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Ji CM, Feng XY, Huang YW, Chen RA. The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research. Viruses 2024; 16:798. [PMID: 38793679 PMCID: PMC11125791 DOI: 10.3390/v16050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.
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Affiliation(s)
- Chun-Miao Ji
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Xiao-Yin Feng
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Yao-Wei Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
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Kabir F, Plaisance E, Portman A, Marfo A, Cirrincione K, Silva D, Amadi V, Stringer J, Short L. Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach. J Infect Dis 2024; 229:S163-S171. [PMID: 37968965 DOI: 10.1093/infdis/jiad504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND In response to Mpox endemic and public health emergency, DCHHS aimed to develop NGS based techniques to streamline Mpox viral clade and lineage analysis. METHODS The Mpox sequencing workflow started with DNA extraction and adapted Illumina's COVIDSeq assay using hMpox primer pools from Yale School of Public Health. Sequencing steps included cDNA amplification, tagmentation, PCR indexing, pooling libraries, sequencing on MiSeq, data analysis, and report generation. The bioinformatic analysis comprised read assembly and consensus sequence mapping to reference genomes and variant identification, and utilized pipelines including Illumina BaseSpace, NextClade, CLC Workbench, Terra.bio for data quality control (QC) and validation. RESULTS In total, 171 mpox samples were sequenced using modified COVIDSeq workflow and QC metrics were assessed for read quality, depth, and coverage. Multiple analysis pipelines identified the West African clade IIb as the only clade during peak Mpox infection from July through October 2022. Analyses also indicated lineage B.1.2 as the dominant variant comprising the majority of Mpox viral genomes (77.7%), implying its geographical distribution in the United States. Viral sequences were uploaded to GISAID EpiPox. CONCLUSIONS We developed NGS workflows to precisely detect and analyze mpox viral clade and lineages aiding in public health genomic surveillance.
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Affiliation(s)
- Farruk Kabir
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Erin Plaisance
- Dallas County Health and Human Services, Dallas, Texas, USA
| | | | - Agnes Marfo
- Dallas County Health and Human Services, Dallas, Texas, USA
| | | | - David Silva
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Victor Amadi
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Joey Stringer
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Luke Short
- Dallas County Health and Human Services, Dallas, Texas, USA
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Obermeier PE, Buder SC, Hillen U. Pockenvirusinfektionen in der Dermatologie: Poxvirus infections in dermatology - the neglected, the notable, and the notorious. J Dtsch Dermatol Ges 2024; 22:56-96. [PMID: 38212918 DOI: 10.1111/ddg.15257_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/20/2023] [Indexed: 01/13/2024]
Abstract
ZusammenfassungDie Familie Poxviridae umfasst derzeit 22 Gattungen, die Wirbeltiere infizieren können. Humanpathogene Pockenviren gehören den Gattungen Ortho‐, Para‐, Mollusci‐ und Yatapoxvirus an. Bis zur Eradikation der Variola vera im Jahr 1979 waren die Pocken, im Volksmund auch Blattern genannt, eine schwerwiegende Gesundheitsbedrohung für die Bevölkerung. Noch heute sind Dermatologen mit zahlreichen Pockenvirusinfektionen konfrontiert, wie den Bauernhofpocken, die als Zoonosen nach Tierkontakten in ländlichen Gebieten oder nach Massenversammlungen auftreten können. In den Tropen können Erkrankungen durch Tanapox‐ oder Vaccinia‐Viren zu den Differenzialdiagnosen gehören. Dellwarzen sind weltweit verbreitet und werden in bestimmten Fällen als sexuell übertragbare Pockenvirusinfektion angesehen. In jüngster Zeit hatten sich Mpox (Affenpocken) zu einer gesundheitlichen Notlage von internationaler Tragweite entwickelt, die eine rasche Identifizierung und angemessene Behandlung durch Dermatologen und Infektiologen erfordert. Fortschritte und neue Erkenntnisse über Epidemiologie, Diagnose, klinische Manifestationen und Komplikationen sowie Behandlung und Prävention von Pockenvirusinfektionen erfordern ein hohes Maß an Fachwissen und interdisziplinärer Zusammenarbeit in den Bereichen Virologie, Infektiologie und Dermatologie. Dieser CME‐Artikel bietet einen aktualisierten systematischen Überblick, um praktizierende Dermatologen bei der Identifizierung, Differenzialdiagnose und Behandlung klinisch relevanter Pockenvirusinfektionen zu unterstützen.
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Affiliation(s)
- Patrick E Obermeier
- Klinik für Dermatologie und Venerologie, Vivantes Klinikum Neukölln, Berlin, Deutschland
- Abteilung für Infektionskrankheiten, Vaccine Safety Initiative, Berlin, Deutschland
| | - Susanne C Buder
- Klinik für Dermatologie und Venerologie, Vivantes Klinikum Neukölln, Berlin, Deutschland
- Konsiliarlabor für Gonokokken, Fachgebiet Sexuell übertragbare bakterielle Krankheitserreger, Robert Koch-Institut, Berlin, Deutschland
| | - Uwe Hillen
- Klinik für Dermatologie und Venerologie, Vivantes Klinikum Neukölln, Berlin, Deutschland
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Obermeier PE, Buder SC, Hillen U. Poxvirus infections in dermatology - the neglected, the notable, and the notorious. J Dtsch Dermatol Ges 2024; 22:56-93. [PMID: 38085140 DOI: 10.1111/ddg.15257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/20/2023] [Indexed: 12/22/2023]
Abstract
The family Poxviridae currently comprises 22 genera that infect vertebrates. Of these, members of the Ortho-, Para-, Mollusci- and Yatapoxvirus genera have been associated with human diseases of high clinical relevance in dermatology. Historically, smallpox had been a notorious health threat until it was declared eradicated by the World Health Organization in 1979. Today, dermatologists are confronted with a variety of poxviral infections, such as farmyard pox, which occurs as a zoonotic infection after contact with animals. In the tropics, tanapox or vaccinia may be in the differential diagnosis as neglected tropical dermatoses. Molluscum contagiosum virus infection accounts for significant disease burden worldwide and is classified as a sexually transmitted infection in certain scenarios. Recently, mpox (monkeypox) has emerged as a public health emergency of international concern, requiring rapid recognition and appropriate management by dermatologists and infectious disease specialists. Advances and new insights into the epidemiology, diagnosis, clinical manifestations and complications, treatment, and prevention of poxviral infections require a high level of expertise and interdisciplinary skills from healthcare professionals linking virology, infectious diseases, and dermatology. This CME article provides a systematic overview and update to assist the practicing dermatologist in the identification, differential diagnosis, and management of poxviral infections.
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Affiliation(s)
- Patrick E Obermeier
- Department of Dermatology and Venereology, Vivantes Hospital Neukölln, Berlin, Germany
- Department of Infectious Diseases, Vaccine Safety Initiative, Berlin, Germany
| | - Susanne C Buder
- Department of Dermatology and Venereology, Vivantes Hospital Neukölln, Berlin, Germany
- German Reference Laboratory for Gonococci, Unit Sexually Transmitted Bacterial Pathogens, Department for Infectious Diseases, Robert Koch-Institute, Berlin, Germany
| | - Uwe Hillen
- Department of Dermatology and Venereology, Vivantes Hospital Neukölln, Berlin, Germany
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Schuele L, Boter M, Nieuwenhuijse DF, Götz H, Fanoy E, de Vries H, Vieyra B, Bavalia R, Hoornenborg E, Molenkamp R, Jonges M, van den Ouden A, Simões M, van den Lubben M, Koopmans M, Welkers MRA, Oude Munnink BB. Circulation, viral diversity and genomic rearrangement in mpox virus in the Netherlands during the 2022 outbreak and beyond. J Med Virol 2024; 96:e29397. [PMID: 38235923 DOI: 10.1002/jmv.29397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Mpox is an emerging zoonotic disease which has now spread to over 113 countries as of August 2023, with over 89,500 confirmed human cases. The Netherlands had one of the highest incidence rates in Europe during the peak of the outbreak. In this study, we generated 158 near-complete mpox virus (MPXV) genomes (12.4% of nationwide cases) that were collected throughout the Netherlands from the start of the outbreak in May 2022 to August 2023 to track viral evolution and investigate outbreak dynamics. We detected 14 different viral lineages, suggesting multiple introductions followed by rapid initial spread within the country. The estimated evolutionary rate was relatively high compared to previously described in orthopoxvirus literature, with an estimated 11.58 mutations per year. Genomic rearrangement events occurred at a rate of 0.63% and featured a large deletion event. In addition, based on phylogenetics, we identified multiple potential transmission clusters which could be supported by direct source- and contact tracing data. This led to the identification of at least two main transmission locations at the beginning of the outbreak. We conclude that whole genome sequencing of MPXV is essential to enhance our understanding of outbreak dynamics and evolution of a relatively understudied and emerging zoonotic pathogen.
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Affiliation(s)
- Leonard Schuele
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hannelore Götz
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Ewout Fanoy
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Dermatology, Amsterdam UMC, Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Bruno Vieyra
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Roisin Bavalia
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Elske Hoornenborg
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Margarida Simões
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Mariken van den Lubben
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Matthijs R A Welkers
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Therrien C, Prévost J, Blais AC, Turcotte S, Gendron-Lepage G, Finzi A, Fafard J. Development and validation of a highly specific in-house chemiluminescent-based serological assay for the detection of antibodies directed against the human monkeypox virus. J Virol Methods 2023; 322:114836. [PMID: 37890729 DOI: 10.1016/j.jviromet.2023.114836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Christian Therrien
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada
| | | | - Sonia Turcotte
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | | | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.
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Martínez-Sanz J, Ponce-Alonso M, Martínez-García L, de la Cueva V, Olavarrieta L, Montero L, Pérez-Elías MJ, Galán JC. Description of mpox reinfection by whole genome sequencing. Int J Infect Dis 2023; 137:111-113. [PMID: 37884258 DOI: 10.1016/j.ijid.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Several possible mpox reinfections have been reported, however, the debate on whether these are confirmed reinfections remains open. A 30-year-old male living with HIV and a history of single-dose mpox vaccination, first diagnosed with mpox in September 2022, presented with genital ulcers in March 2023, testing positive for mpox virus. Real-time polymerase chain reaction revealed the presence of viral DNA with cycle threshold values of 24 and 25, respectively. Whole genome sequencing and phylogenetic approach allowed us to classify these viruses as Clade IIb lineage B.1 and Clade IIb lineage B.1.4, respectively. Twelve nucleotide differences were identified. The observed difference was higher than the estimate of mutations/genome/year described. These data confirm that mpox reinfection is possible and reinforces current vaccination campaigns.
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Affiliation(s)
- Javier Martínez-Sanz
- Department of Infectious Diseases, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
| | - Manuel Ponce-Alonso
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain; Department of Microbiology, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Laura Martínez-García
- Department of Microbiology, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Víctor de la Cueva
- Unidad Central de Apoyo Genómica Traslacional (UCA-GT), IRYCIS, Hospital Ramón y Cajal Madrid, Spain
| | - Leticia Olavarrieta
- Unidad Central de Apoyo Genómica Traslacional (UCA-GT), IRYCIS, Hospital Ramón y Cajal Madrid, Spain
| | - Laura Montero
- Directorate General of Public Health, Regional Ministry of Health of Madrid, Madrid, Spain
| | - María Jesús Pérez-Elías
- Department of Infectious Diseases, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Juan Carlos Galán
- Department of Microbiology, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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Schwartz DA, Mbala-Kingebeni P, Patterson K, Huggins JW, Pittman PR. Congenital Mpox Syndrome (Clade I) in Stillborn Fetus after Placental Infection and Intrauterine Transmission, Democratic Republic of the Congo, 2008. Emerg Infect Dis 2023; 29:2198-2022. [PMID: 37705112 PMCID: PMC10617360 DOI: 10.3201/eid2911.230606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
We report the autopsy pathology findings of a 21-week stillborn fetus with congenital mpox syndrome that occurred in the Democratic Republic of the Congo in 2008. The fetus acquired mpox from the mother after intrauterine transplacental monkeypox virus transmission. We confirmed monkeypox virus infection in the mother, fetus, and placenta by using a monkeypox virus-specific quantitative PCR. Subtyping of the virus was not performed, but the mother and fetus were almost certainly infected with the clade I variant that was endemic in the Democratic Republic of the Congo at the time. Risk for intrauterine infection appears to differ between virus clades, but clinicians should be aware of potential for intrauterine monkeypox virus transmission among pregnant persons during ongoing and future mpox outbreaks.
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Affiliation(s)
| | - Placide Mbala-Kingebeni
- Perinatal Pathology Consulting, Atlanta, Georgia, USA (D.A. Schwartz)
- Institut National de Recherche Biomédicale, Ministère de la Santé Publique, Kinshasa, Democratic Republic of the Congo (P. Mbala-Kingebeni)
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (K. Patterson, J.W. Hudgins, P.R. Pittman)
| | - Kerry Patterson
- Perinatal Pathology Consulting, Atlanta, Georgia, USA (D.A. Schwartz)
- Institut National de Recherche Biomédicale, Ministère de la Santé Publique, Kinshasa, Democratic Republic of the Congo (P. Mbala-Kingebeni)
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (K. Patterson, J.W. Hudgins, P.R. Pittman)
| | - John W. Huggins
- Perinatal Pathology Consulting, Atlanta, Georgia, USA (D.A. Schwartz)
- Institut National de Recherche Biomédicale, Ministère de la Santé Publique, Kinshasa, Democratic Republic of the Congo (P. Mbala-Kingebeni)
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (K. Patterson, J.W. Hudgins, P.R. Pittman)
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