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Bennett C, Coughlan S, Hunt K, Butler F, Fanning S, Ryan E, De Gascun C, O'Gorman J. Detection of hepatitis E RNA in pork products at point of retail in Ireland - Are consumers at risk? Int J Food Microbiol 2024; 410:110492. [PMID: 37988969 DOI: 10.1016/j.ijfoodmicro.2023.110492] [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: 06/29/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023]
Abstract
Hepatitis E (HEV), a zoonotic virus, is the leading cause of acute viral hepatitis in Europe. The presence of HEV in domestic pigs can result in infections in humans through consumption of pork products which are undercooked or where processing methods are insufficient to inactivate the virus. In Ireland, pork accounts for 34 % of all meat consumption (CSO, 2022) and the prevalence of HEV in products at point of retail has not previously been characterised. A sampling strategy was designed in which high pork content sausages, fresh pork liver and raw fermented sausages were systematically purchased from three types of retailers between May 2018 and March 2019. In total, 200 pork products were tested using a lysing agent to release the HEV from the product for detection. RT-PCR for HEV was performed on samples with an extraction efficiency >1 % (n = 188/200) (94 %). Low level HEV RNA was detected in 9/188 (4.8 %) pork products tested. The highest incidence of HEV RNA was in pork liver where 6/25 (24 %) samples were positive. The concentration of HEV ranged from 0.02 - to 9.4 genome copies/g of pork. Based on these data an exposure assessment was performed which found that if consumers followed advice from the Food Safety Authority of Ireland to achieve core temperatures of 70 °C or higher when cooking, the risk was likely to be negligible.
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Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin 4, Ireland
| | - Eoin Ryan
- Central Veterinary Research Laboratory, Department Agriculture Food and the Marine (DAFM), Backweston, Kildare, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
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Bennett C, Hunt K, Butler F, Keaveney S, Fanning S, De Gascun C, Coughlan S, O'Gorman J. Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland. Food Environ Virol 2023; 15:246-254. [PMID: 37528267 PMCID: PMC10499670 DOI: 10.1007/s12560-023-09561-4] [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] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/22/2023] [Indexed: 08/03/2023]
Abstract
Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.
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Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin, 4, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
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Carter SC, Franciosi AN, O’Shea KM, O’Carroll OM, Sharma A, Bell A, Keogan B, O’Reilly P, Coughlan S, Law SM, Gray RD, Hisert KB, Singh PK, Cooke G, Grogan B, De Gascun CF, Gallagher CG, Nicholson TT, Quon BS, McKone EF. Acute Pulmonary Exacerbation Phenotypes in Patients with Cystic Fibrosis. Ann Am Thorac Soc 2022; 19:1818-1826. [PMID: 35713619 PMCID: PMC9667812 DOI: 10.1513/annalsats.202111-1266oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rationale: The etiology of cystic fibrosis (CF) pulmonary exacerbations (PEx) is likely multifactorial with viral, bacterial, and non-infectious pathways contributing. Objectives: To determine whether viral infection status and CRP (C-reactive protein) can classify subphenotypes of PEx that differ in outcomes and biomarker profiles. Methods: Patients were recruited at time of admission for a PEx. Nasal swabs and sputum samples were collected and processed using the respiratory panel of the FilmArray multiplex polymerase chain reaction (PCR). Serum and plasma biomarkers were measured. PEx were classified using serum CRP and viral PCR: "pauci-inflammatory" if CRP < 5 mg/L, "non-viral with systemic inflammation" if CRP ⩾ 5 mg/L and no viral infection detected by PCR and "viral with systemic inflammation" if CRP ⩾ 5 mg/L and viral infection detected by PCR. Results: Discovery cohort (n = 59) subphenotype frequencies were 1) pauci-inflammatory (37%); 2) non-viral with systemic inflammation (41%); and 3) viral with systemic inflammation (22%). Immunoglobulin G, immunoglobulin M, interleukin-10, interleukin-13, serum calprotectin, and CRP levels differed across phenotypes. Reduction from baseline in forced expiratory volume in 1 second as percent predicted (FEV1pp) at onset of exacerbation differed between non-viral with systemic inflammation and viral with systemic inflammation (-6.73 ± 1.78 vs. -13.5 ± 2.32%; P = 0.025). Non-viral with systemic inflammation PEx had a trend toward longer duration of intravenous antibiotics versus pauci-inflammation (18.1 ± 1.17 vs. 14.8 ± 1.19 days, P = 0.057). There were no differences in percent with lung function recovery to <10% of baseline FEV1pp. Similar results were seen in local and external validation cohorts comparing a pauci-inflammatory to viral/non-viral inflammatory exacerbation phenotypes. Conclusions: Subphenotypes of CF PEx exist with differences in biomarker profile, clinical presentation, and outcomes.
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Affiliation(s)
- Suzanne C. Carter
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
- University College Dublin School of Medicine, Dublin, Ireland
| | | | - Kate M. O’Shea
- University College Dublin School of Medicine, Dublin, Ireland
| | - Orla M. O’Carroll
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
| | - Ashutosh Sharma
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aoife Bell
- University College Dublin School of Medicine, Dublin, Ireland
| | - Brian Keogan
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Paul O’Reilly
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Sheonagh M. Law
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, Scotland
| | - Robert D. Gray
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, Scotland
| | - Katherine B. Hisert
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
- University of Washington, Seattle, Washington; and
| | | | - Gordon Cooke
- University College Dublin School of Medicine, Dublin, Ireland
- Technological University Dublin, Dublin, Ireland
| | - Brenda Grogan
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
| | | | - Charles G. Gallagher
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
- University College Dublin School of Medicine, Dublin, Ireland
| | - Trevor T. Nicholson
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
| | - Bradley S. Quon
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edward F. McKone
- National Referral Centre for Adult Cystic Fibrosis, St. Vincent’s University Hospital, Dublin, Ireland
- University College Dublin School of Medicine, Dublin, Ireland
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Kerr C, Kelleher M, Coughlan S, Crowley B, O'Reilly EJ, Bergin C. Changing demographics and immunity to vaccine preventable diseases in people with HIV in Ireland. BMC Infect Dis 2022; 22:582. [PMID: 35768790 PMCID: PMC9245288 DOI: 10.1186/s12879-022-07487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV infection is associated with an increased risk of morbidity and mortality from vaccine preventable infections. This research describes, in the context of changing patient demographics, the seroprevalence of vaccine preventable viral infections among attendees of the largest centre for HIV positive patients in Ireland. METHODS Baseline serum IgG results for measles, mumps, rubella, varicella zoster virus (VZV) & hepatitis A, as well as hepatitis B sAg, cAb and sAb results, were retrieved for 2534 clinic attendees attending in 2018. Results were available for between 990 and 2363 attendees (39-93%), depending on the test, and were compared with 2013 clinic data. RESULTS There was a 35% increase in attendees in 2018 when compared to 2013. The largest increase was in attendees of South American origin. In 2018, males accounted for 73% of the entire cohort and the HIV acquisition risk for 48% of attendees was MSM. 47% of attendees were originally from Ireland. Among those tested, 33% were susceptible to at least one component of the MMR vaccine. 5% were VZV non-immune (significantly associated with younger age and the acquisition risk status of injection drug use). 21% were hepatitis A non-immune (significantly associated with younger age and being of European or South American origin). 32% were hepatitis B cAb seropositive (significantly associated with older age, injection drug use status and being originally from Africa). 3% demonstrated hepatitis B sAg positivity. 64% had hepatitis B sAb ≥ 10mIU. CONCLUSION In a cohort of attendees to an HIV clinic in a large urban setting, the susceptibility to several common vaccine preventable viral infections, in particular MMR and hepatitis A and B, was high. These results highlight the importance of proactive screening and immunisation to help protect this high risk patient group against vaccine preventable diseases.
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Affiliation(s)
- C Kerr
- Department of Infectious Diseases, St. James's Hospital, Dublin, Ireland. .,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
| | - M Kelleher
- Department of Microbiology, St. James's Hospital, Dublin, Ireland
| | - S Coughlan
- National Virus Reference Laboratory, Belfield, Dublin, Ireland
| | - B Crowley
- Department of Microbiology, St. James's Hospital, Dublin, Ireland
| | - E J O'Reilly
- School of Public Health, University College Cork, Cork, Ireland
| | - C Bergin
- Department of Infectious Diseases, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
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Lucey M, Macori G, Mullane N, Sutton-Fitzpatrick U, Gonzalez G, Coughlan S, Purcell A, Fenelon L, Fanning S, Schaffer K. Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks. Clin Infect Dis 2021; 72:e727-e735. [PMID: 32954414 PMCID: PMC7543366 DOI: 10.1093/cid/ciaa1433] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background During the first wave of the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions posed a significant problem. Due to limited evidence, guidance on appropriate infection prevention and control (IPC) measures such as the wearing of face masks varied. Here, we applied whole virus genome sequencing (WvGS) to analyse transmission routes of SARS-CoV-2 in hospital-acquired (HA) COVID-19. Methods An investigation was undertaken for all HA cases of COVID-19 from March to April 2020. Fifty SARS-CoV-2 samples were analysed by WvGS and their phylogenetic relationship established. Results WvGS identified transmission events previously undetected by epidemiological analysis and provided evidence for SARS-CoV-2 transmission between healthcare workers (HCW) and patients and among HCW themselves. The majority of HA COVID-19 cases occurred in patients highly dependent on nursing care, suggesting the likely route of transmission was by close contact or droplet, rather than aerosol, transmission. Mortality among HA COVID-19 infections was recorded as 33%. Conclusions This study provides evidence that SARS-CoV-2 transmission occurs from symptomatic and asymptomatic HCWs to patients. Interventions including comprehensive screening of HCWs for COVID-19 symptoms, PCR testing of asymptomatic HCWs upon identification of HA cases and implementation of universal use of surgical masks for all clinical care is indicated to prevent viral transmission. Our study highlights the importance of close collaboration between guidance bodies and frontline IPC experts for developing control measures in an emergency pandemic situation caused by a virus with undefined transmission modus.
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Affiliation(s)
- Mary Lucey
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Guerrino Macori
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Niamh Mullane
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Una Sutton-Fitzpatrick
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Aisling Purcell
- Department of Occupational Health, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Lynda Fenelon
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kirsten Schaffer
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
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Coughlan S, Elbadry M, Salama M, Divilley R, Stokes HK, O'Neill MB. The Current Use of Lumbar Puncture in a General Paediatric Unit. Ir Med J 2021; 114:354. [PMID: 35015953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Aim This study evaluated the use of Lumbar Puncture (LP) in a general paediatric unit over a 3-year period. Methods Index patients, who had a successful LP, were identified from the microbiology database and failed LP procedures were identified from a chart review of the serum PCR database. Data abstracted included 1) patient age, 2) LP indication, 3) LP procedure outcome; classified as atraumatic, traumatic or failed, 4) grade of doctor undertaking the procedure and 5) the final diagnosis. Results We identified 104 paediatric patients, of whom 29(27.9%) were neonates. LP was indicated for the evaluation of acute undifferentiated illnesses, with 33 (31.7%) patients having fever without source beyond the neonatal period and 16 (15.4%) being neonates with fever. A CSF sample was obtained in 96 (92.4%) patients, with 71 (73.9%) being atraumatic. Successful LP was undertaken by Consultants in 4 (4.1%), Registrars in 83 (86.5%) and SHOs in 9 (9.4%) patients. 14 (14.6%) patients had positive CSF cultures with an additional 23 having positive cultures or serology (9 blood cultures, 11 urine cultures and 3 positive serum PCR). Conclusion Skill in LP performance is still required, to evaluate acute undifferentiated illness, in general paediatric units and ancillary methods to aid SHOs with LP skill development is desirable.
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Affiliation(s)
- S Coughlan
- Dept. of Paediatrics, Mayo University Hospital
| | - M Elbadry
- Dept. of Paediatrics, Mayo University Hospital
| | - M Salama
- Dept. of Paediatrics, Mayo University Hospital
| | - R Divilley
- Dept. of Laboratory Services, Mayo University Hospital
| | - H K Stokes
- Dept. of Paediatrics, Mayo University Hospital
| | - M B O'Neill
- Dept. of Paediatrics, Mayo University Hospital
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Yandle Z, Coughlan S, Dean J, Hare D, De Gascun CF. Indirect impact of rotavirus vaccination on viral causes of acute gastroenteritis in the elderly. J Clin Virol 2021; 137:104780. [PMID: 33647802 DOI: 10.1016/j.jcv.2021.104780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND Rotavirus is considered a childhood infection causing acute gastroenteritis however, it also causes disease in adults which may be underestimated due to less frequent testing in this age-group. OBJECTIVES To determine if paediatric rotavirus vaccination, introduced into Ireland in December 2016, affected the viral aetiology in those aged ≥65 yrs presenting with gastroenteritis in the pre- and post-vaccination years. Additionally, rotavirus genotypes in this age-group will be described. METHODS Faecal samples from 2015 to 2019 for the investigation of gastroenteritis were tested by real-time (RT-) PCR for norovirus, adenovirus, rotavirus, Rotarix, astrovirus and sapovirus. Rotaviruses were genotyped by multiplex real-time RT-PCR or hemi-nested RT-PCR and a proportion confirmed by sequencing. RESULTS 22,593 samples from adults aged ≥65 yrs were tested and 2566 (11 %) had ≥1 virus detected. Of 2566 positive samples, norovirus was detected in 82 %, rotavirus 9 %, sapovirus 6 %, astrovirus 3 % and adenovirus 1 %. Rotavirus and norovirus infections decreased between pre and post-vaccine year groups p < 0.001, whereas sapovirus, astrovirus and adenovirus remained unchanged. Between 2015-16 and 2018-19, G2P[4] increased and G4P[8] decreased, p < 0.001. In 2015-2019 there were 37 rotavirus outbreaks. Five geriatric outbreaks were genotyped and caused by G4P[8] (n = 1), G1P[8] (n = 1), G2P[4] (n = 2) and G12P[8] (n = 1). CONCLUSION Rotavirus causes acute gastroenteritis in older people. Paediatric vaccination may have contributed to a decline in infections in the elderly; nevertheless, rotavirus continued to circulate in older people following vaccine introduction. Genotype distribution changed between the pre- and post-vaccine era however genotypes in outbreak and endemic settings were comparable.
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Affiliation(s)
- Z Yandle
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland.
| | - S Coughlan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
| | - J Dean
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
| | - D Hare
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
| | - C F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
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Coughlan S, Das A, O’Herlihy E, Shanahan F, O’Toole P, Jeffery I. The gut virome in Irritable Bowel Syndrome differs from that of controls. Gut Microbes 2021; 13:1-15. [PMID: 33602058 PMCID: PMC7899630 DOI: 10.1080/19490976.2021.1887719] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/28/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.
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Affiliation(s)
- S. Coughlan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - A. Das
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - E. O’Herlihy
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - F. Shanahan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - P.W. O’Toole
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - I.B. Jeffery
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
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Gujral D, Nazir S, Hunter B, McNaught P, Williams L, Porter S, Coughlan S, Cleator S. PO-0930: Wide tangents versus volumetric arc therapy to treat the internal mammary chain using breath hold. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Yandle Z, Coughlan S, Dean J, Tuite G, Conroy A, De Gascun CF. Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015-2019. Pathogens 2020; 9:pathogens9060449. [PMID: 32517307 PMCID: PMC7350336 DOI: 10.3390/pathogens9060449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Immunisation against rotavirus infection was introduced into Ireland in December 2016. We report on the viruses causing gastroenteritis before (2015–2016) and after (2017–2019) implementation of the Rotarix vaccine, as well as changes in the diversity of circulating rotavirus genotypes. Samples from patients aged ≤ 5 years (n = 11,800) were received at the National Virus Reference Laboratory, Dublin, and tested by real-time RT-PCR for rotavirus, Rotarix, norovirus, sapovirus, astrovirus, and enteric adenovirus. Rotavirus genotyping was performed either by multiplex or hemi-nested RT-PCR, and a subset was characterised by sequence analysis. Rotavirus detection decreased by 91% in children aged 0–12 months between 2015/16 and 2018/19. Rotarix was detected in 10% of those eligible for the vaccine and was not found in those aged >7 months. Rotavirus typically peaks in March–May, but following vaccination, the seasonality became less defined. In 2015–16, G1P[8] was the most common genotype circulating; however, in 2019 G2P[4] was detected more often. Following the introduction of Rotarix, a reduction in numbers of rotavirus infections occurred, coinciding with an increase in genotype diversity, along with the first recorded detection of an equine-like G3 strain in Ireland.
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O Loughlin DW, Coughlan S, De Gascun CF, McNally P, Cox DW. The role of rhinovirus infections in young children with cystic fibrosis. J Clin Virol 2020; 129:104478. [PMID: 32521465 PMCID: PMC7263235 DOI: 10.1016/j.jcv.2020.104478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/22/2020] [Accepted: 05/31/2020] [Indexed: 12/29/2022]
Abstract
Rhinovirus (RV) is an important virus in children with chronic respiratory conditions such as asthma; however, little is known about its role in CF. Our aim was to examine the prevalence and clinical impact of different RV species in young children with CF. We collected clinical data and nasal swabs on patients at home and in the hospital setting. Parents filled out symptom diaries and collected nasal swabs when their children were symptomatic and asymptomatic. A novel RV typing PCR assay was used to determine the RV species present. We collected 55 nasal swab samples from ten preschool CF patients over a six month period. The quality of parent collected samples at home was sufficient for PCR analysis. RV was the most common virus detected in young children with CF. There was no difference in the frequency of RV species between symptomatic and asymptomatic subjects. However, parental home-sampling is an acceptable and feasible approach to monitoring young children with CF.
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Affiliation(s)
- D W O Loughlin
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - S Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - C F De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - P McNally
- Respiratory Department, Children's Health Ireland, Crumlin, Dublin 12, Ireland; Department of Paediatrics, Royal College of Surgeons in Ireland, Ireland
| | - D W Cox
- Respiratory Department, Children's Health Ireland, Crumlin, Dublin 12, Ireland; School of Medicine, University College Dublin, Dublin 4, Ireland
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Bennett C, Dunford L, Coughlan S, De Gascun C, O’Gorman J. A26 Molecular epidemiology of hepatitis E virus in Ireland 2016. Virus Evol 2019. [PMCID: PMC6735873 DOI: 10.1093/ve/vez002.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Foodborne viruses such as hepatitis E virus (HEV) pose an increasing risk to public health and to confidence in Irish food. Hepatitis E has been acknowledged as a significant pathogen of likely zoonotic transmission, with pork products and shellfish being implicated as potential sources. The European Food Safety Authority has recommended that systematic strain typing of viruses in humans, animals, and food commodities is needed to improve understanding of etiological agents and foodborne transmission pathways, in particular for HEV. The dominant autochthonous genotype of HEV in Europe is genotype 3, thought to be associated with consumption of contaminated food, specifically pork products. However, little is known about the epidemiology of HEV in Ireland. In 2016, HEV became a notifiable disease in Ireland. Following this, as part of the Department of Agriculture, Food and the Marine-funded FoVIRA study, the molecular epidemiology of HEV in Irish clinical samples has been characterized for the first time. HEV RNA-positive clinical specimens from 2016 were genetically characterized (n = 14). A 450 nucleotide fragment of the ORF2 region of the HEV genome was amplified, with contiguous sequence assembly performed using DNA Lasergene v14. Sequences were aligned with ClustalW implemented in Bioedit v7.1.9 and compared to reference strains from GenBank. A maximum likelihood phylogenetic tree was constructed using the Hasegawa–Kishino–Yano model and a discrete gamma distribution to model evolutionary rate distances between sites. Evolutionary analyses were conducted in MEGA7. Statistical support was provided by bootstrapping with 1,000 replicates. Fourteen strains belonged to genotype 3 and were classified as the following subtypes: 3c (n = 7), 3e (n = 4), 3f (n = 1), 3 untyped (n = 1), and 1 untyped. Phylogenetic analysis showed the formation of two distinct clusters of genotype 3:3abchij and 3efg, with strong bootstrap support. A genotype 1 was detected and found to be associated with travel. Data generated from this research will contribute to a risk exposure assessment and will be used to identify potential control points and risk mitigation measures for viral foodborne pathogens. This study will provide a unique opportunity to build national capability in the area of food testing within Irish public laboratories.
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Affiliation(s)
- Charlene Bennett
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Linda Dunford
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cillian De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joanne O’Gorman
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
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13
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Carter S, Keogan B, O'Reilly P, Coughlan S, Cooke G, De Gascun C, Gallagher C, McKone E. P176 Detection of respiratory viruses in cystic fibrosis: comparison of nasal FLOQ Swabs™ and sputum using the FilmArray® platform. J Cyst Fibros 2019. [PMCID: PMC7129069 DOI: 10.1016/s1569-1993(19)30470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Cuschieri K, Schuurman R, Coughlan S. Ensuring quality in cervical screening programmes based on molecular human papillomavirus testing. Cytopathology 2019; 30:273-280. [PMID: 30657615 DOI: 10.1111/cyt.12679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/10/2018] [Accepted: 01/11/2019] [Indexed: 01/13/2023]
Abstract
The increased use of human papillomavirus testing within cervical screening programmes necessarily brings about changes to the laboratory services required to support them. A crucial element of such services is to demonstrate initial and ongoing quality of the test (and associated processes). In this review, we outline some of the quality considerations and challenges with an emphasis on the laboratory including assay and platform validation, internal quality control selection and strengths and weaknesses of external quality assurance schemes. The influence and role of key external entities, including regulatory agencies, guideline groups, programme commissioners and commercial providers, are also discussed.
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Affiliation(s)
- Kate Cuschieri
- Scottish HPV Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, Scotland.,HPV Research Group, University of Edinburgh, Edinburgh, Scotland
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Ireland
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15
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Yandle Z, Coughlan S, Drew RJ, Cleary J, De Gascun C. Diagnosis of rotavirus infection in a vaccinated population: Is a less sensitive immunochromatographic method more suitable for detecting wild-type rotavirus than real-time RT-PCR? J Clin Virol 2018; 109:19-21. [PMID: 30388662 DOI: 10.1016/j.jcv.2018.10.006] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Diagnosis of wild-type rotavirus disease may be complicated by the detection of vaccine-derived virus which can be detected in stool samples following immunisation. We evaluate an immunochromatographic assay and real-time RT-PCR to determine which is more suitable for the detection of wild-type rotavirus. OBJECTIVES To compare the Ct values of wild-type rotavirus and Rotarix determined by real-time RT-PCR. To establish the Ct value corresponding to the limit of detection of the immunochromatographic Combi-Strip method (Coris, BioConcept). STUDY DESIGN Retrospective review of real-time RT-PCR Ct values was performed on 100 samples tested by a pan-rotavirus assay (n = 50 wild-type, n = 50 Rotarix). Secondly the limit of detection of the Combi-Strip assay was determined by testing; wild-type rotavirus (n = 33, Ct range 6.85-34.26) samples, Rotarix (n = 9, Ct range 20.86-34.26) samples and rotavirus negative (n = 21) samples. RESULTS The median Ct of 50 wild-type rotavirus was Ct 12.43; range 6.11-32.66 compared with the median of 50 Rotarix, Ct 29.09; range 18.91-35.28, p=<0.0001. The limit of detection of the Combi-Strip method was approximately Ct 18. The 21 rotavirus negative samples were negative by real-time RT-PCR and Combi-Strip. CONCLUSIONS We found the Ct value was significantly lower, and therefore the viral load higher, for wild-type rotavirus compared to detectable Rotarix. The Combi-Strip assay detects most wild-type infections; however, it lacks sensitivity to detect low-level wild-type rotavirus and, beneficially, is unlikely to detect Rotarix. It is not a more suitable method than real-time RT-PCR when a definitive rotavirus result is required.
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Affiliation(s)
- Z Yandle
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland.
| | - S Coughlan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
| | - R J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - J Cleary
- Department of Microbiology, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - C De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
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16
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Dean J, Neary M, Coughlan S, De Gascun CF. A12 Predictors of treatment failure among Irish individuals infected with hepatitis C virus. Virus Evol 2017; 3:vew036.011. [PMID: 28845250 PMCID: PMC5565933 DOI: 10.1093/ve/vew036.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- J Dean
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - M Neary
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - C F De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
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17
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Asif M, McNaught P, Welgemoed C, Coughlan S, Gujral D, Cleator S. Internal Mammary Radiotherapy Planning: a Single Centre Experience. Clin Oncol (R Coll Radiol) 2017. [DOI: 10.1016/j.clon.2017.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Yandle Z, Coughlan S, Drew RJ, O’Flaherty N, O’Gorman J, De Gascun C. Circulating rotavirus genotypes in the Irish paediatric population prior to the introduction of the vaccination programme. Ir J Med Sci 2017; 186:1003-1007. [DOI: 10.1007/s11845-017-1604-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/24/2017] [Indexed: 02/07/2023]
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19
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Linehan E, Brennan M, O'Rourke S, Coughlan S, Clooney L, LeBlanc D, Griffin J, Eogan M, Drew RJ. Impact of introduction of xpert flu assay for influenza PCR testing on obstetric patients: a quality improvement project. J Matern Fetal Neonatal Med 2017; 31:1016-1020. [PMID: 28285563 DOI: 10.1080/14767058.2017.1306048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE The aim of this project was to assess the implementation of a quality improvement project regarding the introduction of on-site influenza PCR testing in a stand-alone obstetric hospital. METHODS As part of a quality improvement project on the management of influenza in obstetric patients, the Xpert Flu assay (Cepheid Inc., Sunnyvale, CA) was introduced on-site and it replaced the previous method of PCR testing which was off-site. The main outcome measures were duration of antimicrobials, rate of admission and administration of oseltamavir in the emergency department. RESULTS Twenty-eight patients were included in the pre-intervention period and 45 patients were included in the post-intervention period. Following the introduction of the test, there was a statistically significant reduction seen in commencement of antimicrobials (76% pre- and 33% post-intervention), and also rate of admission (88% pre- and 45% post-intervention) while there was a statistically significant improvement in the commencement of oseltamavir in the emergency department (72% pre-and 95% post-intervention) (p < .01 for all outcomes). CONCLUSION Introduction of on-site rapid influenza PCR testing can lead to a significant improvement in patient management and should be considered for introduction to other sites.
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Affiliation(s)
- Eimear Linehan
- a Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Marian Brennan
- b Department of Infection Prevention and Control , Rotunda Hospital , Dublin , Ireland
| | - Sadhbh O'Rourke
- c Department of Clinical Microbiology , Temple Street Children's University Hospital , Dublin , Ireland
| | - Suzie Coughlan
- d National Virus Reference Laboratory, University College Dublin , Dublin , Ireland
| | - Lisa Clooney
- e Department of Pharmacy , Rotunda Hospital , Dublin , Ireland
| | - David LeBlanc
- f Department of Clinical Microbiology , Rotunda Hospital , Dublin , Ireland
| | - Joanna Griffin
- g Department of Research , Rotunda Hospital , Dublin , Ireland
| | - Maeve Eogan
- h Department of Obstetrics , Rotunda Hospital , Dublin , Ireland
| | - Richard J Drew
- f Department of Clinical Microbiology , Rotunda Hospital , Dublin , Ireland.,i Department of Clinical Microbiology , Royal College of Surgeons in Ireland , Dublin , Ireland
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20
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Yandle Z, Tuite G, Coughlan S, O’Gorman J, De Gascun C. Detection and characterisation of viral pathogens causing gastroenteritis in Ireland, 2014–2016. J Clin Virol 2016. [DOI: 10.1016/j.jcv.2016.08.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. Infect Genet Evol 2016; 46:169-179. [PMID: 27262355 PMCID: PMC5157885 DOI: 10.1016/j.meegid.2016.05.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their spread around the world over the last 50years and describe significant spread patterns. We show that subtype B travelled from North America to Western Europe in different occasions, while Central/Eastern Europe remained isolated for the most part of the early epidemic. Looking with more detail in European countries we see that the United Kingdom, France and Switzerland exchanged viral isolates with non-European countries than with European ones. The observed pattern is likely to mirror geopolitical landmarks in the post-World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. In conclusion, HIV-1 spread through specific migration routes which are consistent with geopolitical factors that affected human activities during the last 50years, such as migration, tourism and trade. Our findings support the argument that epidemic control policies should be global and incorporate political and socioeconomic factors.
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Affiliation(s)
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Glenn Lawyer
- Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Daniel Struck
- Centre de Recherche Public de la Sante, Luxembourg, Luxembourg
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Annemarie Wensing
- Department of Virology, University Medical Center, Utrecht, The Netherlands
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Perpétua Gomes
- Molecular Biology Lab, LMCBM, SPC, HEM, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Snjezana J Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases "Dr. F. Mihaljevic", Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals", Bucharest, Romania
| | | | - Mario Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | - Maja Stanojevic
- University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | | | | | | | - Georgios Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Samuel R Friedman
- Institute of Infectious Diseases Research, National Development and Research Institutes, Inc., New York, USA
| | - David van de Vijver
- Eijkman Winkler Institute, Department of Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Andrea de Luca
- Institute of Clinical Infectious Diseases, Catholic university, Rome, Italy
| | - Klaus Korn
- University of Erlangen, Erlangen, Germany
| | - Clive Loveday
- International Clinical Virology Centre, Buckinghamshire, England, United Kingdom
| | | | | | | | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece.
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22
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Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [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: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
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Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
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Collins P, Mulherin E, O'Shea H, Cashman O, Lennon G, Pidgeon E, Coughlan S, Hall W, Fanning S. Changing patterns of rotavirus strains circulating in Ireland: Re-emergence of G2P[4] and identification of novel genotypes in Ireland. J Med Virol 2015; 87:764-73. [DOI: 10.1002/jmv.24095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 11/06/2022]
Affiliation(s)
- P.J. Collins
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Emily Mulherin
- UCD-Centre for Food Safety; School of Public Health; Physiotherapy and Population Science; Dublin Ireland
| | - Helen O'Shea
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Olivia Cashman
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Grainne Lennon
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Eugene Pidgeon
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - William Hall
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety; School of Public Health; Physiotherapy and Population Science; Dublin Ireland
- School of Veterinary Medicine; University College Dublin; Dublin Ireland
- Institute for Global Food Security; Queen's University Belfast; Belfast Ireland
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Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, Struck D, Vercauteren J, Wensing AMJ, Alexiev I, Åsjö B, Balotta C, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej S, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CAB, Kaplan L, Vandamme AM, Paraskevis D. Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia. J Infect Dis 2014; 211:1735-44. [PMID: 25512631 DOI: 10.1093/infdis/jiu666] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/24/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. METHODS We assembled a global data set of 2736 CRF01_AE sequences by pooling sequences from public databases and patient-cohort studies. We estimated viral dispersal patterns, using statistical phylogeographic analysis run over bootstrap trees estimated by the maximum likelihood method. RESULTS We show that Thailand has been the source of viral dispersal to most areas worldwide, including 17 of 20 sampled countries in Europe. Japan, Singapore, Vietnam, and other Asian countries have played a secondary role in the viral dissemination. In contrast, China and Taiwan have mainly imported strains from neighboring Asian countries, North America, and Africa without any significant viral exportation. DISCUSSION The central role of Thailand in the global spread of CRF01_AE can be probably explained by the popularity of Thailand as a vacation destination characterized by sex tourism and by Thai emigration to the Western world. Our study highlights the unique case of CRF01_AE, the only globally distributed non-B clade whose global dispersal did not originate in Africa.
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Affiliation(s)
- Konstantinos Angelis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor, and Cell Biology Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece Department of Zoology, University of Oxford, United Kingdom
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | | | | | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | | | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Ricardo J Camacho
- Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | | | | | | | | | | | - Snjezana Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases Dr F. Mihaljevic, Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases Prof Dr Matei Bals, Bucharest, Romania
| | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Center, University of Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Division of Infectious Diseases Division of Clinical Virology, Karolinska Institute Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Lauren Kaplan
- Alcohol Research Group, University California, Berkeley
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
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Jackson V, Ferguson W, Kelleher TB, Lawless M, Eogan M, Nusgen U, Coughlan S, Connell J, Lambert JS. Lamivudine treatment and outcome in pregnant women with high hepatitis B viral loads. Eur J Clin Microbiol Infect Dis 2014; 34:619-23. [PMID: 25381607 DOI: 10.1007/s10096-014-2270-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/20/2014] [Indexed: 01/27/2023]
Abstract
Perinatal transmission is the most common mode of hepatitis B virus (HBV) transmission and is a leading cause of chronic infection worldwide. Maternal treatment with lamivudine (LAM) can result in a rapid and significant reduction in HBV viral load (VL) and, thus, mitigate the risk of mother-to-child transmission (MTCT). The aim of this study was to retrospectively evaluate the safety of LAM treatment administered in the third trimester of pregnancy and determine the influence, if any, on infant outcome. The medical charts of all HBV surface antigen (HBsAg)-positive women eligible for treatment with LAM and who registered for antenatal care between 2007 and 2012 were retrospectively reviewed. During the 6-year period, 45 women met the criteria for LAM treatment. Thirty-six women (80 %) accepted treatment; the remaining women declined treatment (5), defaulted from care (3) or transferred to another maternity unit (1). The median duration of treatment was 11.4 weeks (range 5.3-17.4) and the median baseline VL was 1.4 × 10(8) IU/mL (range 1.8 × 10(7)-1.7 × 10(8)). The median VL at delivery was 2.3 × 10(5) IU/mL and 60 % of women achieved a VL reduction >2 log10 IU/mL before delivery. No cases of perinatal transmission occurred in the infants born to mothers who received treatment; however, one infant, born to a mother who defaulted from care, was HBV-infected at 8 months. The results suggest that LAM therapy in highly viraemic HBV-infected pregnant women could lower the rate of vertical transmission.
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Affiliation(s)
- V Jackson
- Department of Infectious Diseases, The Rotunda Hospital, Dublin, Ireland
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26
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Collison M, Chin JL, Abu Shanab A, Mac Nicholas R, Segurado R, Coughlan S, Connell J, Carr MJ, Merriman RB, McCormick PA, Hall WW. Homozygosity for HLA group 2 alleles predicts treatment failure with interferon-α and ribavirin in chronic hepatitis C virus genotype 1 infection. J Interferon Cytokine Res 2014; 35:126-33. [PMID: 25237729 DOI: 10.1089/jir.2014.0088] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Host genetic factors influence treatment responses to antiviral therapy in chronic hepatitis C virus (HCV) infection. We retrospectively investigated associations between host genetic markers and treatment-induced virologic responses to dual therapy with interferon-α and ribavirin in chronically infected HCV genotype 1 (g1)- and genotype 3 (g3)-infected individuals. A total of 171 patients (89 HCV g1 and 82 HCV g3 infected) were investigated for genetic markers influencing treatment-induced sustained virologic response (SVR). Overall, SVR was observed for 46/89 (52%) HCV g1- and 57/82 (70%) HCV g3-infected patients. Of the 4 interleukin 28B (IL28B) single-nucleotide polymorphisms (SNPs), rs12979860 was the host genetic marker most significantly associated with failure to achieve an SVR in HCV g1-infected individuals [P=3.83×10(-4); odds ratio (OR)=5.61; confidence interval (CI)=2.07-15.18] and gave a positive predictive value for treatment failure of 81.3% for minor homozygotes (TT). Using additive (P=3.54×10(-4)) and dominant models (P=3.83×10(-4)), a dosage effect of the T allele was observed, with the dominance term not significant for this SNP. Logistic regression showed an association between HLA-C1/C1 and rapid virologic response in HCV g1 infections with an OR relative to the heterozygote of 10.0 (95% CI: 1.6-62.5, P=0.014). HLA-C2 homozygosity was a significant predictor of nonresponse to treatment in HCV g1-infected individuals (P=0.023).
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Affiliation(s)
- Meadhbh Collison
- 1 National Virus Reference Laboratory, University College Dublin , Dublin, Ireland
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Affiliation(s)
- C. Devitt
- Glendalough, Co.; Wicklow Bray Ireland
| | - D. A. Graham
- European Studies; MEconSc Animal Health Ireland; Main St, Carrick on Shannon Co. Leitrim Ireland
| | - S. Coughlan
- Irish Cattle Breeding Federation; Shinagh House Bandon Ireland
| | - J. O'Flaherty
- European Studies; MEconSc Animal Health Ireland; Main St, Carrick on Shannon Co. Leitrim Ireland
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Waters A, Jennings K, Fitzpatrick E, Coughlan S, Molloy EJ, De Gascun CF, Hall WW, Knowles SJ. Incidence of congenital cytomegalovirus infection in Ireland: Implications for screening and diagnosis. J Clin Virol 2014; 59:156-60. [DOI: 10.1016/j.jcv.2013.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/11/2013] [Accepted: 12/21/2013] [Indexed: 11/16/2022]
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Graham DA, Lynch M, Coughlan S, Doherty ML, O'Neill R, Sammin D, O'Flaherty J. Development and review of the voluntary phase of a national BVD eradication programme in Ireland. Vet Rec 2014; 174:67. [DOI: 10.1136/vr.101814] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- D. A. Graham
- Animal Health Ireland; Main St, Carrick on Shannon Co. Leitrim Ireland
| | - M. Lynch
- Irish Cattle Breeding Federation; Shinagh House Bandon Ireland
| | - S. Coughlan
- Irish Cattle Breeding Federation; Shinagh House Bandon Ireland
| | - M. L. Doherty
- School of Veterinary Medicine; University College Dublin; Belfield Dublin Ireland
| | - R. O'Neill
- Central Veterinary Research Laboratory; Backweston Celbridge Ireland
| | - D. Sammin
- Central Veterinary Research Laboratory; Backweston Celbridge Ireland
| | - J. O'Flaherty
- Animal Health Ireland; Main St, Carrick on Shannon Co. Leitrim Ireland
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Berry D, Coughlan B, Enright B, Coughlan S, Burke M. Factors associated with milking characteristics in dairy cows. J Dairy Sci 2013; 96:5943-53. [DOI: 10.3168/jds.2012-6162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 05/21/2013] [Indexed: 11/19/2022]
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31
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Frentz D, Wensing AMJ, Albert J, Paraskevis D, Abecasis AB, Hamouda O, Jørgensen LB, Kücherer C, Struck D, Schmit JC, Åsjö B, Balotta C, Beshkov D, Camacho RJ, Clotet B, Coughlan S, De Wit S, Griskevicius A, Grossman Z, Horban A, Kolupajeva T, Korn K, Kostrikis LG, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher CAB, Van de Vijver DAMC. Limited cross-border infections in patients newly diagnosed with HIV in Europe. Retrovirology 2013; 10:36. [PMID: 23551870 PMCID: PMC3626648 DOI: 10.1186/1742-4690-10-36] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND International travel plays a role in the spread of HIV-1 across Europe. It is, however, not known whether international travel is more important for spread of the epidemic as compared to endogenous infections within single countries. In this study, phylogenetic associations among HIV of newly diagnosed patients were determined across Europe. RESULTS Data came from the SPREAD programme which collects samples of newly diagnosed patients that are representative for national HIV epidemics. 4260 pol sequences from 25 European countries and Israel collected in 2002-2007 were included.We identified 457 clusters including 1330 persons (31.2% of all patients). The cluster size ranged between 2 and 28. A number of 987 patients (74.2%) were part of a cluster that consisted only of patients originating from the same country. In addition, 135 patients (10.2%) were in a cluster including only individuals from neighboring countries. Finally, 208 patients (15.6%) clustered with individuals from countries without a common border. Clustering with patients from the same country was less prevalent in patients being infected with B subtype (P-value <0.0001), in men who have sex with men (P-value <0.0001), and in recently infected patients (P-value =0.045). CONCLUSIONS Our findings indicate that the transmission of HIV-1 in Europe is predominantly occurring between patients from the same country. This could have implications for HIV-1 transmission prevention programmes. Because infections through travelling between countries is not frequently observed it is important to have good surveillance of the national HIV-1 epidemics.
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Affiliation(s)
- Dineke Frentz
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
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Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver DAMC, Albert J, Åsjö B, Balotta C, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Hamouda O, Horban A, Korn K, Kostrikis LG, Kücherer C, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Liitsola K, Schmit JC, Schuurman R, Sönnerborg A, Stanekova D, Stanojevic M, Struck D, Van Laethem K, Wensing AMJ, Boucher CAB, Vandamme AM. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology 2012; 9:81. [PMID: 23031662 PMCID: PMC3487874 DOI: 10.1186/1742-4690-9-81] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. RESULTS Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. CONCLUSIONS These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level.
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Affiliation(s)
- Kristof Theys
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jurgen Vercauteren
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jan Albert
- Clinical Microbiology, Karolinska University Hospital and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Birgitta Åsjö
- Section for Microbiology and Immunology, Gade institute, University of Bergen, Bergen, Norway
| | | | - Marie Bruckova
- National Institute of Public Health, Prague, Czech Republic
| | - Ricardo J Camacho
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | | | - Zehava Grossman
- Sheba Medical Center, Tel-Hashomer, and School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Andrzei Horban
- Warsaw Medical University and Hospital for Infectious Diseases, Warsaw, Poland
| | - Klaus Korn
- Institut für Klinische und Molekulare Virologie, University of Erlangen, Erlangen, Germany
| | | | | | | | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology of Medical Statistics, University of Athens, Medical School, Athens, Greece
| | | | | | | | - Lidia Ruiz
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anders Sönnerborg
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institutet, Stockholm, Sweden
| | | | - Maja Stanojevic
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemarie MJ Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Charles AB Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Luu QP, Dean J, Do TTD, Carr MJ, Dunford L, Coughlan S, Connell J, Nguyen HT, Hall WW, Nguyen Thi LA. HIV type 1 coreceptor tropism, CCR5 genotype, and integrase inhibitor resistance profiles in Vietnam: implications for the introduction of new antiretroviral regimens. AIDS Res Hum Retroviruses 2012; 28:1344-8. [PMID: 22264071 DOI: 10.1089/aid.2011.0396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Vietnam, where an estimated 280,000 people will be HIV-positive by 2012, recommended antiretroviral regimens do not include more recently developed therapeutics, such as Integrase inhibitors (INI) and coreceptor antagonists. This study examined HIV-1 coreceptor tropism and INI drug resistance profiles, in parallel with CCR5 genotypes, in a cohort of 60 HIV-positive individuals from different regions of Vietnam. No evidence of INI resistance was detected. Some 40% of individuals had X4-tropic HIV-1, making them unsuitable for treatment with CCR5 antagonists. We identified a novel CCR5 variant-S272P-along with other, previously reported variants: G106R, C178R, W153C, R223Q, and S336I. Interestingly, CCR5 variants known to affect HIV-1 infectivity were observed only in individuals harboring X4-tropic virus. Together, this study presents valuable baseline information on HIV-1 INI resistance, coreceptor tropism, and CCR5 variants in HIV-positive individuals in Vietnam. This should help inform policy on the future use of novel antiretrovirals in Vietnam.
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Affiliation(s)
- Quynh Phuong Luu
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Jonathan Dean
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Trinh Thi Diem Do
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Michael J Carr
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Linda Dunford
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Suzie Coughlan
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Jeff Connell
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - William W. Hall
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Lan Anh Nguyen Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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De Gascun CF, Waters A, Regan CM, O'Halloran J, Farrell G, Coughlan S, Bergin C, Powderly WG, Hall WW. Human immunodeficiency virus type 1 in Ireland: phylogenetic evidence for risk group-specific subepidemics. AIDS Res Hum Retroviruses 2012; 28:1073-81. [PMID: 22176216 DOI: 10.1089/aid.2011.0301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV genetic diversity may have an impact on viral pathogenesis, transmission, response to treatment, and vaccine development. Public health surveillance that monitors the frequency and variety of HIV subtypes in a particular region or patient group is vital to successfully control the pandemic. We present the first comprehensive report on HIV diversity in Ireland. This study comprised all new HIV-1 diagnoses that were confirmed in the National Virus Reference Laboratory, University College Dublin, from January 2004 to December 2008. HIV 1 protease and reverse transcriptase sequences were generated using the Siemens Trugene HIV 1 Genotyping System. Subtypes were determined using web-based genotyping tools. There were 1579 new diagnoses [615 (39%) female and 964 (61%) male], of which 1060 had HIV-1 RNA specimens available for sequencing. Of sequenced samples, HIV-1 subtype B accounted for 50% overall, decreasing from 55.1% in 2004 to 49.5% in 2008. In addition, subtype B accounted for more than 80% of Irish-born individuals and more than 90% of Irish-born injection drug users and men who have sex with men. Subtype C was the second most prevalent in the overall cohort, accounting for 25%, although it accounted for only 6.1% of Irish-born individuals, with no evidence of in country transmission. The prevalence of non-subtype B HIV-1 infection in Ireland is increasing. However, these appear primarily to be imported infections not yet circulating within traditional Irish risk groups. Enhanced HIV-1 molecular epidemiology surveillance is required to monitor the spread of HIV-1, to inform future public health policy, and to ultimately control the HIV-1 epidemic in Ireland.
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Affiliation(s)
- Cillian F. De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Allison Waters
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Ciara M. Regan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Jane O'Halloran
- Department of Infectious Diseases, Mater Misericordiae Hospital, Dublin, Ireland
| | - Gillian Farrell
- Department of GU Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Colm Bergin
- Department of GU Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - William G. Powderly
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - William W. Hall
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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Dunford L, Carr MJ, Dean J, Waters A, Nguyen LT, Ta Thi TH, Thi LAB, Do HD, Thi TTD, Nguyen HT, Diem Do TT, Luu QP, Connell J, Coughlan S, Nguyen HT, Hall WW, Nguyen Thi LA. Hepatitis C virus in Vietnam: high prevalence of infection in dialysis and multi-transfused patients involving diverse and novel virus variants. PLoS One 2012; 7:e41266. [PMID: 22916104 PMCID: PMC3419252 DOI: 10.1371/journal.pone.0041266] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/19/2012] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) is a genetically diverse pathogen infecting approximately 2–3% of the world's population. Herein, we describe results of a large, multicentre serological and molecular epidemiological study cataloguing the prevalence and genetic diversity of HCV in five regions of Vietnam; Ha Noi, Hai Phong, Da Nang, Khanh Hoa and Can Tho. Individuals (n = 8654) with varying risk factors for infection were analysed for the presence of HCV Ab/Ag and, in a subset of positive specimens, for HCV RNA levels (n = 475) and genotype (n = 282). In lower risk individuals, including voluntary blood donors, military recruits and pregnant women, the prevalence of infection was 0.5% (n = 26/5250). Prevalence rates were significantly higher (p<0.001) in intravenous drug users (IDUs; 55.6%, n = 556/1000), dialysis patients (26.6%, n = 153/575) commercial sex workers (CSWs; 8.7%, n = 87/1000), and recipients of multiple blood transfusions (6.0%, n = 32/529). The prevalence of HCV in dialysis patients varied but remained high in all regions (11–43%) and was associated with the receipt of blood transfusions [OR: 2.08 (1.85–2.34), p = 0.001], time from first transfusion [OR: 1.07 (1.01–1.13), p = 0.023], duration of dialysis [OR: 1.31 (1.19–1.43), p<0.001] and male gender [OR: 1.60 (1.06–2.41), p = 0.026]. Phylogenetic analysis revealed high genetic diversity, particularly amongst dialysis and multi-transfused patients, identifying subtypes 1a (33%), 1b (27%), 2a (0.4%), 3a (0.7%), 3b (1.1%), 6a (18.8%), 6e (6.0%), 6h (4.6%), 6l (6.4%) and 2 clusters of novel genotype 6 variants (2.1%). HCV genotype 1 predominated in Vietnam (60%, n = 169/282) but the proportion of infections attributable to genotype 1 varied between regions and risk groups and, in the Southern part of Vietnam, genotype 6 viruses dominated in dialysis and multi-transfused patients (73.9%). This study confirms a high prevalence of HCV infection in Vietnamese IDUs and, notably, reveals high levels of HCV infection associated with dialysis and blood transfusion.
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Affiliation(s)
- Linda Dunford
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Michael J. Carr
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jonathan Dean
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Allison Waters
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Linh Thuy Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Thu Hong Ta Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Lan Anh Bui Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Huy Duong Do
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Thu Thuy Duong Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Ha Thu Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Trinh Thi Diem Do
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Quynh Phuong Luu
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Jeff Connell
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Suzie Coughlan
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - William W. Hall
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- * E-mail: (WWH); (LANT)
| | - Lan Anh Nguyen Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
- * E-mail: (WWH); (LANT)
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Dunford L, Carr MJ, Dean J, Nguyen LT, Ta Thi TH, Nguyen BT, Connell J, Coughlan S, Nguyen HT, Hall WW, Thi LAN. A multicentre molecular analysis of hepatitis B and blood-borne virus coinfections in Viet Nam. PLoS One 2012; 7:e39027. [PMID: 22720022 PMCID: PMC3374772 DOI: 10.1371/journal.pone.0039027] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B (HBV) infection is endemic in Viet Nam, with up to 8.4 million individuals estimated to be chronically infected. We describe results of a large, multicentre seroepidemiological and molecular study of the prevalence of HBV infection and blood-borne viral coinfections in Viet Nam. Individuals with varying risk factors for infection (n = 8654) were recruited from five centres; Ha Noi, Hai Phong, Da Nang, Khanh Hoa and Can Tho. A mean prevalence rate of 10.7% was observed and levels of HBsAg were significantly higher in injecting drug users (IDUs) (17.4%, n = 174/1000) and dialysis patients (14.3%, n = 82/575) than in lower-risk groups (9.4%; p<0.001). Coinfection with HIV was seen in 28% of HBV-infected IDUs (n = 49/174) and 15.2% of commercial sex workers (CSWs; n = 15/99). HCV infection was present in 89.8% of the HBV-HIV coinfected IDUs (n = 44/49) and 40% of HBV-HIV coinfected CSWs (n = 16/40). Anti-HDV was detected in 10.7% (n = 34/318) of HBsAg positive individuals. Phylogenetic analysis of HBV S gene (n = 187) showed a predominance of genotype B4 (82.6%); genotypes C1 (14.6%), B2 (2.7%) and C5 (0.5%) were also identified. The precore mutation G1896A was identified in 35% of all specimens, and was more frequently observed in genotype B (41%) than genotype C (3%; p<0.0001). In the immunodominant 'a' region of the surface gene, point mutations were identified in 31% (n = 58/187) of sequences, and 2.2% (n = 4/187) and 5.3% (n = 10/187) specimens contained the major vaccine escape mutations G145A/R and P120L/Q/S/T, respectively. 368 HBsAg positive individuals were genotyped for the IL28B SNP rs12979860 and no significant association between the IL28B SNP and clearance of HBsAg, HBV viral load or HBeAg was observed. This study confirms the high prevalence of HBV infection in Viet Nam and also highlights the significant levels of blood-borne virus coinfections, which have important implications for hepatitis-related morbidity and development of effective management strategies.
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Affiliation(s)
- Linda Dunford
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Michael J. Carr
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jonathan Dean
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Linh Thuy Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Thu Hong Ta Thi
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Binh Thanh Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Jeff Connell
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Suzie Coughlan
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - William W. Hall
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- * E-mail: (LANT); (WWH)
| | - Lan Anh Nguyen Thi
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
- * E-mail: (LANT); (WWH)
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Muldoon EG, Coughlan S, Mulcahy F. Cerebrospinal fluid HIV viral load may be detectable, despite serum viral load being undetectable, in patients diagnosed with syphilis. Sex Transm Infect 2012; 88:480. [PMID: 22679100 DOI: 10.1136/sextrans-2012-050549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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De Gascun CF, Waters A, Regan C, O'Halloran J, Farrell G, Coughlan S, Bergin C, Powderly WG, Hall WW. Documented prevalence of HIV type 1 antiretroviral transmitted drug resistance in Ireland from 2004 to 2008. AIDS Res Hum Retroviruses 2012; 28:276-81. [PMID: 21770812 DOI: 10.1089/aid.2011.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1-infected individuals with transmitted HIV drug resistance (TDR) begin antiretroviral therapy (ART) with a lower genetic barrier to resistance and a higher risk of both virological failure and of developing further resistance. TDR surveillance informs HIV-1 public health strategies and first line ART. TDR has not been studied nationally in an Irish population. This study includes all new HIV diagnoses from January 2004 to September 2008 from the National Virus Reference Laboratory, University College Dublin. HIV-1 protease and reverse transcriptase sequences were generated, and resistance mutations identified using the Siemens TRUGENE HIV-1 Genotyping System. Subtypes were determined using web-based genotyping tools. The study comprised 1579 patients. There were 305 new diagnoses in 2004 (173 male; 132 female), 298 in 2005 (175M; 123F), 321 in 2006 (197M; 124F), 297 in 2007 (184M; 113F), and 358 (235M; 123F) in 2008. HIV-1 RNA was sequenced from 158/305 patients in 2004, 199/298 in 2005, 225/321 in 2006, 203/297 in 2007, and 275/358 in 2008. The overall TDR rate was 6.3%, peaking in 2006 at 10.4% and declining to 5.3% in 2008. The majority of TDR was seen in Irish born individuals with HIV-1 subtype B infection. The TDR rate in Ireland is comparatively low. Thus, a health technology assessment is required to ascertain the most cost effective use of genotypic antiretroviral resistance testing (GART) in the future: the current approach of performing baseline GART on all new diagnoses, or perhaps a more targeted approach that focuses on patients commencing nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART.
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Affiliation(s)
- Cillian F. De Gascun
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Allison Waters
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Ciara Regan
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jane O'Halloran
- Department of Infectious Diseases, Mater Misericordiae Hospital, Dublin, Ireland
| | - Gillian Farrell
- Department of Genito-Urinary Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Colm Bergin
- Department of Genito-Urinary Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - William G. Powderly
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - William W. Hall
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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39
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Barret AS, Donnell JO, O'Hora A, Collins C, Coughlan S, Joyce M, Moran J, Waters A, O'Malley A, Domegan L, O'Flanagan D. Effectiveness of 2010/2011 seasonal influenza vaccine in Ireland. Ir Med J 2012; 105:39-42. [PMID: 22455236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We conducted a case-control study to estimate the 2010/2011 trivalent influenza vaccine effectiveness (TIVE) using the Irish general practitioners' influenza sentinel surveillance scheme. Cases were influenza-like illness (ILI) patients with laboratory-confirmed influenza. Controls were ILI patients who tested negative for influenza. Participating sentinel general practitioners (GP) collected swabs from patients presenting with ILI along with their vaccination history and other individual characteristics. The TIVE was computed as (1 - odds ratiofor vaccination) x100%. Of 60 sentinel GP practices, 22 expressed interest in participating in the study and 17 (28%) recruited at least one ILI patient. In the analysis, we included 106 cases and 85 controls. Seven controls (8.2%) and one influenza case (0.9%) had been vaccinated in 2010/2011. The estimated TIVE against any influenza subtype was 89.4% [95% CI: 13.8; 99.8%], suggesting a protective effect against GP-attended laboratory confirmed influenza. This study design could be used to monitor influenza vaccine effectiveness annually but sample size and vaccination coverage should be increased to obtain precise and adjusted estimates.
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Affiliation(s)
- A S Barret
- Health Protection Surveillance Centre, 25-27 Middle Gardiner Street, Dublin 1.
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40
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Wickham BW, Amer PR, Berry DP, Burke M, Coughlan S, Cromie A, Kearney JF, Mc Hugh N, McParland S, O'Connell K. Industrial perspective: capturing the benefits of genomics to Irish cattle breeding. Anim Prod Sci 2012. [DOI: 10.1071/an11166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genomics is a technology for increasing the accuracy with which the genetic merit of young potential breeding animals can be determined. It enables earlier selection decisions, thus reducing generation intervals and gives rise to more rapid annual rates of genetic gain. Recently, the cost of genomics has reduced to the point where it enables breeding-program costs to be reduced substantially. Ireland has been a rapid adopter of genomics technology in its dairy-cattle breeding program, with 40% of dairy-cow artificial inseminations in 2010 being from bulls evaluated using genomic information. This rapid adoption has been facilitated by a comprehensive database of phenotypes and genotypes, strong public funding support for applied genomics research, an international network of collaborators, a short path between research and implementation, an overall selection index which farmers use in making breeding decisions, and a motivated and informed breeding industry. The shorter generation interval possible with genomic selection strategies also allows exploitation of the already accelerating rate of genetic progress in Ireland, because elite young dairy bulls are considerably superior to the small numbers of bulls that entered progeny test 6 years ago. In addition, genomics is having a dramatic impact on the artificial-insemination industry by substantially reducing the cost of entry, the cost of operation, and shifting the focus of breeding from bulls to cows. We believe that the current industry structures must evolve substantially if Irish cattle farmers are to realise the full benefits of genomics and be protected from related risks. Our model for future dairy breeding envisages a small number of ‘next generation research herds’, 1000 ‘bull breeder herds’ and an artificial-insemination sector using 30 new genomically selected bulls per year to breed the bulk of replacements in commercial milk-producing herds. Accurate imputation from a low-density to a higher-density chip is a key element of our strategy to enable dairy farmers to afford access to genomics. This model is capable of delivering high rates of genetic gain, realising cost savings, and protecting against the risks of increased inbreeding and suboptimal breeding goals. Our strategy for exploiting genomic selection for beef breeding is currently focussed on genotyping, using a high-density chip, a training population of greater than 2000 progeny-tested bulls representing all the main beef breeds in Ireland. We recognise the need for a larger training population and are seeking collaboration with organisations in other countries and populations.
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Carr MJ, Kajon AE, Lu X, Dunford L, O'Reilly P, Holder P, De Gascun CF, Coughlan S, Connell J, Erdman DD, Hall WW. Deaths associated with human adenovirus-14p1 infections, Europe, 2009-2010. Emerg Infect Dis 2011; 17:1402-8. [PMID: 21801616 DOI: 10.3201/eid1708.101760] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human adenovirus (HAdV) serotype 14 is rarely identified. However, an emerging variant, termed HAdV-14p1, recently has been described in the United States in association with outbreaks of acute respiratory disease with high rates of illness and death. We retrospectively analyzed specimens confirmed positive for HAdV by immunofluorescence, virus culture, or real-time PCR during July 1, 2009-July 31, 2010, and describe 9 cases of HAdV-14p1 infection with characteristic mutations in the fiber and E1A genes that are phylogenetically indistinguishable from the viruses previously detected in the United States. Three patients died; 2 were immunocompromised, and 1 was an immunocompetent adult. We propose that surveillance should be increased for HAdV-14p1 and recommend that this virus be considered in the differential diagnosis of sudden-onset acute respiratory disease, particularly fatal infections, for which an etiology is not clear.
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Affiliation(s)
- Michael J Carr
- National Virus Reference Laboratory-University College Dublin, Dublin, Ireland.
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Carr MJ, Kajon AE, Lu X, Dunford L, O'Reilly P, Holder P, De Gascun CF, Coughlan S, Connell J, Erdman DD, Hall WW. Deaths associated with human adenovirus-14p1 infections, Europe, 2009-2010. Emerg Infect Dis 2011. [PMID: 21801616 PMCID: PMC3381588 DOI: 10.3201/1708.101760] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Michael J Carr
- National Virus Reference Laboratory-University College Dublin, Dublin, Ireland.
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Schaffer K, Hassan J, Staines A, Coughlan S, Holder P, Tuite G, McCormick AP, Traynor O, Hall WW, Connell J. Surveillance of Epstein-Barr virus loads in adult liver transplantation: associations with age, sex, posttransplant times, and transplant indications. Liver Transpl 2011; 17:1420-6. [PMID: 21837744 DOI: 10.1002/lt.22406] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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] [Indexed: 12/11/2022]
Abstract
Epstein-Barr virus (EBV)-associated posttransplant lymphoproliferative disorder (PTLD) is a life-threatening complication after adult orthotopic liver transplantation (AOLT). Besides EBV and immunosuppression, relatively little is known about the pretransplant clinical parameters associated with the risk of PTLD, and the benefit of using EBV surveillance to predict EBV-associated disease in AOLT patients is uncertain. The aims of this single-center study were to monitor EBV viral loads (VLs) in AOLT patients and to investigate any associations with age, sex, cytomegalovirus (CMV) serostatus, posttransplant times, and indications for transplantation. 1275 blood samples that were collected from 197 AOLT patients 1 day to more than 15 years after transplantation were investigated with quantitative polymerase chain reaction for EBV and CMV DNA. Seventy-two percent of the patients had EBV DNAemia less than 100 days after transplantation without clinical manifestations. No association was observed between the EBV copy numbers and the time since transplantation. EBV DNAemia was weakly associated with male sex but was not associated with age, CMV serostatus, or indications for AOLT. The highest EBV VL levels were observed in patients who presented with congenital liver diseases, whereas patients with viral hepatitis maintained high EBV VLs after transplantation. None of the patients developed PTLD during the study period; however, 3 patients presented with EBV-associated diseases. In conclusion, EBV DNAemia is common in AOLT patients, and routine EBV surveillance has limited value for predicting EBV-associated morbidity or mortality.
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Affiliation(s)
- Kirsten Schaffer
- Department of Microbiology, St. Vincent's University Hospital, Dublin, Ireland.
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Nicolay N, McDermott R, Kelly M, Gorby M, Prendergast T, Tuite G, Coughlan S, McKeown P, Sayers G. Potential role of asymptomatic kitchen food handlers during a food-borne outbreak of norovirus infection, Dublin, Ireland, March 2009. Euro Surveill 2011; 16:19931. [PMID: 21813080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Affiliation(s)
- N Nicolay
- Health Protection Surveillance Centre, Dublin, Ireland.
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Nicolay N, McDermott R, Kelly M, Gorby M, Prendergast T, Tuite G, Coughlan S, McKeown P, Sayers G. Potential role of asymptomatic kitchen food handlers during a food-borne outbreak of norovirus infection, Dublin, Ireland, March 2009. Euro Surveill 2011. [DOI: 10.2807/ese.16.30.19931-en] [Citation(s) in RCA: 20] [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] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- N Nicolay
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- Health Protection Surveillance Centre, Dublin, Ireland
| | - R McDermott
- Department of Public Health, Health Service Executive, Dublin, Ireland
| | - M Kelly
- Environmental Health Office, Health Service Executive, Dublin, Ireland
| | - M Gorby
- Environmental Health Office, Health Service Executive, Dublin, Ireland
| | - T Prendergast
- Environmental Health Office, Health Service Executive, Dublin, Ireland
| | - G Tuite
- National Virus Reference Laboratory (NVRL), Dublin, Ireland
| | - S Coughlan
- National Virus Reference Laboratory (NVRL), Dublin, Ireland
| | - P McKeown
- Health Protection Surveillance Centre, Dublin, Ireland
| | - G Sayers
- Department of Public Health, Health Service Executive, Dublin, Ireland
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Dean J, Ta Thi TH, Dunford L, Carr MJ, Nguyen LT, Coughlan S, Connell J, Nguyen HT, Hall WW, Nguyen Thi LA. Prevalence of HIV type 1 antiretroviral drug resistance mutations in Vietnam: a multicenter study. AIDS Res Hum Retroviruses 2011; 27:797-801. [PMID: 21366425 DOI: 10.1089/aid.2011.0013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of HIV-1 drug resistance mutations (DRMs) was determined for a cross-section of individuals (n=8654) in five centers across Vietnam (Hanoi, Hai Phong, Da Nang, Khanh Hoa, and Can Tho) between 2008 and 2009. Following serological screening for HIV infection, HIV-1 viral load was determined, using an in-house real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay. Samples with quantifiable viral loads [all either commercial sex workers (CSW) or intravenous drug users (IDU)] underwent DRM analysis. Sequences were obtained for 92 treatment-naive individuals, the majority of whom were infected with HIV-1 CRF01_AE (99%), with one instance of subtype A1 also detected. DRMs were detected in seven treatment-naive individuals (7.6%). The most common DRMs observed were M184V, V75A/M, M41L, and K65R (NRTI) and K103N, G190A, and Y181C (NNRTI). Overall, the data from this first multicenter survey of DRMs in Vietnam indicate that the problem of transmitted drug resistance is of major concern in the highest-risk groups of IDU and CSW.
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Affiliation(s)
- Jonathan Dean
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Thu Hong Ta Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Linda Dunford
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Michael J. Carr
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Linh Thuy Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Suzie Coughlan
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Jeff Connell
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - William W. Hall
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Lan Anh Nguyen Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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O’Flanagan D, O’Donnell J, Domegan L, Fitzpatrick F, Connell J, Coughlan S, De Gascun C, Carr MJ. First reported cases of human adenovirus serotype 14p1 infection, Ireland, October 2009 to July 2010. Euro Surveill 2011. [DOI: 10.2807/ese.16.08.19801-en] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first nine confirmed cases of human adenovirus 14p1 infection (HAdV-14p1), identified at different locations in Ireland between October 2009 and July 2010. These were the first notifications in Ireland and all were sporadic cases. Following these notifications, the Health Protection Surveillance Centre set up an enhanced surveillance system for HAdV-14p1infection. Seven cases were male and five were aged less than one year. Three patients died, giving a case fatality rate of 33%. It should be noted that cases presented here were diagnosed on presentation to hospital and may represent the severe end of the spectrum of HAdV 14 disease in Ireland.
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Affiliation(s)
- D O’Flanagan
- Health Protection Surveillance Centre, Dublin, Ireland
| | - J O’Donnell
- Health Protection Surveillance Centre, Dublin, Ireland
| | - L Domegan
- Health Protection Surveillance Centre, Dublin, Ireland
| | - F Fitzpatrick
- Health Protection Surveillance Centre, Dublin, Ireland
| | - J Connell
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - S Coughlan
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - C De Gascun
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - M J Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
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48
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O'Flanagan D, O'Donnell J, Domegan L, Fitzpatrick F, Connell J, Coughlan S, De Gascun C, Carr MJ. First reported cases of human adenovirus serotype 14p1 infection, Ireland, October 2009 to July 2010. Euro Surveill 2011; 16:19801. [PMID: 21371411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
We report the first nine confirmed cases of human adenovirus 14p1 infection (HAdV-14p1), identified at different locations in Ireland between October 2009 and July 2010. These were the first notifications in Ireland and all were sporadic cases. Following these notifications, the Health Protection Surveillance Centre set up an enhanced surveillance system for HAdV-14p1 infection. Seven cases were male and five were aged less than one year. Three patients died, giving a case fatality rate of 33%. It should be noted that cases presented here were diagnosed on presentation to hospital and may represent the severe end of the spectrum of HAdV 14 disease in Ireland.
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MESH Headings
- Adenovirus Infections, Human/diagnosis
- Adenovirus Infections, Human/drug therapy
- Adenovirus Infections, Human/epidemiology
- Adenovirus Infections, Human/virology
- Adenoviruses, Human/classification
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adult
- Anti-Bacterial Agents/therapeutic use
- Child
- Child, Preschool
- Comorbidity
- Female
- Fluorescent Antibody Technique
- Humans
- Infant
- Infant, Newborn
- Ireland/epidemiology
- Male
- Middle Aged
- Polymerase Chain Reaction
- Population Surveillance
- Sequence Analysis, DNA
- Serotyping
- Treatment Outcome
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Affiliation(s)
- D O'Flanagan
- Health Protection Surveillance Centre, Dublin, Ireland
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Lonergan RM, Carr MJ, De Gascun CF, Costelloe LF, Waters A, Coughlan S, Duggan M, Doyle K, Jordan S, Hutchinson MW, Hall WW, Tubridy NJ. Reactivation of BK polyomavirus in patients with multiple sclerosis receiving natalizumab therapy. J Neurovirol 2010; 15:351-9. [PMID: 19670070 DOI: 10.3109/13550280903131923] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natalizumab therapy in multiple sclerosis has been associated with JC polyomavirus-induced progressive multifocal leucoencephalopathy. We hypothesized that natalizumab may also lead to reactivation of BK, a related human polyomavirus capable of causing morbidity in immunosuppressed groups. Patients with relapsing remitting multiple sclerosis treated with natalizumab were prospectively monitored for reactivation of BK virus in blood and urine samples, and for evidence of associated renal dysfunction. In this cohort, JC and BK DNA in blood and urine; cytomegalovirus (CMV) DNA in blood and urine; CD4 and CD8 T-lymphocyte counts and ratios in peripheral blood; and renal function were monitored at regular intervals. BK subtyping and noncoding control region sequencing was performed on samples demonstrating reactivation. Prior to commencement of natalizumab therapy, 3 of 36 patients with multiple sclerosis (8.3%) had BK viruria and BK reactivation occurred in 12 of 54 patients (22.2%). BK viruria was transient in 7, continuous in 2 patients, and persistent viruria was associated with transient viremia. Concomitant JC and CMV viral loads were undetectable. CD4:CD8 ratios fluctuated, but absolute CD4 counts did not fall below normal limits. In four of seven patients with BK virus reactivation, transient reductions in CD4 counts were observed at onset of BK viruria: these resolved in three of four patients on resuppression of BK replication. No renal dysfunction was observed in the cohort. BK virus reactivation can occur during natalizumab therapy; however, the significance in the absence of renal dysfunction is unclear. We propose regular monitoring for BK reactivation or at least for evidence of renal dysfunction in patients receiving natalizumab.
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Affiliation(s)
- Roisin M Lonergan
- Department of Neurology, St Vincent's University Hospital, Elm Park, Dublin, Ireland.
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Vercauteren J, Wensing AMJ, van de Vijver DAMC, Albert J, Balotta C, Hamouda O, Kücherer C, Struck D, Schmit JC, Asjö B, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Horban A, Korn K, Kostrikis L, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Riva C, Ruiz L, Salminen M, Schuurman R, Sonnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher CAB. Transmission of drug-resistant HIV-1 is stabilizing in Europe. J Infect Dis 2009; 200:1503-8. [PMID: 19835478 DOI: 10.1086/644505] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The SPREAD Programme investigated prospectively the time trend from September 2002 through December 2005 of transmitted drug resistance (TDR) among 2793 patients in 20 European countries and in Israel with newly diagnosed human immunodeficiency virus type 1 (HIV-1) infection. The overall prevalence of TDR was 8.4% (225 of 2687 patients; 95% confidence interval [CI], 7.4%-9.5%), the prevalence of nucleoside reverse-transcriptase inhibitor (NRTI) resistance was 4.7% (125 of 2687 patients; 95% CI, 3.9%-5.5%), the prevalence of nonucleoside reverse-transcriptase inhibitor (NNRTI) resistance was 2.3% (62 of 2687 patients; 95% CI, 1.8%-2.9%), and the prevalence of protease inhibitor (PI) resistance was 2.9% (79 of 2687 patients; 95% CI, 2.4%-3.6%). There was no time trend in the overall TDR or in NRTI resistance, but there was a statistically significant decrease in PI resistance (P = .04) and in NNRTI resistance after an initial increase (P = .02). We found that TDR appears to be stabilizing in Europe, consistent with recent reports of decreasing drug resistance and improved viral suppression in patients treated for HIV-1 infection.
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