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Zheng SY, Wang LL, Ren L, Luo J, Liao W, Liu EM. Epidemiological analysis and follow-up of human rhinovirus infection in children with asthma exacerbation. J Med Virol 2017; 90:219-228. [PMID: 28500687 PMCID: PMC7167043 DOI: 10.1002/jmv.24850] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 04/19/2017] [Indexed: 12/20/2022]
Abstract
To determine the prevalence of human rhinovirus (HRV) infection in children with acute asthma exacerbations, investigation of HRV viral load and severity of asthma exacerbations is also required. Nasopharyngeal aspirates and swabs were collected and assessed for respiratory viruses. HRV-positive samples were sequenced to identify types and determine viral load. Outpatients with asthma exacerbations underwent follow-up evaluations, their swabs were collected and clinical outcomes were recorded at their next clinic visit 4 weeks later. One hundred forty-three inpatients and 131 outpatients, including 88 patients with asthma exacerbations and 43 controls with stable asthma were recruited. HRV-A was mainly detected in September and February (45.5% and 33.3%, respectively), while HRV-C was mainly detected in November and April (70.0% and 55.6%, respectively). HRV-C was the primary type and was primarily found in inpatients with severe asthma exacerbations. HRV-A viral load in the group of inpatients with severe exacerbations was higher than in the mild and moderate groups (P < 0.001 and P = 0.022). The HRV-A viral load of both inpatients and outpatients was higher than that of HRV-C (P < 0.001 and P = 0.036). The main genotypes were HRV-C53 and HRV-A20 among inpatients, and this genotype caused more severe clinical manifestations. HRV persisted for no more than 4 weeks, and their symptoms or signs of disease were well-controlled well. HRV-C was most frequently detected in asthma exacerbations. HRV-A with high viral load led to severe asthma exacerbations.
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Affiliation(s)
- Shou-Yan Zheng
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Li-Li Wang
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Luo Ren
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Jian Luo
- Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Liao
- Department of Pediatrics, Southwest Hospital of The Third Military Medical University, Chongqing, China
| | - En-Mei Liu
- Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing, China
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52
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Zhou Y, Jiang S, Li KY, Lo ECM, Gao X. Association between oral health and upper respiratory tract infection among children. Int Dent J 2017; 68:122-128. [PMID: 28905361 DOI: 10.1111/idj.12335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The oral cavity is a potential reservoir for respiratory pathogens. This longitudinal study investigated the association between upper respiratory tract infection (URI) and oral health among children. METHODS A total of 288 children aged 4 years were recruited. Their dental caries and oral hygiene status were clinically determined, using the dmft (decayed, missing and filled teeth) index and the Silness-Löe plaque index. Questionnaires were completed by parents to collect information on the child's socio-demographic background and URI episodes and symptoms in the following 12 months. Standard or zero-inflated negative binomial regressions were used to analyse the association between URI and both oral health indicators (dmft and plaque score). RESULTS Some 138 (47.9%) children had URI in 12 months, including 63 (21.9%) and 75 (26.0%) children with 1-2 episodes and ≥3 episodes, respectively. The reported URI episodes fell into two peaks, coinciding with the two influenza peaks in Hong Kong. Significantly a higher dmft was found among children without URI compared with children who had ≥3 URI episodes (1.32 vs. 0.49; P = 0.043). The number of URI episodes was inversely associated with dmft (IRR = 0.851; 95% CI: 0.766-0.945; P = 0.003). There was no significant association between the plaque score and URI (P > 0.05). CONCLUSIONS The children's caries experience was associated with reduced episodes of URI. Whether this inverse association is attributed to the immune response induced by dental caries is yet to be investigated.
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Affiliation(s)
- Ying Zhou
- Department of Preventive Medicine, Health Sciences Center, Shenzhen University, Shenzhen, China
| | - Shan Jiang
- Dental Public Health, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Kar Yan Li
- Centralized Research Laboratories, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Edward Chin Man Lo
- Dental Public Health, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoli Gao
- Dental Public Health, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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53
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Steinke JW, Borish L. Immune Responses in Rhinovirus-Induced Asthma Exacerbations. Curr Allergy Asthma Rep 2017; 16:78. [PMID: 27796793 DOI: 10.1007/s11882-016-0661-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acute asthma exacerbations are responsible for urgent care visits and hospitalizations; they interfere with school and work productivity, thereby driving much of the morbidity and mortality associated with asthma. Approximately 80 to 85 % of asthma exacerbations in children, adolescents, and less frequently adults are associated with viral upper respiratory tract viral infections, and rhinovirus (RV) accounts for ∼60-70 % of these virus-associated exacerbations. Evidence suggests that it is not the virus itself but the nature of the immune response to RV that drives this untoward response. In particular, evidence supports the concept that RV acts to exacerbate an ongoing allergic inflammatory response to environmental allergens present at the time of the infection. The interaction of the ongoing IgE- and T cell-mediated response to allergen superimposed on the innate and adaptive immune responses to the virus and how this leads to triggering of an asthma exacerbation is discussed.
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Affiliation(s)
- John W Steinke
- Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA.,Carter Immunology Center, University of Virginia Health System, Charlottesville, VA, USA.,Asthma and Allergic Disease Center, University of Virginia Health System, Charlottesville, VA, 22908-1355, USA
| | - Larry Borish
- Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA. .,Department of Microbiology, University of Virginia Health System, Charlottesville, VA, USA. .,Carter Immunology Center, University of Virginia Health System, Charlottesville, VA, USA. .,Asthma and Allergic Disease Center, University of Virginia Health System, Charlottesville, VA, 22908-1355, USA.
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54
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Annamalay A, Le Souëf P. Viral-Bacterial Interactions in Childhood Respiratory Tract Infections. VIRAL INFECTIONS IN CHILDREN, VOLUME I 2017. [PMCID: PMC7122469 DOI: 10.1007/978-3-319-54033-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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55
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Chang EH, Willis AL, McCrary HC, Noutsios GT, Le CH, Chiu AG, Mansfield CJ, Reed DR, Brooks SG, Adappa ND, Palmer JN, Cohen NG, Stern DA, Guerra S, Martinez FD. Association between the CDHR3 rs6967330 risk allele and chronic rhinosinusitis. J Allergy Clin Immunol 2016; 139:1990-1992.e2. [PMID: 27923563 DOI: 10.1016/j.jaci.2016.10.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/15/2016] [Accepted: 10/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Eugene H Chang
- Department of Otolaryngology, University of Arizona, Tucson, Ariz.
| | - Amanda L Willis
- Department of Otolaryngology, University of Arizona, Tucson, Ariz
| | - Hilary C McCrary
- Department of Otolaryngology, University of Arizona, Tucson, Ariz
| | | | - Christopher H Le
- Department of Otolaryngology, University of Arizona, Tucson, Ariz
| | - Alexander G Chiu
- Department of Otolaryngology, University of Arizona, Tucson, Ariz
| | | | | | - Steven G Brooks
- Department of Otolaryngology, University of Pennsylvania, Philadelphia, Pa
| | - Nithin D Adappa
- Department of Otolaryngology, University of Pennsylvania, Philadelphia, Pa
| | - James N Palmer
- Department of Otolaryngology, University of Pennsylvania, Philadelphia, Pa
| | - Noam G Cohen
- Monell Chemical Senses Center, Philadelphia, Pa; Department of Otolaryngology, University of Pennsylvania, Philadelphia, Pa; Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pa
| | - Debra A Stern
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
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56
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Bochkov YA, Watters K, Basnet S, Sijapati S, Hill M, Palmenberg AC, Gern JE. Mutations in VP1 and 3A proteins improve binding and replication of rhinovirus C15 in HeLa-E8 cells. Virology 2016; 499:350-360. [PMID: 27743961 PMCID: PMC5110265 DOI: 10.1016/j.virol.2016.09.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 11/21/2022]
Abstract
Viruses in the rhinovirus C species (RV-C) can cause severe respiratory illnesses in children including pneumonia and asthma exacerbations. A transduced cell line (HeLa-E8) stably expressing the CDHR3-Y529 receptor variant, supports propagation of RV-C after infection. C15 clinical or recombinant isolates replicate in HeLa-E8, however progeny yields are lower than those of related strains of RV-A and RV-B. Serial passaging of C15 in HeLa-E8 resulted in stronger cytopathic effects and increased (≥10-fold) virus binding to cells and progeny yields. The adaptation was acquired by two mutations which increased binding (VP1 T125K) and replication (3A E41K), respectively. A similar 3A mutation engineered into C2 and C41 cDNAs also improved viral replication (2-8 fold) in HeLa but the heparan sulfate mediated cell-binding enhancement by the VP1 change was C15-specific. The findings now enable large-scale cost-effective C15 production by infection and the testing of RV-C infectivity by plaque assay.
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Affiliation(s)
- Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA.
| | - Kelly Watters
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarmila Basnet
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Shakher Sijapati
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Marchel Hill
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ann C Palmenberg
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
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57
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Annamalay AA, Jroundi I, Bizzintino J, Khoo SK, Zhang G, Lehmann D, Laing IA, Gern J, Goldblatt J, Mahraoui C, Benmessaoud R, Moraleda C, Bassat Q, Le Souëf P. Rhinovirus C is associated with wheezing and rhinovirus A is associated with pneumonia in hospitalized children in Morocco. J Med Virol 2016; 89:582-588. [PMID: 27677921 PMCID: PMC7166858 DOI: 10.1002/jmv.24684] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2016] [Indexed: 12/03/2022]
Abstract
Human rhinovirus (RV) is commonly associated with severe acute lower respiratory infections (ALRI) in children. We aimed to describe the distribution of RV species and associations between RV species and clinical features in children hospitalized with clinically severe pneumonia (CSP) in Morocco. Nasopharyngeal aspirates (NPAs) were collected from 700 children, 2–59 months of age, admitted with CSP to the Hôpital d'Enfants de Rabat in Morocco. At least one respiratory virus was identified in 92% of children, of which RV was the most common (53%). PCR assays, sequencing, and phylogenetic tree analyses were carried out on 183 RV‐positive NPAs to determine RV species and genotypes. Of 157 successfully genotyped NPAs, 60 (38.2%) were RV‐A, 8 (5.1%) were RV‐B, and 89 (56.7%) were RV‐C. Wheezing and cyanosis were more common in RV‐C‐positive than RV‐A‐positive children (80.9% vs. 56.7%; P = 0.001 for wheezing and 10.1% vs. 0%; P = 0.011 for cyanosis). Physician's discharge diagnosis of pneumonia was more frequent among RV‐A‐positive (40.0%) than RV‐C‐positive children (20.2%; P = 0.009). RV‐A and RV‐C showed distinct seasonal patterns. Our findings suggest that RV‐C is associated with wheezing illness while RV‐A is associated with pneumonia. J. Med. Virol. 89:582–588, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alicia A Annamalay
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Imane Jroundi
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Unit of Training and Research in Public Health, School of Medicine and Pharmacy of Rabat, University Mohamed V, Rabat, Morocco.,École Nationale de Santé Publique (ENSP), Ministère de la Santé, Rabat, Morocco
| | - Joelene Bizzintino
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Siew-Kim Khoo
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Guicheng Zhang
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia.,School of Public Health, Curtin University, Perth, Australia
| | - Deborah Lehmann
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Ingrid A Laing
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - James Gern
- Universityof Wisconsin-Madison, Madison, Wisconsin
| | - Jack Goldblatt
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Chafiq Mahraoui
- Centre Hôpitalier Universitaire (CHU) Ibn Sina, Rabat, Morocco.,Faculté de Médecine et de Pharmacie de Rabat, Rabat, Morocco
| | - Rachid Benmessaoud
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Cinta Moraleda
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Peter Le Souëf
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
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58
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Lee S, Nguyen MT, Currier MG, Jenkins JB, Strobert EA, Kajon AE, Madan-Lala R, Bochkov YA, Gern JE, Roy K, Lu X, Erdman DD, Spearman P, Moore ML. A polyvalent inactivated rhinovirus vaccine is broadly immunogenic in rhesus macaques. Nat Commun 2016; 7:12838. [PMID: 27653379 PMCID: PMC5036149 DOI: 10.1038/ncomms12838] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/05/2016] [Indexed: 11/09/2022] Open
Abstract
As the predominant aetiological agent of the common cold, human rhinovirus (HRV) is the leading cause of human infectious disease. Early studies showed that a monovalent formalin-inactivated HRV vaccine can be protective, and virus-neutralizing antibodies (nAb) correlated with protection. However, co-circulation of many HRV types discouraged further vaccine efforts. Here, we test the hypothesis that increasing virus input titres in polyvalent inactivated HRV vaccine may result in broad nAb responses. We show that serum nAb against many rhinovirus types can be induced by polyvalent, inactivated HRVs plus alhydrogel (alum) adjuvant. Using formulations up to 25-valent in mice and 50-valent in rhesus macaques, HRV vaccine immunogenicity was related to sufficient quantity of input antigens, and valency was not a major factor for potency or breadth of the response. Thus, we have generated a vaccine capable of inducing nAb responses to numerous and diverse HRV types.
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Affiliation(s)
- Sujin Lee
- Department of Pediatrics, Emory University, Atlanta, Georgia 30322, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
| | - Minh Trang Nguyen
- Department of Pediatrics, Emory University, Atlanta, Georgia 30322, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
| | - Michael G Currier
- Department of Pediatrics, Emory University, Atlanta, Georgia 30322, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
| | - Joe B Jenkins
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Elizabeth A Strobert
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Adriana E Kajon
- Infectious Disease Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108, USA
| | - Ranjna Madan-Lala
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53792, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53792, USA.,Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53792, USA
| | - Krishnendu Roy
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xiaoyan Lu
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Dean D Erdman
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Paul Spearman
- Department of Pediatrics, Emory University, Atlanta, Georgia 30322, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
| | - Martin L Moore
- Department of Pediatrics, Emory University, Atlanta, Georgia 30322, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
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59
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Abstract
Allergy and viral respiratory infections have long been recognized as two of the most important risk factors for exacerbations of asthma. These observations have raised questions regarding potential interactions between these two important risk factors. For example, does allergy diminish the antiviral response, thereby promoting exacerbations of asthma? Alternately, do viral respiratory infections potentiate ongoing allergic inflammation in the airway? The answers to these questions are likely to have implications regarding the prevention and treatment of exacerbations of asthma. This article reviews that clinical evidence linking viral infections and allergy to exacerbations of asthma, reviews potential interactions between these two risk factors, and discusses possible application of new insights in virus/allergen interactions to the prevention and treatment of exacerbations of asthma.
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60
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Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
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Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
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61
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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] [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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62
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Ratnamohan VM, Zeng F, Donovan L, MacIntyre CR, Kok J, Dwyer DE. Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia. Influenza Other Respir Viruses 2016; 10:493-503. [PMID: 27383422 PMCID: PMC5059946 DOI: 10.1111/irv.12404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2016] [Indexed: 01/09/2023] Open
Abstract
Background Human rhinoviruses (HRV) cause a wide spectrum of disease, ranging from a mild influenza‐like illness (ILI) to severe respiratory infection. Molecular epidemiological data are limited for HRV circulating in the Southern Hemisphere. Objectives To identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, from 2006 to 2009. Methods Combined nose and throat swabs or nasopharyngeal aspirates collected from individuals with ILI were tested for HRV using real‐time reverse‐transcriptase polymerase chain reaction (RT‐PCR). Sequencing data of 5′UTR and VP4/VP2 coding regions on RT‐PCR‐positive specimens were analysed. Results Human rhinoviruses were detected by real‐time PCR in 20.9% (116/555) of samples tested. Phylogenetic analysis of 5′UTR and VP4/VP2 on HRV‐positive samples was concordant in the grouping of HRV A and B species but not HRV C species. Eighty per cent (16/20) of sequences that grouped as HRV C in the VP4/VP2 tree clustered as HRV A, alongside some previously described C strains as subspecies C/A. Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5′UTR tree, and one sequence showed identity to different HRV A strains in the two genes. The prevalence of HRV C and C/A species was greater in paediatric compared to adult patients (47.9% vs 25.5%, P = .032). Conclusion Human rhinoviruses are a common cause of respiratory infections, and HRV C is present in the Southern Hemisphere. Sequencing of multiple HRV regions may be necessary to determine exact phylogenetic relationships.
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Affiliation(s)
- Vigneswary M Ratnamohan
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia
| | - Frank Zeng
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia
| | - Linda Donovan
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia
| | - Chandini R MacIntyre
- School of Public Health and Community Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia. .,Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. .,Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia.
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia.,Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia
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Fawkner-Corbett DW, Khoo SK, Duarte CM, Bezerra PGM, Bochkov YA, Gern JE, Le Souef PN, McNamara PS. Rhinovirus-C detection in children presenting with acute respiratory infection to hospital in Brazil. J Med Virol 2016; 88:58-63. [PMID: 26100591 PMCID: PMC4682890 DOI: 10.1002/jmv.24300] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 01/28/2023]
Abstract
Human rhinovirus (RV) is a common cause of acute respiratory infection (ARI) in children. We aimed to characterize the clinical and demographic features associated with different RV species detected in children attending hospital with ARI, from low‐income families in North‐east Brazil. Nasopharyngeal aspirates were collected from 630 children <5 years with ARI. Clinical diagnosis and disease severity were also recorded. Samples were analyzed by multiplex PCR for 18 viral and atypical bacterial pathogens; RV positive samples underwent partial sequencing to determine species and type. RV was the fourth commonest pathogen accounting for 18.7% of pathogens detected. RV was commonly detected in children with bronchiolitis, pneumonia, and asthma/episodic viral wheeze (EVW). Species and type were assigned in 112 cases (73% RV‐A; 27% RV‐C; 0% RV‐B). Generally, there were no differences in clinical or demographic characteristics between those infected with RV‐A and RV‐C. However, in children with asthma/EVW, RV‐C was detected relatively more frequently than RV‐A (23% vs. 5%; P = 0.04). Our findings highlight RV as a potentially important pathogen in this setting. Generally, clinical and demographic features were similar in children in whom RV‐A and C species were detected. However, RV‐C was more frequently found in children with asthma/EVW than RV‐A. J. Med. Virol. 88:58–63, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Siew Kim Khoo
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Carminha M Duarte
- Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), Recife, Brazil
| | | | - Yury A Bochkov
- Department of Paediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Wisconsin
| | - James E Gern
- Department of Paediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Wisconsin
| | - Peter N Le Souef
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Paul S McNamara
- Institute of Child Health, Alder Hey Children's Hospital, Liverpool, United Kingdom
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64
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Annamalay AA, Abbott S, Sikazwe C, Khoo SK, Bizzintino J, Zhang G, Laing I, Chidlow GR, Smith DW, Gern J, Goldblatt J, Lehmann D, Green RJ, Le Souëf PN. Respiratory viruses in young South African children with acute lower respiratory infections and interactions with HIV. J Clin Virol 2016; 81:58-63. [PMID: 27317881 PMCID: PMC7106452 DOI: 10.1016/j.jcv.2016.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 01/29/2023]
Abstract
BACKGROUND Human rhinovirus (RV) is the most common respiratory virus and has been associated with frequent and severe acute lower respiratory infections (ALRI). The prevalence of RV species among HIV-infected children in South Africa is unknown. OBJECTIVES To describe the prevalence of respiratory viruses, including RV species, associated with HIV status and other clinical symptoms in children less than two years of age with and without ALRI in Pretoria, South Africa. STUDY DESIGN Nasopharyngeal aspirates were collected from 105 hospitalized ALRI cases and 53 non-ALRI controls less than two years of age. HIV status was determined. Common respiratory viruses were identified by PCR, and RV species and genotypes were identified by semi-nested PCR, sequencing and phylogenetic tree analyses. RESULTS Respiratory viruses were more common among ALRI cases than controls (83.8% vs. 69.2%; p=0.041). RV was the most commonly identified virus in cases with pneumonia (45.6%) or bronchiolitis (52.1%), regardless of HIV status, as well as in controls (39.6%). RV-A was identified in 26.7% of cases and 15.1% of controls while RV-C was identified in 21.0% of cases and 18.9% of controls. HIV-infected children were more likely to be diagnosed with pneumonia than bronchiolitis (p<0.01). RSV was not identified in any HIV-infected cases (n=15) compared with 30.6% of HIV-uninfected cases (n=85, p=0.013), and was identified more frequently in bronchiolitis than in pneumonia cases (43.8% vs. 12.3%; p<0.01). CONCLUSIONS RV-A and RV-C are endemic in South African children and HIV infection may be protective against RSV and bronchiolitis.
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Affiliation(s)
- Alicia A Annamalay
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - Salome Abbott
- Division of Paediatric Pulmonology, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Chisha Sikazwe
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Perth, Australia
| | - Siew-Kim Khoo
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Joelene Bizzintino
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Guicheng Zhang
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; School of Public Health, Curtin University, Perth, Australia
| | - Ingrid Laing
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Glenys R Chidlow
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Perth, Australia
| | - David W Smith
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Perth, Australia
| | - James Gern
- University of Wisconsin-Madison, Madison, USA
| | - Jack Goldblatt
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Deborah Lehmann
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Robin J Green
- Division of Paediatric Pulmonology, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Peter N Le Souëf
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
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Annamalay AA, Lanaspa M, Khoo SK, Madrid L, Acácio S, Zhang G, Laing IA, Gern J, Goldblatt J, Bizzintino J, Lehmann D, Le Souëf PN, Bassat Q. Rhinovirus species and clinical features in children hospitalised with pneumonia from Mozambique. Trop Med Int Health 2016; 21:1171-80. [PMID: 27353724 PMCID: PMC7169728 DOI: 10.1111/tmi.12743] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Objectives To describe the prevalence of human rhinovirus (RV) species in children hospitalised with pneumonia in Manhiça, Mozambique, and the associations between RV species and demographic, clinical and laboratory features. Methods Nasopharyngeal aspirates were collected from children 0 to 10 years of age (n = 277) presenting to Manhiça District Hospital with clinical pneumonia. Blood samples were collected for HIV and malaria testing, blood culture and full blood counts, and a chest X‐ray was performed. A panel of common respiratory viruses was investigated using two independent multiplex RT‐PCR assays with primers specific for each virus and viral type. RV species and genotypes were identified by seminested PCR assays, sequencing and phylogenetic tree analyses. Results At least one respiratory virus was identified in 206 (74.4%) children hospitalised with clinical pneumonia. RV was the most common virus identified in both HIV‐infected (17 of 38, 44.7%) and HIV‐uninfected (74 of 237, 31.2%; P = 0.100) children. RV‐A was the most common RV species identified (47 of 275, 17.0%), followed by RV‐C (35/275, 12.6%) and RV‐B (8/275, 2.9%). Clinical presentation of the different RV species was similar and overlapping, with no particular species being associated with specific clinical features. Conclusions RV‐A and RV‐C were the most common respiratory viruses identified in children hospitalised with clinical pneumonia in Manhiça. Clinical presentation of RV‐A and RV‐C was similar and overlapping.
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Affiliation(s)
- Alicia A Annamalay
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Miguel Lanaspa
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.,ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Siew-Kim Khoo
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Lola Madrid
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.,ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Sozinho Acácio
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Guicheng Zhang
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia.,School of Public Health, Curtin University, Perth, WA, Australia
| | - Ingrid A Laing
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - James Gern
- University of Wisconsin-Madison, Madison, WI, USA
| | - Jack Goldblatt
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - Joelene Bizzintino
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Deborah Lehmann
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Peter N Le Souëf
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - Quique Bassat
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.,ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Bochkov YA, Gern JE. Rhinoviruses and Their Receptors: Implications for Allergic Disease. Curr Allergy Asthma Rep 2016; 16:30. [PMID: 26960297 DOI: 10.1007/s11882-016-0608-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human rhinoviruses (RVs) are picornaviruses that can cause a variety of illnesses including the common cold, lower respiratory tract illnesses such as bronchitis and pneumonia, and exacerbations of asthma. RVs are classified into three species, RV-A, B, and C, which include over 160 types. They utilize three major types of cellular membrane glycoproteins to gain entry into the host cell: intercellular adhesion molecule 1 (ICAM-1) (the majority of RV-A and all RV-B), low-density lipoprotein receptor (LDLR) family members (12 RV-A types), and cadherin-related family member 3 (CDHR3) (RV-C). CDHR3 is a member of cadherin superfamily of transmembrane proteins with yet unknown biological function, and there is relatively little information available about the mechanisms of RV-C interaction with CDHR3. A coding single nucleotide polymorphism (rs6967330) in CDHR3 could promote RV-C infections and illnesses in infancy, which could in turn adversely affect the developing lung to increase the risk of asthma. Further studies are needed to determine how RV infections contribute to pathogenesis of asthma and to develop the optimal treatment approach to control asthma exacerbations.
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Affiliation(s)
- Yury A Bochkov
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.
| | - James E Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
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67
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Lee HG, William T, Menon J, Ralph AP, Ooi EE, Hou Y, Sessions O, Yeo TW. Tuberculous meningitis is a major cause of mortality and morbidity in adults with central nervous system infections in Kota Kinabalu, Sabah, Malaysia: an observational study. BMC Infect Dis 2016; 16:296. [PMID: 27306100 PMCID: PMC4910197 DOI: 10.1186/s12879-016-1640-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Central nervous system (CNS) infections are a significant contributor to morbidity and mortality globally. However, most published studies have been conducted in developed countries where the epidemiology and aetiology differ significantly from less developed areas. Additionally, there may be regional differences due to variation in the socio-economic levels, public health services and vaccination policies. Currently, no prospective studies have been conducted in Sabah, East Malaysia to define the epidemiology and aetiology of CNS infections. A better understanding of these is essential for the development of local guidelines for diagnosis and management. METHODS We conducted a prospective observational cohort study in patients aged 12 years and older with suspected central nervous system infections at Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia between February 2012 and March 2013. Cerebrospinal fluid was sent for microscopy, biochemistry, bacterial and mycobacterial cultures, Mycobacterium tuberculosis polymerase chain reaction (PCR), and multiplex and MassCode PCR for various viral and bacterial pathogens. RESULTS A total of 84 patients with clinically suspected meningitis and encephalitis were enrolled. An aetiological agent was confirmed in 37/84 (44 %) of the patients. The most common diagnoses were tuberculous meningitis (TBM) (41/84, 48.8 %) and cryptococcal meningoencephalitis (14/84, 16.6 %). Mycobacterium tuberculosis was confirmed in 13/41 (31.7 %) clinically diagnosed TBM patients by cerebrospinal fluid PCR or culture. The acute case fatality rate during hospital admission was 16/84 (19 %) in all patients, 4/43 (9 %) in non-TBM, and 12/41 (29 %) in TBM patients respectively (p = 0.02). CONCLUSION TBM is the most common cause of CNS infection in patients aged 12 years or older in Kota Kinabalu, Sabah, Malaysia and is associated with high mortality and morbidity. Further studies are required to improve the management and outcome of TBM.
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Affiliation(s)
- Heng Gee Lee
- Department of Medicine, The Infectious Disease Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia
| | - Timothy William
- Department of Medicine, The Infectious Disease Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia.,Jesselton Medical Centre, Kota Kinabalu, Sabah, Malaysia
| | - Jayaram Menon
- Department of Medicine, The Infectious Disease Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia
| | - Anna P Ralph
- Menzies School of Health Research, Darwin, Australia
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Yan'an Hou
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - October Sessions
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Tsin Wen Yeo
- Menzies School of Health Research, Darwin, Australia. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore. .,Communicable Disease Centre, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore.
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68
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Abstract
Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.
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Affiliation(s)
- Angela L Rasmussen
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA.
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69
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Khaw YS, Chan YF, Jafar FL, Othman N, Chee HY. Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia. Front Microbiol 2016; 7:543. [PMID: 27199901 PMCID: PMC4851184 DOI: 10.3389/fmicb.2016.00543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/04/2016] [Indexed: 11/17/2022] Open
Abstract
Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection.
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Affiliation(s)
- Yam Sim Khaw
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Faizatul Lela Jafar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Norlijah Othman
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
| | - Hui Yee Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
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70
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Lau SKP, Yip CCY, Zhao PSH, Chow WN, To KKW, Wu AKL, Yuen KY, Woo PCY. Enterovirus D68 Infections Associated with Severe Respiratory Illness in Elderly Patients and Emergence of a Novel Clade in Hong Kong. Sci Rep 2016; 6:25147. [PMID: 27121085 PMCID: PMC4848506 DOI: 10.1038/srep25147] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Despite the recent emergence of enterovirus D68 (EV-D68), its clinical impact on adult population is less well defined. To better define the epidemiology of EV-D68, 6,800 nasopharyngeal aspirates (NPAs) from 2010–2014 were subject to EV-D68 detection by RT-PCR and sequencing of 5′UTR and partial VP1. EV-D68 was detected in 30 (0.44%) NPAs from 22 children and 8 adults/elderlies. Sixteen patients (including five elderly) (53%) had pneumonia and 13 (43%) patients were complicated by small airway disease exacerbation. Phylogenetic analysis of VP1, 2C and 3D regions showed four distinct lineages of EV-D68, clade A1, A2, B1 and B3, with adults/elderlies exclusively infected by clade A2. The potentially new clade, B3, has emerged in 2014, while strains closely related to recently emerged B1 strains in the United States were also detected as early as 2011 in Hong Kong. The four lineages possessed distinct aa sequence patterns in BC and DE loops. Amino acid residues 97 and 140, within BC and DE-surface loops of VP1 respectively, were under potential positive selection. EV-D68 infections in Hong Kong usually peak in spring/summer, though with a delayed autumn/winter peak in 2011. This report suggests that EV-D68 may cause severe respiratory illness in adults/elderlies with underlying co-morbidities.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Pyrear Su-Hui Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kelvin K W To
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Alan K L Wu
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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Milanoi S, Ongus JR, Gachara G, Coldren R, Bulimo W. Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008. Influenza Other Respir Viruses 2016; 10:185-91. [PMID: 26822469 PMCID: PMC4814864 DOI: 10.1111/irv.12373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 11/29/2022] Open
Abstract
Background Human rhinoviruses (HRVs) are a well‐established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized. Objectives This study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008. Methods A total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza‐like (ILI) symptoms. Real‐time RT‐PCR was employed for preliminary HRV detection. HRV‐positive samples were amplified using RT‐PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis. Results Twenty‐five percent of the samples tested positive for HRV. Phylogenetic analysis revealed that the Kenyan HRVs clustered into three main species comprising HRV‐A (54%), HRV‐B (12%), and HRV‐C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level. Conclusion These results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRVs contributed substantially to influenza‐like illness in Kenya in 2008.
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Affiliation(s)
- Sylvia Milanoi
- College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Juliette R Ongus
- College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - George Gachara
- Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya
| | - Rodney Coldren
- Department of Emerging Infectious Diseases (DEID), United States Medical Research Directorate- Kenya, Nairobi, Kenya.,A Special Field Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Wallace Bulimo
- Department of Emerging Infectious Diseases (DEID), United States Medical Research Directorate- Kenya, Nairobi, Kenya.,A Special Field Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Department of Biochemistry, University of Nairobi, Nairobi, Kenya
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72
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Royston L, Tapparel C. Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC. Viruses 2016; 8:E16. [PMID: 26761027 PMCID: PMC4728576 DOI: 10.3390/v8010016] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/09/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022] Open
Abstract
Rhinoviruses (RVs) and respiratory enteroviruses (EVs) are leading causes of upper respiratory tract infections and among the most frequent infectious agents in humans worldwide. Both are classified in the Enterovirus genus within the Picornaviridae family and they have been assigned to seven distinct species, RV-A, B, C and EV-A, B, C, D. As viral infections of public health significance, they represent an important financial burden on health systems worldwide. However, the lack of efficient antiviral treatment or vaccines against these highly prevalent pathogens prevents an effective management of RV-related diseases. Current advances in molecular diagnostic techniques have revealed the presence of RV in the lower respiratory tract and its role in lower airway diseases is increasingly reported. In addition to an established etiological role in the common cold, these viruses demonstrate an unexpected capacity to spread to other body sites under certain conditions. Some of these viruses have received particular attention recently, such as EV-D68 that caused a large outbreak of respiratory illness in 2014, respiratory EVs from species C, or viruses within the newly-discovered RV-C species. This review provides an update of the latest findings on clinical and fundamental aspects of RV and respiratory EV, including a summary of basic knowledge of their biology.
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Affiliation(s)
- Léna Royston
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Caroline Tapparel
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
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L'Huillier AG, Kaiser L, Petty TJ, Kilowoko M, Kyungu E, Hongoa P, Vieille G, Turin L, Genton B, D'Acremont V, Tapparel C. Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa. Viruses 2015; 7:6412-23. [PMID: 26670243 PMCID: PMC4690871 DOI: 10.3390/v7122948] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022] Open
Abstract
Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.
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Affiliation(s)
- Arnaud G L'Huillier
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Laurent Kaiser
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Tom J Petty
- Swiss Institute of Bioinformatics, Centre Medical Universitraire, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - Mary Kilowoko
- Amana Regional Referral Hospital, PO box 25411, Dar es Salaam TZ-02, United Republic of Tanzania.
| | - Esther Kyungu
- St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania.
| | - Philipina Hongoa
- St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania.
| | - Gaël Vieille
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Lara Turin
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Blaise Genton
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland.
- Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland.
| | - Valérie D'Acremont
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland.
- Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland.
| | - Caroline Tapparel
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
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Leguia M, Loyola S, Rios J, Juarez D, Guevara C, Silva M, Prieto K, Wiley M, Kasper MR, Palacios G, Bausch DG. Full Genomic Characterization of a Saffold Virus Isolated in Peru. Pathogens 2015; 4:816-25. [PMID: 26610576 PMCID: PMC4693166 DOI: 10.3390/pathogens4040816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/17/2015] [Indexed: 11/16/2022] Open
Abstract
While studying respiratory infections of unknown etiology we detected Saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. The full viral genome recovered by deep sequencing showed 98% identity to a previously described Saffold strain isolated in Japan. Phylogenetic analysis confirmed the Peruvian Saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in Asia. This is the first documented case report of Saffold virus in Peru and the only complete genomic characterization of a Saffold-3 isolate from the Americas.
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Affiliation(s)
- Mariana Leguia
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Steev Loyola
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Jane Rios
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Diana Juarez
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | | | - Maria Silva
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Michael Wiley
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | | | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Daniel G Bausch
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
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Wertheim HFL, Nadjm B, Thomas S, Agustiningsih, Malik S, Nguyen DNT, Vu DVT, Van Nguyen K, Van Nguyen CV, Nguyen LT, Tran ST, Phung TBT, Nguyen TV, Hien TT, Nguyen UH, Taylor W, Truong KH, Ha TM, Chokephaibulkit K, Farrar J, Wolbers M, de Jong MD, van Doorn HR, Puthavathana P. Viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in Thailand, Vietnam and Indonesia. Influenza Other Respir Viruses 2015; 9:315-322. [PMID: 25980749 PMCID: PMC4605413 DOI: 10.1111/irv.12326] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 01/15/2023] Open
Abstract
Background Influenza constitutes a leading cause of morbidity and mortality worldwide. There is limited information about the aetiology of infection presenting clinically as influenza in hospitalised adults and children in South-East Asia. Such data are important for future management of respiratory infections. Objectives To describe the aetiology of infection presenting clinically as influenza in those hospitalised in South-East Asia. Methods Respiratory specimens archived from July 2008 to June 2009 from patients hospitalised with suspected influenza from Indonesia, Thailand and Vietnam were tested for respiratory viruses and atypical bacteria by polymerase chain reaction. Results A total of 1222 patients’ samples were tested. Of 1222, 776 patients (63·5%) were under the age of 5. Viruses detected included rhinoviruses in 229 of 1222 patients (18·7%), bocaviruses in 200 (16·4%), respiratory syncytial viruses in 144 (11·8%), parainfluenza viruses in 140 (11·5%; PIV1: 32; PIV2: 12; PIV3: 71; PIV4: 25), adenovirus in 102 (8·4%), influenza viruses in 93 (7·6%; influenza A: 77; influenza B: 16) and coronaviruses in 23 (1·8%; OC43: 14; E229: 9). Bacterial pathogens were Mycoplasma pneumoniae (n = 33, 2·7%), Chlamydophila psittaci (n = 2), C. pneumoniae (n = 1), Bordetella pertussis (n = 1) and Legionella pneumophila (n = 2). Overall, in-hospital case fatality rate was 29 of 1222 (2·4%). Conclusion Respiratory viruses were the most commonly detected pathogens in patients hospitalised with a clinical suspicion of influenza. Rhinovirus was the most frequently detected virus, and M. pneumoniae, the most common atypical bacterium. The low number of detected influenza viruses demonstrates a low benefit for empirical oseltamivir therapy, unless during an influenza outbreak.
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Affiliation(s)
- Heiman F L Wertheim
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Behzad Nadjm
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Sherine Thomas
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam
| | - Agustiningsih
- National Institute of Health Research and Development, Jakarta, Indonesia
| | - Suhud Malik
- National Institute of Health Research and Development, Jakarta, Indonesia
| | - Diep Ngoc Thi Nguyen
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam
| | - Dung Viet Tien Vu
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | - Tran Tinh Hien
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Uyen Hanh Nguyen
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam
| | - Walter Taylor
- Mahidol Oxford University Clinical Research Unit, Bangkok, Thailand
| | | | - Tuan Manh Ha
- Children's Hospital No 2, Ho Chi Minh City, Vietnam
| | | | - Jeremy Farrar
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Marcel Wolbers
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Menno D de Jong
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - H Rogier van Doorn
- Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Hanoi, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
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76
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Miller EK, Linder J, Kraft D, Johnson M, Lu P, Saville BR, Williams JV, Griffin MR, Talbot HK. Hospitalizations and outpatient visits for rhinovirus-associated acute respiratory illness in adults. J Allergy Clin Immunol 2015; 137:734-43.e1. [PMID: 26255695 DOI: 10.1016/j.jaci.2015.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/15/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Rhinovirus is linked to asthma exacerbations and chronic obstructive pulmonary disease exacerbations in adults. The severity and rates of rhinovirus acute respiratory illnesses (ARIs) in adults are uncertain. OBJECTIVES We sought to determine rhinovirus-associated ARI rates in adults presenting for care in multiple settings and identify factors associated with rhinovirus detection. METHODS This prospective, population-based cohort enrolled Tennessee residents 18 years or older in the emergency department (ED), outpatient clinics, or hospitalized for ARI from December 2008 to May 2010. Nasal/throat swabs were collected and tested for rhinovirus and other viruses by using RT-PCR. Rates of ED visits and hospitalizations were calculated and rhinovirus-positive and rhinovirus-negative patients were compared. RESULTS Among 2351 enrollees, rhinovirus was detected in 247 (11%). There were 7 rhinovirus-associated ED visits and 3 hospitalizations per 1000 adults annually. Patients with rhinovirus, compared with virus-negative ARI, were more likely to present with wheezing (odds ratio [OR], 1.7; 95% CI, 1.23-2.35; P < .001), to be a current smoker (OR, 2.31; 95% CI, 1.68-3.19) or live with a smoker (OR, 1.72; 95% CI, 1.10-2.67), have a history of chronic respiratory disease (OR, 1.61; 95% CI, 1.17-2.22), and were less likely to be hospitalized versus seen in the outpatient setting (OR, 0.58; 95% CI, 0.41-0.83). CONCLUSIONS Rhinovirus is associated with a substantial number of ED visits and hospitalizations for ARIs in adults. There may be modifiable factors that can reduce the likelihood of presenting with rhinovirus-associated ARIs.
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Affiliation(s)
- E Kathryn Miller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn.
| | - Jodell Linder
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - David Kraft
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Monika Johnson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Pengcheng Lu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Benjamin R Saville
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pa
| | - Marie R Griffin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Department of Healthy Policy, Vanderbilt University Medical Center, Nashville, Tenn; Mid-South Geriatric Research Education and Clinical Center and Clinical Research Center of Excellence, VA TN Valley Health Care System, Nashville, Tenn
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
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77
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Jacobs SE, Lamson DM, Soave R, Guzman BH, Shore TB, Ritchie EK, Zappetti D, Satlin MJ, Leonard JP, van Besien K, Schuetz AN, Jenkins SG, George KS, Walsh TJ. Clinical and molecular epidemiology of human rhinovirus infections in patients with hematologic malignancy. J Clin Virol 2015; 71:51-8. [PMID: 26370315 PMCID: PMC4750469 DOI: 10.1016/j.jcv.2015.07.309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/22/2015] [Accepted: 07/25/2015] [Indexed: 10/26/2022]
Abstract
BACKGROUND Human rhinoviruses (HRVs) are common causes of upper respiratory tract infection (URTI) in hematologic malignancy (HM) patients. Predictors of lower respiratory tract infection (LRTI) including the impact of HRV species and types are poorly understood. OBJECTIVES This study aims to describe the clinical and molecular epidemiology of HRV infections among HM patients. STUDY DESIGN From April 2012-March 2013, HRV-positive respiratory specimens from symptomatic HM patients were molecularly characterized by analysis of partial viral protein 1 (VP1) or VP4 gene sequence. HRV LRTI risk-factors and outcomes were analyzed using multivariable logistic regression. RESULTS One hundred and ten HM patients presented with HRV URTI (n=78) and HRV LRTI (n=32). Hypoalbuminemia (OR 3.0; 95% CI, 1.0-9.2; p=0.05) was independently associated with LRTI, but other clinical and laboratory markers of host immunity did not differ between patients with URTI versus LRTI. Detection of bacterial co-pathogens was common in LRTI cases (25%). Among 92 typeable respiratory specimens, there were 58 (64%) HRV-As, 12 (13%) HRV-Bs, and 21 (23%) HRV-Cs, and one Enterovirus 68. LRTI rates among HRV-A (29%), HRV-B (17%), and HRV-C (29%) were similar. HRV-A infections occurred year-round while HRV-B and HRV-C infections clustered in the late fall and winter. CONCLUSIONS HRVs are associated with LRTI in HM patients. Illness severity is not attributable to specific HRV species or types. The frequent detection of bacterial co-pathogens in HRV LRTIs further substantiates the hypothesis that HRVs predispose to bacterial superinfection of the lower airways, similar to that of other community-acquired respiratory viruses.
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Affiliation(s)
- Samantha E Jacobs
- Division of Infectious Diseases, Weill Cornell Medical Center, New York, NY, USA.
| | - Daryl M Lamson
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Weill Cornell Medical Center, New York, NY, USA
| | | | - Tsiporah B Shore
- Division of Hematology and Medical Oncology, Weill Cornell Medical Center, New York, NY, USA
| | - Ellen K Ritchie
- Division of Hematology and Medical Oncology, Weill Cornell Medical Center, New York, NY, USA
| | - Dana Zappetti
- Division of Pulmonary and Critical Care Medicine, New York Presbyterian Hospital/ Weill Cornell Medical College, New York, NY, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medical Center, New York, NY, USA
| | - John P Leonard
- Division of Hematology and Medical Oncology, Weill Cornell Medical Center, New York, NY, USA
| | - Koen van Besien
- Division of Hematology and Medical Oncology, Weill Cornell Medical Center, New York, NY, USA
| | - Audrey N Schuetz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Kirsten St George
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Thomas J Walsh
- Division of Infectious Diseases, Weill Cornell Medical Center, New York, NY, USA
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Abstract
Human rhinoviruses (HRVs) are positive-stranded RNA viruses belonging to the Enterovirus genus in the family of Picornaviridae. Identification of the specific strain in HRV disease has been difficult because the traditional serological method is insensitive, labor intensive, and cumbersome. With the fast progress in molecular biological technique, more sensitive and faster molecular methods have been developed, such as polymerase chain reaction (PCR), reverse transcriptase (RT)-PCR, and real-time RT-PCR. To improve the technique for defining the links between illnesses and specific strains of HRV, we developed RT-PCR specific for HRV as routine base. A multiplex RT-PCR that simultaneously identifies 12 respiratory viruses including HRV is also routinely used in our lab. Here we have described the specific steps of methods for identification of HRV from clinical samples, such as sample preparation, isolation of total RNA, nested-RT-PCR for HRV, Seeplex® RV15 ACE Detection method, gel electrophoresis, how to use the QIAxcel® capillary electrophoresis system, and results interpretation.
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79
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Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Proc Natl Acad Sci U S A 2015; 112:5485-90. [PMID: 25848009 DOI: 10.1073/pnas.1421178112] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Members of rhinovirus C (RV-C) species are more likely to cause wheezing illnesses and asthma exacerbations compared with other rhinoviruses. The cellular receptor for these viruses was heretofore unknown. We report here that expression of human cadherin-related family member 3 (CDHR3) enables the cells normally unsusceptible to RV-C infection to support both virus binding and replication. A coding single nucleotide polymorphism (rs6967330, C529Y) was previously linked to greater cell-surface expression of CDHR3 protein, and an increased risk of wheezing illnesses and hospitalizations for childhood asthma. Compared with wild-type CDHR3, cells transfected with the CDHR3-Y529 variant had about 10-fold increases in RV-C binding and progeny yields. We developed a transduced HeLa cell line (HeLa-E8) stably expressing CDHR3-Y529 that supports RV-C propagation in vitro. Modeling of CDHR3 structure identified potential binding sites that could impact the virus surface in regions that are highly conserved among all RV-C types. Our findings identify that the asthma susceptibility gene product CDHR3 mediates RV-C entry into host cells, and suggest that rs6967330 mutation could be a risk factor for RV-C wheezing illnesses.
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80
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Feldman AS, He Y, Moore ML, Hershenson MB, Hartert TV. Toward primary prevention of asthma. Reviewing the evidence for early-life respiratory viral infections as modifiable risk factors to prevent childhood asthma. Am J Respir Crit Care Med 2015; 191:34-44. [PMID: 25369458 DOI: 10.1164/rccm.201405-0901pp] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A first step in primary disease prevention is identifying common, modifiable risk factors that contribute to a significant proportion of disease development. Infant respiratory viral infection and childhood asthma are the most common acute and chronic diseases of childhood, respectively. Common clinical features and links between these diseases have long been recognized, with early-life respiratory syncytial virus (RSV) and rhinovirus (RV) lower respiratory tract infections (LRTIs) being strongly associated with increased asthma risk. However, there has long been debate over the role of these respiratory viruses in asthma inception. In this article, we systematically review the evidence linking early-life RSV and RV LRTIs with asthma inception and whether they could therefore be targets for primary prevention efforts.
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Affiliation(s)
- Amy S Feldman
- 1 Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, and Center for Asthma Research, Vanderbilt University School of Medicine, Nashville, Tennessee
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81
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A systematic approach to novel virus discovery in emerging infectious disease outbreaks. J Mol Diagn 2015; 17:230-41. [PMID: 25746799 PMCID: PMC7106266 DOI: 10.1016/j.jmoldx.2014.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/03/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
The discovery of novel viruses is of great importance to human health-both in the setting of emerging infectious disease outbreaks and in disease syndromes of unknown etiology. Despite the recent proliferation of many efficient virus discovery methods, careful selection of a combination of methods is important to demonstrate a novel virus, its clinical associations, and its relevance in a timely manner. The identification of a patient or an outbreak with distinctive clinical features and negative routine microbiological workup is often the starting point for virus hunting. This review appraises the roles of culture, electron microscopy, and nucleic acid detection-based methods in optimizing virus discovery. Cell culture is generally slow but may yield viable virus. Although the choice of cell line often involves trial and error, it may be guided by the clinical syndrome. Electron microscopy is insensitive but fast, and may provide morphological clues to choice of cell line or consensus primers for nucleic acid detection. Consensus primer PCR can be used to detect viruses that are closely related to known virus families. Random primer amplification and high-throughput sequencing can catch any virus genome but cannot yield an infectious virion for testing Koch postulates. A systematic approach that incorporates carefully chosen combinations of virus detection techniques is required for successful virus discovery.
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82
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Griggs TF, Bochkov YA, Nakagome K, Palmenberg AC, Gern JE. Production, purification, and capsid stability of rhinovirus C types. J Virol Methods 2015; 217:18-23. [PMID: 25724434 DOI: 10.1016/j.jviromet.2015.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/09/2014] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
Abstract
The rhinovirus C (RV-C) were discovered in 2006 and these agents are an important cause of respiratory morbidity. Little is known about their biology. RV-C15 (C15) can be produced by transfection of recombinant viral RNA into cells and subsequent purification over a 30% sucrose cushion, even though yields and infectivity of other RV-C genotypes with this protocol are low. The goal of this study was to determine whether poor RV-C yields were due to capsid instability, and moreover, to develop a robust protocol suitable for the purification of many RV-C types. Capsid stability assays indicated that virions of RV-C41 (refractory to purification) have similar tolerance for osmotic and temperature stress as RV-A16 (purified readily), although C41 is more sensitive to low pH. Modification to the purification protocol by removing detergent increased the yield of RV-C. Addition of nonfat dry milk to the sucrose cushion increased the virus yield but sacrificed purity of the viral suspension. Analysis of virus distribution following centrifugation indicated that the majority of detectable viral RNA (vRNA) was found in pellets refractory to resuspension. Reduction of the centrifugal force with commiserate increase in spin-time improved the recovery of RV-C for both C41 and C2. Transfection of primary lung fibroblasts (WisL cells) followed by the modified purification protocol further improved yields of infectious C41 and C2. Described herein is a higher yield purification protocol suitable for RV-C types refractory to the standard purification procedure. The findings suggest that aggregation-adhesion problems rather than capsid instability influence RV-C yield during purification.
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Affiliation(s)
- Theodor F Griggs
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, United States; Cellular & Molecular Pathology Graduate Program, University of Wisconsin, Madison, United States; Medical Scientist Training Program, University of Wisconsin, Madison, United States.
| | - Yury A Bochkov
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | - Kazuyuki Nakagome
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | - Ann C Palmenberg
- Institute for Molecular Virology, University of Wisconsin, Madison, United States
| | - James E Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, United States; Cellular & Molecular Pathology Graduate Program, University of Wisconsin, Madison, United States
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Simusika P, Bateman AC, Theo A, Kwenda G, Mfula C, Chentulo E, Monze M. Identification of viral and bacterial pathogens from hospitalized children with severe acute respiratory illness in Lusaka, Zambia, 2011-2012: a cross-sectional study. BMC Infect Dis 2015; 15:52. [PMID: 25888024 PMCID: PMC4391483 DOI: 10.1186/s12879-015-0779-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 01/23/2015] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Morbidity and mortality from respiratory infections are higher in resource-limited countries than developed countries, but limited studies have been conducted in resource-limited settings to examine pathogens from patients with acute respiratory infections. Influenza surveillance has been conducted in Zambia since 2008; however, only 4.3% of patients enrolled in 2011-2012 were positive for influenza. Therefore, we examined non-influenza respiratory pathogens in children with severe acute respiratory illness (SARI) in Zambia, to estimate the scope of disease burden and determine commonly-identified respiratory pathogens. METHODS Two reverse transcriptase polymerase chain reaction (rRT-PCR) methods (single and multiplex) were used to analyze nasopharyngeal and throat swabs collected from SARI cases under five years of age from January 2011 through December 2012. All specimens were negative for influenza by rRT-PCR. The panel of singleplex reactions targeted seven viruses, while the multiplex assay targeted thirty-three bacteria, fungi, and viruses. RESULTS A set of 297 specimens were tested by singleplex rRT-PCR, and a different set of 199 were tested by multiplex rRT-PCR. Using the singleplex assay, 184/297 (61.9%) specimens were positive for one or more viruses. The most prevalent viruses were human rhinovirus (57/297; 19.2%), human adenovirus (50/297; 16.8%), and respiratory syncytial virus (RSV) (45/297; 15.2%). Using multiplex PCR, at least one virus was detected from 167/199 (83.9%) specimens, and at least one bacteria was detected from 197/199 (99.0%) specimens. Cytomegalovirus (415/199; 208.5%) and RSV (67/199; 33.7%) were the most commonly detected viruses, while Streptococcus pneumonie (109/199; 54.8%) and Moraxella catarrhalis (92/199; 46.2%) were the most commonly detected bacteria. CONCLUSIONS Single infections and co-infections of many viruses and bacteria were identified in children with SARI. These results provide an estimate of the prevalence of infection and show which respiratory pathogens are commonly identified in patients. Further studies should investigate causal associations between individual pathogens and SARI.
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Affiliation(s)
- Paul Simusika
- Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia.
| | - Allen C Bateman
- Centre for Infectious Disease Research in Zambia, 34681, Lusaka, Zambia.
| | - Andros Theo
- Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia.
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia.
| | - Christine Mfula
- Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia.
| | - Edward Chentulo
- Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia.
| | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia.
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84
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Loria C, Domm JA, Halasa NB, Heitman E, Miller EK, Xu M, Saville BR, Frangoul H, Williams JV. Human rhinovirus C infections in pediatric hematology and oncology patients. Pediatr Transplant 2015; 19:94-100. [PMID: 25377237 PMCID: PMC4280346 DOI: 10.1111/petr.12383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2014] [Indexed: 12/31/2022]
Abstract
Children with cancer and HSCT recipients are at high risk for common viral infections. We sought to define the viral etiology of ARI and identify risk factors. Nasal wash samples were collected from pediatric hematology-oncology patients and HSCT recipients with ARI during the 2003-2005 winter seasons. Real-time RT-PCR was performed to detect Flu A, influenza B, RSV, PIV 1-3, human MPV, and HRV. HRV specimens were sequenced and genotyped. Seventy-eight samples from 62 children were included. Viruses were detected in 31 of 78 samples (40%). HRV were detected most frequently, in 16 (52%) including five HRVC; followed by seven (22%) RSV, five (16%) Flu A, four (13%) MPV, and two (6%) PIV2. There was a trend toward higher risk of viral infection for children in day care. Only 8% of the study children had received influenza vaccine. HRV, including the recently discovered HRVC, are an important cause of infection in pediatric oncology and HSCT patients. Molecular testing is superior to conventional methods and should be standard of care, as HRV are not detected by conventional methods.
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Affiliation(s)
- Carolina Loria
- Center for Biomedical Ethics and Society, Vanderbilt University School of Medicine, Nashville, TN
| | - Jennifer A. Domm
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Elizabeth Heitman
- Center for Biomedical Ethics and Society, Vanderbilt University School of Medicine, Nashville, TN
| | - E. Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Meng Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN
| | - Benjamin R. Saville
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN
| | - Haydar Frangoul
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - John V. Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN
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85
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Tsatsral S, Xiang Z, Fuji N, Maitsetseg C, Khulan J, Oshitani H, Wang J, Nymadawa P. Molecular Epidemiology of the Human Rhinovirus Infection in Mongolia during 2008-2013. Jpn J Infect Dis 2015; 68:280-7. [PMID: 25672409 DOI: 10.7883/yoken.jjid.2014.090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rhinovirus infections are common in all age groups world-wide, and they occur throughout the year. In this study, we examined 2,689 nasopharyngeal swabs collected in Mongolia during 2008-2013. Human rhinoviruses (HRVs) were detected in 295 (11.0%) samples, and 85 (28.8%) patients were co-infected with other respiratory viruses. HRV was co-detected with bocavirus, human coronavirus, and respiratory syncytial virus in 21 (24.7%), 17 (20.0%), and 14 (16.5%), respectively. We tested 170 (57.6%) of the 295 HRV-positive samples: 117 HRV strains were typed by using the VP4/VP2 method and 53 by using 5' UTR method. We found HVR-A, HVR-C, and HVR-B infections in 80 (47.1%), 76 (44.7%), and 14 (8.2%) samples, respectively.
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86
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Affiliation(s)
- J. E. Gern
- Pediatrics and Medicine; University of Wisconsin-Madison; Madison WI USA
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87
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Ly N, Tokarz R, Mishra N, Sameroff S, Jain K, Rachmat A, An US, Newell S, Harrison DJ, Lipkin WI. Multiplex PCR analysis of clusters of unexplained viral respiratory tract infection in Cambodia. Virol J 2014; 11:224. [PMID: 25514971 PMCID: PMC4280028 DOI: 10.1186/s12985-014-0224-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/05/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Fevers of unknown origin constitute a substantial disease burden in Southeast Asia. In majority of the cases, the cause of acute febrile illness is not identified. METHODS We used MassTag PCR, a multiplex assay platform, to test for the presence of 15 viral respiratory agents from 85 patients with unexplained respiratory illness representing six disease clusters that occurred in Cambodia between 2009 and 2012. RESULTS We detected a virus in 37 (44%) of the cases. Human rhinovirus, the virus detected most frequently, was found in both children and adults. The viruses most frequently detected in children and adults, respectively, were respiratory syncytial virus and enterovirus 68. Sequence analysis indicated that two distinct clades of enterovirus 68 were circulating during this time period. CONCLUSIONS This is the first report of enterovirus 68 in Cambodia and contributes to the appreciation of this virus as an important respiratory pathogen.
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Affiliation(s)
- Nary Ly
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Agus Rachmat
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Ung Sam An
- National Institute of Public Health, Cambodian Ministry of Health, Phnom Penh, Cambodia.
| | - Steven Newell
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Dustin J Harrison
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
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88
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First report of severe parainfluenza virus 4B and rhinovirus C coinfection in a liver transplant recipient treated with immunoglobulin. J Clin Virol 2014; 61:611-4. [PMID: 25453574 DOI: 10.1016/j.jcv.2014.09.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/19/2014] [Accepted: 09/25/2014] [Indexed: 11/22/2022]
Abstract
We describe the first reported case of severe pneumonia due to coinfection by parainfluenza virus type 4B and rhinovirus C in a liver transplant recipient. The patient responded promptly to intravenous immunoglobulin and timely infection control measures prevented spreading of the infections. This report highlights respiratory viral coinfections as a possible cause of severe morbidity in transplant recipients and the importance of efficient molecular diagnostic technologies with major impact on clinical practice in a transplant center. It also describes a potential therapeutic strategy for such patients.
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89
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Linder JE, Plachco TE, Libster R, Miller EK. Sequencing human rhinoviruses: direct sequencing versus plasmid cloning. J Virol Methods 2014; 211:64-9. [PMID: 25286177 DOI: 10.1016/j.jviromet.2014.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 01/08/2023]
Abstract
Human rhinoviruses (RV) are associated with the majority of viral respiratory illnesses in infants, children and adults. Over the last several years, researchers have begun to sequence the many different species and strains of RV in order to determine if certain species were associated with increased disease severity. There are a variety of techniques employed to prepare samples for sequencing. One method utilizes plasmid-cloning, which is expensive and takes several hours to complete. Recently, some investigators have instead used direct sequencing to sequence RV strains, allowing for omission of the time- and labor-intensive cloning step. This study formally compares and contrasts the sequencing results obtained from plasmid-cloning and direct Sanger sequencing of a 500 base pair PCR product covering the VP4/VP2 region of RV. A slightly longer sequence (by 65 base pairs on average) was obtained when specimens were plasmid-cloned, and the sequences were 86% similar. After trimming the extra base pairs from the cloned sequences, the sequences were 99.7% identical. Overall success of directly sequencing samples was similar to that of cloning, 5% on average failed for each technique. Therefore, in many instances, directly sequencing samples may be considered in lieu of the more expensive and time-consuming plasmid-cloning technique.
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Affiliation(s)
- Jodell E Linder
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
| | - Tatyana E Plachco
- Hospital de Pediatria SAMIC Prof. Dr. Juan P Garrahan, Buenos Aires, Argentina; Hospital Materno Infantil Ramon Sarda, Buenos Aires, Argentina.
| | | | - E Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
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90
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Abstract
Human rhinovirus (HRV) infections are now widely accepted as the commonest cause of acute respiratory illnesses (ARIs) in children. Advanced PCR techniques have enabled HRV infections to be identified as causative agents in most common ARIs in childhood including bronchiolitis, acute asthma, pneumonia and croup. However, the long-term implications of rhinovirus infections are less clear. The aim of this review is to examine the relationship between rhinovirus infections and disorders of the lower airways in childhood.
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Affiliation(s)
- D W Cox
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia; Respiratory Department, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - P N Le Souëf
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia; Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia
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91
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McCulloch DJ, Sears MH, Jacob JT, Lyon GM, Burd EM, Caliendo AM, Hill CE, Nix WA, Oberste MS, Kraft CS. Severity of rhinovirus infection in hospitalized adults is unrelated to genotype. Am J Clin Pathol 2014; 142:165-72. [PMID: 25015856 PMCID: PMC4332627 DOI: 10.1309/ajcphikrjc67aazj] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives To determine whether rhinovirus (RV) species is associated with more severe clinical illness in adults. Methods Seventy-two RV-positive viral respiratory samples from adult patients were sequenced and analyzed phylogenetically after reverse transcriptase polymerase chain reaction of the region spanning the VP4 gene and 5′ terminus of the VP2 gene. The clinical features and severity of illness associated with the different RV species were compared. Results Phylogenetic analysis identified three distinct clusters as RV-A (54%), B (11%), or C (35%) species. In an unadjusted model, patients with RV-B infection were significantly more likely to have the composite outcome variable of death or intensive care unit admission (P = .03), but this effect diminished when controlling for patient sex. A logistic model of the relationship between RV species and adverse outcomes produced nonsignificant odds ratios when controlling for patient sex. Conclusions Infection with RV-A or RV-B was associated with greater severity of illness in our adult population; however, the association disappeared after controlling for confounders.
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Affiliation(s)
- Denise J. McCulloch
- Emory University School of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Marti H. Sears
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Jesse T. Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - G. Marshall Lyon
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Eileen M. Burd
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Angela M. Caliendo
- Division of Infectious Diseases, Department of Medicine, Brown University School of Medicine, Providence, RI
| | - Charles E. Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - W. Allan Nix
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
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92
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Abstract
Non-influenza respiratory virus infections are common worldwide and contribute to morbidity and mortality in all age groups. The recently identified Middle East respiratory syndrome coronavirus has been associated with rapidly progressive pneumonia and high mortality rate. Adenovirus 14 has been increasingly recognized in severe acute respiratory illness in both military and civilian individuals. Rhinovirus C and human bocavirus type 1 have been commonly detected in infants and young children with respiratory tract infection and studies have shown a positive correlation between respiratory illness and high viral loads, mono-infection, viremia, and/or serologically-confirmed primary infection.
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Affiliation(s)
- James J Dunn
- Department of Pathology and Laboratory Medicine, Cook Children's Medical Center, 801 Seventh Avenue, Fort Worth, TX 76104, USA.
| | - Melissa B Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Campus Box 7525, Chapel Hill, NC 27599-7525, USA
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93
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Lamson DM, Ramani R, Kleabonas M, Metcalfe M, Humphrey C, St George K. An unusual case of influenza-like illness after yellow fever vaccination. J Clin Virol 2014; 60:67-9. [PMID: 24594082 PMCID: PMC7128991 DOI: 10.1016/j.jcv.2014.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/23/2014] [Accepted: 01/24/2014] [Indexed: 10/25/2022]
Abstract
Yellow fever (YF) is an important public health concern in areas where the disease is endemic. For more than 60 years a highly effective live attenuated vaccine has been available, its widespread use resulting in a dramatic decrease in the number of cases. On rare occasions, YF vaccine can cause mild to severe disease and rare adverse vaccine-associated events have been reported. Additionally, an average viremia of 3-5 days after administration of the YF vaccine has been published. Here we present a case where YF vaccine was isolated in cell culture from a respiratory swab collected from a patient presenting with influenza-like illness. To the best of our knowledge, this is the first report finding replicating YF vaccine in the respiratory sample of a post inoculated individual.
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Affiliation(s)
- Daryl M Lamson
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.
| | - Rama Ramani
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Matthew Kleabonas
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Maureen Metcalfe
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charles Humphrey
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
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94
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Improved molecular typing assay for rhinovirus species A, B, and C. J Clin Microbiol 2014; 52:2461-71. [PMID: 24789198 DOI: 10.1128/jcm.00075-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human rhinoviruses (RVs), comprising three species (A, B, and C) of the genus Enterovirus, are responsible for the majority of upper respiratory tract infections and are associated with severe lower respiratory tract illnesses such as pneumonia and asthma exacerbations. High genetic diversity and continuous identification of new types necessitate regular updating of the diagnostic assays for the accurate and comprehensive detection of circulating RVs. Methods for molecular typing based on phylogenetic comparisons of a variable fragment in the 5' untranslated region were improved to increase assay sensitivity and to eliminate nonspecific amplification of human sequences, which are observed occasionally in clinical samples. A modified set of primers based on new sequence information and improved buffers and enzymes for seminested PCR assays provided higher specificity and sensitivity for virus detection. In addition, new diagnostic primers were designed for unequivocal species and type assignments for RV-C isolates, based on phylogenetic analysis of partial VP4/VP2 coding sequences. The improved assay was evaluated by typing RVs in >3,800 clinical samples. RVs were successfully detected and typed in 99% of the samples that were RV positive in multiplex diagnostic assays.
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95
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Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00203-14. [PMID: 24675858 PMCID: PMC3968336 DOI: 10.1128/genomea.00203-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Human rhinovirus (RV) isolates from the RV-C species are recently discovered infectious agents that are closely linked to asthma and wheezing etiologies in infants. Clinical study samples collected at the University of Wisconsin–Madison describe 41 nearly complete genome sequences representing 21 RV-C genotypes.
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96
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Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
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97
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Rhinoviruses. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7120790 DOI: 10.1007/978-1-4899-7448-8_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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98
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Kaslow RA, Stanberry LR, Le Duc JW. Diagnosis, Discovery and Dissection of Viral Diseases. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7122662 DOI: 10.1007/978-1-4899-7448-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard A. Kaslow
- Department of Epidemiology, University of Alabama, Birmingham School of Public Health, Birmingham, Alabama USA
| | - Lawrence R. Stanberry
- Departmant of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York USA
| | - James W. Le Duc
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas USA
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99
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Kiyota N, Kobayashi M, Tsukagoshi H, Ryo A, Harada S, Kusaka T, Obuchi M, Shimojo N, Noda M, Kimura H. Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012. INFECTION GENETICS AND EVOLUTION 2013; 21:90-102. [PMID: 24200591 DOI: 10.1016/j.meegid.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/25/2013] [Accepted: 10/26/2013] [Indexed: 10/26/2022]
Abstract
We performed detailed genetic analysis of the VP4/VP2 coding region in human rhinovirus species A to C (HRV-ABC) strains detected in patients with a variety of acute respiratory infections in Kumamoto, Japan in the period 2011-12. The phylogenetic tree and evolutionary timescale were obtained by the Bayesian Markov chain Monte Carlo method. Phylogenetic analyses showed that the present HRV-A, -B, and -C strains belonged to 25, 4, and 18 genotypes, respectively. Some new genotypes were confirmed as prevalent strains of HRV-C. An ancestor of the present HRV-ABCs could be dated back to about 20,000 years ago. The present HRV-A and -C strains have wide genetic divergence (pairwise distance >0.2) with rapid evolutionary rates (around 7 × 10(-4) to 4 × 10(-3)substitutions/site/year). Over 100 sites were found to be under negative selection, while no positively selected sites were found in the analyzed region. No evidence of recombination events was found in this region of the present strains. Our results indicate that the present HRV strains have rapidly evolved and subsequently diverged over a long period into multiple genotypes.
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Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Takashi Kusaka
- Maternal Perinatal Center, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Masatsugu Obuchi
- Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
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100
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Tapparel C, Sobo K, Constant S, Huang S, Van Belle S, Kaiser L. Growth and characterization of different human rhinovirus C types in three-dimensional human airway epithelia reconstituted in vitro. Virology 2013; 446:1-8. [DOI: 10.1016/j.virol.2013.06.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/10/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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