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van der Linden L, Bruning AHL, Thomas XV, Minnaar RP, Rebers SPH, Schinkel J, de Jong MD, Pajkrt D, Wolthers KC. A molecular epidemiological perspective of rhinovirus types circulating in Amsterdam from 2007 to 2012. Clin Microbiol Infect 2016; 22:1002.e9-1002.e14. [PMID: 27554204 PMCID: PMC7129042 DOI: 10.1016/j.cmi.2016.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 04/21/2016] [Revised: 07/15/2016] [Accepted: 08/16/2016] [Indexed: 12/03/2022]
Abstract
Rhinoviruses (RVs) are frequently detected respiratory viruses that cause mild common cold symptoms, but may also lead to more severe respiratory tract infections. The large number of RV types, classified into species A, B and C, hampers clear insights into the epidemiology and clinical significance of each RV type. The aim of this study was to map the circulation of RV types in the Amsterdam area. RV-positive nasopharyngeal and oropharyngeal samples, collected from 2007 to 2012 in the Academic Medical Centre (Amsterdam, the Netherlands), were typed based on the sequence of the region coding for capsid proteins VP4 and VP2. RV-A, RV-B and RV-C were found in proportions of of 52.4% (334/637), 11.3% (72/637), and 36.2% (231/637), respectively. We detected 129 of the 167 currently classified types. RVs circulated throughout the entire year with a peak in the autumn and a decline in the summer. Some RV types were observed throughout the entire sampling period and others had a more seasonal pattern. Nine RV-A and four RV-B novel provisionally assigned types were identified. This study provides an insight into the molecular epidemiology of RVs in the Amsterdam area. The RVs circulating are diverse and include several provisionally new types.
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Affiliation(s)
- L van der Linden
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
| | - A H L Bruning
- Department of Paediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - X V Thomas
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - R P Minnaar
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - S P H Rebers
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - J Schinkel
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - M D de Jong
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - D Pajkrt
- Department of Paediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - K C Wolthers
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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Bruning AHL, Thomas XV, van der Linden L, Wildenbeest JG, Minnaar RP, Jansen RR, de Jong MD, Sterk PJ, van der Schee MP, Wolthers KC, Pajkrt D. Clinical, virological and epidemiological characteristics of rhinovirus infections in early childhood: A comparison between non-hospitalised and hospitalised children. J Clin Virol 2015; 73:120-126. [PMID: 26599608 PMCID: PMC7185867 DOI: 10.1016/j.jcv.2015.10.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/21/2015] [Accepted: 10/30/2015] [Indexed: 11/28/2022]
Abstract
Rhinoviruses (RV) frequently cause respiratory tract infections in young children. We evaluated characteristics of RV infections in relation to clinical outcome. In young children clinical outcome was not related to RV species or types. Outcome of RV disease is more likely influenced by multiple (host-specific) factors.
Background Several studies have been published regarding the epidemiology and clinical significance of the different rhinovirus (RV) species (-A, -B and -C). However, data on RV types and the associations with clinical outcome in young children are limited. Here, we investigated the clinical, virological and epidemiological characteristics of RV infections in young children with mild or asymptomatic infection (non-hospitalised children) and in symptomatic young children admitted to the hospital. Objectives The aim of this study was to evaluate associations between different characteristics of RV infections and clinical outcome in young children. Study design RV-infected children were retrospectively selected from a Dutch birth cohort (EUROPA-study) and from hospitalised children admitted to the hospital because of respiratory symptoms. In total 120 RV-typed samples could be selected from 65 non-hospitalised and 49 hospitalised children between November 2009 and December 2012. Results RV-A was the predominant species in both study populations, followed closely by RV-C. RV-B was observed only sporadically. The distribution of the RV species was comparable in non-hospitalised and hospitalised children. In children with respiratory distress who required ICU-admission the distribution of RV species did not differ significantly from the non-hospitalised children. No predominant RV type was present in non-hospitalised nor hospitalised children. However, hospitalised children were younger, had more often an underlying illness, a higher RV load and more frequently a bacterial co-infection. Conclusions Clinical outcome of RV infected young children was not related to RV species or types, but may more likely be influenced by multiple (host-specific) factors.
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Affiliation(s)
- Andrea H L Bruning
- Department of Pediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands.
| | - Xiomara V Thomas
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Lonneke van der Linden
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Joanne G Wildenbeest
- Department of Pediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | - René P Minnaar
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Rogier R Jansen
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Katja C Wolthers
- Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands
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Ho CKY, Welkers MRA, Thomas XV, Sullivan JC, Kieffer TL, Reesink HW, Rebers SPH, de Jong MD, Schinkel J, Molenkamp R. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants. J Virol Methods 2015; 219:28-37. [PMID: 25818622 DOI: 10.1016/j.jviromet.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/09/2023]
Abstract
We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing.
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Affiliation(s)
- Cynthia K Y Ho
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Xiomara V Thomas
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - James C Sullivan
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Tara L Kieffer
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Henk W Reesink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam 1104 AZ, The Netherlands.
| | - Sjoerd P H Rebers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Janke Schinkel
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Richard Molenkamp
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
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Vanhommerig JW, Thomas XV, van der Meer JTM, Geskus RB, Bruisten SM, Molenkamp R, Prins M, Schinkel J. Hepatitis C virus (HCV) antibody dynamics following acute HCV infection and reinfection among HIV-infected men who have sex with men. Clin Infect Dis 2014; 59:1678-85. [PMID: 25186590 DOI: 10.1093/cid/ciu695] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A decline of hepatitis C virus (HCV) antibody titers (anti-HCV), ultimately resulting in seroreversion, has been reported following clearance of viremia in both acute and chronic HCV infection. However, frequency of seroreversion remains unknown in human immunodeficiency virus (HIV)/HCV-coinfected patients. We describe anti-HCV dynamics among HIV-infected men who have sex with men (MSM) following acute HCV infection and reinfection. METHODS Primary acute HCV infection was assumed when a subject was anti-HCV negative prior to the first positive HCV RNA test. Anti-HCV was measured at least annually in 63 HIV-infected MSM, with a median follow-up of 4.0 years (interquartile range [IQR], 2.5-5.7 years). Time from HCV infection to seroconversion, and from seroconversion to seroreversion, was estimated using the Kaplan-Meier method. Longitudinal anti-HCV patterns were studied using a random-effects model to adjust for repeated measures. RESULTS Median time from HCV infection to seroconversion was 74 days (IQR, 47-125 days). Subjects who cleared HCV RNA (n = 36) showed a significant decrease in anti-HCV levels (P < .001). Among 31 subjects with sustained virologic response (SVR), anti-HCV became undetectable during follow-up in 8; cumulative incidence of seroreversion within 3 years after seroconversion was 37% (95% confidence interval, 18%-66%). Eighteen subjects became reinfected during follow-up; this coincided with a subsequent increase in anti-HCV reactivity. CONCLUSIONS A decline of anti-HCV reactivity was associated with HCV RNA clearance. Seroreversion was very common following SVR. Upon reinfection, anti-HCV levels increased again. Monitoring anti-HCV levels might therefore be an effective alternative for diagnosis of HCV reinfection.
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Grady BP, Schinkel J, Thomas XV, Dalgard O. Hepatitis C virus reinfection following treatment among people who use drugs. Clin Infect Dis 2014; 57 Suppl 2:S105-10. [PMID: 23884057 DOI: 10.1093/cid/cit301] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Most new cases of hepatitis C virus (HCV) infections in the developed world are associated with injection drug use. However, treatment for people who inject drugs (PWID) is controversial, as successful treatment risks being followed by new infection. Reinfection after sustained virologic response has been reported, but is the risk so great that treatment should be withheld from this large HCV population? Preliminary evidence suggests that the reinfection incidence is low, but studies to date have been limited by small sample size and few cases of reinfection. In this review, we assess data from studies among PWID of HCV reinfection following treatment to give a reasonable estimate on how frequently reinfection appears and try to characterize those most at risk, The observation that spontaneous clearance of HCV reinfection following treatment occurs is suggestive of a partial protective immunity against persistent infection.
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Affiliation(s)
- Bart P Grady
- Department of Infectious Diseases, Center for Infection and Immunity Amsterdam (CINIMA), Amsterdam, the Netherlands
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de Bruijne J, Thomas XV, Rebers SP, Weegink CJ, Treitel MA, Hughes E, Bergmann JF, de Knegt RJ, Janssen HLA, Reesink HW, Molenkamp R, Schinkel J. Evolutionary dynamics of hepatitis C virus NS3 protease domain during and following treatment with narlaprevir, a potent NS3 protease inhibitor. J Viral Hepat 2013; 20:779-89. [PMID: 24168257 DOI: 10.1111/jvh.12104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 02/03/2013] [Indexed: 12/09/2022]
Abstract
Narlaprevir, a hepatitis C virus (HCV) NS3/4A serine protease inhibitor, has demonstrated robust antiviral activity in a placebo-controlled phase 1 study. To study evolutionary dynamics of resistant variants, the NS3 protease sequence was clonally analysed in thirty-two HCV genotype 1-infected patients following treatment with narlaprevir. Narlaprevir monotherapy was administered for one week (period 1) followed by narlaprevir/pegylated interferon-alpha-2b combination therapy with or without ritonavir (period 2) during two weeks, interrupted by a washout period of one month. Thereafter, all patients initiated pegylated interferon-alpha-2b/ribavirin combination therapy. Longitudinal clonal analysis was performed in those patients with NS3 mutations. After narlaprevir re-exposure, resistance-associated mutations at position V36, T54, R155 and A156 were detected in five patients in >95% of the clones. Narlaprevir retreatment resulted in a 2.58 and 5.06 log10 IU/mL viral load decline in patients with and without mutations, respectively (P=<0.01). After treatment, resistant variants were replaced with wild-type virus within 2-24 weeks in three patients. However, the R155K mutation was still observed 3.1 years after narlaprevir dosing in two patients in 5% and 45% of the viral population. Resistant variants could be detected early during treatment with narlaprevir. A slower viral load decline was observed in those patients with resistance-associated mutations detectable by direct population sequencing. These mutations disappeared within six months following treatment with the exception of R155K mutation, which persisted in two patients.
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Affiliation(s)
- J de Bruijne
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
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Thomas XV, de Bruijne J, Sullivan JC, Kieffer TL, Ho CKY, Rebers SP, de Vries M, Reesink HW, Weegink CJ, Molenkamp R, Schinkel J. Evaluation of persistence of resistant variants with ultra-deep pyrosequencing in chronic hepatitis C patients treated with telaprevir. PLoS One 2012; 7:e41191. [PMID: 22848441 PMCID: PMC3407168 DOI: 10.1371/journal.pone.0041191] [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: 02/20/2012] [Accepted: 06/18/2012] [Indexed: 02/06/2023] Open
Abstract
Background & Aims Telaprevir, a hepatitis C virus NS3/4A protease inhibitor has significantly improved sustained viral response rates when given in combination with pegylated interferon alfa-2a and ribavirin, compared with current standard of care in hepatitis C virus genotype 1 infected patients. In patients with a failed sustained response, the emergence of drug-resistant variants during treatment has been reported. It is unclear to what extent these variants persist in untreated patients. The aim of this study was to assess using ultra-deep pyrosequencing, whether after 4 years follow-up, the frequency of resistant variants is increased compared to pre-treatment frequencies following 14 days of telaprevir treatment. Methods Fifteen patients from 2 previous telaprevir phase 1 clinical studies (VX04-950-101 and VX05-950-103) were included. These patients all received telaprevir monotherapy for 14 days, and 2 patients subsequently received standard of care. Variants at previously well-characterized NS3 protease positions V36, T54, R155 and A156 were assessed at baseline and after a follow-up of 4±1.2 years by ultra-deep pyrosequencing. The prevalence of resistant variants at follow-up was compared to baseline. Results Resistance associated mutations were detectable at low frequency at baseline. In general, prevalence of resistance mutations at follow-up was not increased compared to baseline. Only one patient had a small, but statistically significant, increase in the number of V36M and T54S variants 4 years after telaprevir-dosing. Conclusion In patients treated for 14 days with telaprevir monotherapy, ultra-deep pyrosequencing indicates that long-term persistence of resistant variants is rare.
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Affiliation(s)
- Xiomara V Thomas
- Academic Medical Center, Department of Medical Microbiology, Section of Clinical Virology, Amsterdam, The Netherlands.
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