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Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [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: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
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Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
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Ivin YY, Butusova AA, Gladneva EE, Kolomijtseva GY, Khapchaev YK, Ishmukhametov AA. [The role of the encephalomyocarditis virus type 1 proteins L and 2A in the inhibition of the synthesis of cellular proteins and the accumulation of viral proteins during infection]. Vopr Virusol 2023; 68:428-444. [PMID: 38156577 DOI: 10.36233/0507-4088-195] [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: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2023]
Abstract
INTRODUCTION Infection of cells with encephalomyocarditis virus type 1 (EMCV-1, Cardiovirus A: Picornaviridae) is accompanied by suppression of cellular protein synthesis. The main role in the inhibition of cellular translation is assigned to the L and 2A «security» proteins. The mechanism of the possible influence of the L protein on cellular translation is unknown. There are hypotheses about the mechanism of influence of 2A protein on the efficiency of cap-dependent translation, which are based on interaction with translation factors and ribosome subunits. However, the available experimental data are contradictory, obtained using different approaches, and do not form a unified model of the interaction between the L and 2A proteins and the cellular translation machinery. AIM To study the role of L and 2A «security» proteins in the suppression of translation of cellular proteins and the efficiency of translation and processing of viral proteins in infected cells. MATERIALS AND METHODS Mutant variants of EMCV-1 were obtained to study the properties of L and 2A viral proteins: Zfmut, which has a defective L; Δ2A encoding a partially deleted 2A; Zfmut&Δ2A containing mutations in both proteins. Translational processes in infected cells were studied by Western-blot and the pulse method of incorporating radioactively labeled amino acids (14C) into newly synthesized proteins, followed by radioautography. RESULTS The functional inactivation of the 2A protein does not affect the inhibition of cellular protein synthesis. A direct correlation was found between the presence of active L protein and specific inactivation of cellular protein synthesis at an early stage of viral infection. Nonspecific suppression of the translational processes of the infected cell, accompanied by phosphorylation of eIF2α, occurs at the late stage of infection. Partial removal of the 2A protein from the EMCV-1 genome does not affect the development of this process, while inactivation of the L protein accelerates the onset of complete inhibition of protein synthesis. Partial deletion of the 2A disrupts the processing of viral capsid proteins. Suppression of L protein functions leads to a decrease in the efficiency of viral translation. CONCLUSION A study of the role of EMCV-1 L and 2A proteins during the translational processes of an infected cell, first performed using infectious viral pathogens lacking active L and 2A proteins in one experiment, showed that 2A protein is not implicated in the inhibition of cellular translation in HeLa cells; L protein seems to play an important role not only in the specific inhibition of cellular translation but also in maintaining the efficient synthesis of viral proteins; 2A protein is involved not only in primary but also in secondary processing of EMCV-1 capsid proteins.
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Affiliation(s)
- Y Y Ivin
- Federal State Autonomous Scientific Institution M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences (Polio Institute)
| | - A A Butusova
- Federal State Autonomous Scientific Institution M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences (Polio Institute)
| | - E E Gladneva
- Federal State Autonomous Scientific Institution M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences (Polio Institute)
| | - G Y Kolomijtseva
- A.N. Belozersky Research Institute of Physico-Chemical Biology MSU
| | - Y K Khapchaev
- Federal State Autonomous Scientific Institution M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences (Polio Institute)
| | - A A Ishmukhametov
- Federal State Autonomous Scientific Institution M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences (Polio Institute)
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University
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McGill F, Tokarz R, Thomson EC, Filipe A, Sameroff S, Jain K, Bhuva N, Ashraf S, Lipkin WI, Corless C, Pattabiraman C, Gibney B, Griffiths MJ, Geretti AM, Michael BD, Beeching NJ, McKee D, Hart IJ, Mutton K, Jung A, Miller A, Solomon T. Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis. J Infect 2022; 84:499-510. [PMID: 34990710 DOI: 10.1016/j.jinf.2021.12.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Many patients with meningitis have no aetiology identified leading to unnecessary antimicrobials and prolonged hospitalisation. We used viral capture sequencing to identify possible pathogenic viruses in adults with community-acquired meningitis. METHODS Cerebrospinal fluid (CSF) from 73 patients was tested by VirCapSeq-VERT, a probe set designed to capture viral targets using high throughput sequencing. Patients were categorised as suspected viral meningitis - CSF pleocytosis, no pathogen identified (n = 38), proven viral meningitis - CSF pleocytosis with a pathogen identified (n = 15) or not meningitis - no CSF pleocytosis (n = 20). RESULTS VirCapSeq-VERT detected virus in the CSF of 16/38 (42%) of those with suspected viral meningitis, including twelve individual viruses. A potentially clinically relevant virus was detected in 9/16 (56%). Unexpectedly Toscana virus, rotavirus and Saffold virus were detected and assessed to be potential causative agents. CONCLUSION VirCapSeq-VERT increases the probability of detecting a virus. Using this agnostic approach we identified Toscana virus and, for the first time in adults, rotavirus and Saffold virus, as potential causative agents in adult meningitis. Further work is needed to determine the prevalence of atypical viral candidates as well as the clinical impact of using sequencing methods in real time. This knowledge can help to reduce antimicrobial use and hospitalisations leading to both patient and health system benefits.
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Affiliation(s)
- Fiona McGill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Emma C Thomson
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Ana Filipe
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Nishit Bhuva
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Shirin Ashraf
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Caroline Corless
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Chitra Pattabiraman
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; National Institute for Mental Health and Neurosciences, Bangalore, India
| | - Barry Gibney
- UK Health Security Agency (previously Public Health England), UK
| | - Michael J Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Alder Hey Children's NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Anna Maria Geretti
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Faculty of Medicine, University of Rome Tor Vergata
| | - Benedict D Michael
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Nicholas J Beeching
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Liverpool School of Tropical Medicine, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - David McKee
- Central Manchester Foundation Trust, Manchester, UK
| | - Ian J Hart
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Ken Mutton
- University of Manchester, Manchester, UK
| | - Agam Jung
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alastair Miller
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tom Solomon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
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Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses 2021; 13:v13122365. [PMID: 34960634 PMCID: PMC8704738 DOI: 10.3390/v13122365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/21/2023] Open
Abstract
Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.
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Vandesande H, Edman K, Rondahl E, Falkeborn T, Serrander L, Lindberg AM. Saffold virus infection in elderly people with acute gastroenteritis in Sweden. J Med Virol 2021; 93:3980-3984. [PMID: 32827319 DOI: 10.1002/jmv.26452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022]
Abstract
Viral gastroenteritis is a major source of morbidity and mortality, predominantly caused by so-called NOROAD viruses (norovirus, rotavirus, and adenovirus). In approximately onethird of all cases, however, the exact etiology is unknown. The in 2007 discovered human cardiovirus Saffold virus (SAFV) may prove to be a plausible candidate to explain this diagnostic gap. This virus, a member of the Picornaviridae family which is closely related to the murine viruses Theiler's murine encephalomyelitis virus and Theravirus, is a widespread pathogen and causes infection early in life. Screening of 238 fecal or vomitus samples obtained from NOROAD-negative, elderly patients with acute gastroenteritis at the University Hospital of Linköping showed that SAFV is present in low abundance (4.6%). Phylogenetic analysis of the VP1 gene revealed a Swedish isolate belonging to the highly common and in Europe widespread SAFV-3 genotype. This genotype is also related to previously reported Asian strains. This study describes the first molecular typing of a Swedish SAFV isolate and is the first report to document the circulation of SAFV among elderly people. The pathogenicity of SAFV is, as of yet, still under debate; further studies are necessary to determine its role in the development of disease.
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Affiliation(s)
- Helena Vandesande
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Kjell Edman
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Elin Rondahl
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tina Falkeborn
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
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Abstract
The classification of viruses is relevant to a number of scientific and clinical disciplines, including the practice of diagnostic virology. Here, we provide an update to our previous review of taxonomic changes for disease-causing viruses in humans and vertebrate animals, covering changes between 2018 and 2020. Recent advances in virus taxonomy structure by the International Committee on Taxonomy of Viruses inform this update.
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Bonanno Ferraro G, Mancini P, Veneri C, Iaconelli M, Suffredini E, Brandtner D, La Rosa G. Evidence of Saffold virus circulation in Italy provided through environmental surveillance. Lett Appl Microbiol 2019; 70:102-108. [PMID: 31742735 DOI: 10.1111/lam.13249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
Saffold virus (SAFV) is an emerging human cardiovirus associated with respiratory and gastrointestinal infection, and, more recently, to symptoms related to the endocrine, cardiovascular, and neurological systems. Information about SAFV circulation in Italy is scarce. In order to provide insights into the epidemiology of SAFV in Italy, 141 raw sewage samples collected throughout Italy were tested using broad-range nested RT-PCR primers targeting the 5'-NC region. Seven samples (5·0%) were confirmed as SAFV in samples collected in North, Centre and Southern Italy. Typing was attempted through amplification of the VP1 coding region, using both published and newly designed primers, and one sample was characterized as SAFV-2. SIGNIFICANCE AND IMPACT OF THE STUDY: Prevalence, genetic diversity and geographic distribution of SAFV in Italy is currently unknown. This study represents the first detection of SAFV in sewage samples in Italy, suggesting that it is circulating in the population despite lack of clinical reporting. Whether the virus is associated with asymptomatic cases or with undetected gastroenteritis or respiratory illness is unknown. Further studies are needed to investigate on the occurrence and persistence of SAFV in water environments and its waterborne transmission potential.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
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