1
|
Shaw AG, Mampuela TK, Lofiko EL, Pratt C, Troman C, Bujaki E, O'Toole Á, Akello JO, Aziza AA, Lusamaki EK, Makangara JC, Akonga M, Lay Y, Nsunda B, White B, Jorgensen D, Pukuta E, Riziki Y, Rankin KE, Rambaut A, Ahuka-Mundeke S, Muyembe JJ, Martin J, Grassly NC, Mbala-Kingebeni P. Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study. Nat Microbiol 2023; 8:1634-1640. [PMID: 37591995 PMCID: PMC10465353 DOI: 10.1038/s41564-023-01453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
Collapse
Affiliation(s)
- Alexander G Shaw
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Tresor Kabeya Mampuela
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Catherine Pratt
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Troman
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Erika Bujaki
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Joyce Odeke Akello
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Adrienne Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- TransVIHMI (Recherches Translationnelles sur le VIH et les Maladies Infectieuses endémiques et émergentes), University of Montpellier (UM), French National Research Institute for Sustainable Development (IRD), INSERM, Montpellier, France
| | - Jean Claude Makangara
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Marceline Akonga
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yvonne Lay
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bibiche Nsunda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bailey White
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Elizabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yogolelo Riziki
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Steve Ahuka-Mundeke
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Javier Martin
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Placide Mbala-Kingebeni
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| |
Collapse
|
2
|
Shaw AG, Troman C, Akello JO, O'Reilly KM, Gauld J, Grow S, Grassly N, Steele D, Blazes D, Kumar S. Defining a research agenda for environmental wastewater surveillance of pathogens. Nat Med 2023; 29:2155-2157. [PMID: 37537374 DOI: 10.1038/s41591-023-02457-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Affiliation(s)
- Alexander G Shaw
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Catherine Troman
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Joyce Odeke Akello
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Kathleen M O'Reilly
- Centre for Mathematical Modeling of Infectious Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Nicholas Grassly
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | | | - David Blazes
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | |
Collapse
|
3
|
Akello JO, Bujaki E, Shaw AG, Khurshid A, Arshad Y, Troman C, Majumdar M, O'Toole Á, Rambaut A, Alam MM, Martin J, Grassly NC. Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples. Microbiol Spectr 2023; 11:e0425222. [PMID: 36939356 PMCID: PMC10100708 DOI: 10.1128/spectrum.04252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 nucleic acid extraction methods (7 manual and 4 semiautomated) for poliovirus molecular detection using stool samples (n = 59) that had been previously identified as poliovirus positive by cell culture. To assess the effect of RNA recovery methods, extracted RNA using each of the 11 methods was tested with a poliovirus-specific reverse transcription-quantitative PCR (RT-qPCR), a pan-poliovirus RT-PCR (near-whole-genome amplification), a pan-enterovirus RT-PCR (entire capsid region), and a nested VP1 PCR that is the basis of a direct detection method based on nanopore sequencing. We also assessed extracted RNA integrity and quantity. The overall effect of extraction method on poliovirus PCR amplification assays tested in this study was found to be statistically significant (P < 0.001), thus indicating that the choice of RNA extraction method is an important component that needs to be carefully considered for any diagnostic based on nucleic acid amplification. Performance of the methods was generally consistent across the different assays used. Of the 11 extraction methods tested, the MagMAX viral RNA isolation kit used manually or automatically was found to be the preferable method for poliovirus molecular direct detection considering performance, cost, and processing time. IMPORTANCE Poliovirus, the causative agent of poliomyelitis, is a target of global eradication led by the World Health Organization since 1988. Direct molecular detection and genomic sequencing without virus propagation in cell culture is arguably a critical tool in the final stages of polio eradication. Efficient recovery of good-quality viral RNA from stool samples is a prerequisite for direct detection by nucleic acid amplification. We tested 11 nucleic acid extraction methods to identify those facilitating sensitive, fast, simple, and cost-effective extraction, with flexibility for manual and automated protocols considered. Several different PCR assays were used to compare the recovered viral RNA to test suitability for poliovirus direct molecular detection. Our findings highlight the importance of choosing a suitable RNA extraction protocol and provide useful information to diagnostic laboratories and researchers facing the choice of RNA extraction method for direct molecular virus detection from stool.
Collapse
Affiliation(s)
- Joyce Odeke Akello
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Erika Bujaki
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Alexander G. Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Adnan Khurshid
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Yasir Arshad
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Catherine Troman
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | | | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Nicholas C. Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| |
Collapse
|
4
|
Elviss NC, Allen DJ, Kelly D, Akello JO, Hau S, Fox AJ, Hopkins M, Derrick J, O'Brien S, Iturriza‐Gomara M. Norovirus attribution study: Detection of norovirus from the commercial food preparation environment in outbreak and non-outbreak premises. J Appl Microbiol 2022; 133:3391-3403. [PMID: 35929369 PMCID: PMC9826197 DOI: 10.1111/jam.15761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 01/11/2023]
Abstract
AIMS Norovirus remains the most significant virological risk that is transmitted via food and the environment to cause acute gastroenteritis. This study aimed to investigate the hypothesis that the contamination of the commercial food production environment with norovirus will be higher in premises that have recently reported a foodborne norovirus outbreak than those that have not. METHODS Sampling of commercial food production environments was carried out across a 16-month period between January 2015 and April 2016 in the South East and the North West of England by local authority environmental health departments as part of routine surveillance visits to premises. A total of 2982 samples, 2038 virological and 944 bacteriological, were collected from 256 premises. Sixteen of these premises, six from South East and ten from North West England, were sampled as part of a public health outbreak investigation. RESULTS & CONCLUSIONS Overall, 2038 swabs were submitted for norovirus testing, with an average of eight swabs per premises (range 4 to 23) and a median of seven. Of the premises sampled, 11.7% (30/256) yielded at least one norovirus-positive sample (environmental, and/or food handler hand swab), and 2.5% of the swabs were positive for norovirus. A peak in the positivity rate was seen in the South East in April 2016. No associations were found between norovirus positivity and bacteriology indicators, or between bacteriology indicators and hygiene ratings. SIGNIFICANCE AND IMPACT OF STUDY This study demonstrates that food premises and food handlers remain a potential source of norovirus transmission and outbreaks.
Collapse
Affiliation(s)
- Nicola C. Elviss
- Food, Water and Environmental Microbiology ServicesUnited Kingdom Health Security AgencyLondonUK
| | - David J. Allen
- Department of Infection Biology, Faculty of Infectious and Tropical DiseasesLondon School of Hygiene & Tropical MedicineLondonUK,NIHR Health Protection Research Unit in Gastrointestinal InfectionsLiverpoolUK,Virus Reference DepartmentUnited Kingdom Health Security AgencyLondonUK
| | - Daniel Kelly
- Institute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | | | - Sarah Hau
- Institute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Andrew J. Fox
- Field ServicesUnited Kingdom Health Security AgencyLondonUK
| | - Mark Hopkins
- Liverpool Clinical LaboratoriesLiverpool University Hospitals NHS TrustLiverpoolUK
| | - Jade Derrick
- Virus Reference DepartmentUnited Kingdom Health Security AgencyLondonUK
| | - Sarah O'Brien
- The Farr Institute@HeRC, University of LiverpoolLiverpoolUK
| | - Miren Iturriza‐Gomara
- NIHR Health Protection Research Unit in Gastrointestinal InfectionsLiverpoolUK,Institute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | | |
Collapse
|
5
|
Akello JO, Kamgang R, Barbani MT, Suter-Riniker F, Aebi C, Beuret C, Paris DH, Leib SL, Ramette A. Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients. Sci Rep 2021; 11:24038. [PMID: 34912023 PMCID: PMC8674331 DOI: 10.1038/s41598-021-03445-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2022] Open
Abstract
Human adenoviruses (HAdVs) are highly contagious pathogens of clinical importance, especially among the pediatric population. Studies on comparative viral genomic analysis of cases associated with severe and mild infections due to HAdV are limited. Using whole-genome sequencing (WGS), we investigated whether there were any differences between circulating HAdV strains associated with severe infections (meningitis, sepsis, convulsion, sudden infant death syndrome, death, and hospitalization) and mild clinical presentations in pediatric patients hospitalized between the years 1998 and 2017 in a tertiary care hospital group in Bern, Switzerland covering a population base of approx. 2 million inhabitants. The HAdV species implicated in causing severe infections in this study included HAdV species C genotypes (HAdV1, HAdV2, and HAdV5). Clustering of the HAdV whole-genome sequences of the severe and mild cases did not show any differences except for one sample (isolated from a patient presenting with sepsis, meningitis, and hospitalization) that formed its own cluster with HAdV species C genotypes. This isolate showed intertypic recombination events involving four genotypes, had the highest homology to HAdV89 at complete genome level, but possessed the fiber gene of HAdV1, thereby representing a novel genotype of HAdV species C. The incidence of potential recombination events was higher in severe cases than in mild cases. Our findings confirm that recombination among HAdVs is important for molecular evolution and emergence of new strains. Therefore, further research on HAdVs, particularly among susceptible groups, is needed and continuous surveillance is required for public health preparedness including outbreak investigations.
Collapse
Affiliation(s)
- Joyce Odeke Akello
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland.,Spiez Laboratory, Biology Division, Swiss Federal Office for Civil Protection, Spiez, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Richard Kamgang
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Maria Teresa Barbani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Christoph Aebi
- Department of Pediatrics, Bern University Hospital, Bern, Switzerland
| | - Christian Beuret
- Spiez Laboratory, Biology Division, Swiss Federal Office for Civil Protection, Spiez, Switzerland
| | - Daniel H Paris
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland.
| |
Collapse
|
6
|
Kinsella CM, Santos PD, Postigo-Hidalgo I, Folgueiras-González A, Passchier TC, Szillat KP, Akello JO, Álvarez-Rodríguez B, Martí-Carreras J. Preparedness needs research: How fundamental science and international collaboration accelerated the response to COVID-19. PLoS Pathog 2020; 16:e1008902. [PMID: 33035262 PMCID: PMC7546461 DOI: 10.1371/journal.ppat.1008902] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The first cluster of patients suffering from coronavirus disease 2019 (COVID-19) was identified on December 21, 2019, and as of July 29, 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been linked with 664,333 deaths and number at least 16,932,996 worldwide. Unprecedented in global societal impact, the COVID-19 pandemic has tested local, national, and international preparedness for viral outbreaks to the limits. Just as it will be vital to identify missed opportunities and improve contingency planning for future outbreaks, we must also highlight key successes and build on them. Concomitant to the emergence of a novel viral disease, there is a 'research and development gap' that poses a threat to the overall pace and quality of outbreak response during its most crucial early phase. Here, we outline key components of an adequate research response to novel viral outbreaks using the example of SARS-CoV-2. We highlight the exceptional recent progress made in fundamental science, resulting in the fastest scientific response to a major infectious disease outbreak or pandemic. We underline the vital role of the international research community, from the implementation of diagnostics and contact tracing procedures to the collective search for vaccines and antiviral therapies, sustained by unique information sharing efforts.
Collapse
Affiliation(s)
- Cormac M. Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Pauline Dianne Santos
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ignacio Postigo-Hidalgo
- Charité –Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | | | - Tim Casper Passchier
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Kevin P. Szillat
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Joyce Odeke Akello
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Spiez, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Beatriz Álvarez-Rodríguez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Joan Martí-Carreras
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| |
Collapse
|
7
|
Akello JO, Leib SL, Engler O, Beuret C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses 2020; 12:v12050562. [PMID: 32438629 PMCID: PMC7290855 DOI: 10.3390/v12050562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
Identification and characterization of viral genomes in vectors including ticks and mosquitoes positive for pathogens of great public health concern using metagenomic next generation sequencing (mNGS) has challenges. One such challenge is the ability to efficiently recover viral RNA which is typically dependent on sample processing. We evaluated the quantitative effect of six different extraction methods in recovering viral RNA in vectors using negative tick homogenates spiked with serial dilutions of tick-borne encephalitis virus (TBEV) and surrogate Langat virus (LGTV). Evaluation was performed using qPCR and mNGS. Sensitivity and proof of concept of optimal method was tested using naturally positive TBEV tick homogenates and positive dengue, chikungunya, and Zika virus mosquito homogenates. The amount of observed viral genome copies, percentage of mapped reads, and genome coverage varied among different extractions methods. The developed Method 5 gave a 120.8-, 46-, 2.5-, 22.4-, and 9.9-fold increase in the number of viral reads mapping to the expected pathogen in comparison to Method 1, 2, 3, 4, and 6, respectively. Our developed Method 5 termed ROVIV (Recovery of Viruses in Vectors) greatly improved viral RNA recovery and identification in vectors using mNGS. Therefore, it may be a more sensitive method for use in arbovirus surveillance.
Collapse
Affiliation(s)
- Joyce Odeke Akello
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 4, 3012 Bern, Switzerland
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
| | - Olivier Engler
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
| | - Christian Beuret
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
| |
Collapse
|
8
|
Akello JO, Kamgang R, Barbani MT, Suter-Riniker F, Leib SL, Ramette A. Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland. Clin Epidemiol 2020; 12:353-366. [PMID: 32308491 PMCID: PMC7147615 DOI: 10.2147/clep.s246352] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Human adenovirus (HAdV) is an important pathogen seen in clinical practice. Long-term studies may help better understand epidemiological trends and changes in circulating genotypes over time. PURPOSE Using a large biobank of samples from hospitalized, adenovirus-positive patients over a 20-year period, we aimed to analyze long-term epidemiological trends and genotypic relatedness among circulating HAdV strains. METHODS Based on samples from hospitalized patients confirmed to be HAdV positive in Bern, Switzerland, from 1998 to 2017, and on their associated demographic and clinical data, we identified epidemiological trends and risk factors associated with HAdV infection. HAdV genotyping was performed by PCR amplification and sequencing of the hypervariable hexon gene. The obtained sequences were phylogenetically compared with sequences from international HAdV strains. RESULTS HAdV was identified in 1302 samples tested. Cases of HAdV infection were reported throughout the years with no clear seasonality. Upper respiratory tract samples, conjunctivitis swabs, and stool had the highest positivity rate (56.2%, 18.7%, and 14.2% of the cases, respectively). HAdV infection was highest among children ≤4 years old. Increased number of HAdV cases were observed in years 2009 (n = 110) and 2010 (n =112). HAdV8 was the predominant genotype among patients older than 20 years, and was mostly associated with ophthalmic infection. Predominant genotypes among children ≤4 years old were HAdV1, HAdV2, and HAdV3, which were mostly associated with respiratory tract infections. Recurring peaks of increased HAdV cases were evidenced every 4 years among children ≤4 years old. CONCLUSION Our study gives novel insights on long-term epidemiological trends and phylogenetic relatedness among circulating HAdV strains in Switzerland, country in which little data on HAdV prevalence and diversity was so far available.
Collapse
Affiliation(s)
- Joyce Odeke Akello
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Spiez, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Richard Kamgang
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | | | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| |
Collapse
|