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Rut W, Groborz K, Sun X, Hilgenfeld R, Drag M. Profiling of coronaviral M pro and enteroviral 3C pro specificity provides a framework for the development of broad-spectrum antiviral compounds. Protein Sci 2024; 33:e5139. [PMID: 39150063 DOI: 10.1002/pro.5139] [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: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/20/2024] [Indexed: 08/17/2024]
Abstract
The main protease from coronaviruses and the 3C protease from enteroviruses play a crucial role in processing viral polyproteins, making them attractive targets for the development of antiviral agents. In this study, we employed a combinatorial chemistry approach-HyCoSuL-to compare the substrate specificity profiles of the main and 3C proteases from alphacoronaviruses, betacoronaviruses, and enteroviruses. The obtained data demonstrate that coronavirus Mpros exhibit overlapping substrate specificity in all binding pockets, whereas the 3Cpro from enterovirus displays slightly different preferences toward natural and unnatural amino acids at the P4-P2 positions. However, chemical tools such as substrates, inhibitors, and activity-based probes developed for SARS-CoV-2 Mpro can be successfully applied to investigate the activity of the Mpro from other coronaviruses as well as the 3Cpro from enteroviruses. Our study provides a structural framework for the development of broad-spectrum antiviral compounds.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
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Bianconi I, Battisti L, Staffler A, Giacobazzi E, Masi E, Incrocci E, Bellutti M, Fontana S, Stefanelli P, Buttinelli G, Pagani E. Disseminated Echovirus 11 infection in a newborn in the Province of Bolzano, Italy. Infection 2024:10.1007/s15010-024-02315-9. [PMID: 39150641 DOI: 10.1007/s15010-024-02315-9] [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: 04/23/2024] [Accepted: 05/31/2024] [Indexed: 08/17/2024]
Abstract
PURPOSE Recently, cases of serious illness in newborns infected with Echovirus 11 have been reported in Europe, including Italy. Here, we report the case of a newborn diagnosed with disseminated Echovirus 11 infection, which occurred in October 2023 in the Province of Bolzano, Italy. METHODS A molecular screening, by Real-Time RT-PCR, was employed to analyse the cerebrospinal fluid, blood and stool samples, and nasal swabs. The entire viral genome was sequenced using both Illumina and Nanopore technologies. RESULTS The patient was admitted to hospital due to fever. Molecular testing revealed the presence of enterovirus RNA. Typing confirmed the presence of Echovirus 11. The patient was initially treated with antibiotic therapy and, following the diagnosis of enterovirus infection, also with human immunoglobulins. Over the following days, the patient remained afebrile, with decreasing inflammation indices and in excellent general condition. Genomic and phylogenetic characterization suggested that the strain was similar to strains from severe cases reported in Europe. CONCLUSIONS Despite the low overall risk for the neonatal population in Europe, recent cases of Echovirus 11 have highlighted the importance of surveillance and complete genome sequencing is fundamental to understanding the phylogenetic relationships of Echovirus 11 variants.
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Affiliation(s)
- Irene Bianconi
- Laboratory of Microbiology and Virology, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy.
| | - Laura Battisti
- Division of Paediatrics, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Alex Staffler
- Division of Neonatology/NICU, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Elisabetta Giacobazzi
- Laboratory of Microbiology and Virology, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Elisa Masi
- Laboratory of Microbiology and Virology, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Elisabetta Incrocci
- Laboratory of Microbiology and Virology, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Marion Bellutti
- Division of Paediatrics, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
| | - Stefano Fontana
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Gabriele Buttinelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Pagani
- Laboratory of Microbiology and Virology, Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of Paracelsus Medical University (PMU), Bolzano-Bozen, Italy
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Vlok M, Solis N, Sadasivan J, Mohamud Y, Warsaba R, Kizhakkedathu J, Luo H, Overall CM, Jan E. Identification of the proteolytic signature in CVB3-infected cells. J Virol 2024; 98:e0049824. [PMID: 38953667 PMCID: PMC11265341 DOI: 10.1128/jvi.00498-24] [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: 03/26/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
Coxsackievirus B3 (CVB3) encodes proteinases that are essential for processing of the translated viral polyprotein. Viral proteinases also target host proteins to manipulate cellular processes and evade innate antiviral responses to promote replication and infection. While some host protein substrates of the CVB3 3C and 2A cysteine proteinases have been identified, the full repertoire of targets is not known. Here, we utilize an unbiased quantitative proteomics-based approach termed terminal amine isotopic labeling of substrates (TAILS) to conduct a global analysis of CVB3 protease-generated N-terminal peptides in both human HeLa and mouse cardiomyocyte (HL-1) cell lines infected with CVB3. We identified >800 proteins that are cleaved in CVB3-infected HeLa and HL-1 cells including the viral polyprotein, known substrates of viral 3C proteinase such as PABP, DDX58, and HNRNPs M, K, and D and novel cellular proteins. Network and GO-term analysis showed an enrichment in biological processes including immune response and activation, RNA processing, and lipid metabolism. We validated a subset of candidate substrates that are cleaved under CVB3 infection and some are direct targets of 3C proteinase in vitro. Moreover, depletion of a subset of TAILS-identified target proteins decreased viral yield. Characterization of two target proteins showed that expression of 3Cpro-targeted cleaved fragments of emerin and aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 modulated autophagy and the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway, respectively. The comprehensive identification of host proteins targeted during virus infection provides insights into the cellular pathways manipulated to facilitate infection. IMPORTANCE RNA viruses encode proteases that are responsible for processing viral proteins into their mature form. Viral proteases also target and cleave host cellular proteins; however, the full catalog of these target proteins is incomplete. We use a technique called terminal amine isotopic labeling of substrates (TAILS), an N-terminomics to identify host proteins that are cleaved under virus infection. We identify hundreds of cellular proteins that are cleaved under infection, some of which are targeted directly by viral protease. Revealing these target proteins provides insights into the host cellular pathways and antiviral signaling factors that are modulated to promote virus infection and potentially leading to virus-induced pathogenesis.
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Affiliation(s)
- Marli Vlok
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nestor Solis
- Department of Oral and Biological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jibin Sadasivan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart and Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
- St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Reid Warsaba
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jayachandran Kizhakkedathu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart and Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
- St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral and Biological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Yonsei Frontier Lab, Yonsei University, Seoul, Republic of Korea
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Perillo T, Capasso R, Pinto A. Neuroimaging of the Most Common Meningitis and Encephalitis of Adults: A Narrative Review. Diagnostics (Basel) 2024; 14:1064. [PMID: 38893591 PMCID: PMC11171665 DOI: 10.3390/diagnostics14111064] [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: 04/24/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Meningitis is the infection of the meninges, which are connective tissue membranes covering the brain, and it most commonly affects the leptomeninges. Clinically, meningitis may present with fever, neck stiffness, altered mental status, headache, vomiting, and neurological deficits. Encephalitis is an infection of the brain, which usually presents with fever, altered mental status, neurological deficits, and seizure. Meningitis and encephalitis are serious conditions which could also coexist, with high morbidity and mortality, thus requiring prompt diagnosis and treatment. Imaging plays an important role in the clinical management of these conditions, especially Magnetic Resonance Imaging. It is indicated to exclude mimics and evaluate the presence of complications. The aim of this review is to depict imaging findings of the most common meningitis and encephalitis.
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Affiliation(s)
- Teresa Perillo
- Department of Radiology, CTO Hospital, AORN dei Colli, 80141 Naples, Italy; (R.C.); (A.P.)
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van Ackeren V, Schmutz S, Pichler I, Ziltener G, Zaheri M, Kufner V, Huber M. Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow. Pathogens 2024; 13:390. [PMID: 38787241 PMCID: PMC11124337 DOI: 10.3390/pathogens13050390] [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: 03/21/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0-4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance.
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Affiliation(s)
| | | | | | | | | | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (V.v.A.); (S.S.); (I.P.); (G.Z.); (M.Z.); (V.K.)
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Janse van Rensburg M, Mans J, Mafuyeka RT, Strydom KA, Myburgh M, van Zyl WB. Diversity of enteroviruses in cerebrospinal fluid specimens collected from hospitalised patients in the private and public sector in South Africa. J Med Virol 2024; 96:e29514. [PMID: 38488486 DOI: 10.1002/jmv.29514] [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: 10/09/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
Enteroviruses cause a wide range of neurological illnesses such as encephalitis, meningitis, and acute flaccid paralysis. Two types of enteroviruses, echovirus E4 and E9, have recently been detected in South Africa and are known to be associated with meningitis and encephalitis. The objective of this study was to characterize enterovirus strains detected in cerebrospinal fluid specimens of hospitalized patients in the private and public sector to identify genotypes associated with meningitis and encephalitis. From January 2019 to June 2021 enterovirus positive nucleic acid samples were obtained from a private (n = 116) and a public sector (n = 101) laboratory. These enteroviruses were typed using a nested set of primers targeting the VP1 region of the enterovirus genome, followed by Sanger sequencing and BLASTn analysis. Forty-two percent (91/217) of the strains could be genotyped. Enterovirus B species was the major species detected in 95% (86/91) of the specimens, followed by species C in 3% (3/91) and species A in 2% (2/91) of the specimens. Echovirus E4 and E9 were the two major types identified in this study and were detected in 70% (64/91) and in 10% (9/91) of specimens, respectively. Echovirus E11 has previously been identified in sewage samples from South Africa, but this study is the first to report Echovirus E11 in cerebrospinal fluid specimens from South African patients. The genotypes identified during this study are known to be associated with encephalitis and meningitis. The predominant detection of echovirus E4 followed by E9 corresponds with other studies conducted in South Africa.
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Affiliation(s)
| | - Janet Mans
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Rendani T Mafuyeka
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
| | | | | | - Walda B van Zyl
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
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Kordi R, Chang AJ, Hicar MD. Seasonal Testing, Results, and Effect of the Pandemic on Coxsackievirus Serum Studies. Microorganisms 2024; 12:367. [PMID: 38399771 PMCID: PMC10893248 DOI: 10.3390/microorganisms12020367] [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: 12/10/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Coxsackieviruses (CVs) are common causes of infections and can be life-threatening. Unfortunately, rigorous studies guiding the clinician in interpreting CV serum antibody titer testing is lacking. To explore the epidemiology of circulating CVs and the serological test utility in aiding diagnosis of CV infections in our community, we obtained results of CV immunologic diagnostic tests between 2018 and 2022 from a regional healthcare database. For CV type A, rare individuals had positive CF (complement fixation) tests whereas all 16 individuals with IFA testing showed at least one positive serotype. For CV type B CF testing, 52.2% of 222 patients had at least one serotype positive, with B5 being most common and also the most common with higher titers (14.8% with ≥1:32). We found a significant reduction in seropositivity rate during the pandemic in 2020 compared to 2018, which continued through 2022 (OR: 0.2, 95% CI: 0.08-0.49, p-value < 0.001). During the pandemic, the seasonal pattern of positive tests varied from the pre-pandemic pattern. Testing for CVs was increased after the first year of the pandemic. Overall, the variability by month and seasonal change in our data support that CF testing can be used to identify recent CVB infection.
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Affiliation(s)
- Ramesh Kordi
- Department of Pediatric Infectious Diseases, State University of New York at Buffalo, Buffalo, NY 14203, USA;
| | - Arthur J. Chang
- Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Mark D. Hicar
- Department of Pediatric Infectious Diseases, State University of New York at Buffalo, Buffalo, NY 14203, USA;
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Honorato L, Ferreira NE, Domingues RB, Senne C, Leite FBVDM, Santos MVD, Fernandes GBP, Paião HGO, Vilas Boas LS, da Costa AC, Tozetto-Mendoza TR, Witkin SS, Mendes-Correa MC. Evaluation of enterovirus concentration, species identification, and cerebrospinal fluid parameters in patients of different ages with aseptic meningitis in São Paulo, Brazil. J Med Virol 2024; 96:e29471. [PMID: 38353496 DOI: 10.1002/jmv.29471] [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: 10/17/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Human enteroviruses (EV) are the most common cause of aseptic meningitis worldwide. Data on EV viral load in cerebrospinal fluid (CSF) and related epidemiological studies are scarce in Brazil. This study investigated the influence of EV viral load on CSF parameters, as well as identifying the involved species. CSF samples were collected in 2018-2019 from 140 individuals at The Hospital das Clínicas, São Paulo. The EV viral load was determined using real-time quantitative polymerase chain reaction, while EV species were identified by 5'UTR region sequencing. Median viral load was 5.72 log10 copies/mL and did not differ by subjects' age and EV species. Pleocytosis was observed in 94.3% of cases, with the highest white blood cell (WBC) counts in younger individuals. Viral load and WBC count were correlated in children (p = 0.0172). Elevated lactate levels were observed in 60% of cases and correlated with the viral load in preteen-teenagers (p = 0.0120) and adults (p = 0.0184). Most individuals had normal total protein levels (70.7%), with higher in preteen-teenagers and adults (p < 0.0001). By sequencing, 8.2% were identified as EV species A and 91.8% as species B. Age-specific variations in CSF characteristics suggest distinct inflammatory responses in each group.
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Affiliation(s)
- Layla Honorato
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Noely Evangelista Ferreira
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Heuder Gustavo Oliveira Paião
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lucy Santos Vilas Boas
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tânia Regina Tozetto-Mendoza
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornel Medicine, New York, New York, USA
| | - Maria Cássia Mendes-Correa
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Rai A, Ammi Z, Anes-Boulahbal DL, Assadi AA, Amrane A, Baaloudj O, Mouni L. Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis. Viruses 2024; 16:170. [PMID: 38399946 PMCID: PMC10891896 DOI: 10.3390/v16020170] [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: 01/05/2024] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.
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Affiliation(s)
- Abdelwahab Rai
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Zohra Ammi
- Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Dahbia Leila Anes-Boulahbal
- Laboratoire des Entérovirus, Département de Virologie, Institut Pasteur d’Alger, Annexe de Sidi-Fredj, Alger 16000, Algeria;
| | - Aymen Amin Assadi
- College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, Riyadh 11432, Saudi Arabia;
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Oussama Baaloudj
- Laboratory of Reaction Engineering, Faculty of Mechanical Engineering and Process Engineering, Université des Sciences et de la Technologie Houari Boumediene, BP 32, Algiers 16111, Algeria;
| | - Lotfi Mouni
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
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Pattnaik A, Dhalech AH, Condotta SA, Corn C, Richer MJ, Snell LM, Robinson CM. A viral-specific CD4 + T cell response protects female mice from Coxsackievirus B3 infection. Front Immunol 2024; 14:1327384. [PMID: 38274806 PMCID: PMC10808549 DOI: 10.3389/fimmu.2023.1327384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background Biological sex plays an integral role in the immune response to various pathogens. The underlying basis for these sex differences is still not well defined. Here, we show that Coxsackievirus B3 (CVB3) induces a viral-specific CD4+ T cell response that can protect female mice from mortality. Methods We inoculated C57BL/6 Ifnar-/- mice with CVB3. We investigated the T cell response in the spleen and mesenteric lymph nodes in male and female mice following infection. Results We found that CVB3 can induce expansion of CD62Llo CD4+ T cells in the mesenteric lymph node and spleen of female but not male mice as early as 5 days post-inoculation, indicative of activation. Using a recombinant CVB3 virus expressing a model CD4+ T cell epitope, we found that this response is due to viral antigen and not bystander activation. Finally, the depletion of CD4+ T cells before infection increased mortality in female mice, indicating that CD4+ T cells play a protective role against CVB3 in our model. Conclusions Overall, these data demonstrated that CVB3 can induce an early CD4 response in female but not male mice and further emphasize how sex differences in immune responses to pathogens affect disease.
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Affiliation(s)
| | | | | | | | | | | | - Christopher M. Robinson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
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Sharif F, Shahzad L, Batool M. The association between climatic factors and waterborne infectious outbreaks with a focus on vulnerability in Pakistan: integrative review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-18. [PMID: 38195067 DOI: 10.1080/09603123.2024.2302040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
Climate change affects the spread of waterborne infectious diseases, yet research on vulnerability to outbreaks remains limited. This integrative review examines how climate variables (temperature and precipitation) relate to human vulnerability factors in Pakistan. By 2060, mean temperatures are projected to rise from 21.68°C (2021) to 30°C, with relatively stable precipitation. The epidemiological investigation in Pakistan identified Diarrhea (119,000 cases/year), Malaria (2.6 million cases/year), and Hepatitis (A and E) as the most prevalent infections. This research highlighted vulnerability factors, including poverty (52% of the population), illiteracy (59% of the population), limited healthcare accessibility (55% of the population), malnutrition (38% of the population), dietary challenges (48% of the population), as well as exposure to water pollution (80% of the population) and air pollution (55% of the population). The findings suggest that the coordinated strategies are vital across health, environmental, meteorological, and social sectors, considering climatic variability patterns and population vulnerability determinants.
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Affiliation(s)
- Faiza Sharif
- Sustainable development study center (SDSC), Government College University, Lahore, Pakistan
| | - Laila Shahzad
- Sustainable development study center (SDSC), Government College University, Lahore, Pakistan
| | - Masooma Batool
- Sustainable development study center (SDSC), Government College University, Lahore, Pakistan
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Uribe FR, González VPI, Kalergis AM, Soto JA, Bohmwald K. Understanding the Neurotrophic Virus Mechanisms and Their Potential Effect on Systemic Lupus Erythematosus Development. Brain Sci 2024; 14:59. [PMID: 38248274 PMCID: PMC10813552 DOI: 10.3390/brainsci14010059] [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: 11/07/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Central nervous system (CNS) pathologies are a public health concern, with viral infections one of their principal causes. These viruses are known as neurotropic pathogens, characterized by their ability to infiltrate the CNS and thus interact with various cell populations, inducing several diseases. The immune response elicited by neurotropic viruses in the CNS is commanded mainly by microglia, which, together with other local cells, can secrete inflammatory cytokines to fight the infection. The most relevant neurotropic viruses are adenovirus (AdV), cytomegalovirus (CMV), enterovirus (EV), Epstein-Barr Virus (EBV), herpes simplex virus type 1 (HSV-1), and herpes simplex virus type 2 (HSV-2), lymphocytic choriomeningitis virus (LCMV), and the newly discovered SARS-CoV-2. Several studies have associated a viral infection with systemic lupus erythematosus (SLE) and neuropsychiatric lupus (NPSLE) manifestations. This article will review the knowledge about viral infections, CNS pathologies, and the immune response against them. Also, it allows us to understand the relevance of the different viral proteins in developing neuronal pathologies, SLE and NPSLE.
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Affiliation(s)
- Felipe R. Uribe
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Valentina P. I. González
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile;
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Karen Bohmwald
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma, Santiago 8910060, Chile
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13
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Ndiaye N, Kébé O, Diarra M, Thiaw FD, Dia M, Dia ND, Sall AA, Fall M, Faye O, Faye M. Non-polio enteroviruses circulation in acute flaccid paralysis cases and sewage in Senegal from 2013 to 2021. Int J Infect Dis 2024; 138:54-62. [PMID: 37995831 DOI: 10.1016/j.ijid.2023.11.020] [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: 07/26/2023] [Revised: 10/30/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
OBJECTIVES Several factors can cause acute flaccid paralysis cases including non-polio enteroviruses. In Senegal, few studies on non-polio enteroviruses (NPEV) have been performed. METHODS Our study assess the molecular epidemiology of non-polio enteroviruses in Senegal from 2013 to 2021 through the previously existing programs for surveillance of polioviruses. RESULTS A total of 3815 stool samples and 281 sewage samples were collected. After virus isolation by cell culture, non-polio enteroviruses-positive isolates were confirmed by reverse transcriptase-quantitative polymerase chain reaction. Following this detection, the positive samples were subjected to molecular characterization. Our data showed that 15.22% and 52.66% were positive in cell culture for non-polio enteroviruses in acute flaccid paralysis surveillance and environmental surveillance, respectively. These non-polio enteroviruses-positive isolates were detected all year round but tend to unequal peaks of circulation, and the age group 0-5 years was more vulnerable to infection (84.4%). Genetic characterization revealed the circulation of enteroviruses species infecting humans (Enterovirus A - Enterovirus D): Enterovirus A (29.2%) and Enterovirus B (63.1%) isolates from both the acute flaccid paralysis surveillance and environmental surveillance while Enterovirus C (5.3%) and Enterovirus D (2.4%) were only isolated from the acute flaccid paralysis surveillance. However, the highly prevalent Enterovirus B species from the acute flaccid paralysis surveillance included echovirus 7 and echovirus 13, whereas coxsackievirus A6 was the predominant species from the environmental surveillance. CONCLUSION This first 8-year period study of NPEV in Senegal showed that NPEV represent important viral etiologies associated with acute flaccid paralysis cases and circulating in environmental surveillance in Senegal and highlighted the need to promote effective long-term strategies for monitoring of non-polio enteroviruses infections.
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Affiliation(s)
- Ndack Ndiaye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal; Département de Biologie Animale, Faculté des sciences et techniques, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal.
| | - Ousmane Kébé
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Maryam Diarra
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Mohamed Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - NDongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Malick Fall
- Département de Biologie Animale, Faculté des sciences et techniques, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
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14
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Fang C, Fu W, Liu N, Zhao H, Zhao C, Yu K, Liu C, Yin Z, Xu L, Xia N, Wang W, Cheng T. Investigating the virulence of coxsackievirus B6 strains and antiviral treatments in a neonatal murine model. Antiviral Res 2024; 221:105781. [PMID: 38097049 DOI: 10.1016/j.antiviral.2023.105781] [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: 10/17/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Coxsackievirus B6 (CVB6), a member of the human enterovirus family, is associated with severe diseases such as myocarditis in children. However, to date, only a limited number of CVB6 strains have been identified, and their characterization in animal models has been lacking. To address this gap, in this study, a neonatal murine model of CVB6 infection was established to compare the replication and virulence of three infectious-clone-derived CVB6 strains in vivo. The results showed that following challenge with a lethal dose of CVB6 strains, the neonatal mice rapidly exhibited a series of clinical signs, such as weight loss, limb paralysis, and death. For the two high-virulence CVB6 strains, histological examination revealed myocyte necrosis in skeletal and cardiac muscle, and immunohistochemistry confirmed the expression of CVB6 viral protein in these tissues. Real-time PCR assay also revealed higher viral loads in the skeletal and cardiac muscle than in other tissues at different time points post infection. Furthermore, the protective effect of passive immunization with antisera and a neutralizing monoclonal antibody against CVB6 infection was evaluated in the neonatal mouse model. This study should provide insights into the pathogenesis of CVB6 and facilitate further research in the development of vaccines and antivirals against CVBs.
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Affiliation(s)
- Changjian Fang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wenkun Fu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Nanyi Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Huan Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Canyang Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Kang Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Che Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Zhichao Yin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Longfa Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wei Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
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15
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Ponomareva NV, Novikova NA. Neurotropic enteroviruses (Picornaviridae: Enterovirus): predominant types, basis of neurovirulence. Vopr Virusol 2023; 68:479-487. [PMID: 38156564 DOI: 10.36233/0507-4088-205] [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: 11/26/2023] [Indexed: 12/30/2023]
Abstract
Enteroviruses are one of the most common causative agents of infectious diseases of the central nervous system. They are characterized by genetic variability, the ability to infect a wide range of cells, including brain microglial cells and astrocytes, and persist in the central nervous system tissue, causing delayed and chronic diseases. The review presents data on the basis of neurovirulence of non-polio enteroviruses and the most common pathogens causing enteroviral neuroinfections.
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Affiliation(s)
- N V Ponomareva
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor
| | - N A Novikova
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor
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16
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Chien YS, Chen FJ, Wu HC, Lin CH, Chang WC, Perera D, Yang JY, Lee MS, Liao YC. Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses. Microbiol Spectr 2023; 11:e0250723. [PMID: 37831475 PMCID: PMC10715163 DOI: 10.1128/spectrum.02507-23] [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: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE By employing a cost-effective approach for complete genome sequencing, the study has enabled the identification of novel enterovirus strains and shed light on the genetic exchange events during outbreaks. The success rate of genome sequencing and the scalability of the protocol demonstrate its practical utility for routine enterovirus surveillance. Moreover, the study's findings of recombinant strains of EVA71 and CVA2 contributing to epidemics in Malaysia and Taiwan emphasize the need for accurate detection and characterization of enteroviruses. The investigation of the whole genome and upstream ORF sequences has provided insights into the evolution and spread of enterovirus subgenogroups. These findings have important implications for the prevention, control, and surveillance of enteroviruses, ultimately contributing to the understanding and management of enterovirus-related illnesses.
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Affiliation(s)
- Yeh-Sheng Chien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chieh-Hua Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Chiung Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Jyh-Yuan Yang
- Research and Diagnosis Center, Centers for Disease Control, Taipei, Taiwan
| | - Min-Shi Lee
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
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17
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de Campos GM, de La-Roque DGL, Lima ARJ, Zucherato VS, de Carvalho E, de Lima LPO, de Queiroz Cattony Neto P, dos Santos MM, Ciccozzi M, Giovanetti M, Haddad R, Alcantara LCJ, Elias MC, Sampaio SC, Covas DT, Kashima S, Slavov SN. Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2. Microorganisms 2023; 11:2744. [PMID: 38004755 PMCID: PMC10672962 DOI: 10.3390/microorganisms11112744] [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: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 11/26/2023] Open
Abstract
The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3-7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population.
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Affiliation(s)
- Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Debora Glenda Lima de La-Roque
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Alex Ranieri Jerônimo Lima
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Victória Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Eneas de Carvalho
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Loyze Paola Oliveira de Lima
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Pedro de Queiroz Cattony Neto
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Murilo Marconi dos Santos
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Marta Giovanetti
- Instututo Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil; (M.G.); (L.C.J.A.)
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Rodrigo Haddad
- Campus Ceilândia, University of Brasília, Federal District of Brazil, Brasília 70910-900, Brazil;
| | | | - Maria Carolina Elias
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Sandra Coccuzzo Sampaio
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Dimas Tadeu Covas
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
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18
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Pattnaik A, Dhalech AH, Condotta SA, Corn C, Richer MJ, Snell LM, Robinson CM. A viral-specific CD4 + T cell response protects female mice from Coxsackievirus B3 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563774. [PMID: 37961130 PMCID: PMC10634798 DOI: 10.1101/2023.10.24.563774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Biological sex plays an integral role in the immune response to various pathogens. The underlying basis for these sex differences is still not well defined. Here, we show that Coxsackievirus B3 (CVB3) induces a viral-specific CD4 + T cell response that can protect female mice from mortality. We found that CVB3 can induce expansion of CD62L lo CD4 + T cells in the mesenteric lymph node and spleen of female but not male mice as early as 5 days post-inoculation, indicative of activation. Using a recombinant CVB3 virus expressing a model CD4 + T cell epitope, we found that this response is due to viral antigen and not bystander activation. Finally, the depletion of CD4 + T cells before infection increased mortality in female mice, indicating that CD4 + T cells play a protective role against CVB3 in our model. Overall, these data demonstrated that CVB3 can induce an early CD4 response in female but not male mice and further emphasize how sex differences in immune responses to pathogens affect disease outcomes.
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19
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Itani TM, Chalapa VI, Slautin VN, Bykov RO, Imangaliev BS, Starikova PK, Sergeev AG, Semenov AV. Non-Polio Enterovirus Surveillance in the Ural Federal District and Western Siberia, 2022: Is There a Need for a Vaccine? Vaccines (Basel) 2023; 11:1588. [PMID: 37896990 PMCID: PMC10610881 DOI: 10.3390/vaccines11101588] [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: 09/11/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Human non-polio enteroviruses (NPEVs) are the etiological agents involved in most cases of hand-foot-and-mouth disease (HFMD), herpangina and aseptic meningitis. Information on the epidemiology profiles of NPEV in the Ural Federal District and Western Siberia is very limited, with no published data available. The aim of this study is to describe NPEV incidence in the Ural Federal District and Western Siberia among patients with different forms of non-polio enterovirus infections (NPEVIs) during 2022, stratified by age and clinical manifestations. A total of 265 samples that tested positive for NPEV using a polymerase chain reaction (PCR) were genotyped by semi-nested PCR for the VP1 gene. The results showed that 21 genotypes were identified among patients in this study. CVA6 was the most common genotype for HFMD. CVA6, along with CVA10, accounted for the majority of herpangina cases, while CVA9 was implicated in most meningitis cases. Sequence and phylogenetic analysis showed that nearly all of the CVA6 strains identified in this study displayed a close genetic relationship to strains identified in other cities in Russia and strains from China. NPEV surveillance allows for monitoring the circulation of clinically relevant genotypes, resulting in continuous data about NPEV epidemiology. This is important for improving case prevention, diagnosis and guiding clinical management.
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Affiliation(s)
- Tarek M. Itani
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Vladislav I. Chalapa
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Vasilii N. Slautin
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Roman O. Bykov
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Bolat S. Imangaliev
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Polina K. Starikova
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
| | - Aleksandr G. Sergeev
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
- Department of Microbiology, Virology and Immunology, Ural State Medical University, 620109 Ekaterinburg, Russia
| | - Aleksandr V. Semenov
- Laboratory of Enteric Virus Infections, Federal Budgetary Institution of Science «Federal Scientific Research Institute of Viral Infections «Virome»», Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Yekaterinburg, Russia; (V.I.C.); (V.N.S.); (R.O.B.); (B.S.I.); (P.K.S.); (A.G.S.); (A.V.S.)
- Institute of Natural Sciences and Mathematics, Ural Federal University Named after the First President of Russia B.N. Yeltsin, 620075 Ekaterinburg, Russia
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20
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Álvarez-Rodríguez B, Buceta J, Geller R. Comprehensive profiling of neutralizing polyclonal sera targeting coxsackievirus B3. Nat Commun 2023; 14:6417. [PMID: 37828013 PMCID: PMC10570382 DOI: 10.1038/s41467-023-42144-2] [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: 01/28/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Despite their fundamental role in resolving viral infections, our understanding of how polyclonal neutralizing antibody responses target non-enveloped viruses remains limited. To define these responses, we obtained the full antigenic profile of multiple human and mouse polyclonal sera targeting the capsid of a prototypical picornavirus, coxsackievirus B3. Our results uncover significant variation in the breadth and strength of neutralization sites targeted by individual human polyclonal responses, which contrasted with homogenous responses observed in experimentally infected mice. We further use these comprehensive antigenic profiles to define key structural and evolutionary parameters that are predictive of escape, assess epitope dominance at the population level, and reveal a need for at least two mutations to achieve significant escape from multiple sera. Overall, our data provide a comprehensive analysis of how polyclonal sera target a non-enveloped viral capsid and help define both immune dominance and escape at the population level.
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Affiliation(s)
- Beatriz Álvarez-Rodríguez
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
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21
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Couderé K, Benschop K, van Steen A, Verweij JJ, Pas S, Cremer J, Edridge AWD, Abd-Elfarag GOE, van Hensbroek MB, Pajkrt D, Murk JL, Wolthers KC. First description and phylogenetic analysis of coxsackie virus A non-polio enteroviruses and parechoviruses A in South Sudanese children. J Med Virol 2023; 95:e29194. [PMID: 37881026 DOI: 10.1002/jmv.29194] [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: 07/30/2023] [Revised: 09/19/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Enteroviruses (EV) and parechoviruses A (PeV-A) are commonly circulating viruses able to cause severe disease. Surveillance studies from sub-Saharan Africa are limited and show high but variable infection rates and a high variation in genotypes. This is the first study to describe EV and PeV-A circulation in children in South Sudan. Of the fecal samples collected, 35% and 10% were positive for EV and PeV-A, respectively. A wide range of genotypes were found, including several rarely described EV and PeV-A types. Coxsackie virus A (CVA) EV-C types, particularly CVA13, were the most dominant EV types. The CVA13 types had a high diversity with the majority belonging to four different previously described clusters. PeV-A1 and -A14 were the most common PeV-A genotypes. A lack of representative data from our and other studies from sub-Saharan Africa demonstrates the need for more systematic surveillance of non-polio EV and PeV-A types in this region.
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Affiliation(s)
- Karen Couderé
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Kimberley Benschop
- National Institute for Public Health and the Environment, RIVM, Bilthoven, The Netherlands
| | - Astrid van Steen
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jaco J Verweij
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Suzan Pas
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jeroen Cremer
- National Institute for Public Health and the Environment, RIVM, Bilthoven, The Netherlands
| | | | - Gasim O E Abd-Elfarag
- Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam University Medical Centers, AMC, Amsterdam, The Netherlands
| | - Michaël B van Hensbroek
- Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam University Medical Centers, AMC, Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, OrganoVIR Labs, Emma Children's Hospital, Amsterdam University Medical Centers, University of Amsterdam, AMC, Amsterdam, The Netherlands
| | - Jean-Luc Murk
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Katja C Wolthers
- Department of Medical Microbiology, OrganoVIR Labs, Amsterdam UMC, AMC, Amsterdam, The Netherlands
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22
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Wang Y, Shah PT, Liu Y, Bahoussi AN, Xing L. Genetic Characteristics and Phylogeographic Dynamics of Echovirus. J Microbiol 2023; 61:865-877. [PMID: 37713068 DOI: 10.1007/s12275-023-00078-w] [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: 06/16/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EV-B) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1-G9. Phylogeographic analysis showed that branches G2-G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.
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Affiliation(s)
- Yan Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Yue Liu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Amina Nawal Bahoussi
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China.
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, 030006, People's Republic of China.
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, 030006, People's Republic of China.
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, People's Republic of China.
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23
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Moreni G, van Eijk H, Koen G, Johannesson N, Calitz C, Benschop K, Cremer J, Pajkrt D, Sridhar A, Wolthers K. Non-Polio Enterovirus C Replicate in Both Airway and Intestine Organotypic Cultures. Viruses 2023; 15:1823. [PMID: 37766230 PMCID: PMC10537321 DOI: 10.3390/v15091823] [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: 08/10/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Non-polio enteroviruses (EV) belonging to species C, which are highly prevalent in Africa, mainly among children, are poorly characterized, and their pathogenesis is mostly unknown as they are difficult to culture. In this study, human airway and intestinal organotypic models were used to investigate tissue and cellular tropism of three EV-C genotypes, EV-C99, CVA-13, and CVA-20. Clinical isolates were obtained within the two passages of culture on Caco2 cells, and all three viruses were replicated in both the human airway and intestinal organotypic cultures. We did not observe differences in viral replication between fetal and adult tissue that could potentially explain the preferential infection of infants by EV-C genotypes. Infection of the airway and the intestinal cultures indicates that they both can serve as entry sites for non-polio EV-C. Ciliated airway cells and enterocytes are the target of infection for all three viruses, as well as enteroendocrine cells for EV-C99.
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Affiliation(s)
- Giulia Moreni
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Hetty van Eijk
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
| | - Gerrit Koen
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
| | - Nina Johannesson
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Carlemi Calitz
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Kimberley Benschop
- National Institute for Public Health and Environment, RIVM, 3721 MA Bilthoven, The Netherlands; (K.B.); (J.C.)
| | - Jeroen Cremer
- National Institute for Public Health and Environment, RIVM, 3721 MA Bilthoven, The Netherlands; (K.B.); (J.C.)
| | - Dasja Pajkrt
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Adithya Sridhar
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Katja Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
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24
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Oguzie JU, Petros BA, Oluniyi PE, Mehta SB, Eromon PE, Nair P, Adewale-Fasoro O, Ifoga PD, Odia I, Pastusiak A, Gbemisola OS, Aiyepada JO, Uyigue EA, Edamhande AP, Blessing O, Airende M, Tomkins-Tinch C, Qu J, Stenson L, Schaffner SF, Oyejide N, Ajayi NA, Ojide K, Ogah O, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Okogbenin S, Okokhere PO, Park DJ, Folarin OA, Komolafe I, Ihekweazu C, Frost SDW, Jackson EK, Siddle KJ, Sabeti PC, Happi CT. Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria. Nat Commun 2023; 14:4693. [PMID: 37542071 PMCID: PMC10403498 DOI: 10.1038/s41467-023-40247-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023] Open
Abstract
Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.
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Affiliation(s)
- Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Brittany A Petros
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
- Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samar B Mehta
- Department of Medicine, University of Maryland Medical Center, Baltimore, MA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Opeoluwa Adewale-Fasoro
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Peace Damilola Ifoga
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ikponmwosa Odia
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Otitoola Shobi Gbemisola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Michael Airende
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Christopher Tomkins-Tinch
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liam Stenson
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Nicholas Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nnenna A Ajayi
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley Ojide
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Onwe Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | | | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Simon D W Frost
- Microsoft Premonition, Redmond, WA, USA
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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25
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de Oliveira LF, Filho DM, Marques BL, Maciel GF, Parreira RC, do Carmo Neto JR, Da Silva PEF, Guerra RO, da Silva MV, Santiago HDC, Birbrair A, Kihara AH, Dias da Silva VJ, Glaser T, Resende RR, Ulrich H. Organoids as a novel tool in modelling infectious diseases. Semin Cell Dev Biol 2023; 144:87-96. [PMID: 36182613 DOI: 10.1016/j.semcdb.2022.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022]
Abstract
Infectious diseases worldwide affect human health and have important societal impacts. A better understanding of infectious diseases is urgently needed. In vitro and in vivo infection models have brought notable contributions to the current knowledge of these diseases. Organoids are multicellular culture systems resembling tissue architecture and function, recapitulating many characteristics of human disease and elucidating mechanisms of host-infectious agent interactions in the respiratory and gastrointestinal systems, the central nervous system and the skin. Here, we discuss the applicability of the organoid technology for modeling pathogenesis, host response and features, which can be explored for the development of preventive and therapeutic treatments.
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Affiliation(s)
- Lucas Felipe de Oliveira
- Departamento de Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil; Instituto Nacional de Ciência e Tecnologia de Medicina Regenerativa, Rio de Janeiro, RJ, Brazil
| | - Daniel Mendes Filho
- Departamento de Fisiologia, Escola Médica de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Bruno Lemes Marques
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal deGoiás, Goiânia, GO, Brazil
| | | | | | - José Rodrigues do Carmo Neto
- Departamento de Biociência e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | | | - Rhanoica Oliveira Guerra
- Departamento de Microbiologia, Imunologia eParasitologia, Instituto de Ciências Naturais e Biológicas, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marcos Vinicius da Silva
- Departamento de Microbiologia, Imunologia eParasitologia, Instituto de Ciências Naturais e Biológicas, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Helton da Costa Santiago
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Belo Horizonte, MG, Brazil
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; Department of Radiology, Columbia University Medical Center, New York, NY, USA; Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Belo Horizonte, MG, Brazil
| | - Alexandre H Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Valdo José Dias da Silva
- Departamento de Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil; Instituto Nacional de Ciência e Tecnologia de Medicina Regenerativa, Rio de Janeiro, RJ, Brazil
| | - Talita Glaser
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Rodrigo R Resende
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Belo Horizonte, MG, Brazil
| | - Henning Ulrich
- Instituto Nacional de Ciência e Tecnologia de Medicina Regenerativa, Rio de Janeiro, RJ, Brazil; Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
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26
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Isaacs SR, Roy A, Dance B, Ward EJ, Foskett DB, Maxwell AJ, Rawlinson WD, Kim KW, Craig ME. Enteroviruses and risk of islet autoimmunity or type 1 diabetes: systematic review and meta-analysis of controlled observational studies detecting viral nucleic acids and proteins. Lancet Diabetes Endocrinol 2023:S2213-8587(23)00122-5. [PMID: 37390839 DOI: 10.1016/s2213-8587(23)00122-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Enteroviruses are routinely detected with molecular methods within large cohorts that are at risk of type 1 diabetes. We aimed to examine the association between enteroviruses and either islet autoimmunity or type 1 diabetes. METHODS For this systematic review and meta-analysis, we searched PubMed and Embase for controlled observational studies from inception until Jan 1, 2023. Cohort or case-control studies were eligible if enterovirus RNA or protein were detected in individuals with outcomes of islet autoimmunity or type 1 diabetes. Studies in pregnancy or other types of diabetes were excluded. Data extraction and appraisal involved author contact and deduplication, which was done independently by three reviewers. Study quality was assessed with the Newcastle-Ottawa Scale and National Health and Medical Research Council levels of evidence. Pooled and subgroup meta-analyses were done in RevMan version 5.4, with random effects models and Mantel-Haenszel odds ratios (ORs; 95% CIs). The study is registered with PROSPERO, CRD42021278863. FINDINGS The search returned 3266 publications, with 897 full texts screened. Following deduplication, 113 eligible records corresponded to 60 studies (40 type 1 diabetes; nine islet autoimmunity; 11 both), comprising 12077 participants (5981 cases; 6096 controls). Study design and quality varied, generating substantial statistical heterogeneity. Meta-analysis of 56 studies showed associations between enteroviruses and islet autoimmunity (OR 2·1, 95% CI 1·3-3·3; p=0·002; n=18; heterogeneity χ2/df 2·69; p=0·0004; I2=63%), type 1 diabetes (OR 8·0, 95% CI 4·9-13·0; p<0·0001; n=48; χ2/df 6·75; p<0·0001; I2=85%), or within 1 month of type 1 diabetes (OR 16·2, 95% CI 8·6-30·5; p<0·0001; n=28; χ2/df 3·25; p<0·0001; I2=69%). Detection of either multiple or consecutive enteroviruses was associated with islet autoimmunity (OR 2·0, 95% CI 1·0-4·0; p=0·050; n=8). Detection of Enterovirus B was associated with type 1 diabetes (OR 12·7, 95% CI 4·1-39·1; p<0·0001; n=15). INTERPRETATION These findings highlight the association between enteroviruses and islet autoimmunity or type 1 diabetes. Our data strengthen the rationale for vaccine development targeting diabetogenic enterovirus types, particularly those within Enterovirus B. Prospective studies of early life are needed to elucidate the role of enterovirus timing, type, and infection duration on the initiation of islet autoimmunity and the progression to type 1 diabetes. FUNDING Environmental Determinants of Islet Autoimmunity, European Association for the Study of Diabetes, JDRF, Australian National Health and Medical Research Council, and University of New South Wales.
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Affiliation(s)
- Sonia R Isaacs
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Anju Roy
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Brieana Dance
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Emily J Ward
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Dylan B Foskett
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Anna J Maxwell
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - William D Rawlinson
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ki Wook Kim
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Maria E Craig
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia; Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Westmead, Sydney, NSW, Australia; Specialty of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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27
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Sittikul P, Batty EM, Yodsawat P, Nuanpirom J, Kosoltanapiwat N, Sangket U, Chatchen S, Day NPJ, Thaipadungpanit J. Diversity of Human Enterovirus Co-Circulations in Five Kindergartens in Bangkok between July 2019 and January 2020. Viruses 2023; 15:1397. [PMID: 37376696 DOI: 10.3390/v15061397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Human enterovirus causes various clinical manifestations in the form of rashes, febrile illness, flu-like illness, uveitis, hand-foot-mouth disease (HFMD), herpangina, meningitis, and encephalitis. Enterovirus A71 and coxsackievirus are significant causes of epidemic HFMD worldwide, especially in children aged from birth to five years old. The enterovirus genotype variants causing HFMD epidemics have been reported increasingly worldwide in the last decade. We aim to use simple and robust molecular tools to investigate human enteroviruses circulating among kindergarten students at genotype and subgenotype levels. With the partial 5'-UTR sequencing analysis as a low-resolution preliminary grouping tool, ten enterovirus A71 (EV-A71) and coxsackievirus clusters were identified among 18 symptomatic cases and 14 asymptomatic cases in five kindergartens in Bangkok, Thailand, between July 2019 and January 2020. Two occurrences of a single clone causing an infection cluster were identified (EV-A71 C1-like subgenotype and coxsackievirus A6). Random amplification-based sequencing using MinION (Oxford Nanopore Technology) helped identify viral transmission between two closely related clones. Diverse genotypes co-circulating among children in kindergartens are reservoirs for new genotype variants emerging, which might be more virulent or better at immune escape. Surveillance of highly contagious enterovirus in communities is essential for disease notifications and controls.
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Affiliation(s)
- Pichamon Sittikul
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Elizabeth M Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Prasert Yodsawat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Jiratchaya Nuanpirom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Unitsa Sangket
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Center for Genomics and Bioinformatics Research, Faculty of Science Prince of Songkla University, Songkhla 90110, Thailand
| | - Supawat Chatchen
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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28
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Tomatis Souverbielle C, Erdem G, Sánchez PJ. Update on nonpolio enterovirus and parechovirus infections in neonates and young infants. Curr Opin Pediatr 2023; 35:380-389. [PMID: 36876331 DOI: 10.1097/mop.0000000000001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
PURPOSE OF REVIEW To review the epidemiology, clinical manifestations, and treatment strategies of nonpolio enterovirus and parechovirus (PeV) infections, and identify research gaps. RECENT FINDINGS There is currently no approved antiviral agent for enterovirus or PeV infections, although pocapavir may be provided on a compassionate basis. Elucidation of the structure and functional features of enterovirus and PeV may lead to novel therapeutic strategies, including vaccine development. SUMMARY Nonpolio human enterovirus and PeV are common childhood infections that are most severe among neonates and young infants. Although most infections are asymptomatic, severe disease resulting in substantial morbidity and mortality occurs worldwide and has been associated with local outbreaks. Long-term sequelae are not well understood but have been reported following neonatal infection of the central nervous system. The lack of antiviral treatment and effective vaccines highlight important knowledge gaps. Active surveillance ultimately may inform preventive strategies.
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Affiliation(s)
| | - Guliz Erdem
- Department of Pediatrics, Section of Infectious Diseases
| | - Pablo J Sánchez
- Department of Pediatrics, Section of Infectious Diseases
- Division of Neonatology, Department of Pediatrics, Nationwide Children's Hospital, Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Perinatal Research, The Ohio State University College of Medicine, Columbus, Ohio, USA
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29
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Root-Bernstein R, Chiles K, Huber J, Ziehl A, Turke M, Pietrowicz M. Clostridia and Enteroviruses as Synergistic Triggers of Type 1 Diabetes Mellitus. Int J Mol Sci 2023; 24:ijms24098336. [PMID: 37176044 PMCID: PMC10179352 DOI: 10.3390/ijms24098336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
What triggers type 1 diabetes mellitus (T1DM)? One common assumption is that triggers are individual microbes that mimic autoantibody targets such as insulin (INS). However, most microbes highly associated with T1DM pathogenesis, such as coxsackieviruses (COX), lack INS mimicry and have failed to induce T1DM in animal models. Using proteomic similarity search techniques, we found that COX actually mimicked the INS receptor (INSR). Clostridia were the best mimics of INS. Clostridia antibodies cross-reacted with INS in ELISA experiments, confirming mimicry. COX antibodies cross-reacted with INSR. Clostridia antibodies further bound to COX antibodies as idiotype-anti-idiotype pairs conserving INS-INSR complementarity. Ultraviolet spectrometry studies demonstrated that INS-like Clostridia peptides bound to INSR-like COX peptides. These complementary peptides were also recognized as antigens by T cell receptor sequences derived from T1DM patients. Finally, most sera from T1DM patients bound strongly to inactivated Clostridium sporogenes, while most sera from healthy individuals did not; T1DM sera also exhibited evidence of anti-idiotype antibodies against idiotypic INS, glutamic acid decarboxylase, and protein tyrosine phosphatase non-receptor (islet antigen-2) antibodies. These results suggest that T1DM is triggered by combined enterovirus-Clostridium (and possibly combined Epstein-Barr-virus-Streptococcal) infections, and the probable rate of such co-infections approximates the rate of new T1DM diagnoses.
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Affiliation(s)
| | - Kaylie Chiles
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Jack Huber
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Alison Ziehl
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Miah Turke
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Maja Pietrowicz
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
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30
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Fu L, Zhang XY, Jin WP, Wang C, Qian SS, Wang MJ, Wang WH, Meng SL, Guo J, Wang ZJ, Chen XQ, Shen S. Identification of a Conserved, Linear Epitope on VP3 of Enterovirus A Species Recognized by a Broad-Spectrum Monoclonal Antibody. Viruses 2023; 15:v15041028. [PMID: 37113008 PMCID: PMC10145497 DOI: 10.3390/v15041028] [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: 03/27/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Outbreaks of hand, foot and mouth disease (HFMD) have occurred frequently in the Asian-Pacific region over the last two decades, caused mainly by the serotypes in Enterovirus A species. High-quality monoclonal antibodies (mAbs) are needed to improve the accuracy and efficiency of the diagnosis of enteroviruses associated HFMD. In this study, a mAb 1A11 was generated using full particles of CV-A5 as an immunogen. In indirect immunofluorescence and Western blotting assays, 1A11 bound to the viral proteins of CV-A2, CV-A4, CV-A5, CV-A6, CV-A10, CV-A16, and EV-A71 of the Enterovirus A and targeted VP3. It has no cross-reactivity to strains of Enterovirus B and C. By mapping with over-lapped and truncated peptides, a minimal and linear epitope 23PILPGF28 was identified, located at the N-terminus of the VP3. A BLAST sequence search of the epitope in the NCBI genus Enterovirus (taxid: 12059) protein database indicates that the epitope sequence is highly conserved among the Enterovirus A species, but not among the other enterovirus species, first reported by us. By mutagenesis analysis, critical residues for 1A11 binding were identified for most serotypes of Enterovirus A. It may be useful for the development of a cost-effective and pan-Enterovirus A antigen detection for surveillance, early diagnosis and differentiation of infections caused by the Enterovirus A species.
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Affiliation(s)
- Lie Fu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xiao-Yu Zhang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Wei-Ping Jin
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Chen Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Sha-Sha Qian
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Meng-Jun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Wen-Hui Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Sheng-Li Meng
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Jing Guo
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Ze-Jun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xiao-Qi Chen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Shuo Shen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
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31
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Favoino E, Grapsi E, Barbuti G, Liakouli V, Ruscitti P, Foti C, Giacomelli R, Perosa F. Systemic sclerosis and primary biliary cholangitis share an antibody population with identical specificity. Clin Exp Immunol 2023; 212:32-38. [PMID: 36715304 PMCID: PMC10081109 DOI: 10.1093/cei/uxad012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Anti-centromere (ACA) and antimitochondrial antibodies (AMA) are specific for limited-cutaneous systemic sclerosis (lcSSc) and primary biliary cholangitis (PBC), respectively, and can coexist in up to 25 and 30% of SSc and PBC patients. Here, we evaluated whether anti-centromeric protein A (CENP-A) antibodies cross-react with mitochondrial antigens. To this end, sera from two lcSSc patients (pt1 and pt4), one of them (pt4) also affected by PBC, were used as the source of ACA, previously shown to recognize different groups of amino acids (motifs) in the CENP-A region spanning amino acids 1-17 (Ap1-17). Pt1 and pt4 Ap1-17-specific IgG were purified by affinity-chromatography on insolubilized Ap1-17-peptide column and tested by western blotting with nuclear and cytoplasmic protein extract from HeLa cells. Immunoreactive proteins were identified by mass spectrometry and validated by immunodot. The results showed that affinity-purified SSc/PBC pt4 anti-Ap1-17 and not SSc pt1 anti-Ap1-17 Ab, specifically cross-reacted with the E2 component of the mitochondrial pyruvate dehydrogenase complex (PDC-E2), the major mitochondrial autoantigen in PBC. Sequence homology analysis indicated that the motif A-x-x-P-x-A-P recognized by pt4 anti-Ap1-17 IgG and shared by CENP-A and PDC-E2, is also expressed by some members of the Human Herpesvirus family, suggesting that they may trigger the production of these cross-reacting antibodies.
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Affiliation(s)
- Elvira Favoino
- Department of Interdisciplinary Medicine, Rheumatic and Systemic Autoimmune Diseases Unit, University of Bari Medical School, Bari, Italy
| | - Ettore Grapsi
- Department of Interdisciplinary Medicine, Rheumatic and Systemic Autoimmune Diseases Unit, University of Bari Medical School, Bari, Italy
| | - Giovanna Barbuti
- Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Vasiliki Liakouli
- Department of Precision Medicine, Rheumatology Section, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Piero Ruscitti
- Department of Biotechnological and Applied Clinical Sciences, Rheumatology Unit, University of L’Aquila, L’Aquila, Italy
| | - Caterina Foti
- Department of Biomedical Science and Human Oncology, Unit of Dermatology, University of Bari Medical School, Bari, Italy
| | - Roberto Giacomelli
- Department of Medicine, Rheumatology and Immunology Unit, University of Rome “Campus Biomedico”, Rome, Italy
| | - Federico Perosa
- Department of Interdisciplinary Medicine, Rheumatic and Systemic Autoimmune Diseases Unit, University of Bari Medical School, Bari, Italy
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32
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A One-Step Reverse-transcription Recombinase aided PCR Assay for the Rapid and Sensitive Detection of Human Enteroviruses. BIOSAFETY AND HEALTH 2023. [DOI: 10.1016/j.bsheal.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023] Open
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33
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Kim MJ, Lee JE, Kim KG, Park DW, Cho SJ, Kim TS, Kee HY, Kim SH, Park HJ, Seo MH, Chung JK, Seo JJ. Long-term sentinel surveillance of enteroviruses in Gwangju, South Korea, 2011-2020. Sci Rep 2023; 13:2798. [PMID: 36797345 PMCID: PMC9933826 DOI: 10.1038/s41598-023-29461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Human enteroviruses (EVs) are associated with a broad spectrum of diseases. To understand EV epidemiology, we present longitudinal data reflecting changing EV prevalence patterns in South Korea. We collected 7160 specimens from patients with suspected EV infections in ten hospitals in Gwangju, Korea during 2011-2020. RNA extraction and real-time reverse transcription polymerase chain reaction using EV-specific probes and primers were performed. EV genotyping and phylogenetic analysis were performed; EVs were detected in 3076 samples (43.0%), and the annual EV detection rate varied. EV infection rates did not differ with sex, and children aged ≤ 4 years were the most prone to EV infection; this trend did not change over time. Overall, 35 different EV types belonging to four distinctive species and rhinoviruses were identified. Although serotype distribution changed annually, the most frequently observed EVs were EV-A71 (13.1% of the cases), CVA6 (8.3%), CVB5 (7.6%), CVA16 (7.6%), CVA10 (7.5%), E18 (7.5%), E30 (7.0%), and E11 (5.0%) during 2011-2020. The predominant EV genotypes by clinical manifestation were CVB5 for aseptic meningitis; EV-A71 for hand, foot, and mouth disease cases; and CVA10 for herpangina. These results will aid the development of vaccines against EV infection and allow comprehensive disease control.
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Affiliation(s)
- Min Ji Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea, 61954.
| | - Ji-eun Lee
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Kwang gon Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Duck Woong Park
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Sun Ju Cho
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Tae sun Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Hye-young Kee
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Sun-Hee Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Hye jung Park
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Mi Hee Seo
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Jae Keun Chung
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Jin-jong Seo
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
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Eastman C, Tapprich WE. RNA Structure in the 5' Untranslated Region of Enterovirus D68 Strains with Differing Neurovirulence Phenotypes. Viruses 2023; 15:295. [PMID: 36851509 PMCID: PMC9959730 DOI: 10.3390/v15020295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Enterovirus-D68 (EV-D68) is a positive-sense single-stranded RNA virus within the family Picornaviridae. EV-D68 was initially considered a respiratory virus that primarily affected children. However, in 2014, EV-D68 outbreaks occurred causing the expected increase in respiratory illness cases, but also an increase in acute flaccid myelitis cases (AFM). Sequencing of 2014 outbreak isolates revealed variations in the 5' UTR of the genome compared to the historical Fermon strain. The structure of the 5' UTR RNA contributes to enterovirus virulence, including neurovirulence in poliovirus, and could contribute to neurovirulence in contemporary EV-D68 strains. In this study, the secondary and tertiary structures of 5' UTR RNA from the Fermon strain and 2014 isolate KT347251.1 are analyzed and compared. Secondary structures were determined using SHAPE-MaP and TurboFold II and tertiary structures were predicted using 3dRNAv2.0. Comparison of RNA structures between the EV-D68 strains shows significant remodeling at the secondary and tertiary levels. Notable secondary structure changes occurred in domains II, IV and V. Shifts in the secondary structure changed the tertiary structure of the individual domains and the orientation of the domains. Our comparative structural models for EV-D68 5' UTR RNA highlight regions of the molecule that could be targeted for treatment of neurotropic enteroviruses.
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Affiliation(s)
| | - William E. Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
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35
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Guo Q, Zhao H, Zhang Y, Wang X, Yu Q, Tan Z, Lu H, Xiao J, Ji T, Zhu S, Wang D, Yang Q, Han Z, Xu W, Yan D. Genetic characterization and molecular epidemiology of Coxsackievirus A12 from mainland China during 2010-2019. Front Microbiol 2022; 13:988538. [PMID: 36620057 PMCID: PMC9811122 DOI: 10.3389/fmicb.2022.988538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Coxsackievirus A12 (CVA12) is an enterovirus that has been isolated in many countries in recent years. However, studies on CVA12 are limited, and its effective population size, evolutionary dynamics and recombination patterns have not been clarified now. In this study, we described the phylogenetic characteristics of 16 CVA12 strains isolated from pediatric HFMD patients in mainland China from 2010 to 2019. Comparison of the nucleotide sequences and amino acid sequences with the CVA12 prototype strain revealed that the 16 CVA12 strains are identical in 78.8-79% and 94-94.2%, respectively. A phylodynamic analysis based on the 16 full-length VP1 sequences from this study and 21 sequences obtained from GenBank revealed a mean substitution rate of 6.61 × 10-3 substitutions/site/year (95% HPD: 5.16-8.20 × 10-3), dating the time to most recent common ancestor (tMRCA) of CVA12 back to 1946 (95% HPD: 1942-1947). The Bayesian skyline plot showed that the effective population size has experienced twice dynamic fluctuations since 2007. Phylogeographic analysis identified two significant migration pathways, indicating the existence of cross-provincial transmission of CVA12 in mainland China. Recombination analysis revealed two recombination patterns between 16 CVA12 strains and other EV-A, suggesting that there may be extensive genetic exchange between CVA12 and other enteroviruses. In summary, a total of 16 full-length CVA12 strains were reported in this study, providing valuable references for further studies of CVA12 worldwide.
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Affiliation(s)
- Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Da Zhou Vocational College of Chinese Medicine, Dazhou, China
| | - Hehe Zhao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong, China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, China
| | - Zhaolin Tan
- Tianjin Center for Disease Control and Prevention, Tianjin, China
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Tianjiao Ji
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongyan Wang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Qian Yang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Zhenzhi Han
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,*Correspondence: Dongmei Yan,
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Zhou Y, Zhou C, Wang K, Qiu Q, Cheng Y, Li Y, Cui P, Liang L, Li P, Deng X, Wang L, Zheng W, Gong H, Wang F, Xu M, Chu JJH, Turtle L, Yu H. Diagnostic performance of different specimens in detecting enterovirus A71 in children with hand, foot and mouth disease. Virol Sin 2022; 38:268-275. [PMID: 36371008 PMCID: PMC10176262 DOI: 10.1016/j.virs.2022.11.004] [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: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Hand, foot and mouth disease (HFMD) is a major public health problem among children in the Asia-Pacific region. The optimal specimen for HFMD virological diagnosis remains unclear. Enterovirus A71 (EV-A71) neutralizing antibody titres detected in paired sera were considered the reference standard for calculating the sensitivity, specificity, positive and negative predictive value of throat swabs, rectal swabs, stool, blood samples and cerebrospinal fluid (CSF) by RT-PCR or ELISA assay. In this study, clinical samples from 276 HFMD patients were collected for analysing the sensitivity of different kind of specimens. Our results showed that stool had the highest sensitivity (88%, 95% CI: 74%-96%) and agreement with the reference standard (91%). The order of diagnostic yield for EV-A71 infection was stool sample ≥ rectal swab > throat swab > blood sample > CSF sample, and using a combination of clinical samples improved sensitivity for enterovirus detection. The sensitivity of ELISA for IgM antibody detection in sterile-site specimens was significantly higher than that of RT-PCR (serum/plasma: 62% vs. 2%, CSF: 47% vs. 0%) (P < 0.002). In conclusion, our results suggest that stool has the highest diagnostic yield for EV-A71-infected HFMD. If stool is unavailable, rectal swabs can be collected to achieve a similar diagnostic yield. Otherwise, throat swabs may be useful in detecting positive samples. Although IgM in blood or CSF is diagnostically accurate, it lacks sensitivity, missing 40%-50% of cases. The higher proportion of severe cases and shorter interval between onset and sampling contributed to the increase in congruency between clinical testing and the serological reference standard.
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Affiliation(s)
- Yonghong Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Chongchen Zhou
- Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, 450003, China
| | - Kai Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Yibing Cheng
- Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, 450003, China
| | - Yu Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - Peng Cui
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Lu Liang
- West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Peng Li
- Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, 450003, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Fang Wang
- Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, 450003, China
| | - Meng Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, L69 7BE, UK; Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China.
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37
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Lee CH, Huang PN, Mwale PF, Wang WC, Leu SJ, Tseng SN, Shih SR, Chiang LC, Mao YC, Tsai BY, Dlamini NB, Nguyen TC, Tsai CH, Yang YY. The Bottlenecks of Preparing Virus Particles by Size Exclusion for Antibody Generation. Int J Mol Sci 2022; 23:12967. [PMID: 36361757 PMCID: PMC9653933 DOI: 10.3390/ijms232112967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 08/30/2023] Open
Abstract
Enterovirus 71 (EV71) is the major etiological agent contributing to the development of hand-foot-mouth disease (HFMD). There are not any global available vaccines or antibody drugs against EV71 released yet. In this study, we perform the virus immunization in a cost-effective and convenient approach by preparing virus particles from size exclusion and immunization of chicken. Polyclonal yolk-immunoglobulin (IgY) was simply purified from egg yolk and monoclonal single-chain variable fragments (scFv) were selected via phage display technology with two scFv libraries containing 6.0 × 106 and 1.3 × 107 transformants. Specific clones were enriched after 5 rounds of bio-panning and four identical genes were classified after the sequence analysis. Moreover, the higher mutation rates were revealed in the CDR regions, especially in the CDR3. IgY showed specific binding activities to both EV71-infected and Coxsackievirus 16-infected cell lysates and high infectivity inhibitory activity of EV71. However, while IgY detected a 37 kDa protein, the selected scFv seemingly detected higher size proteins which could be cell protein instead of EV71 proteins. Despite the highly effective chicken antibody generation, the purity of virus particles prepared by size exclusion is the limitation of this study, and further characterization should be carried out rigorously.
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Affiliation(s)
- Chi-Hsin Lee
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan 333423, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | - Pharaoh Fellow Mwale
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Wei-Chu Wang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Sy-Jye Leu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Sung-Nien Tseng
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan 333423, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan 333423, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | - Liao-Chun Chiang
- College of Life Sciences, National Tsing Hua University, Hsinchu 300040, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Bor-Yu Tsai
- Navi Bio-Therapeutics Inc., Taipei 10351, Taiwan
| | - Nhlanhla Benedict Dlamini
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Tien-Cuong Nguyen
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Chen-Hsin Tsai
- Department of Ophthalmology, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Yi-Yuan Yang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
- Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei 110301, Taiwan
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Faleye TO, Skidmore P, Elyaderani A, Adhikari S, Kaiser N, Smith A, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.09.25.22280344. [PMID: 36203558 PMCID: PMC9536034 DOI: 10.1101/2022.09.25.22280344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.
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Affiliation(s)
- Temitope O.C. Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Skidmore
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Amir Elyaderani
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicole Kaiser
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Abriana Smith
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Allan Yanez
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Tyler Perleberg
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
- OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, Tempe, AZ, USA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
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Hu L, Zhou L, Wang P, Maimaiti H, Lu Y. Molecular characteristics of a coxsackievirus A12 strain in Zhejiang of China, 2019. Virol J 2022; 19:160. [PMID: 36224635 PMCID: PMC9555000 DOI: 10.1186/s12985-022-01892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Background Enterovirus A (EV-A), such as enterovirus A71 (EV-A71), generally causes hand, foot, and mouth disease (HFMD). However, limited studies focused on uncommon enterovirus serotypes such as coxsackievirus A12 (CV-A12). This study aimed to provide evidence to determine the molecular characteristics of a CV-A12 strain isolated in Zhejiang province, China. Methods In routine surveillance of HFMD, we identified a child case with CV-A12 infection in 2019 in Zhejiang province, China. Enterovirus was examined by using real-time reverse transcription-PCR (qRT-PCR). A partial VP1 sequence was amplified to determine the serotype, and then a full-length CV-A12 genome was sequenced. Nucleotide and amino acid similarity was calculated with those CV-A12 strains available in GenBank. Recombination was detected using RDP 4 and SimPlot. Furthermore, phylogenetic analysis was conducted by using BEAST 1.10, and protein modeling was performed with I-TASSER webserver. Results A full-length CV-A12 genome PJ201984 was isolated in a Chinese child with HFMD. The similarities with complete coding sequences of the CV-A12 strains in GenBank ranged between 79.3–100% (nucleotide) and 94.4–100% (amino acid), whereas it was 88.7–100.0% (nucleotide) and 97.2–100% (amino acid) when excluding the CV-A12 prototype strain Texas-12. In PJ201984, amino acid variations were more divergent in P2 and P3 regions than those in P1; the majority of those variations in VP1 (13/15) and VP4 (7/8) were similar to those documented in recently isolated CV-A12 strains in China. Furthermore, recombination was identified in P2 region, which involved a CV-A5 strain collected in China. Phylogenetic analysis revealed that PJ201984 clustered together with multiple CV-A12 strains isolated in China and the Netherlands during 2013–2018, as compared to another cluster consisting of CV-A12 strains in China and France during 2009–2015. Additionally, protein models of VP1 and VP4 in PJ201984 were well predicted to be similar to VP1 protein of EV-A71 and VP4 protein of coxsackievirus A21, respectively. Conclusions The full-length CV-A12 genome was characterized to have common recombination in P2 region and be phylogenetically related to those CV-A12 strains isolated in recent years, suggesting a continual spread in China. It warrants strengthening the routine surveillance for uncommon enterovirus serotypes, particularly on possible recombination and variation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01892-1.
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Affiliation(s)
- Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Pingping Wang
- Pujiang Center for Disease Control and Prevention, Jinhua, 321000, Zhejiang, China
| | - Hairenguli Maimaiti
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China.
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40
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Novikov DV, Melentev DA. [Enteroviral (Picornaviridae: Enterovirus) (nonpolio) vaccines]. Vopr Virusol 2022; 67:185-192. [PMID: 35831961 DOI: 10.36233/0507-4088-111] [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: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Non-polio enteroviruses (NPEVs) are ubiquitous and are one of the main causative agents of viral infections in children. NPEVs most commonly infect newborns and young children, due to their lack of antibodies. In children, clinical manifestations can range from acute febrile illness to severe complications that require hospitalization and lead in some cases to disability or death. NPEV infections can have severe consequences, such as polio-like diseases, serous meningitis, meningoencephalitis, myocarditis, etc. The most promising strategy for preventing such diseases is vaccination. No less than 53 types of NPEVs have been found to circulate in Russia. However, of epidemic importance are the causative agents of exanthemic forms of the disease, aseptic meningitis and myocarditis. At the same time, the frequency of NPEV detection in the constituent entities of the Russian Federation is characterized by uneven distribution and seasonal upsurges. The review discusses the epidemic significance of different types of enteroviruses, including those relevant to the Russian Federation, as well as current technologies used to create enterovirus vaccines for the prevention of serious diseases.
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Affiliation(s)
- D V Novikov
- 1Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology
| | - D A Melentev
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology; N.I. Lobachevsky State University of Nizhny Novgorod
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41
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Puri BK, Lee GS, Schwarzbach A. Human enteroviral infection in fibromyalgia: a case-control blinded study. Rev Assoc Med Bras (1992) 2022; 68:xxx. [PMID: 35830017 PMCID: PMC9574953 DOI: 10.1590/1806-9282.20220139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/20/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE This study aimed to test the hypothesis that fibromyalgia is associated with a human enteroviral infection. METHODS Venous peripheral blood samples from 27 patients fulfilling the American College of Rheumatology revised diagnostic criteria for fibromyalgia and from 26 age- and sex-matched controls, who underwent immunofluorescence assays for coxsackievirus A7 IgG, coxsackievirus B1 IgG, coxsackievirus A7 IgA, coxsackievirus B1 IgA, echovirus IgG, and echovirus IgA. These immunological tests were performed blind to group status. RESULTS There were no significant differences between the patient and control groups in respect of positive results for coxsackievirus A7 IgG (p=0.467), coxsackievirus B1 IgG (p=0.491), coxsackievirus A7 IgA (p=0.586), coxsackievirus B1 IgA (p=0.467), echovirus IgG (p=0.236), and echovirus IgA (p=1). CONCLUSIONS The results of this systematic study do not support the hypothesis that fibromyalgia is associated with infection by a human enterovirus.
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Affiliation(s)
- Basant K Puri
- University of Winchester - Winchester, United Kingdom
| | - Gary S Lee
- University of Southampton - Southampton, United Kingdom
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Human FcRn Is a Two-in-One Attachment-Uncoating Receptor for Echovirus 18. mBio 2022; 13:e0116622. [PMID: 35862785 PMCID: PMC9426509 DOI: 10.1128/mbio.01166-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virus-receptor interactions determine viral host range and tissue tropism. CD55 and human neonatal Fc receptor (FcRn) were found to be the binding and uncoating receptors for some of the echovirus-related enterovirus species B serotypes in our previous study. Echovirus 18 (E18), as a member of enterovirus species B, is a significant causative agent of aseptic meningitis and viral encephalitis in children. However, it does not use CD55 as a critical host factor. We conducted CRISPR/Cas9 knockout screening to determine the receptors and entry mechanisms and identified FcRn working as a dual-function receptor for E18. Knockout of FCGRT and B2M, which encode the two subunits of FcRn, prevented infection by E18 and other echoviruses in the same physiological cluster. We then elucidated the underlying molecular mechanism of receptor recognition by E18 using cryogenic electron microscopy. The binding of the FCGRT subunit to the canyon region rotates the residues around the pocket, triggering the release of the pocket factor as observed for other enterovirus species B members.
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43
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O’Neal AJ, Glass KA, Emig CJ, Vitug AA, Henry SJ, Shungu DC, Mao X, Levine SM, Hanson MR. Survey of Anti-Pathogen Antibody Levels in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Proteomes 2022; 10:proteomes10020021. [PMID: 35736801 PMCID: PMC9228258 DOI: 10.3390/proteomes10020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/06/2023] Open
Abstract
Infectious pathogens are implicated in the etiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) because of the occurrence of outbreaks of the disease. While a number of different infectious agents have been associated with the onset of ME/CFS, the identity of a specific organism has been difficult to determine in individual cases. The aim of our study is to survey ME/CFS subjects for evidence of an infectious trigger and/or evidence of immune dysregulation via serological testing of plasma samples for antibodies to 122 different pathogen antigens. Immune profiles were compared to age-, sex-, and BMI-matched controls to provide a basis for comparison. Antibody levels to individual antigens surveyed in this study do not implicate any one of the pathogens in ME/CFS, nor do they rule out common pathogens that frequently infect the US population. However, our results revealed sex-based differences in steady-state humoral immunity, both within the ME/CFS cohort and when compared to trends seen in the healthy control cohort.
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Affiliation(s)
- Adam J. O’Neal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; (A.J.O.); (K.A.G.); (S.M.L.)
| | - Katherine A. Glass
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; (A.J.O.); (K.A.G.); (S.M.L.)
| | - Christopher J. Emig
- Augmenta Bioworks, Inc., Menlo Park, CA 94025, USA; (C.J.E.); (A.A.V.); (S.J.H.)
| | - Adela A. Vitug
- Augmenta Bioworks, Inc., Menlo Park, CA 94025, USA; (C.J.E.); (A.A.V.); (S.J.H.)
| | - Steven J. Henry
- Augmenta Bioworks, Inc., Menlo Park, CA 94025, USA; (C.J.E.); (A.A.V.); (S.J.H.)
| | - Dikoma C. Shungu
- Department of Radiology, Weill Cornell Medicine, New York, NY 10021, USA; (D.C.S.); (X.M.)
| | - Xiangling Mao
- Department of Radiology, Weill Cornell Medicine, New York, NY 10021, USA; (D.C.S.); (X.M.)
| | - Susan M. Levine
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; (A.J.O.); (K.A.G.); (S.M.L.)
| | - Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; (A.J.O.); (K.A.G.); (S.M.L.)
- Correspondence:
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Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proc Natl Acad Sci U S A 2022; 119:e2121335119. [PMID: 35639694 PMCID: PMC9191635 DOI: 10.1073/pnas.2121335119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that only a small fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics. Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits, in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semiindependent epidemiological niches that are not regionally or seasonally defined. Typically, intralineage mutational signatures are similar to interlineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage defining. Interlineage turnover is slower than expected under a neutral model, whereas intralineage turnover is faster than the neutral expectation, further supporting the existence of independent niches. The persistence of virus lineages appears to stem from limited outbreaks within small communities, so that only a small fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.
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Heckenberg E, Steppe JT, Coyne CB. Enteroviruses: The role of receptors in viral pathogenesis. Adv Virus Res 2022; 113:89-110. [DOI: 10.1016/bs.aivir.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Botvinkin AD. [Viruses and bats: interdisciplinary issues]. Vopr Virusol 2021; 66:383-389. [PMID: 34545718 DOI: 10.36233/0507-4088-79] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022]
Abstract
The virologists' attention to bats (Сhiroptera) changed in the late 20th century as the concept of emerging infections grew in popularity. Since the beginning of the COVID-19 pandemic, the number of publications on bat viruses has increased profoundly.History of the problem; biodiversity of Chiroptera and related viruses; medical and veterinary significance of some viral genera and subgenera (Lyssavirus, Henipavirus, Marburgvirus, Ebolavirus, Sarbecovirus, Merbecovirus), as well as problems of bat protection, are addressed in a concise form. Literature search was carried out in electronic databases, mainly for the period of 2000-2021. Publications in Russian that are poorly represented in English-language reviews are also included. The purpose of the review is to substantiate the importance of an interdisciplinary approach in the context of increased interest in the study of viral infections in bats. This review was written for researchers who have not previously dealt with this problem.Since the beginning of this century, the number of known virus species associated with bats has increased by an order of magnitude (>200). The families Rhabdoviridae, Coronaviridae, Paramyxoviridae are in the first ranks according to the number of findings, and the highest diversity of viruses has been established for the families Vespertilionidae, Pteropodidae, Molossidae. Interdisciplinary cooperation positively influences the efficiency, biological safety and practical significance of the ongoing research. The best results were achieved by multidisciplinary teams with good cross-training in several specialties. Many papers emphasize the need to balance health and conservation interests.The analysis of scientific publications indicates a change in research approaches in this area: from collecting individual facts within the framework of narrow specialties to a comprehensive assessment of new knowledge from ecological, evolutionary and socio-economic positions. Results of the research emphasize the need to maintain complex approaches addressing public health needs and environmental protection. The importance of bat-borne viral infections determines the necessity for correction and interdepartmental coordination of scientific research and surveillance of wildlife zoonoses in the Russian Federation.
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Affiliation(s)
- A D Botvinkin
- FSBEI HE «Irkutsk State Medical University» of the Ministry of Health of Russia
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Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020. Viruses 2021; 13:v13091803. [PMID: 34578384 PMCID: PMC8472758 DOI: 10.3390/v13091803] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022] Open
Abstract
We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900-2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.
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Development of Group B Coxsackievirus as an Oncolytic Virus: Opportunities and Challenges. Viruses 2021; 13:v13061082. [PMID: 34198859 PMCID: PMC8227215 DOI: 10.3390/v13061082] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Oncolytic viruses have emerged as a promising strategy for cancer therapy due to their dual ability to selectively infect and lyse tumor cells and to induce systemic anti-tumor immunity. Among various candidate viruses, coxsackievirus group B (CVBs) have attracted increasing attention in recent years. CVBs are a group of small, non-enveloped, single-stranded, positive-sense RNA viruses, belonging to species human Enterovirus B in the genus Enterovirus of the family Picornaviridae. Preclinical studies have demonstrated potent anti-tumor activities for CVBs, particularly type 3, against multiple cancer types, including lung, breast, and colorectal cancer. Various approaches have been proposed or applied to enhance the safety and specificity of CVBs towards tumor cells and to further increase their anti-tumor efficacy. This review summarizes current knowledge and strategies for developing CVBs as oncolytic viruses for cancer virotherapy. The challenges arising from these studies and future prospects are also discussed in this review.
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