum RW, Thimmaiah S, Jacobs JL, Taufour V, Kreyssig A, Houk RS, Bud'ko SL, Canfield PC. Giant magnetic anisotropy and tunnelling of the magnetization in Li₂(Li(1-x)Fe(x))N. Nat Commun 2014; 5:3333. [PMID: 24566374 DOI: 10.1038/ncomms4333] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/28/2014] [Indexed: 11/09/2022] Open
Abstract
Large magnetic anisotropy and coercivity are key properties of functional magnetic materials and are generally associated with rare earth elements. Here we show an extreme, uniaxial magnetic anisotropy and the emergence of magnetic hysteresis in Li₂(Li(1-x)Fe(x))N. An extrapolated, magnetic anisotropy field of 220 T and a coercivity field of over 11 T at 2 K outperform all known hard ferromagnets and single-molecular magnets. Steps in the hysteresis loops and relaxation phenomena in striking similarity to single-molecular magnets are particularly pronounced for x≪1 and indicate the presence of nanoscale magnetic centres. Quantum tunnelling, in the form of temperature-independent relaxation and coercivity, deviation from Arrhenius behaviour and blocking of the relaxation, dominates the magnetic properties up to 10 K. The simple crystal structure, the availability of large single crystals and the ability to vary the Fe concentration make Li₂(Li(1-x)Fe(x))N an ideal model system to study macroscopic quantum effects at elevated temperatures and also a basis for novel functional magnetic materials.
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Affiliation(s)
- A Jesche
- The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - R W McCallum
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - S Thimmaiah
- The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - J L Jacobs
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - V Taufour
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA
| | - A Kreyssig
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA
| | - R S Houk
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - S L Bud'ko
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA
| | - P C Canfield
- 1] The Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA [2] Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA
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Muir SK, Ward GN, Jacobs JL. Milk production and composition of mid-lactation cows consuming perennial ryegrass-and chicory-based diets. J Dairy Sci 2014; 97:1005-15. [PMID: 24290818 DOI: 10.3168/jds.2013-7183] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/22/2013] [Indexed: 11/19/2022]
Abstract
Dry matter intakes (DMI), nutrient selection, and milk production responses of dairy cows grazing 3 herbage-based diets offered at 2 allowances were measured. The 2 allowances were 20 (low) and 30 (high) kg of dry matter (DM)/cow per day and these were applied to 3 herbage types: perennial ryegrass (PRG) and chicory (CHIC+) monocultures and a mixed sward of chicory and perennial ryegrass (MIX). The CHIC+ diet was supplemented with alfalfa hay (approximately 2 kg of DM/cow per day) to maintain dietary neutral detergent fiber (NDF) concentration and all diets were supplemented with energy-based pellets (6 kg of DM/cow per day). Holstein-Friesian dairy cows averaging 136 ± 30 d in milk were allocated to 4 replicates of the 6 treatments using stratified randomization procedures. Cows were adapted to their experimental diets over a 14-d period, with measurements of DMI, milk yield, and composition conducted over the following 10 d. Herbage DMI was lowest (12.8 vs. 14.0 kg of DM/d) for CHIC+ compared with the MIX and PRG, although total forage intake (grazed herbage plus hay) was similar (14.0 to 15.0 kg of DM/d) across the 3 treatments. Milk production, milk protein, and milk fat concentrations were not different between herbage types. Grazed herbage DMI increased with increasing herbage allowance and this was associated with increased milk protein concentration (3.23 to 3.34%) and total casein production (41.7 to 43.6 mg/g). Concentrations of polyunsaturated fatty acids in milk fat, particularly linoleic acid, were increased in milk from cows offered the CHIC+ or the MIX diets, indicating potential benefits of chicory herbage on milk fatty acid concentrations. Although feeding CHIC+ or MIX did not increase milk yield, these herbage types could be used as an alternative to perennial ryegrass pasture in spring.
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Affiliation(s)
- S K Muir
- Department of Environment and Primary Industries, 78 Henna Street, Warrnambool, Victoria 3280, Australia.
| | - G N Ward
- Department of Environment and Primary Industries, 78 Henna Street, Warrnambool, Victoria 3280, Australia
| | - J L Jacobs
- Department of Environment and Primary Industries, 78 Henna Street, Warrnambool, Victoria 3280, Australia
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Oriot P, Selvais P, Radikov J, Jacobs JL, Gilleman U, Loumaye R, Fernandez C. Assessing the incidence of gestational diabetes and neonatal outcomes using the IADPSG guidelines in comparison with the Carpenter and Coustan criteria in a Belgian general hospital. Acta Clin Belg 2014; 69:8-11. [PMID: 24635392 DOI: 10.1179/0001551213z.0000000004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
We have conducted a systematic universal screening for gestational diabetes mellitus (GDM) since 2008, following the criteria outlined by the International Association of Diabetes and Pregnancy Study Group (IADPSG) since 2011. However, we recently replaced the IADPSG standards with those established by the Belgian French Language Gynecologists and Obstetricians Group (GGOLFB). These new criteria indicate GDM when fasting plasma glucose (FPG) is ≥0·92 g/l at the beginning of pregnancy or when an orally provoked hyperglycaemia test (75 g of glucose) between the twenty-fourth and twenty-eighth week results in an FPG of ≥0·92 g/l and/or ≥1·80 g/l after 1 hour and/or ≥1·53 g/l after 2 hours. The goal of this retrospective study was to evaluate the incidence of GDM, neonatal outcomes, and the use of insulin therapy 21 months post-implementation of the IADPSG criteria within our centre. A total of 393 patients were diagnosed with GDM from January 2009 to December 2012. After applying the new criteria, the incidence of GDM rose significantly from 8 to 23% (P<0·0001). However, there were no significant changes in the proportion of GDM patients requiring insulin therapy (34·2% versus 34·7%) or the rate of foetal large for gestational age (11·2% versus 8·8%). In addition, the ≥90% percentile decreased non-significantly from 96·3±0·6% to 94·3±0·70% (P = 0·057), whereas the lower quartiles and the proportion of cesarean deliveries (27·0% versus 25·6%) did not change significantly. Therefore, non-targeted screening significantly increased the incidence of GDM in our centre without significantly decreasing large for gestational age or the number of cesarean deliveries.
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Jacobs JL, Zhu J, Sarkar SN, Coyne CB. Regulation of mitochondrial antiviral signaling (MAVS) expression and signaling by the mitochondria-associated endoplasmic reticulum membrane (MAM) protein Gp78. J Biol Chem 2013; 289:1604-16. [PMID: 24285545 DOI: 10.1074/jbc.m113.520254] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In a previous study, we identified the E3 ubiquitin ligase Gp78 by RNAi high-throughput screening as a gene whose depletion restricted enterovirus infection. In the current study, we show that Gp78, which localizes to the ER-mitochondria interface, is a regulator of RIG-I-like receptor (RLR) antiviral signaling. We show that depletion of Gp78 results in a robust decrease of vesicular stomatitis virus (VSV) infection and a corresponding enhancement of type I interferon (IFN) signaling. Mechanistically, we show that Gp78 modulates type I IFN induction by altering both the expression and signaling of the mitochondria-localized RLR adaptor mitochondrial antiviral signaling (MAVS). Expression of mutants of Gp78 that abolish its E3 ubiquitin ligase and its participation in ER-associated degradation (ERAD) lost their ability to degrade MAVS, but surprisingly maintained their ability to repress RLR signaling. In contrast, Gp78 lacking its entire C terminus lost both its ability to degrade MAVS and repress RLR signaling. We show that Gp78 interacts with both the N- and C-terminal domains of MAVS via its C-terminal RING domain, and that this interaction is required to abrogate Gp78-mediated attenuation of MAVS signaling. Our data thus implicate two parallel pathways by which Gp78 regulates MAVS signaling; one pathway requires its E3 ubiquitin ligase and ERAD activity to directly degrade MAVS, whereas the other pathway occurs independently of these activities, but requires the Gp78 RING domain and occurs via a direct association between this region and MAVS.
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Affiliation(s)
- Jana L Jacobs
- From the Department of Infectious Diseases and Microbiology, Graduate School of Public Health
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Jacobs JL, Coyne CB. Mechanisms of MAVS regulation at the mitochondrial membrane. J Mol Biol 2013; 425:5009-19. [PMID: 24120683 DOI: 10.1016/j.jmb.2013.10.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [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: 08/29/2013] [Revised: 10/02/2013] [Accepted: 10/02/2013] [Indexed: 12/24/2022]
Abstract
Mitochondria have emerged as critical platforms for antiviral innate immune signaling. This is due in large part to the mitochondrial localization of the innate immune signaling adaptor MAVS (mitochondrial antiviral signaling protein), which coordinates signals received from two independent cytosolic pathogen recognition receptors (PRRs) to induce antiviral genes. The existence of a shared adaptor for two central PRRs presents an ideal target by which the host cell can prevent cellular damage induced by uncontrolled inflammation through alteration of MAVS expression and/or signaling. In this review, we focus on the MAVS regulome and review the cellular factors that regulate MAVS by (1) protein-protein interactions, (2) alterations in mitochondrial dynamics, and/or (3) post-translational modifications.
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Affiliation(s)
- Jana L Jacobs
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Abstract
Soybean vein necrosis virus (SVNV) is associated with an emerging disease in soybean producing regions of the United States. Soybean leaves with necrotic vein symptoms were initially noted in 2008 or 2009 in fields across Arkansas, Kansas, Missouri, Illinois, Mississippi, Tennessee, and Kentucky and SVNV was determined to be the causal agent (2). In 2012, widespread reports of SVNV were made across most soybean (Glycine max) producing states including the recent confirmation of SVNV in Iowa and Wisconsin (1). Foliar symptoms similar to those reported for SVNV were observed at approximately 1 to 10% incidence in soybean fields across Michigan in late August and September of 2012, including fields located in Cass, Ingham, Midland, Saginaw, and Van Buren counties. Symptoms included chlorosis and necrosis which initiated on the veins with subsequent spread across the leaf. An initial sample collected from the East Lansing Agricultural Research Station was confirmed to have SVNV with a polyclonal antibody using double antibody sandwich (DAS)-ELISA at AC Diagnostics, Inc. (Fayetteville, AR) and with reverse transcription PCR by Ioannis Tzanetakis, University of Arkansas, Fayetteville. Additional samples from five fields were subsequently collected from Cass, Ingham, and Van Buren counties. Duplicate leaf tissue samples were tested with DAS-ELISA using the SVNV test kit (AC Diagnostics). All symptomatic leaf samples exhibited a strong positive reaction based on the optical density reading at 405 nm. Absorbance reading that exceeded the healthy soybean tissue by a standard deviation of +3× were considered positive. Total RNA was also extracted from each sample using the RNeasy Plant Mini Kit (Qiagen, Germantown, MD). Complementary DNA (cDNA) was generated using virus-specific LdetR and SdetR primers (2) with the High Capacity RT cDNA kit (Life Technologies; Carlsbad, CA). The cDNA was used as template for PCR with the SVNV-specific primers that amplify regions of the L (LdetF/LdetR) and the S (SdetF/SdetR) RNAs (1). Amplification products of the expected 297 and 861 bp size, respectively, were detected in all symptomatic samples while no amplification products were generated from healthy soybean plant tissues grown under greenhouse conditions. Significantly, this is the first documentation and confirmation of the widespread prevalence of SVNV across the state of Michigan in 2012. References: (1) D. L. Smith et al. Plant Dis. http://dx.doi.org/10.1094/PDIS-11-12-1096-PDN . (2) J. Zhou et al. Virus Genes 43:289, 2011.
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Affiliation(s)
- J L Jacobs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824
| | - M I Chilvers
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824
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Moate PJ, Williams SRO, Hannah MC, Eckard RJ, Auldist MJ, Ribaux BE, Jacobs JL, Wales WJ. Effects of feeding algal meal high in docosahexaenoic acid on feed intake, milk production, and methane emissions in dairy cows. J Dairy Sci 2013; 96:3177-88. [PMID: 23498011 DOI: 10.3168/jds.2012-6168] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/21/2013] [Indexed: 11/19/2022]
Abstract
This study examined effects on milk yield and composition, milk fatty acid concentrations and methane (CH4) emissions when dairy cows were offered diets containing different amounts of algal meal. The algal meal contained 20% docosahexaenoic acid (DHA) and cows were offered either 0, 125, 250, or 375 g/cow per d of algal meal corresponding to 0, 25, 50, or 75 g of DHA/cow per d. Thirty-two Holstein cows in mid lactation were allocated to 4 treatment groups, and cows in all groups were individually offered 5.9k g of dry matter (DM) per day of concentrates [683 g/kg of cracked wheat (Triticum aestivum), 250 g/kg of cold-pressed canola, 46 g/kg of granulated dried molasses, and 21 g/kg of mineral mix] and ad libitum alfalfa (Medicago sativa) hay. The algal meal supplement was added to the concentrate allowance and was fed during the morning and afternoon milking, whereas the alfalfa hay was fed individually in pens. Cows were gradually introduced to their diets over 7d and then fed their treatment diets for a further 16d. Dry matter intake and milk yield were measured daily, and milk composition was measured on a sample representative of the daily milk yield on Thursday of each week. For the last 2d of the experiment, cows were individually housed in respiration chambers to allow measurement of CH4 emissions. Dry matter intake, milk yield and milk composition were also measured while cows were in the respiration chambers. Cows ate all their offered concentrates, but measured intake of alfalfa decreased with increasing dose of DHA by 16.2, 16.4, 15.1, and 14.3 kg of DM/d, respectively. Milk yield (22.6, 23.5, 22.6, and 22.6 kg/cow per d) was not affected by DHA dose, but milk fat concentrations (49.7, 37.8, 37.0, and 38.3g/kg) and, consequently, milk fat yields (1.08, 0.90, 0.83, and 0.85 kg/d) decreased with addition of DHA. The feeding of algal meal high in DHA was associated with substantial increases in the concentrations of DHA (0.04, 0.36, 0.60, and 0.91 g/100g of milk fatty acids) and conjugated linoleic acid C18:2 cis-9,trans-11 (0.36, 1.09, 1.79, and 1.87 g/100g of milk fatty acids). Addition of DHA did not affect total emissions of CH4 (543, 563, 553, and 520 g/cow per d), nor emissions in terms of milk production (24.9, 22.1, 24.3, and 23.4 g of CH4/kg of milk), but emissions were increased with respect to total intake (22.6, 23.5, 24.5, and 24.4 g of CH4/kg of DM). These findings indicate that CH4 emissions were not reduced when dairy cows were fed a forage-based diet supplemented with DHA from algal meal.
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Affiliation(s)
- P J Moate
- Future Farming Systems Research Division, Department of Primary Industries, Ellinbank, Victoria 3821, Australia.
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Auldist MJ, Marett LC, Greenwood JS, Hannah M, Jacobs JL, Wales WJ. Effects of different strategies for feeding supplements on milk production responses in cows grazing a restricted pasture allowance. J Dairy Sci 2012; 96:1218-31. [PMID: 23219117 DOI: 10.3168/jds.2012-6079] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/19/2012] [Indexed: 11/19/2022]
Abstract
Milk production responses of grazing cows offered supplements in different ways were measured. Holstein-Friesian cows, averaging 227 d in milk, were allocated into 6 groups of 36, with 2 groups randomly assigned to each of 3 feeding strategies: (1) cows grazed perennial ryegrass pasture supplemented with milled barley grain fed in the milking parlor and pasture silage offered in the paddock (control); (2) same pasture and allotment supplemented with the same amounts of milled barley grain and pasture silage, but presented as a mixed ration after each milking (PMR 1); and (3) same pasture and allotment, supplemented with a mixed ration of milled barley grain, alfalfa hay, corn silage, and crushed corn grain (PMR 2). For all strategies, supplements provided the same metabolizable energy and grain:forage ratio. [75:25, dry matter (DM) basis]. Each group of 36 cows was further allocated into 4 groups of 9, which were assigned to receive 6, 8, 10, or 12 kg of supplement DM/cow per day. Thus, there were 2 replicated groups per supplement amount per dietary strategy. The experiment had a 14-d adaptation period and an 11-d measurement period. Pasture allotment was approximately 14 kg of DM/d for all cows and was offered in addition to the supplement. Positive quadratic responses to increasing amounts of supplement were observed for yield of milk, energy-corrected milk (ECM), and fat and protein, and positive linear responses for concentrations of fat and protein for cows on all 3 supplement feeding strategies. No difference existed between feeding strategy groups in yield of milk, ECM, or protein at any amount of supplement offered, but yield and concentration of fat was higher in PMR 2 cows compared with control and PMR 1 cows at the highest amounts of supplementation. Responses in marginal ECM production per additional kilogram of supplement were also greater for PMR 2 than control and PMR 1 cows when large amounts of supplement were consumed. For all diets, marked daily variation occurred in ruminal fluid volatile fatty acids and pH, especially in cows fed the largest amounts of supplement. It was concluded that when supplements are fed to grazing dairy cows, a simple mix of grain and pasture silage has no benefit over traditional strategies of feeding grain in the parlor and forage in the paddock. However, yield of milk fat and marginal milk production responses can be greater if the strategy uses an isoenergetic ration that also contains alfalfa hay, corn silage, and corn grain.
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Affiliation(s)
- M J Auldist
- Future Farming Systems Research Division, Department of Primary Industries, Ellinbank, VIC 3821, Australia.
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Si Y, Liu S, Liu X, Jacobs JL, Cheng M, Niu Y, Jin Q, Wang T, Yang W. A human claudin-1-derived peptide inhibits hepatitis C virus entry. Hepatology 2012; 56:507-15. [PMID: 22378192 PMCID: PMC3406249 DOI: 10.1002/hep.25685] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 02/16/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED Hepatitis C virus (HCV) entry is a complicated process that requires multiple host factors, such as CD81, scavenger receptor BI, claudin-1 (CLDN1), and occludin. The interaction of virus and cellular entry factors represents a promising target for novel anti-HCV drug development. In this study, we sought to identify peptide inhibitors for HCV entry by screening a library of overlapping peptides covering the four above-mentioned entry factors. An 18-amino acid peptide (designated as CL58) that was derived from the CLDN1 intracellular and first transmembrane region inhibited both de novo and established HCV infection in vitro. Unlike previously reported peptides corresponding to CLDN1 extracellular loops, CL58 did not alter the normal distribution of CLDN1 and was not cytotoxic in vitro at concentrations nearly 100-fold higher than the effective antiviral dose. The inhibitory effect of CL58 appeared to occur at a late step during viral entry, presumably after initial binding. Finally, overexpressed CL58 was able to interact with HCV envelope proteins. CONCLUSION We identified a novel CLDN1-derived peptide that inhibits HCV entry at a postbinding step. The findings expand our knowledge of the roles that CLDN1 play in HCV entry and highlight the potential for developing a new class of inhibitors targeting the viral entry process.
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Affiliation(s)
- Youhui Si
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shufeng Liu
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, PA
| | - Xiuying Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jana L. Jacobs
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, PA
| | - Min Cheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuqiang Niu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyi Wang
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, PA
| | - Wei Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Yu C, Zhang X, Sun G, Guo X, Li H, You Y, Jacobs JL, Gardner K, Yuan D, Xu Z, Du Q, Dai C, Qian Z, Jiang K, Zhu Y, Li QQ, Miao Y. RNA interference-mediated silencing of the polo-like kinase 1 gene enhances chemosensitivity to gemcitabine in pancreatic adenocarcinoma cells. J Cell Mol Med 2008; 12:2334-49. [PMID: 18266952 PMCID: PMC4514112 DOI: 10.1111/j.1582-4934.2008.00257.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [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: 10/07/2007] [Accepted: 01/18/2008] [Indexed: 12/30/2022] Open
Abstract
Gemcitabine is the first-line chemotherapeutic agent for advanced adenocarcinoma of the pancreas; however, chemoresistance to gemcitabine remains a major cause of failure for the clinical treatment of this disease. Polo-like kinase 1 (Plk-1) is highly expressed in pancreatic cancer cell lines and pancreatic tumour tissues, and is involved in a wide variety of cell cycle processes. Nevertheless, its biological role and implication for gemcitabine resistance are not clearly defined. In this study, we used RNA-interference (RNAi)-mediated depletion of Plk-1 to determine its potential for sensitizing pancreatic tumour cells to gemcitabine. We showed that the level of Plk-1 protein was correlated significantly with gemcitabine resistance in human pancreatic adenocarcinoma cells and that overexpression of Plk-1 reduced sensitivity to gemcitabine in these cells. In addition, small interfering RNA (siRNA)-mediated knockdown of Plk-1 caused cell cycle arrest at G2/M and the reduction of cellular proliferation. More importantly, the treatment of pancreatic cancer cells with Plk-1 siRNA followed by exposure to gemcitabine dramatically decreased cell viability and increased cellular apoptosis, as compared with treatment with either agent alone. These observations indicate that down-regulation of Plk-1 expression by RNAi enhances gemcitabine sensitivity and increases gemcitabine cytotoxicity in pancreatic tumour cells. This is the first demonstration that the combination of Plk-1 gene therapy and gemcitabine chemotherapy has synergistic anti-tumour activity against pancreatic carcinoma in vitro. This combination treatment warrants further investigation as an effective therapeutic regimen for patients with resistant pancreatic cancer and other tumours.
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Affiliation(s)
- C Yu
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
- Department of Surgery, Beijing Aerospace General HospitalBeijing, P. R. China
| | - X Zhang
- Institute of Pediatric Medicine, Nanjing Medical UniversityNanjing, P. R. China
| | - G Sun
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - X Guo
- Institute of Pediatric Medicine, Nanjing Medical UniversityNanjing, P. R. China
| | - H Li
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - Y You
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - J L Jacobs
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - K Gardner
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - D Yuan
- Laboratory of Pathophysiology Medical School ofHubei Institute for NationalitiesEnshi, P. R. China
| | - Z Xu
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - Q Du
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - C Dai
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - Z Qian
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - K Jiang
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - Y Zhu
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
| | - Q Q Li
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - Y Miao
- Department of Surgery, First Affiliated Hospital, Nanjing Medical UniversityNanjing, P. R. China
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Jacobs JL, Carroll TL, Sundin GW. The role of pigmentation, ultraviolet radiation tolerance, and leaf colonization strategies in the epiphytic survival of phyllosphere bacteria. Microb Ecol 2005; 49:104-13. [PMID: 15883865 DOI: 10.1007/s00248-003-1061-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Accepted: 11/19/2003] [Indexed: 05/02/2023]
Abstract
Phenotypic mechanisms that enhance bacterial UVR survival typically include pigmentation and DNA repair mechanisms which provide protection from UVA and UVB wavelengths, respectively. In this study, we examined the contribution of pigmentation to field survival in Clavibacter michiganensis and evaluated differences in population dynamics and leaf colonization strategies. Two C. michiganensis pigment-deficient mutants were significantly reduced in UVA radiation survival in vitro; one of these mutants also exhibited reduced field populations on peanut when compared to the wild-type strain over the course of replicate 25-day experiments. The UVR-tolerant C. michiganensis strains G7.1 and G11.1 maintained larger epiphytic field populations on peanut compared to the UVR-sensitive C. michiganensis T5.1. Epiphytic field populations of C. michiganensis utilized the strategy of solar UVR avoidance during leaf colonization resulting in increased strain survival on leaves after UVC irradiation. These results further demonstrate the importance of UVR tolerance in the ability of bacterial strains to maintain population size in the phyllosphere. However, an examination of several bacterial species from the peanut phyllosphere and a collection of environmental Pseudomonas spp. revealed that sensitivity to UVA and UVC radiation was correlated in some but not all of these bacteria. These results underscore a need to further understand the biological effects of different solar wavelength groups on microbial ecology.
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Affiliation(s)
- J L Jacobs
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX 77843, USA
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Abstract
The effect of solar UV-B radiation on the population dynamics and composition of the culturable bacterial community from peanut (Arachis hypogeae L.) was examined in field studies using plants grown under UV-B-transmitting (UV-B+) or UV-B-excluding (UV-B-) plastic filters. Our data demonstrate that solar UV-B selection alters phyllosphere bacterial community composition and that UV tolerance is a prevalent phenotype late in the season. The total bacterial population size was not affected by either UV-B treatment. However, isolates from the UV-B+ plots (n = 368) were significantly more UV tolerant than those from the UV-B- (n = 363) plots. UV sensitivity was determined as the minimal inhibitory dose of UV that resulted in an inhibition of growth compared to the growth of a nonirradiated control. The difference in minimal inhibitory doses among bacterial isolates from UV-B+ and UV-B- treatments was mainly partitioned among nonpigmented isolates, with pigmented isolates as a group being characterized as UV tolerant. A large increase in UV tolerance was observed within isolate groups collected late (89 and 96 days after planting) in the season. Identification of 200 late-season isolates indicated that the predominant UV-tolerant members of this group were Bacillus coagulans, Clavibacter michiganensis, and Curtobacterium flaccumfaciens. We selected C. michiganensis as a model UV-tolerant epiphyte to study if cell survival on UV-irradiated peanut leaves was increased relative to UV survival in vitro. The results showed an enhancement in the survival of C. michiganensis G7.1, especially following high UV-C doses (300 and 375 J m(-2)), that was evident between 24 and 96 h after inoculation. A dramatic increase in the in planta/in vitro survival ratio was observed over the entire 96-h experiment period for C. michiganensis T5.1.
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Affiliation(s)
- J L Jacobs
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843-2132, USA
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Sundin GW, Jacobs JL, Murillo J. Sequence diversity of rulA among natural isolates of Pseudomonas syringae and effect on function of rulAB-mediated UV radiation tolerance. Appl Environ Microbiol 2000; 66:5167-73. [PMID: 11097885 PMCID: PMC92439 DOI: 10.1128/aem.66.12.5167-5173.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rulAB locus confers tolerance to UV radiation and is borne on plasmids of the pPT23A family in Pseudomonas syringae. We sequenced 14 rulA alleles from P. syringae strains representing seven pathovars and found sequence differences of 1 to 12% within pathovar syringae, and up to 15% differences between pathovars. Since the sequence variation within rulA was similar to that of P. syringae chromosomal alleles, we hypothesized that rulAB has evolved over a long time period in P. syringae. A phylogenetic analysis of the deduced amino acid sequences of rulA resulted in seven clusters. Strains from the same plant host grouped together in three cases; however, strains from different pathovars grouped together in two cases. In particular, the rulA alleles from P. syringae pv. lachrymans and P. syringae pv. pisi were grouped but were clearly distinct from the other sequenced alleles, suggesting the possibility of a recent interpathovar transfer. We constructed chimeric rulAB expression clones and found that the observed sequence differences resulted in significant differences in UV (wavelength) radiation sensitivity. Our results suggest that specific amino acid changes in RulA could alter UV radiation tolerance and the competitiveness of the P. syringae host in the phyllosphere.
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Affiliation(s)
- G W Sundin
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132, USA.
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Jacobs JL, Porter WD. Preventing workplace violence: looking at your hiring and termination processes. Director 2000; 7:66-9; quiz 79-80. [PMID: 10703331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Sundin GW, Jacobs JL. Ultraviolet Radiation (UVR) Sensitivity Analysis and UVR Survival Strategies of a Bacterial Community from the Phyllosphere of Field-Grown Peanut (Arachis hypogeae L.). Microb Ecol 1999; 38:27-38. [PMID: 10384007 DOI: 10.1007/s002489900152] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
> Abstract The short-term population dynamics of the culturable bacterial community from field-grown peanut (Arachis hypogeae L.) was analyzed over three 2-day periods. As in other phyllosphere studies, significant numbers of pigmented organisms were detected, suggesting the importance of pigmentation in the colonization of this habitat. Isolates were grouped according to pigmentation (orange, pink, yellow, nonpigmented), and the sensitivity of each isolate in the collection (n = 617) to ultraviolet radiation (UVR) was determined as the minimal inhibitory dose (MIDC) of UVR that resulted in an inhibition of growth compared to an unirradiated control. The majority of isolates recovered (56.1%) had an MIDC equal to or exceeding that of Pseudomonas syringae 8B48, a known UV-tolerant strain. Among pigmentation groups, the mean MIDC of pink- and orange-pigmented isolates was significantly greater than that of yellow- or nonpigmented isolates at each sampling time of day. Identification of 213 of the isolates using fatty acid methyl ester analysis indicated that a large proportion of the isolates were gram-positive, with Bacillus spp. alone accounting for 35.7% of the total. The genus Curtobacterium contained the largest percentage of highly UVR-tolerant strains. Nonpigmented mutants of four Curtobacterium strains were selected following ethyl methane sulfonate mutagenesis; these nonpigmented mutants were significantly altered in survival following irradiation with UV-A wavelengths. The strategy of avoidance of UVR through colonization of the abaxial leaf surface was evaluated on three separate occasions by leaf imprint sampling. Only 3 of 120 leaves (2.5%) contained larger bacterial populations on the adaxial surface, indicating that colonization of the abaxial leaf surface is important to phyllosphere survival. Our results indicate that tolerance to UVR is a common phenotype among phyllosphere bacteria, suggesting that solar radiation has a strong influence on the microbial ecology of the phyllosphere.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p27.html
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Affiliation(s)
- GW Sundin
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
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Jacobs JL, Porter WD. Workplace violence: dealing with the abusive patient. Balance 1999; 3:22-4. [PMID: 10557766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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Jacobs JL, Porter WD. The dynamics of workplace violence. Balance 1999; 3:27-9. [PMID: 10346526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Abstract
PURPOSE This study of volume replacement in anophthalmic sockets compares the volume replaced by the implant and prosthesis with the volume removed from the socket and evaluates A-scan ultrasonography as a tool to predict an ideal implant size before enucleation. METHODS In this retrospective study of 59 anophthalmic patients, the volume replaced by the implant and the prosthesis was compared with the volume of the enucleated eye. The volume removed was estimated by calculating the volume of the fellow eye using A-scan ultrasonography. Enophthalmos and superior sulcus deformity were measured and correlated with the percent volume replacement in the anophthalmic sockets. RESULTS Greater enophthalmos and superior sulcus deformity were found in patients with less than 100% volume replacement compared with those with 100% or more volume replacement. The axial length determined by A-scan ultrasonography of the fellow eye suggested that a larger implant size should have been placed in 76.3% of those patients with less than 100% volume replacement. Sixty-three percent of adult patients could have received an implant more than 22 mm in diameter to fill 80% of the volume removed at enucleation. CONCLUSIONS A-scan ultrasonography of the fellow eye provides a useful tool for predicting the implant size before surgery for optimal volume replacement.
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Affiliation(s)
- S A Kaltreider
- Department of Ophthalmology, University of Virginia, Charlottesville, USA
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