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Polat C, Ayhan N, Ergünay K, Charrel RN. Comprehensive evaluation of nucleic acid amplification methods widely used for generic detection of sandfly-borne phleboviruses. Microbiol Spectr 2024; 12:e0342823. [PMID: 38456695 PMCID: PMC10986501 DOI: 10.1128/spectrum.03428-23] [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: 09/22/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024] Open
Abstract
Sandfly-borne phleboviruses (SBPs), which cause sandfly fever, aseptic meningitis, encephalitis, and meningoencephalitis, are emerging pathogens of major public health concern. Virus nucleic acid testing is essential for SBP diagnosis, especially in the early stages of infection, and for the discovery of novel SBPs. The efficacy of utilizing generic primers that target conserved nucleotide sequences for the detection of both known and novel SBPs has not been extensively evaluated. We aimed to compare and evaluate the performance of five generic primer sets, widely used to detect S- and L-segments of arthropod-borne phleboviruses and designed as singleplex (n = 3) and nested (n = 2) formats, including both well-known and recently characterized 15 Old World virus strains. Furthermore, we performed in silico analysis to assess the detection capabilities of these generic primer sets. The initial evaluation of previously published generic primer sets for SBP detection yielded two singleplex primer sets with the potential to be adapted for use in real-time or high-throughput detection settings. Studies are ongoing to develop and further optimize a preliminary assay and test various hosts and vectors to assess their capacity to detect known and novel viruses. IMPORTANCE Virus nucleic acid testing is the primary diagnostic method, particularly in the early stages of illness. Virus-specific or syndromic tests are widely used for this purpose. The use of generic primers has had a considerable impact on the discovery, identification, and detection of Old World sandfly-borne phleboviruses (OWSBP). The study is significant because it is the first to carry out a comparative evaluation of all published OWSBP generic primer sets.
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Affiliation(s)
- Ceylan Polat
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
| | - Nazli Ayhan
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- National Reference Center for Arboviruses, National Institute of Health, and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Koray Ergünay
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, Maryland, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Remi N. Charrel
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- Laboratoire des Infections Virales Aigues et Tropicales, Pole des Maladies Infectieuses, AP-HM Hopitaux Universitaires de Marseille, Marseille, France
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Gámbaro F, Pérez AB, Prot M, Agüera E, Baidaliuk A, Sánchez-Seco MP, Martínez-Martínez L, Vázquez A, Fernandez-Garcia MD, Simon-Loriere E. Untargeted metagenomic sequencing identifies Toscana virus in patients with idiopathic meningitis, southern Spain, 2015 to 2019. Euro Surveill 2023; 28:2200913. [PMID: 37943504 PMCID: PMC10636744 DOI: 10.2807/1560-7917.es.2023.28.45.2200913] [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: 11/21/2022] [Accepted: 04/15/2023] [Indexed: 11/10/2023] Open
Abstract
BackgroundVarious pathogens, including bacteria, fungi, parasites, and viruses can lead to meningitis. Among viruses causing meningitis, Toscana virus (TOSV), a phlebovirus, is transmitted through sandfly bites. TOSV infection may be suspected if patients with enterovirus- and herpesvirus-negative aseptic (non-bacterial) meningitis recall recent insect bites. Other epidemiological factors (season, rural area) may be considered. The broad range of possible meningitis aetiologies poses considerable diagnosis challenges. Untargeted metagenomic next-generation sequencing (mNGS) can potentially identify pathogens, which are not considered or detected in routine diagnostic panels.AimIn this retrospective, single-centre observational study, we investigated mNGS usefulness to understand the cause of meningitis when conventional approaches fail.MethodsCerebrospinal fluid (CSF) samples from patients hospitalised in southern Spain in 2015-2019 with aseptic meningitis and no aetiology found by conventional testing, were subjected to mNGS. Patients' demographic characteristics had been recorded and physicians had asked them about recent insect bites. Obtained viral genome sequences were phylogenetically analysed.ResultsAmong 23 idiopathic cases, TOSV was identified in eight (all male; median age: 39 years, range: 15-78 years). Five cases lived in an urban setting, three occurred in autumn and only one recalled insect bites. Phylogenetic analysis of TOSV segment sequences supported one intra-genotype reassortment event.ConclusionsOur study highlights the usefulness of mNGS for identifying viral pathogens directly in CSF. In southern Spain, TOSV should be considered regardless of recalling of insect bites or other epidemiological criteria. Detection of a disease-associated reassortant TOSV emphasises the importance of monitoring the spread and evolution of phleboviruses in Mediterranean countries.
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Affiliation(s)
- Fabiana Gámbaro
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ana Belén Pérez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Eduardo Agüera
- Universidad de Córdoba, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Artem Baidaliuk
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - María Paz Sánchez-Seco
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Universidad de Córdoba, Córdoba, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Ana Vázquez
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - María Dolores Fernandez-Garcia
- These authors contributed equally to this work and share last authorship and correspondence
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Etienne Simon-Loriere
- These authors contributed equally to this work and share last authorship and correspondence
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
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Hiraldo JDG, Fuerte-Hortigón A, Domínguez-Mayoral A, De la Rosa Riestra S, Palacios-Baena ZR, Fernández FS, Ruiz RL, Pascual-Vaca D, de León CM, Hurtado RJ, Sanbonmatsu-Gámez S. Uncovering the neurological effects of West Nile virus during a record-breaking southern Spain outbreak in 2020-2021. J Neuroimmunol 2023; 383:578179. [PMID: 37657130 DOI: 10.1016/j.jneuroim.2023.578179] [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: 03/23/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
The 2020-21 West Nile Virus (WNV) outbreak in Andalusia, Spain, was the largest reported in the country, with eight cases of West Nile Neuroinvasive Disease (WNND) diagnosed in a tertiary hospital. Diagnosis of WNND is based on detecting WNV RNA, viral isolation, or demonstrating a specific immune response against the virus, with additional tests used to support the diagnosis. Treatment remains supportive, with variable outcomes. The potential efficacy of plasma exchange (PLEX) in select cases raises the possibility of an autoimmune component secondary to infectious pathology of the central nervous system. The influence of climate change on the expansion of WNV into new regions is a significant concern. It is crucial for physicians practicing in high-risk areas to be knowledgeable about the disease for early prevention and effective control measures.
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Affiliation(s)
| | | | | | - Sandra De la Rosa Riestra
- Unit of Infectious Diseases and Clinical Microbiology, University Hospital Virgen Macarena/Institute of Biomedicine of Seville (IBIS), Spain
| | - Zaira R Palacios-Baena
- Unit of Infectious Diseases and Clinical Microbiology, University Hospital Virgen Macarena/Institute of Biomedicine of Seville (IBIS), Spain
| | | | - Rocio López Ruiz
- Department of Neurology, University Hospital Virgen Macarena, Seville, Spain
| | - Diego Pascual-Vaca
- Department of Paediatric Neurology, University Hospital Virgen Macarena, Seville, Spain
| | | | - Rafael Jiménez Hurtado
- Department of Clinical Neurophysiology, University Hospital Virgen Macarena, Seville, Spain
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Xu H, Chen P, Guo S, Shen X, Lu Y. Progress in etiological diagnosis of viral meningitis. Front Neurol 2023; 14:1193834. [PMID: 37583954 PMCID: PMC10423822 DOI: 10.3389/fneur.2023.1193834] [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: 03/25/2023] [Accepted: 06/05/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, with the rapid development of molecular biology techniques such as polymerase chain reaction and molecular biochip, the etiological diagnosis of viral encephalitis has a very big step forward. At present, the etiological examination of viral meningitis mainly includes virus isolation, serological detection and molecular biological nucleic acid detection. This article reviews the progress in etiological diagnosis of viral meningitis.
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Affiliation(s)
- Hongyan Xu
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of General Practice, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzong Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Peng Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shihan Guo
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaokai Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Lu
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Benbetka C, Hachid A, Benallal KE, Khardine FA, Ayhan N, Bouredjoul N, Boulehbal WM, Bellila D, Khaldi A, Charrel R. Epidemiology, Isolation, and Genetic Characterization of Toscana Virus in Algerian Patients Displaying Neurological Infection, 2016-2018. IJID REGIONS 2023; 7:193-198. [PMID: 37123383 PMCID: PMC10131063 DOI: 10.1016/j.ijregi.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/02/2023]
Abstract
Purpose The current study reports the results of the diagnosis of neuro-invasive Toscana virus (TOSV) infection in Algeria between 2016 and 2018 and describes the first isolation of TOSV strain from human samples in North Africa. Materiel and methods Cerebrospinal fluid (CSF) and sera samples were obtained from 720 hospitalized patients displaying neurological infection symptoms of unknown etiology, of which 604 were screened for TOSV. The diagnosis was performed by serological and/or RT-PCR tests. In addition, TOSV was isolated in vivo and in vitro from CSF and genetically characterized. Results 23 cases of TOSV neurological infections were detected. Cases were located in 11 Wilayas (administrative provinces), mainly in northern Algeria. In addition, we report the isolation of TOSV strain belonging to lineage A from human samples with its complete coding sequence. Conclusion Even though the number of infections is probably underestimated, TOSV is endemic in Algeria, with several cases of neuro-invasive diseases in humans recorded each year. Therefore, the diagnosis of TOSV should be included in the differential diagnosis of neurological diseases, especially aseptic meningitis, during the period of activity of the phlebotomine vector. Further studies are required to measure precisely the nationwide prevalence of TOSV in Algeria.
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Affiliation(s)
- Chahrazed Benbetka
- Laboratory of Arboviruses and Emerging Viruses, Institut Pasteur of Algeria, 16000, Algiers, Algeria
- Department of Immunology, Béni-Messous Teaching Hospital, University of Algiers, 16000, Algiers, Algeria
- Faculty of Pharmacy, University of Algiers 1, 16000, Algiers, Algeria
- Co-first authors.
| | - Aissam Hachid
- Laboratory of Arboviruses and Emerging Viruses, Institut Pasteur of Algeria, 16000, Algiers, Algeria
- Faculty of Pharmacy, University of Algiers 1, 16000, Algiers, Algeria
- Co-first authors.
| | - Kamal Eddine Benallal
- Laboratory of Parasitic Eco-epidemiology and Population Genetics, Institut Pasteur of Algeria, 16000, Algiers, Algeria
| | - Fayez Ahmed Khardine
- Laboratory of Arboviruses and Emerging Viruses, Institut Pasteur of Algeria, 16000, Algiers, Algeria
| | - Nazli Ayhan
- Unité des Virus Emergents, UVE: Aix Marseille Université, IRD 190, Inserm 1207, AP-HM Hôpitaux Universitaires de Marseille, 13005, Marseille, France
| | - Nesrine Bouredjoul
- Laboratory of Arboviruses and Emerging Viruses, Institut Pasteur of Algeria, 16000, Algiers, Algeria
| | | | - Djamila Bellila
- Faculty of Natural Sciences, University of Algiers 1, 16000, Algiers, Algeria
| | - Aldjia Khaldi
- Laboratory of Arboviruses and Emerging Viruses, Institut Pasteur of Algeria, 16000, Algiers, Algeria
- Faculty of Pharmacy, University of Algiers 1, 16000, Algiers, Algeria
| | - Rémi Charrel
- Unité des Virus Emergents, UVE: Aix Marseille Université, IRD 190, Inserm 1207, AP-HM Hôpitaux Universitaires de Marseille, 13005, Marseille, France
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Sandfly-Borne Phleboviruses in Portugal: Four and Still Counting. Viruses 2022; 14:v14081768. [PMID: 36016390 PMCID: PMC9413822 DOI: 10.3390/v14081768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
According to ICTV, there are currently 66 known phlebovirus species. More than 40 of these viruses were isolated or detected in phlebotomine sandflies and some of them are known pathogens. In Portugal, information about sandfly-borne phleboviruses is scarce and scattered sandfly-borne diseases are neglected and often not considered in differential diagnoses. The main objective of this work was to gather the existing information and to raise awareness about the circulating phleboviruses in this country. To date, Massilia and Alcube phleboviruses have been isolated from sandflies in southern Portugal. Human infections with Toscana and Sicilian phleboviruses have been reported, as well as seroprevalence in cats and dogs. More studies are needed in order to understand if the viruses isolated during the entomological surveys have an impact on human health and to fully understand the real importance of the already recognized pathogens in our country.
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