1
|
Abstract
PURPOSE OF REVIEW The majority of norovirus outbreaks in the United States occur in healthcare facilities. With the growing population of immunocompromised hosts who are in frequent contact with healthcare facilities, norovirus is not only a threat to hospitals and nursing homes but also to these individuals. This review summarizes the impact of norovirus infection on healthcare facilities and immunocompromised hosts. RECENT FINDINGS The natural history of norovirus infection in immunocompromised individuals remains poorly understood. Although host immune responses play a critical role in reducing duration of viral shedding and viral load in norovirus-infected individuals, why some immunocompromised patients spontaneously recover while others develop a chronic and protracted course of illness remains unclear. Norovirus outbreaks occur in healthcare facilities because the virus is highly contagious, resistant to disinfection and efficiently transmitted. The use of real-time metagenomic next-generation sequencing and phylogenetic analyses has provided valuable information on transmission patterns in complex hospital-associated norovirus outbreaks. The development of human intestinal enteroid cultures enables the determination of effectiveness of disinfectants against human noroviruses, circumventing the validity questions with surrogate virus models due to differences in susceptibility to inactivation and disinfectants. SUMMARY Metagenomics next-generation sequencing can enhance our understanding of norovirus transmission and lead to more timely mitigation strategies to curb norovirus outbreaks in healthcare facilities. With new in-vitro cultivation methods for human noroviruses, candidate vaccines and effective antivirals could be available in the near future.
Collapse
|
2
|
Brown JR, Roy S, Shah D, Williams CA, Williams R, Dunn H, Hartley J, Harris K, Breuer J. Norovirus Transmission Dynamics in a Pediatric Hospital Using Full Genome Sequences. Clin Infect Dis 2020; 68:222-228. [PMID: 29800111 PMCID: PMC6321856 DOI: 10.1093/cid/ciy438] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Norovirus is a leading cause of worldwide and nosocomial gastroenteritis. The study aim was to assess the utility of molecular epidemiology using full genome sequences compared to routine infection prevention and control (IPC) investigations. Methods Norovirus genomes were generated from new episodes of norovirus at a pediatric tertiary referral hospital over a 19-month period (n = 182). Phylogeny identified clusters of related sequences that were verified using epidemiological and clinical data. Results Twenty-four clusters of related norovirus sequences (“sequence clusters”) were observed, including 8 previously identified by IPC investigations (“IPC outbreaks”). Seventeen sequence clusters (involving 77/182 patients) were corroborated by epidemiological data (“epidemiologically supported clusters”), suggesting transmission between patients. Linked infections were identified among 44 patients who were missed by IPC investigations. Thirty-three percent of norovirus sequences were linked, suggesting nosocomial transmission; 24% of patients had nosocomial infections from an unknown source; and 43% were norovirus positive on admission. Conclusions We show there are frequent introductions of multiple norovirus strains with extensive onward nosocomial transmission of norovirus in a pediatric hospital with a high proportion of immunosuppressed patients nursed in isolation. Phylogenetic analysis using full genome sequences is more sensitive than classic IPC investigations for identifying linked cases and should be considered when investigating norovirus nosocomial transmission. Sampling of staff, visitors, and the environment may be required for complete understanding of infection sources and transmission routes in patients with nosocomial infections not linked to other patients and among patients with phylogenetically linked cases but no evidence of direct contact.
Collapse
Affiliation(s)
- Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Sunando Roy
- Infection and Immunity, University College London, United Kingdom
| | - Divya Shah
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | | | - Rachel Williams
- Infection and Immunity, University College London, United Kingdom
| | - Helen Dunn
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - John Hartley
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Kathryn Harris
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust.,Infection and Immunity, University College London, United Kingdom
| |
Collapse
|
3
|
Fischer TK, Rasmussen LD, Fonager J. Taking gastro-surveillance into the 21st century. J Clin Virol 2019; 117:43-48. [PMID: 31176211 DOI: 10.1016/j.jcv.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Enteric viruses, particularly rotaviruses and noroviruses, are leading causes of gastroenteritis worldwide. Human rotaviruses are ubiquitous and globally almost every child has been infected by 3-5 years of age. Noroviruses affect people of all ages and is the leading cause of foodborne outbreaks. Rota- and noroviruses account for ˜40% and ˜17% of diarrhea-associated hospitalizations, and ˜200,000 deaths annually respectively, with most deaths occurring in developing countries. Two rotavirus vaccines have currently been implemented in ˜95 countries and several norovirus vaccine candidates are currently in development and/or clinical testing. Surveillance of enteric viruses is an important part of outbreak investigations as well as pre- and post-vaccine impact studies but is even in developed countries often limited to investigation of sporadic cases or comprehensive outbreaks. Conventional methods for enteric virus detection and subtyping relies on standard RT-PCR methods, supplemented with Sanger-sequencing. However, for viruses with even moderate mutationrates, PCR-based-typing of only limited parts of the virus genome is challenging and requires regular update of primers. Full-genomecharacterization technologies based on sequence independent methods based on next generation sequencing (NGS), have demonstrated great potential for enteric virus detection and/or typing in both clinical and environmental samples. However, cost-benefits must balance for such methods to be widely accepted for public health purposes. In Europe as also globally, routine use of NGS-methods for surveillance of enteric viruses is currently limited to few national public health laboratories. What important lessons can be learned from these and what is the future of NGS-based surveillance?
Collapse
Affiliation(s)
- Thea K Fischer
- Department of Clinical Research, Nordsjaellands Hospital, Hilleroed, Denmark; Departments of Infectious Diseases and Global Health, Clinical Institute, University of Southern Denmark, Denmark; National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
| | - Lasse D Rasmussen
- National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research & Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
4
|
Fonager J, Stegger M, Rasmussen LD, Poulsen MW, Rønn J, Andersen PS, Fischer TK. A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants. Sci Rep 2017; 7:813. [PMID: 28400558 PMCID: PMC5429772 DOI: 10.1038/s41598-017-00926-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 03/21/2017] [Indexed: 12/16/2022] Open
Abstract
Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.
Collapse
Affiliation(s)
- Jannik Fonager
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Mille Weismann Poulsen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Rønn
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thea Kølsen Fischer
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Infectious Diseases and Centre for Global health, Clinical Unit, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
5
|
Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers. Appl Environ Microbiol 2017; 83:AEM.03187-16. [PMID: 27940545 DOI: 10.1128/aem.03187-16] [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] [Received: 11/21/2016] [Accepted: 12/01/2016] [Indexed: 11/20/2022] Open
Abstract
Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. IMPORTANCE Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.
Collapse
|
6
|
Nasheri N, Petronella N, Ronholm J, Bidawid S, Corneau N. Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach. Front Microbiol 2017; 8:73. [PMID: 28197136 PMCID: PMC5282449 DOI: 10.3389/fmicb.2017.00073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/11/2017] [Indexed: 01/14/2023] Open
Abstract
Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens.
Collapse
Affiliation(s)
- Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada
| | - Sabah Bidawid
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nathalie Corneau
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| |
Collapse
|
7
|
Bok K, Prevots DR, Binder AM, Parra GI, Strollo S, Fahle GA, Behrle-Yardley A, Johnson JA, Levenson EA, Sosnovtsev SV, Holland SM, Palmore TN, Green KY. Epidemiology of Norovirus Infection Among Immunocompromised Patients at a Tertiary Care Research Hospital, 2010-2013. Open Forum Infect Dis 2016; 3:ofw169. [PMID: 27800529 PMCID: PMC5084716 DOI: 10.1093/ofid/ofw169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 11/13/2022] Open
Abstract
Background. Noroviruses are a major cause of infectious gastroenteritis worldwide, and viruses can establish persistent infection in immunocompromised individuals. Risk factors and transmission in this population are not fully understood. Methods. From 2010 through 2013, we conducted a retrospective review among immunocompromised patients (n = 268) enrolled in research studies at the National Institutes of Health Clinical Center and identified a subset of norovirus-positive patients (n = 18) who provided stool specimens for norovirus genotyping analysis. Results. Norovirus genome was identified by reverse-transcription quantitative polymerase chain reaction in stools of 35 (13%) of the 268 immunocompromised patients tested, and infection prevalence was 21% (11 of 53) in persons with primary immune deficiencies and 12% (20 of 166) among persons with solid tumors or hematologic malignancies. Among 18 patients with norovirus genotyping information, norovirus GII.4 was the most prevalent genotype (14 of 18, 78%). Persistent norovirus infection (≥6 months) was documented in 8 of 18 (44%) individuals. Phylogenetic analysis of the GII.4 capsid protein sequences identified at least 5 now-displaced GII.4 variant lineages, with no evidence of their nosocomial transmission in the Clinical Center. Conclusions. Norovirus was a leading enteric pathogen identified in this immunocompromised population. Both acute and chronic norovirus infections were observed, and these were likely community-acquired. Continued investigation will further define the role of noroviruses in these patients and inform efforts toward prevention and treatment.
Collapse
Affiliation(s)
- Karin Bok
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | | | | | - Gabriel I Parra
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | - Sara Strollo
- Laboratory of Clinical Infectious Disease, NIAID
| | - Gary A Fahle
- Microbiology Service, Clinical Center , National Institutes of Health , Bethesda, Maryland
| | - Allison Behrle-Yardley
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | - Jordan A Johnson
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | - Eric A Levenson
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | - Stanislav V Sosnovtsev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| | | | - Tara N Palmore
- Laboratory of Clinical Infectious Disease, NIAID; Hospital Epidemiology Service, National Institutes of Health Clinical Center
| | - Kim Y Green
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID)
| |
Collapse
|
8
|
Norovirus shedding among food and healthcare workers exposed to the virus in outbreak settings. J Clin Virol 2016; 82:119-125. [PMID: 27479175 DOI: 10.1016/j.jcv.2016.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 07/01/2016] [Accepted: 07/23/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Noroviruses (NoV) are highly contagious and the leading cause of nonbacterial outbreaks of gastroenteritis worldwide. Individuals who are infected asymptomatically may act as reservoirs and facilitate the transmission of NoV, but the likelihood of workers of becoming infected in outbreak settings has not been systematically studied. OBJECTIVES We evaluated the occurrence of norovirus infections among workers exposed to the virus in different outbreak settings. STUDY DESIGN We screened feces from food handlers and healthcare workers related with gastroenteritis outbreaks, and shedding concentrations over time were calculated from serial samples of infected individuals. Sequence analyses of the capsid P2 domain and region C were used to evaluate linkage between asymptomatic employees and outbreak cases. RESULTS Of all employees, 59.1% were positive for NoV, and more than 70% of them were asymptomatic. Asymptomatic infections were significantly more frequent in foodborne compared to person-to-person transmitted outbreaks; and in restaurants and hotels, compared to nursing homes and healthcare institutions. Mean viral loads were similar between symptomatic and asymptomatic individuals, starting at 7.51±1.80 and 6.49±1.93 log10 genome copies/g, respectively, and decreasing to 5.28±0.76 and 4.52±1.45 log10 genome copies/g after 19days. CONCLUSIONS The likelihood of becoming infected when a NoV outbreak occurs at the work place is high and similar between food handlers and healthcare workers, but asymptomatic infections are more frequently identified among food handlers. Since shed amounts of viruses in the absence of symptoms are also high, reinforcement of hygiene practices among workers is especially relevant to reduce the risk of virus secondary transmissions.
Collapse
|
9
|
Cuevas JM, Combe M, Torres-Puente M, Garijo R, Guix S, Buesa J, Rodríguez-Díaz J, Sanjuán R. Human norovirus hyper-mutation revealed by ultra-deep sequencing. INFECTION GENETICS AND EVOLUTION 2016; 41:233-239. [PMID: 27094861 PMCID: PMC7172324 DOI: 10.1016/j.meegid.2016.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023]
Abstract
Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. Norovirus U-to-C hyper-mutants are present in patient samples. Analysis of hyper-mutants in cell culture suggests ADAR-mediated RNA edition. Hyper-mutation may contribute to norovirus diversity and evolution.
Collapse
Affiliation(s)
- José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Marine Combe
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Manoli Torres-Puente
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Susana Guix
- Departament de Microbiologia, Universitat de Barcelona, Barcelona, Spain
| | - Javier Buesa
- Departament de Microbiologia, Universitat de València, Valencia, Spain
| | | | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain.
| |
Collapse
|
10
|
Complete Genome Sequence of Human Norovirus GII.4_2006b, a Variant of Minerva 2006. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01648-15. [PMID: 26823589 PMCID: PMC4732342 DOI: 10.1128/genomea.01648-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In 2006, the National Calicivirus Laboratory at the U.S. Centers for Disease Control and Prevention (CDC) confirmed multistate outbreaks of norovirus infection and identified two new GII.4 norovirus strains (Minerva and Laurens) through partial sequencing of the major capsid (VP1) gene. Here, we report the first complete genome sequence of the GII.4 Minerva isolate.
Collapse
|
11
|
Bavelaar HH, Rahamat-Langendoen J, Niesters HG, Zoll J, Melchers WJ. Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus. J Clin Virol 2015; 72:122-5. [DOI: 10.1016/j.jcv.2015.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 11/16/2022]
|
12
|
Franck KT, Nielsen RT, Holzknecht BJ, Ersbøll AK, Fischer TK, Böttiger B. Norovirus Genotypes in Hospital Settings: Differences Between Nosocomial and Community-Acquired Infections. J Infect Dis 2015; 212:881-8. [PMID: 25701867 DOI: 10.1093/infdis/jiv105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/11/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Norovirus (NoV) is a major cause of gastroenteritis and hospital outbreaks, leading to substantial morbidity and direct healthcare expenses as well as indirect societal costs. The aim of the study was to estimate the proportion of nosocomial NoV infections among inpatients testing positive for NoV in Denmark, 2002-2010, and to study the distribution of NoV genotypes among inpatients with nosocomial and community-acquired NoV infections, respectively. METHODS Admission and stool sampling dates from 3656 NoV-infected patients were used to estimate the proportion of nosocomial infections. The associations between nosocomial infection and patient age, sex, and NoV genotype GII.4 were examined. RESULTS Of the 3656 inpatients, 63% were classified as having nosocomial infections. Among these, 9 capsid and 8 polymerase NoV genotypes were detected, whereas in the smaller group of inpatients with community-acquired infections, 12 capsid and 9 polymerase genotypes were detected. Nosocomial NoV infections were associated with age ≥60 years and infections with genotype GII.4. CONCLUSIONS The majority of NoV infections in hospitalized patients were nosocomial. Nosocomial infection was mainly associated with older age but also with the specific genotype GII.4. The genotypes in community-acquired NoV infections were more heterogeneous than in nosocomial infections.
Collapse
Affiliation(s)
- Kristina Træholt Franck
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen Research Unit for Clinical Microbiology, University of Southern Denmark, Odense
| | | | | | - Annette Kjær Ersbøll
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Thea Kølsen Fischer
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen
| | - Blenda Böttiger
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen Department of Laboratory Medicine Malmö, Lund University, Sweden
| |
Collapse
|