1
|
Neeb ZT, Ritter AJ, Chauhan LV, Katzman S, Lipkin WI, Mishra N, Sanford JR. A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression. Sci Rep 2022; 12:21694. [PMID: 36522444 PMCID: PMC9753033 DOI: 10.1038/s41598-022-26135-9] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, with symptoms ranging from mild to severe, including fatality. The molecular mechanisms surrounding the effects of viral infection on the host RNA machinery remain poorly characterized. We used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression machinery in a human lung epithelial cell line (Calu-3) and an African green monkey kidney cell line (Vero-E6). Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Additionally, we discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs) predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. 52 of the 67 svRNAs identified in Calu-3 cells are predicted to interact with differentially expressed miRNAs, with many svRNAs having multiple targets. Accordingly, we speculate that these svRNAs may play a role in SARS-CoV-2 propagation by modulating post-transcriptional gene regulation, and that methods for antagonizing them may have therapeutic value.
Collapse
Affiliation(s)
- Zachary T Neeb
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alexander J Ritter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lokendra V Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sol Katzman
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
2
|
Mishra M, Zahra A, Chauhan LV, Thakkar R, Ng J, Joshi S, Spitzer ED, Marcos LA, Lipkin WI, Mishra N. A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses 2022; 14:v14050934. [PMID: 35632677 PMCID: PMC9145915 DOI: 10.3390/v14050934] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 01/08/2023] Open
Abstract
Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
Collapse
Affiliation(s)
- Mitali Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Aleena Zahra
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Shreyas Joshi
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Eric D. Spitzer
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Luis A. Marcos
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
| |
Collapse
|
3
|
O’Donnell MR, Grinsztejn B, Cummings MJ, Justman JE, Lamb MR, Eckhardt CM, Philip NM, Cheung YK, Gupta V, João E, Pilotto JH, Diniz MP, Cardoso SW, Abrams D, Rajagopalan KN, Borden SE, Wolf A, Sidi LC, Vizzoni A, Veloso VG, Bitan ZC, Scotto DE, Meyer BJ, Jacobson SD, Kantor A, Mishra N, Chauhan LV, Stone EF, Dei Zotti F, La Carpia F, Hudson KE, Ferrara SA, Schwartz J, Stotler BA, Lin WHW, Wontakal SN, Shaz B, Briese T, Hod EA, Spitalnik SL, Eisenberger A, Lipkin WI. A randomized double-blind controlled trial of convalescent plasma in adults with severe COVID-19. J Clin Invest 2021; 131:150646. [PMID: 33974559 PMCID: PMC8245169 DOI: 10.1172/jci150646] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUNDAlthough convalescent plasma has been widely used to treat severe coronavirus disease 2019 (COVID-19), data from randomized controlled trials that support its efficacy are limited.METHODSWe conducted a randomized, double-blind, controlled trial among adults hospitalized with severe and critical COVID-19 at 5 sites in New York City (USA) and Rio de Janeiro (Brazil). Patients were randomized 2:1 to receive a single transfusion of either convalescent plasma or normal control plasma. The primary outcome was clinical status at 28 days following randomization, measured using an ordinal scale and analyzed using a proportional odds model in the intention-to-treat population.RESULTSOf 223 participants enrolled, 150 were randomized to receive convalescent plasma and 73 to receive normal control plasma. At 28 days, no significant improvement in the clinical scale was observed in participants randomized to convalescent plasma (OR 1.50, 95% confidence interval [CI] 0.83-2.68, P = 0.180). However, 28-day mortality was significantly lower in participants randomized to convalescent plasma versus control plasma (19/150 [12.6%] versus 18/73 [24.6%], OR 0.44, 95% CI 0.22-0.91, P = 0.034). The median titer of anti-SARS-CoV-2 neutralizing antibody in infused convalescent plasma units was 1:160 (IQR 1:80-1:320). In a subset of nasopharyngeal swab samples from Brazil that underwent genomic sequencing, no evidence of neutralization-escape mutants was detected.CONCLUSIONIn adults hospitalized with severe COVID-19, use of convalescent plasma was not associated with significant improvement in day 28 clinical status. However, convalescent plasma was associated with significantly improved survival. A possible explanation is that survivors remained hospitalized at their baseline clinical status.TRIAL REGISTRATIONClinicalTrials.gov, NCT04359810.FUNDINGAmazon Foundation, Skoll Foundation.
Collapse
Affiliation(s)
- Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Department of Epidemiology, and
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Jessica E. Justman
- Department of Epidemiology, and
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew R. Lamb
- Department of Epidemiology, and
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Christina M. Eckhardt
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Neena M. Philip
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Ying Kuen Cheung
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Vinay Gupta
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, USA
| | - Esau João
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Jose Henrique Pilotto
- Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil and Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz – Fiocruz, Rio de Janeiro, Brazil
| | - Maria Pia Diniz
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | | | - Darryl Abrams
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Kartik N. Rajagopalan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarah E. Borden
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Leon Claude Sidi
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Alexandre Vizzoni
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Valdilea G. Veloso
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Zachary C. Bitan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Dawn E. Scotto
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Benjamin J. Meyer
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Samuel D. Jacobson
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Alex Kantor
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Elizabeth F. Stone
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Flavia Dei Zotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Francesca La Carpia
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Krystalyn E. Hudson
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Stephen A. Ferrara
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Joseph Schwartz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Brie A. Stotler
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Wen-Hsuan W. Lin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Sandeep N. Wontakal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Beth Shaz
- New York Blood Center, New York, New York, USA
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Eldad A. Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Steven L. Spitalnik
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrew Eisenberger
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Walter I. Lipkin
- Department of Epidemiology, and
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
4
|
Dugue R, Cay-Martínez KC, Thakur KT, Garcia JA, Chauhan LV, Williams SH, Briese T, Jain K, Foca M, McBrian DK, Bain JM, Lipkin WI, Mishra N. Neurologic manifestations in an infant with COVID-19. Neurology 2020; 94:1100-1102. [PMID: 32327489 PMCID: PMC7455334 DOI: 10.1212/wnl.0000000000009653] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Rachelle Dugue
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY.
| | - Karla C Cay-Martínez
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Kiran T Thakur
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Joel A Garcia
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Lokendra V Chauhan
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Simon H Williams
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Thomas Briese
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Komal Jain
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Marc Foca
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Danielle K McBrian
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Jennifer M Bain
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - W Ian Lipkin
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| | - Nischay Mishra
- From the Department of Neurology (R.D., K.C.C.-M., K.T.T., D.K.M., J.M.B.), Columbia University Irving Medical Center; Center for Infection and Immunity (J.A.G., L.V.C., S.H.W., T.B., K.J., W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Epidemiology (W.I.L., N.M.), Mailman School of Public Health, Columbia University; Department of Pediatric Infectious Disease (M.F.), Columbia University Irving Medical Center; and New York Presbyterian Hospital (R.D., K.C.C.-M., K.T.T., M.F., D.K.M., J.M.B.), Columbia University Medical Center, New York, NY
| |
Collapse
|
5
|
Tokarz R, Tagliafierro T, Caciula A, Mishra N, Thakkar R, Chauhan LV, Sameroff S, Delaney S, Wormser GP, Marques A, Lipkin WI. Identification of immunoreactive linear epitopes of Borrelia miyamotoi. Ticks Tick Borne Dis 2019; 11:101314. [PMID: 31636001 DOI: 10.1016/j.ttbdis.2019.101314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 08/22/2019] [Revised: 09/30/2019] [Accepted: 10/13/2019] [Indexed: 11/19/2022]
Abstract
Borrelia miyamotoi is an emerging tick-borne spirochete transmitted by ixodid ticks. Current serologic assays for B. miyamotoi are impacted by genetic similarities to other Borrelia and limited understanding of optimal antigenic targets. In this study, we employed the TBD-Serochip, a peptide array platform, to identify new linear targets for serologic detection of B. miyamotoi. We examined a wide range of suspected B. miyamotoi antigens and identified 352 IgM and 91 IgG reactive peptides, with the majority mapping to variable membrane proteins. These included peptides within conserved fragments of variable membrane proteins that may have greater potential for differential diagnosis. We also identified reactive regions on FlaB, and demonstrate crossreactivity of B. burgdorferi s.l. C6 with a B. miyamotoi C6-like peptide. The panel of linear peptides identified in this study can be used to enhance serodiagnosis of B. miyamotoi.
Collapse
Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States.
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Adrian Caciula
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lokendra V Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shannon Delaney
- Department of Psychiatry, Columbia University, New York, NY, United States
| | - Gary P Wormser
- Division of Infectious Diseases, New York Medical College, Valhalla, NY, United States
| | - Adriana Marques
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| |
Collapse
|
6
|
Trivedi S, Murthy S, Sharma H, Hartlage AS, Kumar A, Gadi S, Simmonds P, Chauhan LV, Scheel TKH, Billerbeck E, Burbelo PD, Rice CM, Lipkin WI, Vandergrift K, Cullen JM, Kapoor A. Viral persistence, liver disease, and host response in a hepatitis C-like virus rat model. Hepatology 2018; 68:435-448. [PMID: 28859226 PMCID: PMC5832584 DOI: 10.1002/hep.29494] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/01/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022]
Abstract
UNLABELLED The lack of a relevant, tractable, and immunocompetent animal model for hepatitis C virus (HCV) has severely impeded investigations of viral persistence, immunity, and pathogenesis. In the absence of immunocompetent models with robust HCV infection, homolog hepaciviruses in their natural host could potentially provide useful surrogate models. We isolated a rodent hepacivirus from wild rats (Rattus norvegicus), RHV-rn1; acquired the complete viral genome sequence; and developed an infectious reverse genetics system. RHV-rn1 resembles HCV in genomic features including the pattern of polyprotein cleavage sites and secondary structures in the viral 5' and 3' untranslated regions. We used site-directed and random mutagenesis to determine that only the first of the two microRNA-122 seed sites in the viral 5' untranslated region is required for viral replication and persistence in rats. Next, we used the clone-derived virus progeny to infect several inbred and outbred rat strains. Our results determined that RHV-rn1 possesses several HCV-defining hallmarks: hepatotropism, propensity to persist, and the ability to induce gradual liver damage. Histological examination of liver samples revealed the presence of lymphoid aggregates, parenchymal inflammation, and macrovesicular and microvesicular steatosis in chronically infected rats. Gene expression analysis demonstrated that the intrahepatic response during RHV-rn1 infection in rats mirrors that of HCV infection, including persistent activation of interferon signaling pathways. Finally, we determined that the backbone drug of HCV direct-acting antiviral therapy, sofosbuvir, effectively suppresses chronic RHV-rn1 infection in rats. CONCLUSION We developed RHV-rn1-infected rats as a fully immunocompetent and informative surrogate model to delineate the mechanisms of HCV-related viral persistence, immunity, and pathogenesis. (Hepatology 2018).
Collapse
Affiliation(s)
- Sheetal Trivedi
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Satyapramod Murthy
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Himanshu Sharma
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Alex S. Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA,Medical Scientist Training Program, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210
| | - Arvind Kumar
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Sashi Gadi
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | - Troels K. H. Scheel
- Copenhagen Hepatitis C Program, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | - Eva Billerbeck
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | | | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | - Kurt Vandergrift
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - John M. Cullen
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210,Corresponding author. , Amit Kapoor, Ph.D., Associate Professor, Department of Pediatrics, College of Medicine, The Ohio State University, Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, Ohio 43205
| |
Collapse
|