1
|
Gonzalez G, Carr M, Kelleher TM, O'Byrne E, Banka W, Keogan B, Bennett C, Franzoni G, Keane P, Kenna C, Meredith LW, Fletcher N, Urtasun-Elizari JM, Dean J, Browne C, Lyons F, Crowley B, Igoe D, Robinson E, Martin G, Connell J, De Gascun CF, Hare D. Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023. Euro Surveill 2024; 29:2300505. [PMID: 38639093 PMCID: PMC11027473 DOI: 10.2807/1560-7917.es.2024.29.16.2300505] [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: 09/18/2023] [Accepted: 02/05/2024] [Indexed: 04/20/2024] Open
Abstract
BackgroundMpox, caused by monkeypox virus (MPXV), was considered a rare zoonotic disease before May 2022, when a global epidemic of cases in non-endemic countries led to the declaration of a Public Health Emergency of International Concern. Cases of mpox in Ireland, a country without previous mpox reports, could reflect extended local transmission or multiple epidemiological introductions.AimTo elucidate the origins and molecular characteristics of MPXV circulating in Ireland between May 2022 and October 2023.MethodsWhole genome sequencing of MPXV from 75% of all Irish mpox cases (182/242) was performed and compared to sequences retrieved from public databases (n = 3,362). Bayesian approaches were used to infer divergence time between sequences from different subclades and evaluate putative importation events from other countries.ResultsOf 242 detected mpox cases, 99% were males (median age: 35 years; range: 15-60). All 182 analysed genomes were assigned to Clade IIb and, presence of 12 distinguishable subclades suggests multiple introductions into Ireland. Estimation of time to divergence of subclades further supports the hypothesis for multiple importation events from numerous countries, indicative of extended and sustained international spread of mpox. Further analysis of sequences revealed that 92% of nucleotide mutations were from cytosine to thymine (or from guanine to adenine), leading to a high number of non-synonymous mutations across subclades; mutations associated with tecovirimat resistance were not observed.ConclusionWe provide insights into the international transmission dynamics supporting multiple introductions of MPXV into Ireland. Such information supported the implementation of evidence-informed public health control measures.
Collapse
Affiliation(s)
- Gabriel Gonzalez
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Japan Initiative for World-leading Vaccine Research and Development Centers, Hokkaido University, Institute for Vaccine Research and Development, Sapporo, Japan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Michael Carr
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Tomás M Kelleher
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Emer O'Byrne
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Weronika Banka
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Brian Keogan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Charlene Bennett
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Geraldine Franzoni
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Patrice Keane
- Department of Virology, St. James's Hospital, Dublin, Ireland
| | - Cliona Kenna
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicola Fletcher
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Veterinary Sciences Centre, University College Dublin, Dublin, Ireland
| | | | - Jonathan Dean
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Ciaran Browne
- National MPOX Crisis Management Lead, Acute Operations, Health Service Executive, Dublin, Ireland
| | - Fiona Lyons
- Sexual Health and Crisis Pregnancy Programme, Health and Wellbeing, Strategy and Research, Healthcare Strategy, Health Service Executive, Dublin, Ireland
| | - Brendan Crowley
- Department of Virology, St. James's Hospital, Dublin, Ireland
| | - Derval Igoe
- Health Service Executive Public Health: National Health Protection, Ireland
| | - Eve Robinson
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Greg Martin
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Jeff Connell
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Cillian F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Daniel Hare
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| |
Collapse
|
2
|
Shridas P, Ji A, Trumbauer AC, Noffsinger VP, Meredith LW, de Beer FC, Mullick AE, Webb NR, Karounos DG, Tannock LR. Antisense oligonucleotide targeting hepatic Serum Amyloid A limits the progression of angiotensin II-induced abdominal aortic aneurysm formation. Atherosclerosis 2024; 391:117492. [PMID: 38461759 PMCID: PMC11006562 DOI: 10.1016/j.atherosclerosis.2024.117492] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/07/2024] [Accepted: 02/23/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND AND AIMS Obesity increases the risk for abdominal aortic aneurysms (AAA) in humans and enhances angiotensin II (AngII)-induced AAA formation in C57BL/6 mice. We reported that deficiency of Serum Amyloid A (SAA) significantly reduces AngII-induced inflammation and AAA in both hyperlipidemic apoE-deficient and obese C57BL/6 mice. The aim of this study is to investigate whether SAA plays a role in the progression of early AAA in obese C57BL/6 mice. METHODS Male C57BL/6J mice were fed a high-fat diet (60% kcal as fat) throughout the study. After 4 months of diet, the mice were infused with AngII until the end of the study. Mice with at least a 25% increase in the luminal diameter of the abdominal aorta after 4 weeks of AngII infusion were stratified into 2 groups. The first group received a control antisense oligonucleotide (Ctr ASO), and the second group received ASO that suppresses SAA (SAA-ASO) until the end of the study. RESULTS Plasma SAA levels were significantly reduced by the SAA ASO treatment. While mice that received the control ASO had continued aortic dilation throughout the AngII infusion periods, the mice that received SAA-ASO had a significant reduction in the progression of aortic dilation, which was associated with significant reductions in matrix metalloprotease activities, decreased macrophage infiltration and decreased elastin breaks in the abdominal aortas. CONCLUSIONS We demonstrate for the first time that suppression of SAA protects obese C57BL/6 mice from the progression of AngII-induced AAA. Suppression of SAA may be a therapeutic approach to limit AAA progression.
Collapse
Affiliation(s)
- Preetha Shridas
- Department of Internal Medicine, University of Kentucky, Lexington, 40536, Kentucky, USA; Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA.
| | - Ailing Ji
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| | - Andrea C Trumbauer
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| | - Victoria P Noffsinger
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| | - Luke W Meredith
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| | - Frederick C de Beer
- Department of Internal Medicine, University of Kentucky, Lexington, 40536, Kentucky, USA; Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| | | | - Nancy R Webb
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA; Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, 40536, Kentucky, USA
| | - Dennis G Karounos
- Department of Internal Medicine, University of Kentucky, Lexington, 40536, Kentucky, USA; Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, 40536, Kentucky, USA; Department of Veterans Affairs, Lexington, 40536, Kentucky, USA
| | - Lisa R Tannock
- Department of Internal Medicine, University of Kentucky, Lexington, 40536, Kentucky, USA; Saha Cardiovascular Research Center, University of Kentucky, Lexington, 40536, Kentucky, USA
| |
Collapse
|
3
|
Meredith LW, Aboualy M, Ochola R, Ozel M, Abubakar A, Barakat A. A phased strengthening of laboratory capacity in the Eastern Mediterranean Region during the COVID-19 pandemic. Influenza Other Respir Viruses 2024; 18:e13225. [PMID: 38322196 PMCID: PMC10844753 DOI: 10.1111/irv.13225] [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: 05/17/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 02/08/2024] Open
Abstract
The Eastern Mediterranean Region (EMR) faces ongoing challenges in its public health system due to limited resources, logistical issues, and political disruptions. The COVID-19 pandemic accelerated the need for stronger laboratory capacities to handle the increased demand for testing. In a phased response, EMR countries utilized the National Influenza Centers to rapidly establish and scale molecular testing for SARS-CoV-2, the causative agent of COVID-19. The expansion of capacity included strong collaborations between public health bodies and private and academic sectors to decentralize and expand testing to the subnational level. To ensure that the quality of testing was not impacted by rapid expansion, national and subnational laboratories were enrolled in external quality assurance programs for the duration of the response. Implementation of genomic surveillance was prioritized for variant tracking, leading to the establishment of regional sequencing reference laboratories and the distribution of MinION sequencing platforms to complex emergency countries who previously had limited experience with pathogen sequencing. Challenges included a lack of technical expertise, including in implementing novel diagnostic assays and sequencing, a lack of bioinformatics expertise in the region, and significant logistical and procurement challenges. The collaborative approach, coordinated through the WHO Eastern Mediterranean Regional Office, enabled all 22 countries to achieve SARS-CoV-2 diagnostic capabilities, highlighting the pivotal role of laboratories in global health security.
Collapse
Affiliation(s)
- Luke W. Meredith
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mustafa Aboualy
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Rachel Ochola
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mehmet Ozel
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Abdinasir Abubakar
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Amal Barakat
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| |
Collapse
|
4
|
Ji A, Trumbauer AC, Noffsinger VP, Meredith LW, Dong B, Wang Q, Guo L, Li X, De Beer FC, Webb NR, Tannock LR, Starr ME, Waters CM, Shridas P. Deficiency of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality and Lung Injury in Mice. Int J Mol Sci 2023; 24:17501. [PMID: 38139330 PMCID: PMC10744229 DOI: 10.3390/ijms242417501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated with chemokine production, chemokine and cytokine-mediated signaling, neutrophil chemotaxis, and neutrophil migration in SAA-TKO compared to WT mice. Consistently, myeloperoxidase activity and neutrophil counts were significantly increased in the lungs of septic SAA-TKO mice compared to WT mice. The in vitro treatment of HL-60, neutrophil-like cells, with SAA or SAA bound to a high-density lipoprotein (SAA-HDL), significantly decreased cellular transmigration through laminin-coated membranes compared to untreated cells. Thus, SAA potentially prevents neutrophil transmigration into injured lungs, thus reducing exacerbated tissue injury and mortality. In conclusion, we demonstrate for the first time that endogenous SAA plays a protective role in sepsis, including ameliorating lung injury.
Collapse
Affiliation(s)
- Ailing Ji
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Andrea C. Trumbauer
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Victoria P. Noffsinger
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Luke W. Meredith
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Brittany Dong
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA; (B.D.); (C.M.W.)
| | - Qian Wang
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Ling Guo
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
| | - Xiangan Li
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA; (B.D.); (C.M.W.)
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA;
| | - Frederick C. De Beer
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA;
| | - Nancy R. Webb
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA;
| | - Lisa R. Tannock
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA;
| | - Marlene E. Starr
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA;
- Department of Surgery, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Christopher M. Waters
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA; (B.D.); (C.M.W.)
| | - Preetha Shridas
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY 40536, USA; (A.J.); (A.C.T.); (V.P.N.); (L.W.M.); (Q.W.); (L.G.); (X.L.); (N.R.W.); (L.R.T.)
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA;
| |
Collapse
|
5
|
Meredith LW, Aboualy M, Ochola R, Ozel M, Abubakar A, Barakat A. Monitoring the quality of SARS-CoV-2 virus detection in molecular diagnostic laboratories in the Eastern Mediterranean Region during the COVID-19 pandemic. Influenza Other Respir Viruses 2023; 17:e13217. [PMID: 38019698 PMCID: PMC10654553 DOI: 10.1111/irv.13217] [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: 05/17/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION The COVID-19 pandemic placed unprecedented stress on laboratories in the Eastern Mediterranean Region. Building on existing capacity for influenza diagnostics, countries introduced COVID-19 diagnostic support to ~100% regional coverage. A key challenge during the expansion was maintaining quality testing in laboratories, ensuring that correct results were shared with medical facilities. METHODS WHO organized two rounds of independently monitored severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) external quality assurance programs (EQAP). The Public Health Laboratory (PHL) division of WHO supplied external quality assurance (EQA) panels, from the Royal College of Pathologists of Australasia Quality Assurance Programme (RCPAQAP) Australia to laboratories not enrolled in recurring Global Influenza Surveillance and Response System (GISRS) quality assurance programs, in which national influenza centers routinely participate. RESULTS Fifteen and 14 countries participated in PHL/EQAP for SARS-CoV-2 between 2020 and 2022. Concordance was consistent between rounds, reaching 96.4% and 89.9%. A separate assessment of GISRS/EQAP to national-level laboratories identified high levels of response and concordance for SARS-CoV-2 (100% response, 93% concordance), which was reduced for influenza (50% response rate, 80% concordance), reflecting the challenge of prioritizing pathogens during outbreaks. CONCLUSION The proliferation of laboratories in response to COVID-19 was a success story from the pandemic. However, monitoring the quality of laboratories was challenging via existing EQAP. The addition of PHL/EQAP provided a mechanism to monitor performance of laboratories that were not designated as national influenza centers. While a high proportion of laboratories attained good results, continual emphasis on quality and enrollment in EQAP is key to ensuring sustainability of laboratory testing in future.
Collapse
Affiliation(s)
- Luke W. Meredith
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mustafa Aboualy
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Rachel Ochola
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mehmet Ozel
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Abdinasir Abubakar
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Amal Barakat
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| |
Collapse
|
6
|
Khan MM, Tahoun MM, Meredith LW, Barakat A, Safi H, Hanifi AN, Mashal MO, Amiri AW, Abouzeid A. Implementation and expansion of laboratory capacity for molecular diagnostics in response to COVID-19 and preparedness for other emerging infectious diseases in the Islamic Emirate of Afghanistan. Influenza Other Respir Viruses 2023; 17:e13210. [PMID: 37964989 PMCID: PMC10640962 DOI: 10.1111/irv.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023] Open
Abstract
Background Afghanistan experienced various outbreaks before and during the Covid-19 pandemic, including dengue, Crimean Congo hemorrhagic fever (CCHF), measles, and acute watery diarrhea (AWD). Diagnostic and surveillance support was limited, with only the Central Public Health Laboratory equipped to handle outbreak responses. This article highlights initiatives taken to improve diagnostic capabilities for COVID-19 and other outbreaks of public health concern encountered during the pandemic. Background The World Health Organization (WHO) Afghanistan Country Office collaborated with the WHO Eastern Mediterranean Regional Office (EMRO), Central Public Health Laboratory (CPHL), and National Influenza Center (NIC) to enhance COVID-19 diagnostic capacity at national and subnational facilities. To alleviate pressure on CPHL, a state-of-the-art laboratory was established at the National Infectious Disease Hospital (NIDH) in Kabul in 2021-2022, while WHO EMRO facilitated the regionalization of testing to subnational facilities for dengue, CCHF, and AWD in 2022-2023. Results COVID-19 testing capacity expanded nationwide to 34 Biosafety Level II labs, improving diagnosis time. Daily testing rose from 1000 in 2020 to 9200 in 2023, with 848,799 cumulative tests. NIDH identified 229 CCHF cases and 45 cases nationally. Dengue and CCHF testing, decentralized to Nangarhar and Kandahar labs, identified 338 dengue and 18 CCHF cases. AWD testing shifted to NIDH and five subnational facilities (Kandahar, Paktia, Balkh, Herat, and Nangarhar labs), while measles testing also decentralized to nine subnational facilities. Conclusion Afghanistan implemented a remarkable, multisectoral response to priority pathogens. The nation now possesses diagnostic expertise at national and subnational levels, supported by genomic surveillance. Future efforts should concentrate on expanding and sustaining this capacity to enhance public health responses.
Collapse
Affiliation(s)
- Murad Momin Khan
- Afghanistan Country OfficeWorld Health OrganizationKabulAfghanistan
| | - Mohamed Mostafa Tahoun
- Afghanistan Country OfficeWorld Health OrganizationKabulAfghanistan
- High Institute of Public HealthAlexandria UniversityAlexandriaEgypt
| | - Luke W. Meredith
- Eastern Mediterranean Regional OfficeWorld Health OrganizationCairoEgypt
| | - Amal Barakat
- Eastern Mediterranean Regional OfficeWorld Health OrganizationCairoEgypt
| | - Hafizullah Safi
- Afghanistan Country OfficeWorld Health OrganizationKabulAfghanistan
| | - Ahmed Nasir Hanifi
- Directorate of Diagnostic ServicesMinistry of Public HealthKabulAfghanistan
| | | | | | - Alaa Abouzeid
- Afghanistan Country OfficeWorld Health OrganizationKabulAfghanistan
- Faculty of MedicineCairo UniversityCairoEgypt
| |
Collapse
|
7
|
Shridas P, Ji A, Trumbauer AC, Noffsinger VP, Meredith LW, de Beer FC, Mullick AE, Webb NR, Karounos DG, Tannock LR. Antisense Oligonucleotide Targeting Hepatic Serum Amyloid A Limits the Progression of Angiotensin II-Induced Abdominal Aortic Aneurysm Formation. bioRxiv 2023:2023.08.22.554377. [PMID: 37662383 PMCID: PMC10473661 DOI: 10.1101/2023.08.22.554377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
OBJECTIVE Obesity increases the risk for abdominal aortic aneurysms (AAA) in humans and enhances angiotensin II (AngII)-induced AAA formation in C57BL/6 mice. Obesity is also associated with increases in serum amyloid A (SAA). We previously reported that deficiency of SAA significantly reduces AngII-induced inflammation and AAA in both hyperlipidemic apoE-deficient and obese C57BL/6 mice. In this study, we investigated whether SAA plays a role in the progression of early AAA in obese C57BL/6 mice. APPROACH AND RESULTS Male C57BL/6J mice were fed a high-fat diet (60% kcal as fat) throughout the study. After 4 months of diet, the mice were infused with angiotensin II (AngII) until the end of the study. Mice with at least a 25% increase in the luminal diameter of the abdominal aorta after 4 weeks of AngII infusion were stratified into 2 groups. The first group received a control antisense oligonucleotide (Ctr ASO), and the second group received ASO that suppresses SAA (SAA-ASO) until the end of the study. Plasma SAA levels were significantly reduced by the SAA ASO treatment. While mice that received the control ASO had continued aortic dilation throughout the AngII infusion periods, the mice that received SAA-ASO had a significant reduction in the progression of aortic dilation, which was associated with significant reductions in matrix metalloprotease activities, decreased macrophage infiltration and decreased elastin breaks in the abdominal aortas. CONCLUSION We demonstrate for the first time that suppression of SAA protects obese C57BL/6 mice from the progression of AngII-induced AAA. Suppression of SAA may be a therapeutic approach to limit AAA progression.
Collapse
|
8
|
Meredith LW, Aboualy M, Ochola R, Okwarah P, Ozel M, Abubakar A, Barakat A. Key aspects defining the development and implementation of a regional genomic surveillance strategy for the Eastern Mediterranean Region. Influenza Other Respir Viruses 2023; 17:e13205. [PMID: 37859974 PMCID: PMC10583647 DOI: 10.1111/irv.13205] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
The COVID-19 pandemic highlighted the critical role of pathogen sequencing in making informed public health decisions. Initially, the Eastern Mediterranean Region faced limitations in sequencing capacity. However, with robust WHO and stakeholder support, the situation significantly improved. By 2022, COVID-19 sequencing was underway in 22 out of 23 regional countries, with varying throughput and capacity. Notably, three genomic hubs were established in Oman, UAE, and Morocco, playing a key role in providing expanded genomics training and support across the region. While primarily for COVID-19 surveillance, this sequencing capacity offers an opportunity to integrate genomic surveillance into existing networks. This integration can enable early detection and response to high-threat pathogens with pandemic potential. To advance this, WHO/EMRO collaborated with stakeholders to formulate the Eastern Mediterranean Regional Genomic Surveillance Strategy for Emerging Pathogens of Pandemic Concern. Consultative meetings with regional and international genomic surveillance experts identified strategy focal points, key partners, priority pathogens, and implementation steps. As the strategy awaits member states' ratification in Q4 2023, this manuscript outlines pivotal facets defined by member states and the strategic document's key deliverables and opportunities. These efforts aim to yield a substantial positive impact within the region.
Collapse
Affiliation(s)
- Luke W. Meredith
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mustafa Aboualy
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Rachel Ochola
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Patrick Okwarah
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mehmet Ozel
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Abdinasir Abubakar
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Amal Barakat
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| |
Collapse
|
9
|
Abu‐Dayyeh I, Naber Z, Meredith LW, Alsawalha L, Nassar D, Sumrain L, Ghunaim M, Hasan T, Abdelnour A. A model for public-private partnership during the COVID-19 pandemic: Lessons from Biolab and public laboratories working in the Hashemite Kingdom of Jordan. Influenza Other Respir Viruses 2023; 17:e13209. [PMID: 37885370 PMCID: PMC10627090 DOI: 10.1111/irv.13209] [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: 05/17/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
INTRODUCTION The global COVID-19 pandemic overwhelmed national public health and laboratory capacity in Jordan and globally. In response, Biolab, a private laboratory group with 27 branches across Jordan, assisted with testing. Biolab was equipped to quickly increase molecular testing capacity without compromising quality or turnaround time, allowing them to contribute to national COVID-19 surveillance efforts. METHODS Biolab expanded testing in Jordan by operationalizing automated testing platforms at various locations, including 16 branches, 2 drive-through and 2 walk-through centres, and entry points for airports and marine passenger arrivals. Genomic and molecular testing were implemented to track variants. Information technology platforms were introduced for sample management, registration, and commercial sample payments. Data were directly provided to the Ministry of Health through these platforms to support public health decision-making and responses. Biolab prioritized staff well-being by providing mental, financial, and physical health support during the pandemic. RESULTS Biolab processed more than two million samples, with a turnaround time of ~1.5 h. Results were transmitted directly to key stakeholders in near real time. Biolab conducted variant evaluations on >1.4 million samples using molecular variant testing and >1000 samples using whole genome sequencing. Biolab prioritized staff well-being, improving staff satisfaction from 74% to 91%, a remarkable achievement when many laboratory systems experienced staff burnout and dissatisfaction. CONCLUSION The collaboration between public and private laboratories during COVID-19 established a model for future joint efforts to prevent outbreaks from becoming pandemics. Biolab's focus on efficiency, quality, and staff well-being enabled consistent, high-quality performance. The introduction of innovative information technology platforms ensured swift information dissemination. Biolab plans to continue investing in these platforms and expand pathogen testing, creating a top-tier testing infrastructure in Jordan with a demonstrated ability to cooperate with the government for public benefit.
Collapse
Affiliation(s)
- Issa Abu‐Dayyeh
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Zein Naber
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Luke W. Meredith
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Lora Alsawalha
- Jordan Country OfficeWorld Health OrganizationAmmanJordan
| | - Dana Nassar
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Lara Sumrain
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Mohammad Ghunaim
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Thaer Hasan
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| | - Amid Abdelnour
- Department of Research and DevelopmentBiolab Diagnostic LaboratoriesAmmanJordan
| |
Collapse
|
10
|
van Loben Sels JM, Meredith LW, Sosnovtsev SV, de Graaf M, Koopmans MP, Lindesmith LC, Baric RS, Green KY, Goodfellow IG. A luciferase-based approach for measuring HBGA blockade antibody titers against human norovirus. J Virol Methods 2021; 297:114196. [PMID: 34019938 PMCID: PMC9924141 DOI: 10.1016/j.jviromet.2021.114196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Noroviruses are the most common cause of viral gastroenteritis worldwide, yet there is a deficit in the understanding of protective immunity. Surrogate neutralization assays have been widely used that measure the ability of antibodies to block virus-like particle (VLP) binding to histo-blood group antigens (HBGAs). However, screening large sample sets against multiple antigens using the traditional HBGA blocking assay requires significant investment in terms of time, equipment, and technical expertise, largely associated with the generation of purified VLPs. METHODS To address these issues, a luciferase immunoprecipitation system (LIPS) assay was modified to measure the norovirus-specific HBGA blockade activity of antibodies. The assay (designated LIPS-Blockade) was validated using a panel of well-characterized homotypic and heterotypic hyperimmune sera as well as strain-specific HBGA blocking monoclonal antibodies. RESULTS The LIPS-Blockade assay was comparable in specificity to a standard HBGA blocking protocol performed with VLPs. Using time-ordered patient sera, the luciferase-based approach was also able to detect changes in HBGA blocking titers following viral challenge and natural infection with norovirus. CONCLUSION In this study we developed a rapid, robust, and scalable surrogate neutralization assay for noroviruses that circumvented the need for purified VLPs. This LIPS-Blockade assay should streamline the process of large-scale immunological studies, ultimately aiding in the characterization of protective immunity to human noroviruses.
Collapse
Affiliation(s)
- Jessica M. van Loben Sels
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK,Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA
| | - Luke W. Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK
| | - Stanislav V. Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Marion P.G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, 3015 CN Rotterdam, NL
| | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Kim Y. Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA,Corresponding author at: Dr. Kim Y. Green, Caliciviruses Section, LID/DIR/NIAID, National Institutes of Health (NIH), Building 50, Room 6318, 50 South Drive, Bethesda, MD 20892 USA –
| | - Ian G. Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK
| |
Collapse
|
11
|
Illingworth CJR, Hamilton WL, Warne B, Routledge M, Popay A, Jackson C, Fieldman T, Meredith LW, Houldcroft CJ, Hosmillo M, Jahun AS, Caller LG, Caddy SL, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran MD, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Ferris M, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Goodfellow IG, Gouliouris T, de Angelis D, Török ME. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife 2021; 10:e67308. [PMID: 34425938 PMCID: PMC8384420 DOI: 10.7554/elife.67308] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.
Collapse
Affiliation(s)
- Christopher JR Illingworth
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical SciencesCambridgeUnited States
| | - William L Hamilton
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ben Warne
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Forvie Site, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Jackson
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
| | - Tom Fieldman
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sarah L Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sushmita Sridhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
| | - Sally Forrest
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Mark Ferris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic ScienceCambridgeUnited Kingdom
- University of Cambridge, School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Michael P Weekes
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Stephen Baker
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Theodore Gouliouris
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Daniela de Angelis
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - M Estée Török
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| |
Collapse
|
12
|
Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | | |
Collapse
|
13
|
Hamilton WL, Tonkin-Hill G, Smith ER, Aggarwal D, Houldcroft CJ, Warne B, Meredith LW, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Brown CS, Gonçalves S, Amato R, Harrison EM, Brown NM, Beale MA, Spencer Chapman M, Jackson DK, Johnston I, Alderton A, Sillitoe J, Langford C, Dougan G, Peacock SJ, Kwiatowski DP, Goodfellow IG, Torok ME. Genomic epidemiology of COVID-19 in care homes in the east of England. eLife 2021; 10:e64618. [PMID: 33650490 PMCID: PMC7997667 DOI: 10.7554/elife.64618] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/25/2021] [Indexed: 01/12/2023] Open
Abstract
COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.
Collapse
Affiliation(s)
- William L Hamilton
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Emily R Smith
- Cambridgeshire County CouncilCambridgeUnited Kingdom
| | - Dinesh Aggarwal
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
- Public Health EnglandColindaleUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
- The Francis Crick InstituteLondonUnited Kingdom
| | - Sarah L Caddy
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | | | | | | | | | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | | | - Michael Spencer Chapman
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS TrustLondonUnited Kingdom
| | | | | | | | | | | | - Gordon Dougan
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - M Estee Torok
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | |
Collapse
|
14
|
Meredith LW, Hamilton WL, Warne B, Houldcroft CJ, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Forrest S, Sridhar S, Weekes MP, Baker S, Brown N, Moore E, Popay A, Roddick I, Reacher M, Gouliouris T, Peacock SJ, Dougan G, Török ME, Goodfellow I. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis 2020; 20:1263-1272. [PMID: 32679081 PMCID: PMC7806511 DOI: 10.1016/s1473-3099(20)30562-4] [Citation(s) in RCA: 276] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures. METHODS In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases. FINDINGS Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting. INTERPRETATION We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings. FUNDING COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.
Collapse
Affiliation(s)
- Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Ben Warne
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | | | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Aminu S Jahun
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Laura G Caller
- Department of Pathology, University of Cambridge, Cambridge, UK; Francis Crick Institute, London, UK
| | - Sarah L Caddy
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Fahad A Khokhar
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Anna Yakovleva
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Grant Hall
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Sally Forrest
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Sushmita Sridhar
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Michael P Weekes
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Nicholas Brown
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Elinor Moore
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Ashley Popay
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Iain Roddick
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Mark Reacher
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; National Infection Service, Public Health England, London, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK.
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
15
|
Fletcher NF, Meredith LW, Tidswell EL, Bryden SR, Gonçalves-Carneiro D, Chaudhry Y, Shannon-Lowe C, Folan MA, Lefteri DA, Pingen M, Bailey D, McKimmie CS, Baird AW. A novel antiviral formulation inhibits a range of enveloped viruses. J Gen Virol 2020; 101:1090-1102. [PMID: 32692647 DOI: 10.1099/jgv.0.001472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Some free fatty acids derived from milk and vegetable oils are known to have potent antiviral and antibacterial properties. However, therapeutic applications of short- to medium-chain fatty acids are limited by physical characteristics such as immiscibility in aqueous solutions. We evaluated a novel proprietary formulation based on an emulsion of short-chain caprylic acid, ViroSAL, for its ability to inhibit a range of viral infections in vitro and in vivo. In vitro, ViroSAL inhibited the enveloped viruses Epstein-Barr, measles, herpes simplex, Zika and orf parapoxvirus, together with Ebola, Lassa, vesicular stomatitis and severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) pseudoviruses, in a concentration- and time-dependent manner. Evaluation of the components of ViroSAL revealed that caprylic acid was the main antiviral component; however, the ViroSAL formulation significantly inhibited viral entry compared with caprylic acid alone. In vivo, ViroSAL significantly inhibited Zika and Semliki Forest virus replication in mice following the inoculation of these viruses into mosquito bite sites. In agreement with studies investigating other free fatty acids, ViroSAL had no effect on norovirus, a non-enveloped virus, indicating that its mechanism of action may be surfactant disruption of the viral envelope. We have identified a novel antiviral formulation that is of great interest for the prevention and/or treatment of a broad range of enveloped viruses, particularly those of the skin and mucosal surfaces.
Collapse
Affiliation(s)
- Nicola F Fletcher
- Institute of Immunity and Infection, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Luke W Meredith
- Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma L Tidswell
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Steven R Bryden
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Gonçalves-Carneiro
- Present address: Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA.,Virus Host Interaction Team, Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS9 7TF, UK
| | - Yasmin Chaudhry
- Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - Claire Shannon-Lowe
- School of Cancer Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Michael A Folan
- Westgate Biomedical Ltd, Lough Eske, Donegal Town, Co. Donegal, Ireland.,Institute of Immunity and Infection, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Daniella A Lefteri
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Marieke Pingen
- Present address: Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Dalan Bailey
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.,Virus Host Interaction Team, Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS9 7TF, UK
| | - Clive S McKimmie
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Alan W Baird
- Institute of Immunity and Infection, The University of Birmingham, Birmingham, B15 2TT, UK
| |
Collapse
|
16
|
Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
Collapse
Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| |
Collapse
|
17
|
Scott JT, Sharma R, Meredith LW, Dunning J, Moore CE, Sahr F, Ward S, Goodfellow I, Horby P. Pharmacokinetics of TKM-130803 in Sierra Leonean patients with Ebola virus disease: plasma concentrations exceed target levels, with drug accumulation in the most severe patients. EBioMedicine 2020; 52:102601. [PMID: 31953031 PMCID: PMC7033524 DOI: 10.1016/j.ebiom.2019.102601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Background TKM-130803 is a specific anti-EBOV therapeutic comprised of two small interfering RNAs (siRNA) siLpol-2 and siVP35-2. The pharmacokinetics (PK) of these siRNAs was defined in Ebola virus disease (EVD) patients, with reference to efficacy (ET) and toxicology thresholds (TT). The relationship between PK and patient survival was explored. Methods Pharmacokinetic (PK) and pharmacodynamic (PD) data were available for seven participants with EVD in Sierra Leone who received 0·3 mg/kg of TKM-130803 by intravenous infusion over 2 h daily for up to 7 days. Plasma concentration of siRNA was compared to survival at 14 days. PK data were fitted to two-compartment models then Monte Carlo simulated PK profiles were compared to ET (Cmax 0·04–0·57 ng/mL and mean concentration 1·43 ng/mL), and TT (3000 ng/mL). Findings Viral loads (VL) were not significantly different at treatment onset or during treatment (p = 0·1) in subjects who survived or died. siRNA was in quantitative excess of virus genomes throughout treatment, but the 95% percentile exceeded TT. The maximum AUC for which the 95% percentile remained under TT was a continuous infusion of 0·15 mg/kg/day. Plasma concentration of both siRNAs were higher in subjects who died compared to subjects who survived (p<0·025 both siRNAs). Interpretation TKM-130803 was circulating in molar excess of circulating virus; a level considered needed for efficacy. Given extremely high viral loads it seems likely that the patients died because they were physiologically beyond the point of no return. Subjects who died exhibited some indication of impaired drug clearance, justifying caution in dosing strategies for such patients. This analysis has given a useful insight into the pharmacokinetics of the siRNA in the disease state and illustrates the value of designing PKPD studies into future clinical trials in epidemic situations. Funding This work was supported by the Wellcome Trust of Great Britain (grant number 106491/Z/14/Z and 097997/Z/11/A) and by the EU FP7 project PREPARE (602525). The PHE laboratory was funded by the UK Department for International Development. The funders had no role in trial design, data collection or analysis. The views expressed are those of the authors and not necessarily those of Public Health England, the Department of Health, or the EU. Trial registration Pan African Clinical Trials Registry PACTR201501000997429.
Collapse
Affiliation(s)
- Janet T Scott
- MRC-University of Glasgow Centre for Virus Research, G61 1QH, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
| | - Raman Sharma
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luke W Meredith
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1QP, UK; Department of Public Health, University of Makeni, Makeni, Sierra Leone
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Catrin E Moore
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Foday Sahr
- Republic Sierra Leone Armed Forces, Military Hosp 34, Freetown, Sierra Leone
| | - Steve Ward
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ian Goodfellow
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1QP, UK; Department of Public Health, University of Makeni, Makeni, Sierra Leone
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | -
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| |
Collapse
|
18
|
Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Accepted: 12/30/2019] [Indexed: 08/27/2023] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
Collapse
Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| |
Collapse
|
19
|
Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA. COMRADES determines in vivo RNA structures and interactions. Nat Methods 2018; 15:785-788. [PMID: 30202058 PMCID: PMC6168409 DOI: 10.1038/s41592-018-0121-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023]
Abstract
The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs.
Collapse
Affiliation(s)
- Omer Ziv
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Marta M Gabryelska
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zhong-Yu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| |
Collapse
|
20
|
Chavali PL, Stojic L, Meredith LW, Joseph N, Nahorski MS, Sanford TJ, Sweeney TR, Krishna BA, Hosmillo M, Firth AE, Bayliss R, Marcelis CL, Lindsay S, Goodfellow I, Woods CG, Gergely F. Neurodevelopmental protein Musashi-1 interacts with the Zika genome and promotes viral replication. Science 2017; 357:83-88. [PMID: 28572454 PMCID: PMC5798584 DOI: 10.1126/science.aam9243] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [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: 02/08/2017] [Accepted: 05/16/2017] [Indexed: 12/21/2022]
Abstract
A recent outbreak of Zika virus in Brazil has led to a simultaneous increase in reports of neonatal microcephaly. Zika targets cerebral neural precursors, a cell population essential for cortical development, but the cause of this neurotropism remains obscure. Here we report that the neural RNA-binding protein Musashi-1 (MSI1) interacts with the Zika genome and enables viral replication. Zika infection disrupts the binding of MSI1 to its endogenous targets, thereby deregulating expression of factors implicated in neural stem cell function. We further show that MSI1 is highly expressed in neural progenitors of the human embryonic brain and is mutated in individuals with autosomal recessive primary microcephaly. Selective MSI1 expression in neural precursors could therefore explain the exceptional vulnerability of these cells to Zika infection.
Collapse
Affiliation(s)
- Pavithra L Chavali
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Lovorka Stojic
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Luke W Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Michael S Nahorski
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Thomas J Sanford
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Trevor R Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Ben A Krishna
- Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Richard Bayliss
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carlo L Marcelis
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - C Geoffrey Woods
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.
| |
Collapse
|
21
|
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro J, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kargbo B, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll M, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 2017; 544:309-315. [PMID: 28405027 PMCID: PMC5712493 DOI: 10.1038/nature22040] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [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: 08/31/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
Abstract
The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.
Collapse
Affiliation(s)
- Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J. Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Daniel J. Park
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason T. Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Armando Arias
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Danny Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Sarah L. Caddy
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jonathan D’Ambrozio
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Institute for Infectious Diseases ”L. Spallanzani” – IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - JosephW. Diclaro
- Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo, 11517, Egypt
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Michael J. Elmore
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
| | | | - Ousmane Faye
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Merle L. Gilbert
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Stephen Gire
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Andreas Gnirke
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
| | - Umaru Jah
- University of Makeni, Makeni, Sierra Leone
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Jeffrey R. Kugelman
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Di Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia Lu
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | | | - Suzanne Mate
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | | | - Luke W. Meredith
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Suzan D. Pas
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - My VT Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
| | - Chantal B. Reusken
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | - John S. Schieffelin
- Department of Pediatrics, Section of Infectious Diseases, New Orleans, LA 70112, USA
| | - Rachel S. Sealfon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Etienne Simon-Loriere
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, Paris 75015, France
| | - Saskia L. Smits
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Lucy Thorne
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Ekaete Alice Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Mohamed A. Vandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Simon J. Watson
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kendra West
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Michael R. Wiley
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | - Sarah M. Winnicki
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shirlee Wohl
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Nathan L. Yozwiak
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Sylvia O. Blyden
- Ministry of Social Welfare, Gender and Children’s Affairs, New Englandville, Freetown, Sierra Leone
| | - Fatorma Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - MilesW. Carroll
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
- University of Southampton, South General Hospital, Southampton SO16 6YD, UK
| | | | | | | | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George F. Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Robert F. Garry
- Department of Microbiology and Immunology, New Orleans, LA 70112, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - Stephan Günther
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Christian T. Happi
- Department of Biological Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, NSW 2006, Australia
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | | | - Paul Kellam
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Division of Infectious Diseases, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Stuart T. Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | | | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Pardis C. Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amadou Sall
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Ute Ströher
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Isatta Wurie
- University of Sierra Leone, Freetown, Sierra Leone
| | - Marc A. Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
22
|
Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S. Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days. Clin Infect Dis 2016; 63:1353-1356. [PMID: 27585800 PMCID: PMC5091350 DOI: 10.1093/cid/ciw601] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/17/2016] [Indexed: 11/17/2022] Open
Abstract
We report on an Ebola virus disease (EVD) survivor who showed Ebola virus in seminal fluid 531 days after onset of disease. The persisting virus was sexually transmitted in February 2016, about 470 days after onset of symptoms, and caused a new cluster of EVD in Guinea and Liberia.
Collapse
Affiliation(s)
| | - Daouda Sissoko
- INSERM U1219, Bordeaux University.,Bordeaux University Hospital, France
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, United Kingdom
| | - Hadja Aïssatou Bah
- Laboratoire des Fièvres Hémorragiques en Guinée, Hôpital Donka et N'Zérékoré
| | - Hawa Bah
- World Health Organization, Conakry, Guinea
| | - Mary Claire Worrell
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,Center for Global Health, CDC, Atlanta, Georgia
| | | | | | | | | | | | - Ngozi A Erondu
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry
| | - Benjamin A Dahl
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,Center for Global Health, CDC, Atlanta, Georgia
| | - Susann Handrick
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, United Kingdom.,Department of Public Health, University of Makeni, Sierra Leone
| | - Luke W Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, United Kingdom.,Department of Public Health, University of Makeni, Sierra Leone
| | - Matthew Cotten
- Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Umaru Jah
- Department of Public Health, University of Makeni, Sierra Leone
| | - Raoul Emeric Guetiya Wadoum
- Department of Public Health, University of Makeni, Sierra Leone.,Department of Biology, University of Rome II "Tor Vergata," Italy
| | - Pierre Rollin
- Centers for Disease Control and Prevention (CDC) Guinea Response Team, Conakry.,National Center for Emerging and Zoonotic Infectious Diseases, CDC, Atlanta, Georgia
| | - N'Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Guinea
| | - Denis Malvy
- INSERM U1219, Bordeaux University.,Bordeaux University Hospital, France
| | - Xavier Anglaret
- INSERM U1219, Bordeaux University.,Programme ANRS Coopération Côte d'Ivoire, Agence Nationale de Recherche sur le Sida Research Site, Treichville University Hospital, Abidjan, Côte d'Ivoire
| | - Miles W Carroll
- European Mobile Laboratory Consortium.,Public Health England, Porton Down, Salisbury.,University of Southampton, South General Hospital, United Kingdom
| | | | | | | | | | | | - Stephan Günther
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andrew Rambaut
- Institute for Evolutionary Biology, Centre for Infection, Immunity and Evolution, Ashworth Laboratories, University of Edinburgh, United Kingdom
| | - Sophie Duraffour
- European Mobile Laboratory Consortium.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
23
|
Meredith LW, Hu K, Cheng X, Howard CR, Baumert TF, Balfe P, van de Graaf KF, Protzer U, McKeating JA. Lentiviral hepatitis B pseudotype entry requires sodium taurocholate co-transporting polypeptide and additional hepatocyte-specific factors. J Gen Virol 2015; 97:121-127. [PMID: 26474824 DOI: 10.1099/jgv.0.000317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is one of the world's major unconquered infections, resulting in progressive liver disease, and current treatments rarely cure infection. A limitation to discovering new therapies is our limited knowledge of HBV entry and dissemination pathways that hinders the development of in vitro culture systems. To address this gap in our understanding we optimized the genesis of infectious lentiviral pseudoparticles (HBVpps). The recent discovery that the bile salt transporter sodium taurocholate co-transporting polypeptide (NTCP) acts as a receptor for HBV enabled us to assess the receptor dependency of HBVpp infection. HBVpps preferentially infect hepatoma cells expressing NTCP, whereas other non-liver cells engineered to express NTCP do not support infection, suggesting that additional hepatocyte-specific factors are required for HBVpp internalization. These results highlight the value of the HBVpp system to dissect the pathways of HBV entry and dissemination.
Collapse
Affiliation(s)
- L W Meredith
- Centre for Human Virology, Viral Hepatitis Laboratory, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - K Hu
- Centre for Human Virology, Viral Hepatitis Laboratory, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - X Cheng
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - C R Howard
- Centre for Human Virology, Viral Hepatitis Laboratory, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - T F Baumert
- INSERM U1110, Institut de Recherche sur les Maladies Virales et Hépatiques and Université de Strasbourg, Strasbourg, France
| | - P Balfe
- Centre for Human Virology, Viral Hepatitis Laboratory, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - K F van de Graaf
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology and Hepatology, AMC, Amsterdam, The Netherlands
| | - U Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - J A McKeating
- Institute for Advanced Study, Technische Universität München, Garching, Germany.,Centre for Human Virology, Viral Hepatitis Laboratory, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
24
|
Meredith LW, Farquhar MJ, Tarr AW, McKeating JA. Type I interferon rapidly restricts infectious hepatitis C virus particle genesis. Hepatology 2014; 60:1891-901. [PMID: 25066844 PMCID: PMC4265257 DOI: 10.1002/hep.27333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/24/2014] [Indexed: 12/19/2022]
Abstract
UNLABELLED Interferon-alpha (IFNα) has been used to treat chronic hepatitis C virus (HCV) infection for over 20 years with varying efficacy, depending on the infecting viral genotype. The mechanism of action of IFNα is not fully understood, but is thought to target multiple stages of the HCV lifecycle, inhibiting viral transcription and translation leading to a degradation of viral RNA and protein expression in the infected cell. IFNα induces the expression of an array of interferon-stimulated genes within minutes of receptor engagement; however, the impact of these early responses on the viral lifecycle are unknown. We demonstrate that IFNα inhibits the genesis of infectious extracellular HCV particles within 2 hours of treating infected cells, with minimal effect on the intracellular viral burden. Importantly, this short duration of IFNα treatment of infected cells significantly reduced cell-free and cell-to-cell dissemination. The secreted viral particles showed no apparent change in protein content or density, demonstrating that IFNα inhibits particle infectivity but not secretion rates. To investigate whether particles released from IFNα-treated cells have a reduced capacity to establish infection we used HCV lentiviral pseudotypes (HCVpp) and demonstrated a defect in cell entry. Using a panel of monoclonal antibodies targeting the E2 glycoprotein, we demonstrate that IFNα alters glycoprotein conformation and receptor utilization. CONCLUSION These observations show a previously unreported and rapid effect of IFNα on HCV particle infectivity that inhibits de novo infection events. Evasion of this response may be a contributing factor in whether a patient achieves early or rapid virological response, a key indicator of progression to sustained virological response or clearance of viral infection.
Collapse
Affiliation(s)
- Luke W Meredith
- Viral Hepatitis Research Group, Centre for Human Virology, University of BirminghamBirmingham, UK
| | - Michelle J Farquhar
- Viral Hepatitis Research Group, Centre for Human Virology, University of BirminghamBirmingham, UK
| | - Alexander W Tarr
- School of Molecular Medical Sciences and the Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical CentreNottingham, UK
| | - Jane A McKeating
- Viral Hepatitis Research Group, Centre for Human Virology, University of BirminghamBirmingham, UK,NIHR Liver Biomedical Research Unit, University of BirminghamBirmingham, UK
| |
Collapse
|
25
|
Fletcher NF, Sutaria R, Jo J, Barnes A, Blahova M, Meredith LW, Cosset FL, Curbishley SM, Adams DH, Bertoletti A, McKeating JA. Activated macrophages promote hepatitis C virus entry in a tumor necrosis factor-dependent manner. Hepatology 2014; 59:1320-30. [PMID: 24259385 PMCID: PMC4255687 DOI: 10.1002/hep.26911] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/19/2013] [Indexed: 02/06/2023]
Abstract
UNLABELLED Macrophages are critical components of the innate immune response in the liver. Chronic hepatitis C is associated with immune infiltration and the infected liver shows a significant increase in total macrophage numbers; however, their role in the viral life cycle is poorly understood. Activation of blood-derived and intrahepatic macrophages with a panel of Toll-like receptor agonists induce soluble mediators that promote hepatitis C virus (HCV) entry into polarized hepatoma cells. We identified tumor necrosis factor α (TNF-α) as the major cytokine involved in this process. Importantly, this effect was not limited to HCV; TNF-α increased the permissivity of hepatoma cells to infection by Lassa, measles and vesicular stomatitis pseudoviruses. TNF-α induced a relocalization of tight junction protein occludin and increased the lateral diffusion speed of HCV receptor tetraspanin CD81 in polarized HepG2 cells, providing a mechanism for their increased permissivity to support HCV entry. High concentrations of HCV particles could stimulate macrophages to express TNF-α, providing a direct mechanism for the virus to promote infection. CONCLUSION This study shows a new role for TNF-α to increase virus entry and highlights the potential for HCV to exploit existing innate immune responses in the liver to promote de novo infection events.
Collapse
Affiliation(s)
- Nicola F Fletcher
- Hepatitis C Research Group, Institute for Biomedical Research, University of BirminghamBirmingham, UK
| | - Rupesh Sutaria
- NIHR Liver Biomedical Research Unit, University of BirminghamBirmingham, UK
| | - Juandy Jo
- Viral Hepatitis Laboratory, Singapore Institute for Clinical Sciences, Agency of Science Technology and Research (A*STAR)Singapore
| | - Amy Barnes
- Hepatitis C Research Group, Institute for Biomedical Research, University of BirminghamBirmingham, UK
| | - Miroslava Blahova
- NIHR Liver Biomedical Research Unit, University of BirminghamBirmingham, UK
| | - Luke W Meredith
- Hepatitis C Research Group, Institute for Biomedical Research, University of BirminghamBirmingham, UK
| | | | | | - David H Adams
- NIHR Liver Biomedical Research Unit, University of BirminghamBirmingham, UK
| | - Antonio Bertoletti
- Viral Hepatitis Laboratory, Singapore Institute for Clinical Sciences, Agency of Science Technology and Research (A*STAR)Singapore
| | - Jane A McKeating
- Hepatitis C Research Group, Institute for Biomedical Research, University of BirminghamBirmingham, UK,NIHR Liver Biomedical Research Unit, University of BirminghamBirmingham, UK
| |
Collapse
|
26
|
Meredith LW, Zitzmann N, McKeating JA. Differential effect of p7 inhibitors on hepatitis C virus cell-to-cell transmission. Antiviral Res 2013; 100:636-9. [PMID: 24157306 PMCID: PMC3851685 DOI: 10.1016/j.antiviral.2013.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/19/2013] [Accepted: 10/14/2013] [Indexed: 12/13/2022]
Abstract
p7 Inhibitors were tested for their ability to block HCV cell-free and cell-to-cell transmission. p7 Inhibitor BIT225 reduced the infectivity of diverse HCV extracellular virus. p7 Inhibitors had minimal effect on HCV cell-to-cell transmission. Important to consider HCV transmission route when assessing assembly inhibitors.
Inhibitors targeting the hepatitis C virus (HCV) encoded viroporin, p7 prevent virus release in vitro. HCV can transmit by cell-free particle infection of new target cells and via cell-to-cell dependent contact with limited exposure to the extracellular environment. The role of assembly inhibitors in preventing HCV transmission via these pathways has not been studied. We compared the efficacy of three published p7 inhibitors to inhibit cell-free and cell-to-cell transmission of two chimeric HCV strains encoding genotype 2 (GT2) or 5 (GT5) p7 using a recently developed single cycle co-culture assay. The inhibitors reduced the infectivity of extracellular GT2 and GT5 virus by 80–90% and GT2 virus cell-to-cell transmission by 50%. However, all of the p7 inhibitors had minimal effect on GT5 cell contact dependent transmission. Screening a wider panel of diverse viral genotypes demonstrated that p7 viroporin inhibitors were significantly more effective at blocking cell-free virus than cell-to-cell transmission. These results suggest an altered assembly or trafficking of cell-to-cell transmitted compared to secreted virus. These observations have important implications for the validation, therapeutic design and testing of HCV assembly inhibitors.
Collapse
Affiliation(s)
- L W Meredith
- Centre for Human Virology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
| | | | | |
Collapse
|
27
|
Meredith LW, Harris HJ, Wilson GK, Fletcher NF, Balfe P, McKeating JA. Early infection events highlight the limited transmissibility of hepatitis C virus in vitro. J Hepatol 2013; 58:1074-80. [PMID: 23353869 DOI: 10.1016/j.jhep.2013.01.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/10/2012] [Accepted: 01/09/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) poses a global health problem, with over 170 million chronically infected individuals at risk of developing progressive liver disease. The ability of a virus to spread within a host is a key determinant of its persistence and virulence. HCV can transmit in vitro by cell-free particle diffusion or via contact(s) between infected and naïve hepatocytes. However, limited information is available on the relative efficiency of these routes, our aim is to develop physiologically relevant assays to quantify these processes. METHODS We developed a single-cycle infection assay to measure HCV transmission rates. RESULTS We compared HCV spread in proliferating and arrested cell systems and demonstrated a significant reduction in cell-to-cell infection of arrested target cells. Comparison of cell-free and cell-to-cell virus spread demonstrated relatively poor transmission rates, with 10-50 infected producer cells required to infect a single naïve target cell. We found HCV strain J6/JFH to be 10-fold more efficient at spreading via the cell-to-cell route than cell-free, whereas SA13/JFH and HK6/JFH strains showed comparable rates of infection via both routes. Importantly, the level of infectious virus released from cells did not predict the ability of a virus to spread in vitro, highlighting the importance of studying cell-associated viruses. CONCLUSIONS These studies demonstrate the relatively poor infectivity of HCV and highlight differences between strains in their efficiency and preferred route of transmission that may inform future therapeutic strategies that target virus entry.
Collapse
Affiliation(s)
- Luke W Meredith
- Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, UK
| | | | | | | | | | | |
Collapse
|
28
|
Meredith LW, Wilson GK, Fletcher NF, McKeating JA. Hepatitis C virus entry: beyond receptors. Rev Med Virol 2012; 22:182-93. [PMID: 22392805 DOI: 10.1002/rmv.723] [Citation(s) in RCA: 76] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/30/2011] [Accepted: 10/09/2011] [Indexed: 12/11/2022]
Abstract
HCV is a blood-borne pathogen that affects approximately 3% of the global population and leads to progressive liver disease. Recent advances have identified an essential role for host cell molecules: tetraspanin CD81, scavenger receptor B1 and the tight junction proteins claudin-1 and occludin in HCV entry, suggesting a complex multi-step process. The conserved nature of this receptor-dependent step in the viral life cycle offers an attractive target for therapeutic intervention. Evidence is emerging that additional factors other than classical receptors, such as inflammatory mediators regulate the ability of hepatocytes to support HCV entry, and as such may provide potential avenues for drug design and development. In this review, we summarise the recent literature on HCV entry mechanisms with a view to realising the future potential of therapeutically targeting this process.
Collapse
Affiliation(s)
- Luke W Meredith
- Institute for Biomedical Research, University of Birmingham, Birmingham, UK
| | | | | | | |
Collapse
|
29
|
Fletcher NF, Wilson GK, Murray J, Hu K, Lewis A, Reynolds GM, Stamataki Z, Meredith LW, Rowe IA, Luo G, Lopez–ramirez MIGUELA, Baumert TF, Weksler B, Couraud PO, Kim KS, Romero IA, Jopling C, Morgello S, Balfe P, Mckeating JA. Hepatitis C virus infects the endothelial cells of the blood-brain barrier. Gastroenterology 2012; 142:634-643.e6. [PMID: 22138189 PMCID: PMC3801216 DOI: 10.1053/j.gastro.2011.11.028] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 10/18/2011] [Accepted: 11/15/2011] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) infection leads to progressive liver disease and is associated with a variety of extrahepatic syndromes, including central nervous system (CNS) abnormalities. However, it is unclear whether such cognitive abnormalities are a function of systemic disease, impaired hepatic function, or virus infection of the CNS. METHODS We measured levels of HCV RNA and expression of the viral entry receptor in brain tissue samples from 10 infected individuals (and 3 uninfected individuals, as controls) and human brain microvascular endothelial cells by using quantitative polymerase chain reaction and immunochemical and confocal imaging analyses. HCV pseudoparticles and cell culture-derived HCV were used to study the ability of endothelial cells to support viral entry and replication. RESULTS Using quantitative polymerase chain reaction, we detected HCV RNA in brain tissue of infected individuals at significantly lower levels than in liver samples. Brain microvascular endothelia and brain endothelial cells expressed all of the recognized HCV entry receptors. Two independently derived brain endothelial cell lines, hCMEC/D3 and HBMEC, supported HCV entry and replication. These processes were inhibited by antibodies against the entry factors CD81, scavenger receptor BI, and claudin-1; by interferon; and by reagents that inhibit NS3 protease and NS5B polymerase. HCV infection promotes endothelial permeability and cellular apoptosis. CONCLUSIONS Human brain endothelial cells express functional receptors that support HCV entry and replication. Virus infection of the CNS might lead to HCV-associated neuropathologies.
Collapse
Affiliation(s)
- Nicola F. Fletcher
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Garrick K. Wilson
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Jacinta Murray
- School of Pharmacy, University of Nottingham, Nottingham, England
| | - Ke Hu
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Andrew Lewis
- School of Pharmacy, University of Nottingham, Nottingham, England
| | - Gary M. Reynolds
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Zania Stamataki
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Luke W. Meredith
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Ian A. Rowe
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Guangxiang Luo
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky
| | | | - Thomas F. Baumert
- Université de Strasbourg and Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Pierre-Olivier Couraud
- Institut Cochin, CNRS UMR 8104, INSERM Unité 567, Université Paris Descartes, Paris, France
| | - Kwang Sik Kim
- Division of Infectious Diseases, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Ignacio A. Romero
- Department of Life Sciences, The Open University, Milton Keynes, England
| | | | - Susan Morgello
- Department of Pathology, Mount Sinai School of Medicine, New York, New York
| | - Peter Balfe
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| | - Jane A. Mckeating
- Hepatitis C Research Group, Institute for Biomedical Research, University of Birmingham, Birmingham, England
| |
Collapse
|
30
|
Brimacombe CL, Grove J, Meredith LW, Hu K, Syder AJ, Flores MV, Timpe JM, Krieger SE, Baumert TF, Tellinghuisen TL, Wong-Staal F, Balfe P, McKeating JA. Neutralizing antibody-resistant hepatitis C virus cell-to-cell transmission. J Virol 2011; 85:596-605. [PMID: 20962076 PMCID: PMC3014195 DOI: 10.1128/jvi.01592-10] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [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: 07/30/2010] [Accepted: 10/04/2010] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) can initiate infection by cell-free particle and cell-cell contact-dependent transmission. In this study we use a novel infectious coculture system to examine these alternative modes of infection. Cell-to-cell transmission is relatively resistant to anti-HCV glycoprotein monoclonal antibodies and polyclonal immunoglobulin isolated from infected individuals, providing an effective strategy for escaping host humoral immune responses. Chimeric viruses expressing the structural proteins representing the seven major HCV genotypes demonstrate neutralizing antibody-resistant cell-to-cell transmission. HCV entry is a multistep process involving numerous receptors. In this study we demonstrate that, in contrast to earlier reports, CD81 and the tight-junction components claudin-1 and occludin are all essential for both cell-free and cell-to-cell viral transmission. However, scavenger receptor BI (SR-BI) has a more prominent role in cell-to-cell transmission of the virus, with SR-BI-specific antibodies and small-molecule inhibitors showing preferential inhibition of this infection route. These observations highlight the importance of targeting host cell receptors, in particular SR-BI, to control viral infection and spread in the liver.
Collapse
Affiliation(s)
- Claire L. Brimacombe
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Joe Grove
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Luke W. Meredith
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Ke Hu
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Andrew J. Syder
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Maria Victoria Flores
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Jennifer M. Timpe
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Sophie E. Krieger
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Thomas F. Baumert
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Timothy L. Tellinghuisen
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Flossie Wong-Staal
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Peter Balfe
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| | - Jane A. McKeating
- Hepatitis C Research Group, Institute For Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom, iTherX Pharmaceuticals, Inc., P.O. Box 910530, San Diego, California 92191-0530, Pfizer Ltd., Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom, Inserm U748, Université de Strasbourg and Pôle Hépato-Digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France, Department of Infectology, The Scripps Research Institute, Jupiter, Florida 33458
| |
Collapse
|
31
|
Abstract
The role of Tat in HIV-1 reverse transcription has been controversial largely because different studies have observed disparate effects of the Tat protein on reverse transcription. Studies of HIV-1 lacking a functional tat gene demonstrated a decrease in reverse transcription efficiency following infection of T-cells however, in vitro recombinant Tat(1-86) has been shown to inhibit RT activity. Here we show that 20-200 nM of both N-terminally histidine-tagged recombinant Tat(1-72) and Tat(1-86) stimulated reverse transcription by HIV-1 reverse transcriptase (RT) in vitro by 2-3 fold. However, both Tat species were efficient inhibitors of RT activity at 400 nM. The lower concentrations of Tat increased reverse transcription efficiency by facilitating multiple rounds of DNA synthesis, and this increase was either not seen or reduced when Tat proteins with multiply-mutated cysteine or basic domains were used. Tat-enhanced reverse transcription occurred in a RNA-independent manner, and required formation of a Tat-RT complex. Pull-down and immunoprecipitation experiments confirmed that Tat could interact with the RT p51 subunit, and mammalian two-hybrid experiments showed interaction between Tat and both the p51 and p66 subunits. Together these results provide evidence that Tat can stimulate reverse transcription through an interaction with RT.
Collapse
Affiliation(s)
- Ann Apolloni
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
| | | | | | | | | |
Collapse
|