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Hartmann JA, Cardoso MR, Talarico MCR, Kenney DJ, Leone MR, Reese DC, Turcinovic J, O'Connell AK, Gertje HP, Marino C, Ojeda PE, De Paula EV, Orsi FA, Velloso LA, Cafiero TR, Connor JH, Ploss A, Hoelzemer A, Carrington M, Barczak AK, Crossland NA, Douam F, Boucau J, Garcia-Beltran WF. Evasion of NKG2D-mediated cytotoxic immunity by sarbecoviruses. Cell 2024; 187:2393-2410.e14. [PMID: 38653235 DOI: 10.1016/j.cell.2024.03.026] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
SARS-CoV-2 and other sarbecoviruses continue to threaten humanity, highlighting the need to characterize common mechanisms of viral immune evasion for pandemic preparedness. Cytotoxic lymphocytes are vital for antiviral immunity and express NKG2D, an activating receptor conserved among mammals that recognizes infection-induced stress ligands (e.g., MIC-A/B). We found that SARS-CoV-2 evades NKG2D recognition by surface downregulation of MIC-A/B via shedding, observed in human lung tissue and COVID-19 patient serum. Systematic testing of SARS-CoV-2 proteins revealed that ORF6, an accessory protein uniquely conserved among sarbecoviruses, was responsible for MIC-A/B downregulation via shedding. Further investigation demonstrated that natural killer (NK) cells efficiently killed SARS-CoV-2-infected cells and limited viral spread. However, inhibition of MIC-A/B shedding with a monoclonal antibody, 7C6, further enhanced NK-cell activity toward SARS-CoV-2-infected cells. Our findings unveil a strategy employed by SARS-CoV-2 to evade cytotoxic immunity, identify the culprit immunevasin shared among sarbecoviruses, and suggest a potential novel antiviral immunotherapy.
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Affiliation(s)
- Jordan A Hartmann
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | | | - Devin J Kenney
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Madison R Leone
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Dagny C Reese
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Caitlin Marino
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Pedro E Ojeda
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Erich V De Paula
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
| | - Fernanda A Orsi
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
| | - Licio Augusto Velloso
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Obesity and Comorbidities Research Center, University of Campinas, Campinas, SP, Brazil
| | - Thomas R Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Angelique Hoelzemer
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Institute for Infection and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Research Department Virus Immunology, Leibniz Institute for Virology, Hamburg, Germany
| | - Mary Carrington
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amy K Barczak
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Crossland
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. bioRxiv 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
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Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
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Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Alekseyev YO, Doucette-Stamm L, Hamer DH, Klapperich C, Landsberg HE, Connor JH. Transmission Dynamics and Rare Clustered Transmission Within an Urban University Population Before Widespread Vaccination. J Infect Dis 2024; 229:485-492. [PMID: 37856283 DOI: 10.1093/infdis/jiad397] [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: 05/09/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Universities returned to in-person learning in 2021 while SARS-CoV-2 spread remained high. At the time, it was not clear whether in-person learning would be a source of disease spread. METHODS We combined surveillance testing, universal contact tracing, and viral genome sequencing to quantify introductions and identify likely on-campus spread. RESULTS Ninety-one percent of viral genotypes occurred once, indicating no follow-on transmission. Less than 5% of introductions resulted in >3 cases, with 2 notable exceptions of 40 and 47 cases. Both partially overlapped with outbreaks defined by contact tracing. In both cases, viral genomics eliminated over half the epidemiologically linked cases but added an equivalent or greater number of individuals to the transmission cluster. CONCLUSIONS Public health interventions prevented within-university transmission for most SARS-CoV-2 introductions, with only 2 major outbreaks being identified January to May 2021. The genetically linked cases overlap with outbreaks identified by contact tracing; however, they persisted in the university population for fewer days and rounds of transmission than estimated via contact tracing. This underscores the effectiveness of test-trace-isolate strategies in controlling undetected spread of emerging respiratory infectious diseases. These approaches limit follow-on transmission in both outside-in and internal transmission conditions.
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Affiliation(s)
- Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
| | | | | | - Lena Landaverde
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | | | | | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories
- Precision Diagnostics Center
- Department of Global Health, School of Public Health
- Section of Infectious Disease, Department of Medicine, Chobanian & Avedisian School of Medicine
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
| | - Catherine Klapperich
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | - John H Connor
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
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Ma Q, Srivastav SP, Gamez S, Dayama G, Feitosa-Suntheimer F, Patterson EI, Johnson RM, Matson EM, Gold AS, Brackney DE, Connor JH, Colpitts TM, Hughes GL, Rasgon JL, Nolan T, Akbari OS, Lau NC. Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. Genome Res 2024; 34:160. [PMID: 38326031 PMCID: PMC10903936 DOI: 10.1101/gr.278898.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
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Overbeck V, Taylor BP, Turcinovic J, Qiu X, Schaeffer B, Seitz S, Curry SR, Hanage WP, Connor JH, Kuppalli K. Successful treatment of SARS-CoV-2 in an immunocompromised patient with persistent infection for 245 days: A case report. Heliyon 2024; 10:e23699. [PMID: 38223743 PMCID: PMC10784163 DOI: 10.1016/j.heliyon.2023.e23699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024] Open
Abstract
Background Immunocompromised patients receiving B-cell-depleting therapies are at increased risk of persistent SARS-CoV-2 infection, with many experiencing fatal outcomes. We report a successful outcome in a patient with rheumatoid arthritis (RA) on rituximab diagnosed with COVID-19 in July 2020 with persistent infection for over 245 days. Results The patient received numerous treatment courses for persistent COVID-19 infection, including remdesivir, baricitinib, immunoglobulin and high doses of corticosteroids followed by a prolonged taper due to persistent respiratory symptoms and cryptogenic organizing pneumonia. Her clinical course was complicated by Pseudomonas aeruginosa sinusitis with secondary bacteremia, and cytomegalovirus (CMV) viremia and pneumonitis. SARS-CoV-2 positive RNA samples were extracted from two nasopharyngeal swabs and sequenced using targeted amplicon Next-Generation Sequencing which were analyzed for virus evolution over time. Viral sequencing indicated lineage B.1.585.3 SARS-CoV-2 accumulated Spike protein mutations associated with immune evasion and resistance to therapeutics. Upon slowly decreasing the patient's steroids, she had resolution of her symptoms and had a negative nasopharyngeal SARS-CoV-2 PCR and serum CMV PCR in March 2021. Conclusion A patient with RA on B-cell depleting therapy developed persistent SARS-CoV-2 infection allowing for virus evolution and had numerous complications, including viral and bacterial co-infections with opportunistic pathogens. Despite intra-host evolution with a more immune evasive SARS-CoV-2 lineage, it was cleared after 245 days with reconstitution of the patient's immune system.
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Affiliation(s)
- Victoria Overbeck
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Bradford P. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Beau Schaeffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott R. Curry
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Krutika Kuppalli
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
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Hume AJ, Olejnik J, White MR, Huang J, Turcinovic J, Heiden B, Bawa PS, Williams CJ, Gorham NG, Alekseyev YO, Connor JH, Kotton DN, Mühlberger E. Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality. Pathogens 2024; 13:62. [PMID: 38251369 PMCID: PMC10818917 DOI: 10.3390/pathogens13010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus-host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.
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Affiliation(s)
- Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Mitchell R. White
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Baylee Heiden
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Pushpinder S. Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
| | - Christopher J. Williams
- Department of Medicine, Single Cell Sequencing Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Nickolas G. Gorham
- Microarray and Sequencing Resource Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Yuriy O. Alekseyev
- Department of Pathology and Laboratory Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - John H. Connor
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
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Woolsey C, Strampe J, Fenton KA, Agans KN, Martinez J, Borisevich V, Dobias NS, Deer DJ, Geisbert JB, Cross RW, Connor JH, Geisbert TW. A Recombinant Vesicular Stomatitis Virus-Based Vaccine Provides Postexposure Protection Against Bundibugyo Ebolavirus Infection. J Infect Dis 2023; 228:S712-S720. [PMID: 37290053 PMCID: PMC10651203 DOI: 10.1093/infdis/jiad207] [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: 03/29/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND The filovirus Bundibugyo virus (BDBV) causes severe disease with a mortality rate of approximately 20%-51%. The only licensed filovirus vaccine in the United States, Ervebo, consists of a recombinant vesicular stomatitis virus (rVSV) vector that expresses Ebola virus (EBOV) glycoprotein (GP). Ervebo was shown to rapidly protect against fatal Ebola disease in clinical trials; however, the vaccine is only indicated against EBOV. Recent outbreaks of other filoviruses underscore the need for additional vaccine candidates, particularly for BDBV infections. METHODS To examine whether the rVSV vaccine candidate rVSVΔG/BDBV-GP could provide therapeutic protection against BDBV, we inoculated seven cynomolgus macaques with 1000 plaque-forming units of BDBV, administering rVSVΔG/BDBV-GP vaccine to 6 of them 20-23 minutes after infection. RESULTS Five of the treated animals survived infection (83%) compared to an expected natural survival rate of 21% in this macaque model. All treated animals showed an early circulating immune response, while the untreated animal did not. Surviving animals showed evidence of both GP-specific IgM and IgG production, while animals that succumbed did not produce significant IgG. CONCLUSIONS This small, proof-of-concept study demonstrated early treatment with rVSVΔG/BDBV-GP provides a survival benefit in this nonhuman primate model of BDBV infection, perhaps through earlier initiation of adaptive immunity.
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Affiliation(s)
- Courtney Woolsey
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jamie Strampe
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Karla A Fenton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Krystle N Agans
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jasmine Martinez
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Viktoriya Borisevich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Natalie S Dobias
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Daniel J Deer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Joan B Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
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8
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Xia Q, Guo Z, Zong H, Seitz S, Yurdakul C, Ünlü MS, Wang L, Connor JH, Cheng JX. Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy. Nat Commun 2023; 14:6655. [PMID: 37863905 PMCID: PMC10589364 DOI: 10.1038/s41467-023-42439-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 01/25/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.
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Affiliation(s)
- Qing Xia
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Haonan Zong
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Scott Seitz
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Celalettin Yurdakul
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Le Wang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Photonics Center, Boston University, Boston, MA, 02215, USA.
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9
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Carmola LR, Turcinovic J, Draper G, Webner D, Putukian M, Silvers-Granelli H, Bombin A, Connor BA, Angelo KM, Kozarsky P, Libman M, Huits R, Hamer DH, Fairley JK, Connor JH, Piantadosi A, Bourque DL. Genomic Epidemiology of a Severe Acute Respiratory Syndrome Coronavirus 2 Outbreak in a US Major League Soccer Club: Was It Travel Related? Open Forum Infect Dis 2023; 10:ofad235. [PMID: 37323423 PMCID: PMC10264064 DOI: 10.1093/ofid/ofad235] [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: 02/01/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
Background Professional soccer athletes are at risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). United States Major League Soccer (MLS) uses protocol-based SARS-CoV-2 testing for identification of individuals with coronavirus disease 2019. Methods Per MLS protocol, fully vaccinated players underwent SARS-CoV-2 real-time polymerase chain reaction testing weekly; unvaccinated players were tested every other day. Demographic and epidemiologic data were collected from individuals who tested positive, and contact tracing was performed. Whole genome sequencing (WGS) was performed on positive specimens, and phylogenetic analyses were used to identify potential transmission patterns. Results In the fall of 2021, all 30 players from 1 MLS team underwent SARS-CoV-2 testing per protocol; 27 (90%) were vaccinated. One player who had recently traveled to Africa tested positive for SARS-CoV-2; within the following 2 weeks, 10 additional players and 1 staff member tested positive. WGS yielded full genome sequences for 10 samples, including 1 from the traveler. The traveler's sample was Delta sublineage AY.36 and was closely related to a sequence from Africa. Nine samples yielded other Delta sublineages including AY.4 (n = 7), AY.39 (n = 1), and B.1.617.2 (n = 1). The 7 AY.4 sequences clustered together; suggesting a common source of infection. Transmission from a family member visiting from England to an MLS player was identified as the potential index case. The other 2 AY.4 sequences differed from this group by 1-3 nucleotides, as did a partial genome sequence from an additional team member. Conclusions WGS is a useful tool for understanding SARS-CoV-2 transmission dynamics in professional sports teams.
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Affiliation(s)
- Ludy R Carmola
- Correspondence: Daniel L. Bourque, MD, Section of Infectious Diseases, Boston University Chobanian & Avedisian School of Medicine, 801 Massachusetts Ave, Boston, MA 02118 (); Ludy R. Carmola, PhD, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Road NE, Atlanta, GA 30322 ()
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratory, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | - Garrison Draper
- Department of Sport and Exercise Science, School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- Player and Health Performance, 6 Philadelphia Union, Chester, Pennsylvania, USA
| | - David Webner
- Player and Health Performance, 6 Philadelphia Union, Chester, Pennsylvania, USA
- Crozer Health, Sports Medicine, Springfield, Pennsylvania, USA
| | | | | | - Andrei Bombin
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bradley A Connor
- Deparment of Medicine, Weill Cornell Medicine and the New York Center for Travel and Tropical Medicine, New York, New York, USA
| | - Kristina M Angelo
- Travelers’ Health Branch, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phyllis Kozarsky
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael Libman
- J.D. MacLean Centre for Tropical Diseases, McGill University, Montreal, Canada
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS) Ospedale Sacro Cuore Don Calabria, Negrar, Verona, Italy
| | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratory, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Section of Infectious Diseases, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Global Health, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jessica K Fairley
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John H Connor
- Department of Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratory, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daniel L Bourque
- Correspondence: Daniel L. Bourque, MD, Section of Infectious Diseases, Boston University Chobanian & Avedisian School of Medicine, 801 Massachusetts Ave, Boston, MA 02118 (); Ludy R. Carmola, PhD, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Road NE, Atlanta, GA 30322 ()
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10
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Chen DY, Turcinovic J, Feng S, Kenney DJ, Chin CV, Choudhary MC, Conway HL, Semaan M, Close BJ, Tavares AH, Seitz S, Khan N, Kapell S, Crossland NA, Li JZ, Douam F, Baker SC, Connor JH, Saeed M. Cell culture systems for isolation of SARS-CoV-2 clinical isolates and generation of recombinant virus. iScience 2023; 26:106634. [PMID: 37095858 PMCID: PMC10083141 DOI: 10.1016/j.isci.2023.106634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/22/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
A simple and robust cell culture system is essential for generating authentic SARS-CoV-2 stocks for evaluation of viral pathogenicity, screening of antiviral compounds, and preparation of inactivated vaccines. Evidence suggests that Vero E6, a cell line commonly used in the field to grow SARS-CoV-2, does not support efficient propagation of new viral variants and triggers rapid cell culture adaptation of the virus. We generated a panel of 17 human cell lines overexpressing SARS-CoV-2 entry factors and tested their ability to support viral infection. Two cell lines, Caco-2/AT and HuH-6/AT, demonstrated exceptional susceptibility, yielding highly concentrated virus stocks. Notably, these cell lines were more sensitive than Vero E6 cells in recovering SARS-CoV-2 from clinical specimens. Further, Caco-2/AT cells provided a robust platform for producing genetically reliable recombinant SARS-CoV-2 through a reverse genetics system. These cellular models are a valuable tool for the study of SARS-CoV-2 and its continuously emerging variants.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Shuchen Feng
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Devin J Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Marc Semaan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Brianna J Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Seitz
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Sebastian Kapell
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
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11
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Tseng AE, Carossino M, Gertje HP, O'Connell AK, Gummuluru S, Kolachalama VB, Balasuriya UBR, Connor JH, Bennett RS, Liu DX, Hensley LE, Crossland NA. Hepatic proinflammatory myeloid phenotypes are a hallmark of Ebola virus Kikwit pathogenesis in rhesus monkeys. Vet Pathol 2023:3009858231171906. [PMID: 37170900 DOI: 10.1177/03009858231171906] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The liver is an early systemic target of Ebola virus (EBOV), but characterization beyond routine histopathology and viral antigen distribution is limited. We hypothesized Ebola virus disease (EVD) systemic proinflammatory responses would be reflected in temporally altered liver myeloid phenotypes. We utilized multiplex fluorescent immunohistochemistry (mfIHC), multispectral whole slide imaging, and image analysis to quantify molecular phenotypes of myeloid cells in the liver of rhesus macaques (Macaca mulatta; n = 21) infected with EBOV Kikwit. Liver samples included uninfected controls (n = 3), 3 days postinoculation (DPI; n = 3), 4 DPI (n = 3), 5 DPI (n = 3), 6 DPI (n = 3), and terminal disease (6-8 DPI; n = 6). Alterations in hepatic macrophages occurred at ≥ 5 DPI characterized by a 1.4-fold increase in CD68+ immunoreactivity and a transition from primarily CD14-CD16+ to CD14+CD16- macrophages, with a 2.1-fold decrease in CD163 expression in terminal animals compared with uninfected controls. An increase in the neutrophil chemoattractant and alarmin S100A9 occurred within hepatic myeloid cells at 5 DPI, followed by rapid neutrophil influx at ≥ 6 DPI. An acute rise in the antiviral myxovirus resistance protein 1 (MxA) occurred at ≥ 4 DPI, with a predilection for enhanced expression in uninfected cells. Distinctive expression of major histocompatibility complex (MHC) class II was observed in hepatocytes during terminal disease. Results illustrate that EBOV causes macrophage phenotype alterations as well as neutrophil influx and prominent activation of interferon host responses in the liver. Results offer insight into potential therapeutic strategies to prevent and/or modulate the host proinflammatory response to normalize hepatic myeloid functionality.
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Affiliation(s)
- Anna E Tseng
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory (LADDL), Louisiana State University, Baton Rouge, LA, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
| | - Suryaram Gummuluru
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Vijaya B Kolachalama
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Computer Science, Boston University, Boston, MA, USA
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory (LADDL), Louisiana State University, Baton Rouge, LA, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Richard S Bennett
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland, USA
| | - David X Liu
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland, USA
| | - Lisa E Hensley
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland, USA
| | - Nicholas A Crossland
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, NEIDL Comparative Pathology Laboratory, Boston University, Boston, MA, USA
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12
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Chen DY, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature 2023; 615:143-150. [PMID: 36630998 DOI: 10.1038/s41586-023-05697-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
The SARS-CoV-2 Omicron variant is more immune evasive and less virulent than other major viral variants that have so far been recognized1-12. The Omicron spike (S) protein, which has an unusually large number of mutations, is considered to be the main driver of these phenotypes. Here we generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron (BA.1 lineage) in the backbone of an ancestral SARS-CoV-2 isolate, and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escaped vaccine-induced humoral immunity, mainly owing to mutations in the receptor-binding motif; however, unlike naturally occurring Omicron, it efficiently replicated in cell lines and primary-like distal lung cells. Similarly, in K18-hACE2 mice, although virus bearing Omicron S caused less severe disease than the ancestral virus, its virulence was not attenuated to the level of Omicron. Further investigation showed that mutating non-structural protein 6 (nsp6) in addition to the S protein was sufficient to recapitulate the attenuated phenotype of Omicron. This indicates that although the vaccine escape of Omicron is driven by mutations in S, the pathogenicity of Omicron is determined by mutations both in and outside of the S protein.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Adams
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Markus Bosmann
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yachana Kataria
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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13
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Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer M. Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations. Clin Infect Dis 2023; 76:e400-e408. [PMID: 35616119 PMCID: PMC9213864 DOI: 10.1093/cid/ciac413] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area. METHODS We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs. RESULTS We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5-12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections. CONCLUSIONS We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5-12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.
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Affiliation(s)
- Brittany A Petros
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura F White
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Eric D Kolaczyk
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts, USA.,Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, Massachusetts, USA
| | - Matthew R Bauer
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Harvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Cleary
- Harvard University Clinical Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Sabrina T Dobbins
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Lynn Doucette-Stamm
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA
| | - Mitch Gore
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Tien G Nguyen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Scott Rose
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Daniel Tsang
- Integrated DNA Technologies, Inc, Coralville, Iowa, USA
| | | | - Michele Hope
- Harvard University Clinical Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Judy T Platt
- Boston University Student Health Services, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Tara Bouton
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Seyho Yune
- Student Affairs, Northeastern University, Boston, Massachusetts, USA
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.,Life Sciences Testing Center, Northeastern University, Burlington, Massachusetts, USA.,Biopharmaceutical Analysis and Training Laboratory, Burlington, Massachusetts, USA
| | - Lena Landaverde
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA.,Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Catherine M Klapperich
- Boston University Clinical Testing Laboratory, Boston University Boston, Massachusetts, USA.,Boston University Student Health Services, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA.,Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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14
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Bouton TC, Atarere J, Turcinovic J, Seitz S, Sher-Jan C, Gilbert M, White L, Zhou Z, Hossain MM, Overbeck V, Doucette-Stamm L, Platt J, Landsberg HE, Hamer DH, Klapperich C, Jacobson KR, Connor JH. Viral Dynamics of Omicron and Delta Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants With Implications for Timing of Release from Isolation: A Longitudinal Cohort Study. Clin Infect Dis 2023; 76:e227-e233. [PMID: 35737948 PMCID: PMC9278204 DOI: 10.1093/cid/ciac510] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In January 2022, US guidelines shifted to recommend isolation for 5 days from symptom onset, followed by 5 days of mask-wearing. However, viral dynamics and variant and vaccination impact on culture conversion are largely unknown. METHODS We conducted a longitudinal study on a university campus, collecting daily anterior nasal swabs for at least 10 days for reverse-transcription polymerase chain reaction (RT-PCR) testing and culture, with antigen rapid diagnostic testing (RDT) on a subset. We compared culture positivity beyond day 5, time to culture conversion, and cycle threshold trend when calculated from diagnostic test, from symptom onset, by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, and by vaccination status. We evaluated sensitivity and specificity of RDT on days 4-6 compared with culture. RESULTS Among 92 SARS-CoV-2 RT-PCR-positive participants, all completed the initial vaccine series; 17 (18.5%) were infected with Delta and 75 (81.5%) with Omicron. Seventeen percent of participants had positive cultures beyond day 5 from symptom onset, with the latest on day 12. There was no difference in time to culture conversion by variant or vaccination status. For 14 substudy participants, sensitivity and specificity of day 4-6 RDT were 100% and 86%, respectively. CONCLUSIONS The majority of our Delta- and Omicron-infected cohort culture-converted by day 6, with no further impact of booster vaccination on sterilization or cycle threshold decay. We found that rapid antigen testing may provide reassurance of lack of infectiousness, though guidance to mask for days 6-10 is supported by our finding that 17% of participants remained culture-positive after isolation.
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Affiliation(s)
- Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA.,Boston Medical Center, Boston, Massachusetts, USA
| | | | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,BioInformatics Program, Boston University, Boston, Massachusetts, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cole Sher-Jan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Madison Gilbert
- Boston Medical Center, Boston, Massachusetts, USA.,Graduate Medical Sciences, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Mohammad M Hossain
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Victoria Overbeck
- Boston Medical Center, Boston, Massachusetts, USA.,Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Judy Platt
- Boston University Student Health Services, Boston, Massachusetts, USA
| | | | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA.,Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Boston University School of Public Health, Boston, Massachusetts, USA.,Boston University Clinical Testing Laboratory, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA.,Boston Medical Center, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,BioInformatics Program, Boston University, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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15
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Chen DY, Kenney D, Chin CV, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. bioRxiv 2023:2022.10.13.512134. [PMID: 36263066 PMCID: PMC9580375 DOI: 10.1101/2022.10.13.512134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The recently identified, globally predominant SARS-CoV-2 Omicron variant (BA.1) is highly transmissible, even in fully vaccinated individuals, and causes attenuated disease compared with other major viral variants recognized to date. The Omicron spike (S) protein, with an unusually large number of mutations, is considered the major driver of these phenotypes. We generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron in the backbone of an ancestral SARS-CoV-2 isolate and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S.
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16
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Seymour E, Ünlü MS, Connor JH. A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies. Sci Rep 2023; 13:306. [PMID: 36609657 PMCID: PMC9821353 DOI: 10.1038/s41598-022-27281-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023] Open
Abstract
Monoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases. Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30 mAbs against Ebola, Sudan, and Lassa viruses (EBOV, SUDV, and LASV) to find out the ideal capture antibodies for whole virus detection using recombinant vesicular stomatitis virus (rVSV) models expressing surface glycoproteins (GPs) of EBOV, SUDV, and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the antibody epitopes on the GP structure. mAbs that bind to mucin-like domain or glycan cap of the EBOV surface GP show the highest signal on SP-IRIS, followed by mAbs that target the GP1-GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best performance on SP-IRIS. This antibody binds to a unique region on the surface GP compared to other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher efficacy compared to the other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do not compete with each other for binding to EBOV GP. In fact, the binding of 13C6 enhances the binding of 2G4 and 4G7 antibodies. Our results establish SP-IRIS as a versatile tool that can provide high-throughput screening of mAbs, multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails.
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Affiliation(s)
- Elif Seymour
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - M Selim Ünlü
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA.
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17
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Boytz R, Seitz S, Gaudiano E, Patten JJ, Keiser PT, Connor JH, Sharpe AH, Davey RA. Inactivation of Ebola Virus and SARS-CoV-2 in Cell Culture Supernatants and Cell Pellets by Gamma Irradiation. Viruses 2022; 15:43. [PMID: 36680083 PMCID: PMC9866162 DOI: 10.3390/v15010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Viral pathogens with the potential to cause widespread disruption to human health and society continue to emerge or re-emerge around the world. Research on such viruses often involves high biocontainment laboratories (BSL3 or BSL4), but the development of diagnostics, vaccines and therapeutics often uses assays that are best performed at lower biocontainment. Reliable inactivation is necessary to allow removal of materials to these spaces and to ensure personnel safety. Here, we validate the use of gamma irradiation to inactivate culture supernatants and pellets of cells infected with a representative member of the Filovirus and Coronavirus families. We show that supernatants and cell pellets containing SARS-CoV-2 are readily inactivated with 1.9 MRad, while Ebola virus requires higher doses of 2.6 MRad for supernatants and 3.8 MRad for pellets. While these doses of radiation inactivate viruses, proinflammatory cytokines that are common markers of virus infection are still detected with low losses. The doses required for virus inactivation of supernatants are in line with previously reported values, but the inactivation of cell pellets has not been previously reported and enables new approaches for analysis of protein-based host responses to infection.
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Affiliation(s)
- RuthMabel Boytz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Scott Seitz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Emily Gaudiano
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - J. J. Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Patrick T. Keiser
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - John H. Connor
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Arlene H. Sharpe
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
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18
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Landaverde L, Turcinovic J, Doucette-Stamm L, Gonzales K, Platt J, Connor JH, Klapperich C. Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs. Microbiol Spectr 2022; 10:e0130722. [PMID: 36255297 PMCID: PMC9769721 DOI: 10.1128/spectrum.01307-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
The COVID-19 pandemic has increased use of rapid diagnostic tests (RDTs). In winter 2021 to 2022, the Omicron variant surge made it apparent that although RDTs are less sensitive than quantitative reverse transcription-PCR (qRT-PCR), the accessibility, ease of use, and rapid readouts made them a sought after and often sold-out item at local suppliers. Here, we sought to qualify the Abbott BinaxNOW RDT for use in our university testing program as a method to rule in positive or rule out negative individuals quickly at our priority qRT-PCR testing site. To perform this qualification study, we collected additional swabs from individuals attending this site. All swabs were tested using BinaxNOW. Initially as part of a feasibility study, test period 1 (n = 110) samples were stored cold before testing. In test period 2 (n = 209), samples were tested immediately. Combined, 102/319 samples tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive via qRT-PCR. All sequenced samples were Omicron (n = 92). We calculated 53.9% sensitivity, 100% specificity, a 100% positive predictive value, and an 82.2% negative predictive value for BinaxNOW (n = 319). Sensitivity would be improved (75.3%) by changing the qRT-PCR positivity threshold from a threshold cycle (CT) value of 40 to a CT value of 30. The receiver operating characteristic (ROC) curve shows that for qRT-PCR-positive CT values of between 24 and 40, the BinaxNOW test is of limited value diagnostically. Results suggest BinaxNOW could be used in our setting to confirm SARS-CoV-2 infection in individuals with substantial viral load, but a significant fraction of infected individuals would be missed if we used RDTs exclusively to rule out infection. IMPORTANCE Our results suggest BinaxNOW can rule in SARS-CoV-2 infection but would miss infections if RDTs were exclusively used.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | | | - Kevin Gonzales
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
- Office of Research, Boston University, Boston, Massachusetts, USA
| | - Judy Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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19
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Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Doucette-Stamm L, Hanage WP, Hamer DH, Klapperich C, Landsberg HE, Connor JH. Linking contact tracing with genomic surveillance to deconvolute SARS-CoV-2 transmission on a university campus. iScience 2022; 25:105337. [PMID: 36246573 PMCID: PMC9554197 DOI: 10.1016/j.isci.2022.105337] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/12/2022] [Accepted: 10/10/2022] [Indexed: 11/26/2022] Open
Abstract
Contact tracing and genomic data, approaches often used separately, have both been important tools in understanding the nature of SARS-CoV-2 transmission. Linked analysis of contact tracing and sequence relatedness of SARS-CoV-2 genomes from a regularly sampled university environment were used to build a multilevel transmission tracing and confirmation system to monitor and understand transmission on campus. Our investigation of an 18-person cluster stemming from an athletic team highlighted the importance of linking contact tracing and genomic analysis. Through these findings, it is suggestive that certain safety protocols in the athletic practice setting reduced transmission. The linking of traditional contact tracing with rapid-return genomic information is an effective approach for differentiating between multiple plausible transmission scenarios and informing subsequent public health protocols to limit disease spread in a university environment. Contact tracing and sequencing provide more information than either approach alone Primary exposures in an athletic group occurred outside structured athletic events Genomic and contact tracing data can inform effective public health decisions
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Affiliation(s)
- Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Madison Sullivan
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA,BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA 02215, USA
| | - Judy T. Platt
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Lynn Doucette-Stamm
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA 02215, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Davidson H. Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA,Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA,Section of Infectious Disease, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA,Center for Emerging Infectious Disease Policy and Research, Boston University, Boston, MA 02118, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA
| | | | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Program in Bioinformatics, Boston University, Boston, MA 02215, USA,Center for Emerging Infectious Disease Policy and Research, Boston University, Boston, MA 02118, USA,Corresponding author
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20
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Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP. Understanding early pandemic SARS-CoV-2 transmission in a medical center by incorporating public sequencing databases to mitigate bias. J Infect Dis 2022; 226:1704-1711. [PMID: 35993116 PMCID: PMC9452097 DOI: 10.1093/infdis/jiac348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
Background Throughout the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inform hospital infection control policy. Here we show how the incorporation of sequences from public genomic databases aided genomic surveillance early in the pandemic when circulating viral diversity was limited. Methods We sequenced a subset of discarded, diagnostic SARS-CoV-2 isolates between March and May 2020 from Boston Medical Center HCWs and combined this data set with publicly available sequences from the surrounding community deposited in GISAID with the goal of inferring specific transmission routes. Results Contextualizing our data with publicly available sequences reveals that 73% (95% confidence interval, 63%–84%) of coronavirus disease 2019 cases in HCWs are likely novel introductions rather than nosocomial spread. Conclusions We argue that introductions of SARS-CoV-2 into the hospital environment are frequent and that expanding public genomic surveillance can better aid infection control when determining routes of transmission.
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Affiliation(s)
- Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, MA, USA
| | - Beau Schaeffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Aubrey R Odom-Mabey
- Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sarah E Weber
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Sara Lodi
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Elizabeth J Ragan
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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21
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Kuhfeldt K, Turcinovic J, Sullivan M, Landaverde L, Doucette-Stamm L, Hamer DH, Platt JT, Klapperich C, Landsberg HE, Connor JH. Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology. JAMA Netw Open 2022; 5:e2225430. [PMID: 35930286 PMCID: PMC9356317 DOI: 10.1001/jamanetworkopen.2022.25430] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, has displayed person-to-person transmission in a variety of indoor situations. This potential for robust transmission has posed significant challenges and concerns for day-to-day activities of colleges and universities where indoor learning is a focus for students, faculty, and staff. OBJECTIVE To assess whether in-class instruction without any physical distancing, but with other public health mitigation strategies, is a risk for driving SARS-CoV-2 transmission. DESIGN, SETTING, AND PARTICIPANTS This cohort study examined the evidence for SARS-CoV-2 transmission on a large urban US university campus using contact tracing, class attendance, and whole genome sequencing during the 2021 fall semester. Eligible participants were on-campus and off-campus individuals involved in campus activities. Data were analyzed between September and December 2021. EXPOSURES Participation in class and work activities on a campus with mandated vaccination and indoor masking but that was otherwise fully open without physical distancing during a time of ongoing transmission of SARS-CoV-2, both at the university and in the surrounding counties. MAIN OUTCOMES AND MEASURES Likelihood of in-class infection was assessed by measuring the genetic distance between all potential in-class transmission pairings using polymerase chain reaction testing. RESULTS More than 600 000 polymerase chain reaction tests were conducted throughout the semester, with 896 tests (0.1%) showing detectable SARS-CoV-2; there were over 850 cases of SARS-CoV-2 infection identified through weekly surveillance testing of all students and faculty on campus during the fall 2021 semester. The rolling mean average of positive tests ranged between 4 and 27 daily cases. Of more than 140 000 in-person class events and a total student population of 33 000 between graduate and undergraduate students, only 9 instances of potential in-class transmission were identified, accounting for 0.0045% of all classroom meetings. CONCLUSIONS AND RELEVANCE In this cohort study, the data suggested that under robust transmission abatement strategies, in-class instruction was not an appreciable source of disease transmission.
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Affiliation(s)
- Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, Massachusetts
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Program in Bioinformatics, Boston University, Boston, Massachusetts
| | - Madison Sullivan
- Student Health Services, Boston University, Boston, Massachusetts
| | - Lena Landaverde
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, Massachusetts
- Boston University Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Lynn Doucette-Stamm
- Boston University Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Davidson H. Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
- Section of Infectious Disease, Department of Medicine, Boston University School of Medicine; Boston, Massachusetts
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts
| | - Judy T. Platt
- Student Health Services, Boston University, Boston, Massachusetts
| | - Catherine Klapperich
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, Massachusetts
| | | | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Program in Bioinformatics, Boston University, Boston, Massachusetts
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts
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22
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Cosimi LA, Kelly C, Esposito S, Seitz S, Turcinovic J, Connor JH, Hung D. Duration of Symptoms and Association With Positive Home Rapid Antigen Test Results After Infection With SARS-CoV-2. JAMA Netw Open 2022; 5:e2225331. [PMID: 35921111 PMCID: PMC9350709 DOI: 10.1001/jamanetworkopen.2022.25331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This cohort study assesses the duration of symptoms and association with positive rapid antigen test results after SARS-CoV-2 infection.
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Affiliation(s)
- Lisa A. Cosimi
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Christina Kelly
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Samantha Esposito
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Scott Seitz
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Deborah Hung
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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23
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Kenney DJ, O’Connell AK, Turcinovic J, Montanaro P, Hekman RM, Tamura T, Berneshawi AR, Cafiero TR, Al Abdullatif S, Blum B, Goldstein SI, Heller BL, Gertje HP, Bullitt E, Trachtenberg AJ, Chavez E, Nono ET, Morrison C, Tseng AE, Sheikh A, Kurnick S, Grosz K, Bosmann M, Ericsson M, Huber BR, Saeed M, Balazs AB, Francis KP, Klose A, Paragas N, Campbell JD, Connor JH, Emili A, Crossland NA, Ploss A, Douam F. Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection. Cell Rep 2022; 39:110714. [PMID: 35421379 PMCID: PMC8977517 DOI: 10.1016/j.celrep.2022.110714] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/17/2022] [Accepted: 03/29/2022] [Indexed: 01/11/2023] Open
Abstract
The human immunological mechanisms defining the clinical outcome of SARS-CoV-2 infection remain elusive. This knowledge gap is mostly driven by the lack of appropriate experimental platforms recapitulating human immune responses in a controlled human lung environment. Here, we report a mouse model (i.e., HNFL mice) co-engrafted with human fetal lung xenografts (fLX) and a myeloid-enhanced human immune system to identify cellular and molecular correlates of lung protection during SARS-CoV-2 infection. Unlike mice solely engrafted with human fLX, HNFL mice are protected against infection, severe inflammation, and histopathological phenotypes. Lung tissue protection from infection and severe histopathology associates with macrophage infiltration and differentiation and the upregulation of a macrophage-enriched signature composed of 11 specific genes mainly associated with the type I interferon signaling pathway. Our work highlights the HNFL model as a transformative platform to investigate, in controlled experimental settings, human myeloid immune mechanisms governing lung tissue protection during SARS-CoV-2 infection.
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Affiliation(s)
- Devin J. Kenney
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Bioinformatics Program, Boston University, Boston, MA, USA
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ryan M. Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Tomokazu Tamura
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Thomas R. Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Salam Al Abdullatif
- Single Cell RNA Sequencing Core, Boston University, Boston, MA, USA,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Stanley I. Goldstein
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Brigitte L. Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Alexander J. Trachtenberg
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Elizabeth Chavez
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Evans Tuekam Nono
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Catherine Morrison
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Anna E. Tseng
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Amira Sheikh
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susanna Kurnick
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Animal Science Center, Boston University, Boston, MA, USA
| | - Kyle Grosz
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Animal Science Center, Boston University, Boston, MA, USA
| | - Markus Bosmann
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - Bertrand R. Huber
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | | | | | - Neal Paragas
- In Vivo Analytics, Inc., New York, NY, USA,Department of Radiology Imaging Research Lab, University of Washington, Seattle, WA, USA
| | - Joshua D. Campbell
- Single Cell RNA Sequencing Core, Boston University, Boston, MA, USA,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,Department of Biology, Boston University School of Medicine, Boston, MA, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA,Corresponding author
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA,Corresponding author
| | - Florian Douam
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Corresponding author
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24
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Bouton TC, Atarere J, Turcinovic J, Seitz S, Sher-Jan C, Gilbert M, White L, Zhou Z, Hossain MM, Overbeck V, Doucette-Stamm L, Platt J, Landsberg HE, Hamer DH, Klapperich C, Jacobson KR, Connor JH. Viral dynamics of Omicron and Delta SARS-CoV-2 variants with implications for timing of release from isolation: a longitudinal cohort study. medRxiv 2022:2022.04.04.22273429. [PMID: 35411341 PMCID: PMC8996632 DOI: 10.1101/2022.04.04.22273429] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 12/16/2022]
Abstract
Background In January 2022, United States guidelines shifted to recommend isolation for 5 days from symptom onset, followed by 5 days of mask wearing. However, viral dynamics and variant and vaccination impact on culture conversion are largely unknown. Methods We conducted a longitudinal study on a university campus, collecting daily anterior nasal swabs for at least 10 days for RT-PCR and culture, with antigen rapid diagnostic testing (RDT) on a subset. We compared culture positivity beyond day 5, time to culture conversion, and cycle threshold trend when calculated from diagnostic test, from symptom onset, by SARS-CoV-2 variant, and by vaccination status. We evaluated sensitivity and specificity of RDT on days 4-6 compared to culture. Results Among 92 SARS-CoV-2 RT-PCR positive participants, all completed the initial vaccine series, 17 (18.5%) were infected with Delta and 75 (81.5%) with Omicron. Seventeen percent of participants had positive cultures beyond day 5 from symptom onset with the latest on day 12. There was no difference in time to culture conversion by variant or vaccination status. For the 14 sub-study participants, sensitivity and specificity of RDT were 100% and 86% respectively. Conclusions The majority of our Delta- and Omicron-infected cohort culture-converted by day 6, with no further impact of booster vaccination on sterilization or cycle threshold decay. We found that rapid antigen testing may provide reassurance of lack of infectiousness, though masking for a full 10 days is necessary to prevent transmission from the 17% of individuals who remain culture positive after isolation. Main Point Beyond day 5, 17% of our Delta and Omicron-infected cohort were culture positive. We saw no significant impact of booster vaccination on within-host Omicron viral dynamics. Additionally, we found that rapid antigen testing may provide reassurance of lack of infectiousness.
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Affiliation(s)
- Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
- Boston Medical Center, Boston, MA, USA
| | | | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- BioInformatics Program, Boston University, Boston, MA, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Cole Sher-Jan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Madison Gilbert
- Boston Medical Center, Boston, MA, USA
- Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mohammad M Hossain
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Victoria Overbeck
- Boston Medical Center, Boston, MA, USA
- Boston University School of Public Health, Boston, MA, USA
| | | | - Judy Platt
- Boston University Student Health Services, Boston, MA, USA
| | | | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA, USA
| | - Catherine Klapperich
- Boston University Clinical Testing Laboratory, Boston, MA, USA
- Boston University Student Health Services, Boston, MA, USA
- Boston University Precision Diagnostics Center, Boston University, Boston, MA, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
- Boston Medical Center, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Boston University Precision Diagnostics Center, Boston University, Boston, MA, USA
- BioInformatics Program, Boston University, Boston, MA, USA
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25
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Kuhfeldt K, Turcinovic J, Sullivan M, Landaverde L, Doucette-Stamm L, Hamer DH, Platt J, Klapperich C, Landsberg HE, Connor JH. Minimal SARS-CoV-2 classroom transmission at a large urban university experiencing repeated into campus introduction. medRxiv 2022:2022.03.16.22271983. [PMID: 35313596 PMCID: PMC8936094 DOI: 10.1101/2022.03.16.22271983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
SARS-CoV-2, the causative agent of COVID-19, has displayed person to person transmission in a variety of indoor situations. This potential for robust transmission has posed significant challenges to day-to-day activities of colleges and universities where indoor learning is a focus. Concerns about transmission in the classroom setting have been of concern for students, faculty and staff. With the simultaneous implementation of both non-pharmaceutical and pharmaceutical control measures meant to curb the spread of the disease, defining whether in-class instruction without any physical distancing is a risk for driving transmission is important. We examined the evidence for SARS-CoV-2 transmission on a large urban university campus that mandated vaccination and masking but was otherwise fully open without physical distancing during a time of ongoing transmission of SARS-CoV-2 both at the university and in the surrounding counties. Using weekly surveillance testing of all on-campus individuals and rapid contact tracing of individuals testing positive for the virus we found little evidence of in-class transmission. Of more than 140,000 in-person class events, only nine instances of potential in-class transmission were identified. When each of these events were further interrogated by whole-genome sequencing of all positive cases significant genetic distance was identified between all potential in-class transmission pairings, providing evidence that all individuals were infected outside of the classroom. These data suggest that under robust transmission abatement strategies, in-class instruction is not an appreciable source of disease transmission.
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Affiliation(s)
- Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, MA USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Lena Landaverde
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, MA, USA
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA
| | - Lynn Doucette-Stamm
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA
| | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Global Health, Boston University School of Public Health, Boston, MA
- Section of Infectious Disease, Department of Medicine, Boston University School of Medicine; Boston, MA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA
| | - Judy Platt
- Department of Global Health, Boston University School of Public Health, Boston, MA
| | - Catherine Klapperich
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, MA, USA
| | | | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA
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26
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Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog 2022; 18:e1010268. [PMID: 35120176 PMCID: PMC8849519 DOI: 10.1371/journal.ppat.1010268] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/16/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2023] Open
Abstract
Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness. Due to increasing utilization of high-throughput sequencing technologies, RNA sequences of many unknown viruses have been discovered in bats and other animal species. Research on the pathogenic potential of these viruses is hampered by incomplete viral genome sequences and difficulties in isolating infectious virus from the animal hosts. One example of these potentially zoonotic pathogens is Lloviu virus (LLOV), a filovirus which is closely related to Ebola virus. Here we applied molecular virological approaches, including minigenome assays, to complement the incomplete LLOV genome ends with sequences from related viruses and identify cis-acting elements required for LLOV replication and transcription that were missing in the published LLOV sequence. The resulting full-length clones were used to generate infectious recombinant LLOV. We used this virus for electron microscopic analyses, infection studies in human cells, host response analysis, and antiviral drug testing. Our results provide new insights into the pathogenic potential of LLOV and delineate a roadmap for studying uncultured viruses.
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Affiliation(s)
- Adam J. Hume
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
| | - Baylee Heiden
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Stephen Ross
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Whitney A. Scoon
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Maria Ericsson
- Department of Cell Biology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Mitchell R. White
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Program in Bioinformatics, Boston University; Boston, Massachusetts, United States of America
| | - Tran T. N. Thao
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - Ryan M. Hekman
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
| | - Joseph E. Kaserman
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Gabor E. Toth
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center; Boston, Massachusetts, United States of America
| | - Andrew A. Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
- Department of Biology, Boston University; Boston, Massachusetts, United States of America
| | - Volker Thiel
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Gabor Kemenesi
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
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27
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Bean DJ, Monroe J, Turcinovic J, Moreau Y, Connor JH, Sagar M. SARS-CoV-2 reinfection associates with unstable housing and occurs in the presence of antibodies. Clin Infect Dis 2021; 75:e208-e215. [PMID: 34755830 PMCID: PMC8689949 DOI: 10.1093/cid/ciab940] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background The factors associated with severe acute respiratory coronavirus 2 (SARS-CoV-2) reinfection remain poorly defined. Methods We identified patients with SARS-CoV-2 infection and at least 1 repeat reverse transcription polymerase chain reaction result a minimum of 90 days after the initial positive test and before 21 January 2021. Those with a repeat positive test were deemed to have reinfection (n = 75), and those with only negative tests were classified as convalescents (n = 1594). Demographics, coronavirus disease 2019 (COVID-19) severity, and treatment histories were obtained from the Boston Medical Center electronic medical record. Humoral responses were analyzed using SARS-CoV-2–specific enzyme-linked immunosorbent assays and pseudovirus neutralizations in a subset of reinfection (n = 16) and convalescent samples (n = 32). Univariate, multivariate, and time to event analyses were used to identify associations. Results Individuals with reinfection had more frequent testing at shorter intervals compared with the convalescents. Unstable housing was associated with more than 2-fold greater chance of reinfection. Preexisting comorbidities and COVID-19 severity after the initial infection were not associated with reinfection. SARS-CoV-2 immunoglobulin G levels and pseudovirus neutralization were not different within the early weeks after primary infection and at a timepoint at least 90 days later in the 2 groups. In the convalescents, but not in those with reinfection, the late as compared with early humoral responses were significantly higher. Conclusions Reinfection associates with unstable housing, which is likely a marker for virus exposure, and reinfection occurs in the presence of SARS-CoV-2 antibodies.
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Affiliation(s)
- David J Bean
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Janet Monroe
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Yvetane Moreau
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Manish Sagar
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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28
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Fuchs SY, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J Virol 2021; 95:e0086221. [PMID: 34260266 PMCID: PMC8428404 DOI: 10.1128/jvi.00862-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectible human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectible human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Brianna J. Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Raghuveera K. Goel
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Benjamin Blum
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Alexander H. Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hasahn L. Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Vipul C. Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Boston Veterans Affairs Healthcare System, Boston, Massachusetts, USA
- Institute of Medical Engineering and Sciences, MA Institute of Technology, Cambridge, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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29
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Rajeeva Pandian NK, Connor JH, Cooke JP, Jain A. Abstract 111: Vein-Chip Is A New Experimental Model To Predict Pathophysiology Of SARS-CoV-2 Induced Thrombosis. Arterioscler Thromb Vasc Biol 2021. [DOI: 10.1161/atvb.41.suppl_1.111] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is a serious limitation of experimental models that can improve our limited knowledge of the mechanisms that regulate endotheliopathy and venous thrombosis (VT) clinically observed frequently amongst the most severe COVID-19 patients. Also, while observation and study of VT in humans are difficult due to the deep-lying nature of the deep veins in which VT develops, lab animal models do not include the venous valves, which are the sites for thrombus development in humans. We develop a Vein-chip microfluidic platform that includes venous valve architecture, endothelial cells (ECs), and whole blood flow, which can include the three factors of Virchow’s triad - endothelial inflammation, stasis of blood flow, and coagulable nature of blood. Our
in silico
and
in vitro
observations with Vein-Chip reveal that incompetent valves and thrombosis changes the blood flow pattern in and around the venous valves. We show that healthy endothelium at the venous valve cusps adapt to the complex flow patterns and have an anti-thrombotic phenotype compared to the venous lumen. But exposure of the lumen to living and replicating SARS-CoV-2 virus and inflammatory cytokines found in COVID-19 patient samples inflames the lumen and the valve endothelium becomes pro-thrombotic. Interestingly, when we directed our investigation to analyze the ACE2 expression on these cells, as ACE2 is the functional receptor of the SARS-CoV-2 virus, we found that ACE2 expression was poor under a static culture, but increased dramatically when venous ECs were exposed to shear stress within the vein-chip. This data supports our hypothesis that ACE2 expression (and therefore, SARS-CoV-2 entry into the endothelium) is dependent on venous hemodynamics and the Vein-Chip model is a highly dissectible platform that will help us to unravel the molecular mechanisms that lead to VT and its treatment strategies for COVID-19 and beyond.
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Ma Q, Srivastav SP, Gamez S, Dayama G, Feitosa-Suntheimer F, Patterson EI, Johnson RM, Matson EM, Gold AS, Brackney DE, Connor JH, Colpitts TM, Hughes GL, Rasgon JL, Nolan T, Akbari OS, Lau NC. A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. Genome Res 2021; 31:512-528. [PMID: 33419731 PMCID: PMC7919454 DOI: 10.1101/gr.265157.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Although mosquitoes are major transmission vectors for pathogenic arboviruses, viral infection has little impact on mosquito health. This immunity is caused in part by mosquito RNA interference (RNAi) pathways that generate antiviral small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). RNAi also maintains genome integrity by potently repressing mosquito transposon activity in the germline and soma. However, viral and transposon small RNA regulatory pathways have not been systematically examined together in mosquitoes. Therefore, we developed an integrated mosquito small RNA genomics (MSRG) resource that analyzes the transposon and virus small RNA profiles in mosquito cell cultures and somatic and gonadal tissues across four medically important mosquito species. Our resource captures both somatic and gonadal small RNA expression profiles within mosquito cell cultures, and we report the evolutionary dynamics of a novel Mosquito-Conserved piRNA Cluster Locus (MCpiRCL) made up of satellite DNA repeats. In the larger culicine mosquito genomes we detected highly regular periodicity in piRNA biogenesis patterns coinciding with the expansion of Piwi pathway genes. Finally, our resource enables detection of cross talk between piRNA and siRNA populations in mosquito cells during a response to virus infection. The MSRG resource will aid efforts to dissect and combat the capacity of mosquitoes to tolerate and spread arboviruses.
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Affiliation(s)
- Qicheng Ma
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Satyam P Srivastav
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Gargi Dayama
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Fabiana Feitosa-Suntheimer
- Department of Microbiology and the National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Edward I Patterson
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Rebecca M Johnson
- Department of Entomology, Center for Infectious Disease Dynamics, and the Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Erik M Matson
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alexander S Gold
- Department of Microbiology and the National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Douglas E Brackney
- Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06511, USA
| | - John H Connor
- Department of Microbiology and the National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Tonya M Colpitts
- Department of Microbiology and the National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Jason L Rasgon
- Department of Entomology, Center for Infectious Disease Dynamics, and the Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tony Nolan
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Boston University Genome Science Institute and the National Emerging Infectious Disease Laboratory, Boston, Massachusetts 02118, USA
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31
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Abstract
Here, we demonstrate real-time multiplexed virus detection by applying a DNA-directed antibody immobilization technique in a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing for specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant vesicular stomatitis viruses (rVSVs), which are genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in the solution phase prior to incubation in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/mL in 1 h. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104 PFU/mL was detectable under 10 min for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe that these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.
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Affiliation(s)
- Elif Seymour
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Nese Lortlar Ünlü
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Erik P. Carter
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02218, United States
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02218, United States
| | - M. Selim Ünlü
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
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32
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Strampe J, Asogun DA, Speranza E, Pahlmann M, Soucy A, Bockholt S, Pallasch E, Becker-Ziaja B, Duraffour S, Bhadelia N, Ighodalo Y, Oyakhilome J, Omomoh EO, Olokor T, Adomeh DI, Ikponwonsa O, Aire C, Tobin E, Akpede N, Okokhere PO, Okogbenin SA, Akpede GO, Muñoz-Fontela C, Ogbaini-Emovon E, Günther S, Connor JH, Oestereich L. Factors associated with progression to death in patients with Lassa fever in Nigeria: an observational study. Lancet Infect Dis 2021; 21:876-886. [PMID: 33484646 DOI: 10.1016/s1473-3099(20)30737-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/29/2020] [Accepted: 08/21/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Lassa fever is endemic in several west African countries. Case-fatality rates ranging from 21% to 69% have been reported. The pathophysiology of the disease in humans and determinants of mortality remain poorly understood. We aimed to determine host protein biomarkers capable of determining disease outcome. METHODS In this observational study, we analysed left-over blood samples from patients who tested positive for Lassa fever at Irrua Specialist Teaching Hospital, Nigeria, between January, 2014, and April, 2017. We measured viral load, concentrations of clinical chemistry parameters, and levels of 62 circulating proteins involved in inflammation, immune response, and haemostasis. Patients with a known outcome (survival or death) and at least 200 μL of good-quality diagnostic sample were included in logistic regression modelling to assess the correlation of parameters with Lassa fever outcome. Individuals who gave consent could further be enrolled into a longitudinal analysis to assess the association of parameters with Lassa fever outcome over time. Participants were divided into two datasets for the statistical analysis: a primary dataset (samples taken between Jan 1, 2014, and April 1, 2016), and a secondary dataset (samples taken between April 1, 2016, and April 1, 2017). Biomarkers were ranked by area under the receiver operating characteristic curve (AUC) from highest (most predictive) to lowest (least predictive). FINDINGS Of 554 patients who tested positive for Lassa fever during the study period, 201 (131 in the primary dataset and 70 in the secondary dataset) were included in the biomarker analysis, of whom 74 (49 in the primary dataset and 25 in the secondary dataset) had died and 127 (82 in the primary dataset and 45 in the secondary dataset) had survived. Cycle threshold values (indicating viral load) and levels of 18 host proteins at the time of admission to hospital were significantly correlated with fatal outcome. The best predictors of outcome in both datasets were plasminogen activator inhibitor-1 (PAI-1; AUC 0·878 in the primary dataset and 0·876 in the secondary dataset), soluble thrombomodulin (TM; 0·839 in the primary dataset and 0·875 in the secondary dataset), and soluble tumour necrosis factor receptor superfamily member 1A (TNF-R1; 0·807 in the primary dataset and 0·851 in the secondary dataset), all of which had higher prediction accuracy than viral load (0·774 in the primary dataset and 0·837 in the secondary dataset). Longitudinal analysis (150 patients, of whom 36 died) showed that of the biomarkers that were predictive at admission, PAI-1 levels consistently decreased to normal levels in survivors but not in those who died. INTERPRETATION The identification of PAI-1 and soluble TM as markers of fatal Lassa fever at admission, and of PAI-1 as a marker of fatal Lassa fever over time, suggests that dysregulated coagulation and fibrinolysis and endothelial damage have roles in the pathophysiology of Lassa fever, providing a mechanistic explanation for the association of Lassa fever with oedema and bleeding. These novel markers might aid in clinical risk stratification and disease monitoring. FUNDING German Research Foundation, Leibniz Association, and US National Institutes of Health.
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Affiliation(s)
- Jamie Strampe
- Bioinformatics Program, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Danny A Asogun
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Emily Speranza
- Bioinformatics Program, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston, MA, USA; National Institutes of Health, National Institute of Allergy and Infectious disease, Laboratory of Virology, Laboratory of Immune System Biology, Bethesda, MD, USA
| | - Meike Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Ali Soucy
- Department of Microbiology, School of Medicine, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Sabrina Bockholt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Elisa Pallasch
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Beate Becker-Ziaja
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany; Robert Koch Institute, Berlin, Germany
| | - Sophie Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Nahid Bhadelia
- National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Yemisi Ighodalo
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Thomas Olokor
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Odia Ikponwonsa
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Chris Aire
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ekaete Tobin
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Nosa Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - George O Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | | | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - John H Connor
- Bioinformatics Program, Boston University, Boston, MA, USA; Department of Microbiology, School of Medicine, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston, MA, USA.
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany.
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33
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2021; 81:212. [PMID: 33417854 PMCID: PMC7831449 DOI: 10.1016/j.molcel.2020.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Cooke JP, Connor JH, Jain A. Acute and Chronic Cardiovascular Manifestations of COVID-19: Role for Endotheliopathy. Methodist Debakey Cardiovasc J 2021; 17:53-62. [PMID: 34992723 PMCID: PMC8680072 DOI: 10.14797/mdcvj.1044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2, the virus that causes coronavirus disease 19 (COVID-19), is associated with a bewildering array of cardiovascular manifestations, including myocardial infarction and stroke, myocarditis and heart failure, atrial and ventricular arrhythmias, venous thromboembolism, and microvascular disease. Accumulating evidence indicates that a profound disturbance of endothelial homeostasis contributes to these conditions. Furthermore, the pulmonary infiltration and edema, and later pulmonary fibrosis, in patients with COVID-19 is promoted by endothelial alterations including the expression of endothelial adhesion molecules and chemokines, increased intercellular permeability, and endothelial-to-mesenchyme transitions. The cognitive disturbance occurring in this disease may also be due in part to an impairment of the blood-brain barrier. Venous thrombosis and pulmonary thromboembolism are most likely associated with an endothelial defect caused by circulating inflammatory cytokines and/or direct endothelial invasion by the virus. Endothelial-targeted therapies such as statins, nitric oxide donors, and antioxidants may be useful therapeutic adjuncts in COVID-19 by restoring endothelial homeostasis.
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Affiliation(s)
- John P Cooke
- Houston Methodist Research Institute, Houston Methodist, Houston, TX, US
| | - John H Connor
- Boston University Medical Center and National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, US
| | - Abhishek Jain
- Texas A&M University, College Station, TX, US.,Texas A&M Health Science Center, Bryan, TX, US
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35
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2020; 80:1104-1122.e9. [PMID: 33259812 PMCID: PMC7674017 DOI: 10.1016/j.molcel.2020.11.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [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: 09/01/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.
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Affiliation(s)
- Ryan M Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ellen L Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Indranil Paul
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Ahmed Youssef
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Dmitry Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Mamta Verma
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, Miami, FL, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Anne Hinds
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Tilston-Lunel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Benjamin L Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA; Department of Biology, University of Miami, Miami, FL, USA; Miami Institute of Data Science and Computing, Miami, FL, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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36
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Kapell S, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. bioRxiv 2020. [PMID: 33140044 DOI: 10.1101/2020.10.27.358259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.
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37
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Gold AS, Feitosa-Suntheimer F, Asad S, Adeoye B, Connor JH, Colpitts TM. Examining the Role of Niemann-Pick C1 Protein in the Permissiveness of Aedes Mosquitoes to Filoviruses. ACS Infect Dis 2020; 6:2023-2028. [PMID: 32609483 DOI: 10.1021/acsinfecdis.0c00018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aedes mosquitoes vector many viruses with divergent characteristics, yet the criteria needed for a virus to be vectored by an arthropod remain unknown. The intracellular cholesterol transporter protein Niemann-Pick C1 (NPC1) has been identified as the necessary entry receptor for filoviruses such as Ebola and Marburg viruses. While homologues of NPC1 are observed in mosquitoes, currently no filovirus has been identified as circulating in mosquitoes. This work aimed at increasing the understanding of the mosquito vector by examining the capability of a virus to gain the ability to enter mosquito cells. We developed a model system of Aedes cells expressing human NPC1 (hNPC1) and attempted to infect these cells with recombinant vesicular stomatitis virus expressing the Ebola virus glycoprotein. As compared to the control cells, no significant increase in infection was observed in cells expressing hNPC1, demonstrating that the expression of human NPC1 alone is not sufficient to support filovirus infection, and that host factors other than NPC1 determine filovirus susceptibility of mosquito cells.
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Affiliation(s)
- Alexander S. Gold
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Fabiana Feitosa-Suntheimer
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Sultan Asad
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Bukola Adeoye
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Tonya M. Colpitts
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, 620 Albany Street, Boston, Massachusetts 02118, United States
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38
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Greenberg A, Huber BR, Liu DX, Logue JP, Hischak AMW, Hart RJ, Abbott M, Isic N, Hisada YM, Mackman N, Bennett RS, Hensley LE, Connor JH, Crossland NA. Quantification of Viral and Host Biomarkers in the Liver of Rhesus Macaques: A Longitudinal Study of Zaire Ebolavirus Strain Kikwit (EBOV/Kik). Am J Pathol 2020; 190:1449-1460. [PMID: 32275904 PMCID: PMC7322367 DOI: 10.1016/j.ajpath.2020.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022]
Abstract
Zaire ebolavirus (EBOV) causes Ebola virus disease (EVD), which carries a fatality rate between 25% and 90% in humans. Liver pathology is a hallmark of terminal EVD; however, little is known about temporal disease progression. We used multiplexed fluorescent immunohistochemistry and in situ hybridization in combination with whole slide imaging and image analysis (IA) to quantitatively characterize temporospatial signatures of viral and host factors as related to EBOV pathogenesis. Eighteen rhesus monkeys euthanized between 3 and 8 days post-infection, and 3 uninfected controls were enrolled in this study. Compared with semiquantitative histomorphologic ordinal scoring, quantitative IA detected subtle and progressive features of early and terminal EVD that was not feasible with routine approaches. Sinusoidal macrophages were the earliest cells to respond to infection, expressing proinflammatory cytokine interleukin 6 (IL6) mRNA, which was subsequently also observed in fibrovascular compartments. The mRNA of interferon-stimulated gene-15 (ISG-15), also known as ISG15 ubiquitin like modifier (ISG15), was observed early, with a progressive and ubiquitous hybridization signature involving mesenchymal and epithelial compartments. ISG-15 mRNA was prominent near infected cells, but not in infected cells, supporting the hypothesis that bystander cells produce a robust interferon gene response. This study contributes to our current understanding of early EVD progression and illustrates the value that digital pathology and quantitative IA serve in infectious disease research.
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Affiliation(s)
- Alexandra Greenberg
- Graduate Medical Sciences, Boston University School of Medicine, Boston, Massachusetts
| | - Bertrand R Huber
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - David X Liu
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - James P Logue
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Amanda M W Hischak
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Randy J Hart
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Maureen Abbott
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Nejra Isic
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Yohei M Hisada
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nigel Mackman
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard S Bennett
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - John H Connor
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Nicholas A Crossland
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts.
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39
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Yurdakul C, Avci O, Matlock A, Devaux AJ, Quintero MV, Ozbay E, Davey RA, Connor JH, Karl WC, Tian L, Ünlü MS. High-Throughput, High-Resolution Interferometric Light Microscopy of Biological Nanoparticles. ACS Nano 2020; 14:2002-2013. [PMID: 32003974 DOI: 10.1021/acsnano.9b08512] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Label-free, visible light microscopy is an indispensable tool for studying biological nanoparticles (BNPs). However, conventional imaging techniques have two major challenges: (i) weak contrast due to low-refractive-index difference with the surrounding medium and exceptionally small size and (ii) limited spatial resolution. Advances in interferometric microscopy have overcome the weak contrast limitation and enabled direct detection of BNPs, yet lateral resolution remains as a challenge in studying BNP morphology. Here, we introduce a wide-field interferometric microscopy technique augmented by computational imaging to demonstrate a 2-fold lateral resolution improvement over a large field-of-view (>100 × 100 μm2), enabling simultaneous imaging of more than 104 BNPs at a resolution of ∼150 nm without any labels or sample preparation. We present a rigorous vectorial-optics-based forward model establishing the relationship between the intensity images captured under partially coherent asymmetric illumination and the complex permittivity distribution of nanoparticles. We demonstrate high-throughput morphological visualization of a diverse population of Ebola virus-like particles and a structurally distinct Ebola vaccine candidate. Our approach offers a low-cost and robust label-free imaging platform for high-throughput and high-resolution characterization of a broad size range of BNPs.
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Affiliation(s)
- Celalettin Yurdakul
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Oguzhan Avci
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alex Matlock
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alexander J Devaux
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Maritza V Quintero
- Department of Biochemistry and Structural Biology , University of Texas Health San Antonio , San Antonio , Texas 78229 , United States
| | - Ekmel Ozbay
- Department of Electrical and Electronics Engineering , Bilkent University , 06800 Ankara , Turkey
| | - Robert A Davey
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - W Clem Karl
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Lei Tian
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
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40
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Sebba D, Lastovich AG, Kuroda M, Fallows E, Johnson J, Ahouidi A, Honko AN, Fu H, Nielson R, Carruthers E, Diédhiou C, Ahmadou D, Soropogui B, Ruedas J, Peters K, Bartkowiak M, Magassouba N, Mboup S, Ben Amor Y, Connor JH, Weidemaier K. A point-of-care diagnostic for differentiating Ebola from endemic febrile diseases. Sci Transl Med 2019; 10:10/471/eaat0944. [PMID: 30541788 DOI: 10.1126/scitranslmed.aat0944] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 11/09/2018] [Indexed: 12/25/2022]
Abstract
Hemorrhagic fever outbreaks such as Ebola are difficult to detect and control because of the lack of low-cost, easily deployable diagnostics and because initial clinical symptoms mimic other endemic diseases such as malaria. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need. Although rapid tests such as lateral flow can be broadly deployed, they are typically not well-suited for differentiating among multiple diseases presenting with similar symptoms. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect and differentiate infection with Ebola virus from other more common febrile diseases. Here, we developed and tested an immunoassay technology that uses surface-enhanced Raman scattering (SERS) tags to simultaneously detect antigens from Ebola, Lassa, and malaria within a single blood sample. Results are provided in <30 min for individual or batched samples. Using 190 clinical samples collected from the 2014 West African Ebola outbreak, along with 163 malaria positives and 233 negative controls, we demonstrated Ebola detection with 90.0% sensitivity and 97.9% specificity and malaria detection with 100.0% sensitivity and 99.6% specificity. These results, along with corresponding live virus and nonhuman primate testing of an Ebola, Lassa, and malaria 3-plex assay, indicate the potential of the SERS technology as an important tool for outbreak detection and clinical triage in low-resource settings.
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Affiliation(s)
- David Sebba
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Alexander G Lastovich
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Melody Kuroda
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Eric Fallows
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Joshua Johnson
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, MD 21702, USA
| | - Ambroise Ahouidi
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal.,Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF), Diamniadio, BP 7325, Dakar, Senegal
| | - Anna N Honko
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, MD 21702, USA
| | - Henry Fu
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Rex Nielson
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Erin Carruthers
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Cyrille Diédhiou
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Doré Ahmadou
- Hemorrhagic Fever Laboratory, Université Gamal Abdel Nasser de Conakry, BP 5680, Conakry, Guinea
| | - Barré Soropogui
- Hemorrhagic Fever Laboratory, Université Gamal Abdel Nasser de Conakry, BP 5680, Conakry, Guinea
| | - John Ruedas
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Kristen Peters
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Miroslaw Bartkowiak
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - N'Faly Magassouba
- Hemorrhagic Fever Laboratory, Université Gamal Abdel Nasser de Conakry, BP 5680, Conakry, Guinea
| | - Souleymane Mboup
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal.,Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF), Diamniadio, BP 7325, Dakar, Senegal
| | - Yanis Ben Amor
- Center for Sustainable Development, Earth Institute at Columbia University, 475 Riverside Drive, Suite 1040, New York, NY 10115, USA
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA.
| | - Kristin Weidemaier
- Becton, Dickinson and Company, 21 Davis Drive, Research Triangle Park, NC 27709, USA.
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41
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Speranza E, Ruibal P, Port JR, Feng F, Burkhardt L, Grundhoff A, Günther S, Oestereich L, Hiscox JA, Connor JH, Muñoz-Fontela C. T-Cell Receptor Diversity and the Control of T-Cell Homeostasis Mark Ebola Virus Disease Survival in Humans. J Infect Dis 2019; 218:S508-S518. [PMID: 29986035 DOI: 10.1093/infdis/jiy352] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differences in T-cell phenotype, particularly the expression of markers of T-cell homeostasis, have been observed in fatal and nonfatal Ebola virus disease (EVD). However, the relationship between these markers with T-cell function and virus clearance during EVD is poorly understood. To gain biological insight into the role of T cells during EVD, combined transcriptomics and T-cell receptor sequencing was used to profile blood samples from fatal and nonfatal EVD patients from the recent West African EVD epidemic. Fatal EVD was characterized by strong T-cell activation and increased abundance of T-cell inhibitory molecules. However, the early T-cell response was oligoclonal and did not result in viral clearance. In contrast, survivors mounted highly diverse T-cell responses, maintained low levels of T-cell inhibitors, and cleared Ebola virus. Our findings highlight the importance of T-cell immunity in surviving EVD and strengthen the foundation for further research on targeting of the dendritic cell-T cell interface for postexposure immunotherapy.
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Affiliation(s)
- Emily Speranza
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Paula Ruibal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia R Port
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Lia Burkhardt
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Julian A Hiscox
- Institute for Infection and Global Health, University of Liverpool, United Kingdom.,Singapore Immunology Network, A*STAR, Singapore
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
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42
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Cross RW, Speranza E, Borisevich V, Widen SG, Wood TG, Shim RS, Adams RD, Gerhardt DM, Bennett RS, Honko AN, Johnson JC, Hensley LE, Geisbert TW, Connor JH. Comparative Transcriptomics in Ebola Makona-Infected Ferrets, Nonhuman Primates, and Humans. J Infect Dis 2018; 218:S486-S495. [PMID: 30476250 PMCID: PMC6249602 DOI: 10.1093/infdis/jiy455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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] [Indexed: 01/29/2023] Open
Abstract
The domestic ferret is a uniformly lethal model of infection for 3 species of Ebolavirus known to be pathogenic in humans. Reagents to systematically analyze the ferret host response to infection are lacking; however, the recent publication of a draft ferret genome has opened the potential for transcriptional analysis of ferret models of disease. In this work, we present comparative analysis of longitudinally sampled blood taken from ferrets and nonhuman primates infected with lethal doses of the Makona variant of Zaire ebolavirus. Strong induction of proinflammatory and prothrombotic signaling programs were present in both ferrets and nonhuman primates, and both transcriptomes were similar to previously published datasets of fatal cases of human Ebola virus infection.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Steven G Widen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Thomas G Wood
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Rebecca S Shim
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Ricky D Adams
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Dawn M Gerhardt
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Richard S Bennett
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - John H Connor
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
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43
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Olsen ME, Cressey TN, Mühlberger E, Connor JH. Differential Mechanisms for the Involvement of Polyamines and Hypusinated eIF5A in Ebola Virus Gene Expression. J Virol 2018; 92:e01260-18. [PMID: 30045993 PMCID: PMC6158423 DOI: 10.1128/jvi.01260-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 02/06/2023] Open
Abstract
Polyamines and hypusinated eIF5A have been implicated in the replication of diverse viruses; however, defining their roles in supporting virus replication is still under investigation. We have previously reported that Ebola virus (EBOV) requires polyamines and hypusinated eIF5A for replication. Using a replication-deficient minigenome construct, we show that gene expression, in the absence of genome replication, requires hypusinated eIF5A. Additional experiments demonstrated that the block in gene expression upon hypusine depletion was posttranscriptional, as minigenome reporter mRNA transcribed by the EBOV polymerase accumulated normally in the presence of drug treatment where protein did not. When this mRNA was isolated from cells with low levels of hypusinated eIF5A and transfected into cells with normal eIF5A function, minigenome reporter protein accumulation was normal, demonstrating that the mRNA produced was functional but required hypusinated eIF5A function for translation. Our results support a mechanism in which hypusinated eIF5A is required for the translation, but not synthesis, of EBOV transcripts. In contrast, depletion of polyamines with difluoromethylornithine (DFMO) resulted in a strong block in the accumulation of EBOV polymerase-produced mRNA, indicating a different mechanism of polyamine suppression of EBOV gene expression. Supplementing with exogenous polyamines after DFMO treatment restored mRNA accumulation and luciferase activity. These data indicate that cellular polyamines are required for two distinct aspects of the EBOV life cycle. The bifunctional requirement for polyamines underscores the importance of these cellular metabolites in EBOV replication and suggests that repurposing existing inhibitors of this pathway could be an effective approach for EBOV therapeutics.IMPORTANCE Ebola virus is a genetically simple virus that has a small number of proteins. Because of this, it requires host molecules and proteins to produce new infectious virus particles. Though attention is often focused on cellular proteins required for this process, it has recently been shown that cellular metabolites such as polyamines are also necessary for EBOV replication. Here we show that polyamines such as spermine and spermidine are required for the accumulation of EBOV mRNA and that eIF5A, a molecule modified by spermidine, is required for the translation, but not the production, of EBOV mRNAs. These findings suggest that effectively targeting this pathway could provide a biphasic block of EBOV replication.
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Affiliation(s)
- Michelle E Olsen
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Tessa N Cressey
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - John H Connor
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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44
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Speranza E, Bixler SL, Altamura LA, Arnold CE, Pratt WD, Taylor-Howell C, Burrows C, Aguilar W, Rossi F, Shamblin JD, Wollen SE, Zelko JM, Minogue T, Nagle E, Palacios G, Goff AJ, Connor JH. A conserved transcriptional response to intranasal Ebola virus exposure in nonhuman primates prior to onset of fever. Sci Transl Med 2018; 10:10/434/eaaq1016. [PMID: 29593102 PMCID: PMC9986849 DOI: 10.1126/scitranslmed.aaq1016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/13/2018] [Indexed: 12/18/2022]
Abstract
Ebola virus disease (EVD), caused by Ebola virus (EBOV), is a severe illness characterized by case fatality rates of up to 90%. The sporadic nature of outbreaks in resource-limited areas has hindered the ability to characterize the pathogenesis of EVD at all stages of infection but particularly early host responses. Pathogenesis is often studied in nonhuman primate (NHP) models of disease that replicate major aspects of human EVD. Typically, NHP models use a large infectious dose, are carried out through intramuscular or aerosol exposure, and have a fairly uniform disease course. By contrast, we report our analysis of the host response to EBOV after intranasal exposure. Twelve cynomolgus macaques were infected with 100 plaque-forming units of EBOV/Makona through intranasal exposure and presented with varying times to onset of EVD. We used RNA sequencing and a newly developed NanoString CodeSet to monitor the host response via changes in RNA transcripts over time. When individual animal gene expression data were phased based on the onset of sustained fever, the first clinical sign of severe disease, mathematical models indicated that interferon-stimulated genes appeared as early as 4 days before fever onset. This demonstrates that lethal EVD has a uniform and predictable response to infection regardless of time to onset. Furthermore, expression of a subset of genes could predict disease development before other host-based indications of infection such as fever.
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Affiliation(s)
- Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Sandra L Bixler
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Louis A Altamura
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Catherine E Arnold
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - William D Pratt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Cheryl Taylor-Howell
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Christina Burrows
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - William Aguilar
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Franco Rossi
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Joshua D Shamblin
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Suzanne E Wollen
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Justine M Zelko
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Timothy Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Elyse Nagle
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Arthur J Goff
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - John H Connor
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
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Abstract
Mosquito-borne viruses, including Zika virus (ZIKV) and dengue virus (DENV), are global threats that continue to infect millions annually. Historically, efforts to combat the spread of these diseases have sought to eradicate the mosquito population. This has had limited success. Recent efforts to combat the spread of these diseases have targeted the mosquito population and the mosquito's ability to transmit viruses by altering the mosquito's microbiome. The introduction of particular strains of Wolbachia bacteria into mosquitos suppresses viral growth and blocks disease transmission. This novel strategy is being tested worldwide to reduce DENV and has early indications of success. The Wolbachia genus comprised divergent strains that are divided in major phylogenetic clades termed supergroups. All Wolbachia field trials currently utilize supergroup A Wolbachia in Aedes aegypti mosquitos to limit virus transmission. Here we discuss our studies of Wolbachia strains not yet used in virus control strategies but that show strong potential to reduce ZIKV replication. These strains are important opportunities in the search for novel tools to reduce the levels of mosquito-borne viruses and provide additional models for mechanistic studies.
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Affiliation(s)
- Michaela J Schultz
- 1 Department of Biology, Boston University , Boston Massachusetts.,2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts
| | - John H Connor
- 2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts.,3 Department of Microbiology, Boston University School of Medicine , Boston, Massachusetts
| | - Horacio M Frydman
- 1 Department of Biology, Boston University , Boston Massachusetts.,2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts
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46
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Speranza E, Altamura LA, Kulcsar K, Bixler SL, Rossi CA, Schoepp RJ, Nagle E, Aguilar W, Douglas CE, Delp KL, Minogue TD, Palacios G, Goff AJ, Connor JH. Comparison of Transcriptomic Platforms for Analysis of Whole Blood from Ebola-Infected Cynomolgus Macaques. Sci Rep 2017; 7:14756. [PMID: 29116224 PMCID: PMC5676990 DOI: 10.1038/s41598-017-15145-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/17/2017] [Indexed: 11/09/2022] Open
Abstract
Ebola virus disease (EVD) is a serious illness with mortality rates of 20-90% in various outbreaks. EVD is characterized by robust virus replication and strong host inflammatory response. Analyzing host immune responses has increasingly involved multimodal approaches including transcriptomics to profile gene expression. We studied cynomolgus macaques exposed to Ebola virus Makona via different routes with the intent of comparing RNA-Seq to a NanoString nCounter codeset targeting 769 non-human primate (NHP) genes. RNA-Seq analysis of serial blood samples showed different routes led to the same overall transcriptional response seen in previously reported EBOV-exposed NHP studies. Both platforms displayed a strong correlation in gene expression patterns, including a strong induction of innate immune response genes at early times post-exposure, and neutrophil-associated genes at later time points. A 41-gene classifier was tested in both platforms for ability to cluster samples by infection status. Both NanoString and RNA-Seq could be used to predict relative abundances of circulating immune cell populations that matched traditional hematology. This demonstrates the complementarity of RNA-Seq and NanoString. Moreover, the development of an NHP-specific NanoString codeset should augment studies of filoviruses and other high containment infectious diseases without the infrastructure requirements of RNA-Seq technology.
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Affiliation(s)
- Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, United States
| | - Louis A Altamura
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Kirsten Kulcsar
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Sandra L Bixler
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Cynthia A Rossi
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Randal J Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Elyse Nagle
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - William Aguilar
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Christina E Douglas
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Korey L Delp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Timothy D Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Arthur J Goff
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States.
| | - John H Connor
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, United States.
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47
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Lo J, Zhang D, Speranza E, Negron JA, Connor JH. HoTResDB: host transcriptional response database for viral hemorrhagic fevers. Bioinformatics 2017; 34:321-322. [PMID: 29028885 PMCID: PMC5860212 DOI: 10.1093/bioinformatics/btx599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 11/12/2022] Open
Abstract
Summary High-throughput screening of the host transcriptional response to various viral infections provides a wealth of data, but utilization of microarray and next generation sequencing (NGS) data for analysis can be difficult. The Host Transcriptional Response DataBase (HoTResDB), allows visitors to access already processed microarray and NGS data from non-human primate models of viral hemorrhagic fever to better understand the host transcriptional response. Availability HoTResDB is freely available at http://hotresdb.bu.edu
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Affiliation(s)
- Jonathan Lo
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA, USA
| | - Deric Zhang
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA, USA
| | - Emily Speranza
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA, USA.,Department of Microbiology, National Emerging Infectious Diseases Laboratories (NEIDL), Boston Univeristy, 620 Albany St, Boston, MA, USA
| | - Jose A Negron
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA, USA
| | - John H Connor
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA, USA.,Department of Microbiology, National Emerging Infectious Diseases Laboratories (NEIDL), Boston Univeristy, 620 Albany St, Boston, MA, USA
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48
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Abstract
Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by the Ebolavirus and currently there are no licensed therapeutics or vaccines to treat EVD. Due to its high mortality rates and potential as a bioterrorist weapon, a better understanding of the disease is of high priority. Multiparametric analysis techniques allow for a more complete understanding of a disease and the host response. Analysis of RNA species present in a sample can lead to a greater understanding of activation or suppression of different states of the immune response. Transcriptomic analyses such as microarrays and RNA-Sequencing (RNA-Seq) have been important tools to better understand the global gene expression response to EVD. In this review, we outline the current knowledge gained by transcriptomic analysis of EVD.
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Affiliation(s)
- Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Boston, MA 02118, USA.
| | - John H Connor
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Boston, MA 02118, USA.
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49
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Daaboul GG, Freedman DS, Scherr SM, Carter E, Rosca A, Bernstein D, Mire CE, Agans KN, Hoenen T, Geisbert TW, Ünlü MS, Connor JH. Enhanced light microscopy visualization of virus particles from Zika virus to filamentous ebolaviruses. PLoS One 2017. [PMID: 28651016 PMCID: PMC5484481 DOI: 10.1371/journal.pone.0179728] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light microscopy is a powerful tool in the detection and analysis of parasites, fungi, and prokaryotes, but has been challenging to use for the detection of individual virus particles. Unlabeled virus particles are too small to be visualized using standard visible light microscopy. Characterization of virus particles is typically performed using higher resolution approaches such as electron microscopy or atomic force microscopy. These approaches require purification of virions away from their normal millieu, requiring significant levels of expertise, and can only enumerate small numbers of particles per field of view. Here, we utilize a visible light imaging approach called Single Particle Interferometric Reflectance Imaging Sensor (SP-IRIS) that allows automated counting and sizing of thousands of individual virions. Virions are captured directly from complex solutions onto a silicon chip and then detected using a reflectance interference imaging modality. We show that the use of different imaging wavelengths allows the visualization of a multitude of virus particles. Using Violet/UV illumination, the SP-IRIS technique is able to detect individual flavivirus particles (~40 nm), while green light illumination is capable of identifying and discriminating between vesicular stomatitis virus and vaccinia virus (~360 nm). Strikingly, the technology allows the clear identification of filamentous infectious ebolavirus particles and virus-like particles. The ability to differentiate and quantify unlabeled virus particles extends the usefulness of traditional light microscopy and can be embodied in a straightforward benchtop approach allowing widespread applications ranging from rapid detection in biological fluids to analysis of virus-like particles for vaccine development and production.
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Affiliation(s)
| | | | - Steven M. Scherr
- Department of Mechanical Engineering, Boston University, Boston, MA, United States of America
| | - Erik Carter
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Alexandru Rosca
- nanoView Diagnostics Inc., Boston, MA, United States of America
| | - David Bernstein
- nanoView Diagnostics Inc., Boston, MA, United States of America
| | - Chad E. Mire
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Krystle N. Agans
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Thomas Hoenen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, United States of America
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald–Isle of Riems, Germany
| | - Thomas W. Geisbert
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - M. Selim Ünlü
- Department of Electrical Engineering, Boston University, Boston, MA, United States of America
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Physics Department, Boston University, Boston, MA, United States of America
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- * E-mail:
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50
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Rossignol ED, Peters KN, Connor JH, Bullitt E. Zika virus induced cellular remodelling. Cell Microbiol 2017; 19. [PMID: 28318141 DOI: 10.1111/cmi.12740] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 01/18/2017] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
Abstract
Zika virus (ZIKV) has been associated with morbidities such as Guillain-Barré, infant microcephaly, and ocular disease. The spread of this positive-sense, single-stranded RNA virus and its growing public health threat underscore gaps in our understanding of basic ZIKV virology. To advance knowledge of the virus replication cycle within mammalian cells, we use serial section 3-dimensional electron tomography to demonstrate the widespread remodelling of intracellular membranes upon infection with ZIKV. We report extensive structural rearrangements of the endoplasmic reticulum and reveal stages of the ZIKV viral replication cycle. Structures associated with RNA genome replication and virus assembly are observed integrated within the endoplasmic reticulum, and we show viruses in transit through the Golgi apparatus for viral maturation, and subsequent cellular egress. This study characterises in detail the 3-dimensional ultrastructural organisation of the ZIKV replication cycle stages. Our results show close adherence of the ZIKV replication cycle to the existing flavivirus replication paradigm.
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Affiliation(s)
- Evan D Rossignol
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Kristen N Peters
- Department of Microbiology and National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology and National Emerging Infectious Disease Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
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