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Papagiannis D, Perlepe G, Tendolouri T, Karakitsiou P, Damagka G, Kalaitzi A, Alevra S, Malli F, Gourgoulianis KI. Proportion of Respiratory Syncytial Virus, SARS-CoV-2, Influenza A/B, and Adenovirus Cases via Rapid Tests in the Community during Winter 2023-A Cross Sectional Study. Diseases 2023; 11:122. [PMID: 37754318 PMCID: PMC10529898 DOI: 10.3390/diseases11030122] [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: 07/26/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Respiratory infections constitute a major reason for infants and children seeking medical advice and visiting health facilities, thus remaining a significant public threat with high morbidity and mortality. The predominant viruses causing viral respiratory infections are influenza A and B viruses (Flu-A, Flu-B), respiratory syncytial virus (RSV), adenovirus and coronaviruses. We aimed to record the proportion of RSV, SARS-CoV-2, influenza A/B and adenovirus cases with rapid antigen tests and validate the results with RT-PCR assays of upper respiratory specimens with a wide range of viral loads and (co)-infection patterns in children. Clinical samples were collected from early symptomatic children (presenting with fever and/or cough and/or headache within 5-7 days). The surveillance program was conducted in five private pediatric dispensaries and one pediatric care unit, from 10 January 2023 to 30 March 2023 in central Greece. The total sample of specimens collected was 784 young children and infants, of which 383 (48.8%) were female and 401 were male (51.2%). The mean age of participants was 7.3 + 5.5 years. The sensitivity of the FLU A & B test was 91.15% (95% CI: 84.33-95.67%), and the specificity was 98.96% (95% CI: 97.86-99.58%). The sensitivity and specificity of the adenovirus and RSV test was {92.45% (95% CI: 81.79-97.91%), 99.32% (95% CI: 98.41-99.78%)} and {92.59% (95% CI: 75.71-99.09%), 99.47% (95% CI: 98.65-99.86%)} respectively. Lastly, the sensitivity of the SARS-CoV-2 test was 100.00% (95% CI: 79.41-100.00%) and the specificity was 99.74% (95% CI: 99.06-99.97%). We recorded a proportion of 14.3% and 3.44% for influenza A and B, respectively, followed by a proportion of 6.9% for adenovirus, a proportion of 3.7% for RSV, and finally, a proportion of 2.3% for SARS-CoV-2. The combination of a new multiple rapid test with multiple antigens will probably be a useful tool with a financial impact for health systems targeting the early detection and appropriate treatment of respiratory infections in emergency departments in primary health care facilities.
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Affiliation(s)
- Dimitrios Papagiannis
- Public Health & Vaccines Laboratory, Department of Nursing, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| | - Garifallia Perlepe
- Respiratory Medicine Department, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (G.P.); (K.I.G.)
| | - Theodora Tendolouri
- MD Private Sector of Greek Health System, Kanouta 1 Str. Trikala Thessaly, 42100 Trikala, Greece;
| | - Polyxeni Karakitsiou
- MD Private Sector of Greek Health System, Annas Komninis 1-3 Str. Trikala Thessaly, 42100 Trikala, Greece;
| | - Georgia Damagka
- MD Private Sector of Greek Health System, Lefkosias Str. 3 Larissa Thessaly, 41335 Larissa, Greece;
| | - Anna Kalaitzi
- Pediatric Department, General Hospital of Larissa, Tsakalof 1 Str. Larissa Thessaly, 41221 Larissa, Greece; (A.K.); (S.A.)
| | - Sofia Alevra
- Pediatric Department, General Hospital of Larissa, Tsakalof 1 Str. Larissa Thessaly, 41221 Larissa, Greece; (A.K.); (S.A.)
| | - Foteini Malli
- Respiratory Disorders Laboratory, Department of Nursing, University of Thessaly, 41110 Larissa, Greece;
| | - Konstantinos I. Gourgoulianis
- Respiratory Medicine Department, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (G.P.); (K.I.G.)
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Georgakopoulou VE, Petsinis G, Mantzouranis K, Damaskos C, Melemeni D, Gkoufa A, Chlapoutakis S, Garmpis N, Sklapani P, Trakas N, Tsiafaki X. First Detection of Human Coronavirus HKU1 in Greece, in an Immunocompromised Patient With Severe Lower Respiratory Tract Infection. Acta Med Litu 2021; 28:121-126. [PMID: 34393634 PMCID: PMC8311844 DOI: 10.15388/amed.2021.28.1.21] [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: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
Human coronavirus HKU1 (HCoV-HKU1) is a RNA virus which gets in the human cells by binding to the receptor of N-acetyl-9-O-acetylneuraminic acid. Human Coronaviruses (HCoVs), including HCoV-HKU1, are globally found. HCoV-HKU1 is responsible for upper and lower respiratory tract infections, usually with mild symptoms. In severe cases, HCoV-HKU1 can cause life-threatening respiratory illness especially in vulnerable hosts such as elderly, children and immunocompromised patients. In Greece, Respiratory Syncytial Virus (RSV) and influenza are the most common viruses causing respiratory tract infections. Traditionally, HCoVs are responsible for less than 3% of respiratory infections in Greek population. HCoVs 229E and OC43 have been shown to circulate in Greece. We report the first case of lung infection in an immunocompromised woman due to HCoV-HKU1, that has never been before detected in Greece. HCoV-HKU1 is related to severe disease even in healthy individuals and must be considered in the differential diagnosis of severe respiratory infections.
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Affiliation(s)
| | | | | | - Christos Damaskos
- Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens
| | | | - Aikaterini Gkoufa
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos Garmpis
- Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens Greece
| | | | - Nikolaos Trakas
- Department of Biochemistry, Sismanogleio Hospital, Athens, Greece
| | - Xanthi Tsiafaki
- 1 Pulmonology Department Sismanogleio Hospital, Athens, Greece
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Rapid functionalisation and detection of viruses via a novel Ca 2+-mediated virus-DNA interaction. Sci Rep 2019; 9:16219. [PMID: 31700064 PMCID: PMC6838052 DOI: 10.1038/s41598-019-52759-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/22/2019] [Indexed: 11/28/2022] Open
Abstract
Current virus detection methods often take significant time or can be limited in sensitivity and specificity. The increasing frequency and magnitude of viral outbreaks in recent decades has resulted in an urgent need for diagnostic methods that are facile, sensitive, rapid and inexpensive. Here, we describe and characterise a novel, calcium-mediated interaction of the surface of enveloped viruses with DNA, that can be used for the functionalisation of intact virus particles via chemical groups attached to the DNA. Using DNA modified with fluorophores, we have demonstrated the rapid and sensitive labelling and detection of influenza and other viruses using single-particle tracking and particle-size determination. With this method, we have detected clinical isolates of influenza in just one minute, significantly faster than existing rapid diagnostic tests. This powerful technique is easily extendable to a wide range of other enveloped pathogenic viruses and holds significant promise as a future diagnostic tool.
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Tsoumakas K, Giamaiou K, Goussetis E, Graphakos S, Kossyvakis A, Horefti E, Mentis A, Elefsiniotis I, Pavlopoulou ID. Epidemiology of viral infections among children undergoing hematopoietic stem cell transplant: Α prospective single‐center study. Transpl Infect Dis 2019; 21:e13095. [DOI: 10.1111/tid.13095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/09/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Konstantinos Tsoumakas
- Faculty of Nursing Pediatric Clinic, "P & A Kyriakou" Children's Hospital, National and Kapodistrian University of Athens Athens Greece
- Pediatric Research Laboratory, Faculty of Nursing National and Kapodistrian University of Athens Athens Greece
| | - Konstantina Giamaiou
- Pediatric Research Laboratory, Faculty of Nursing National and Kapodistrian University of Athens Athens Greece
- Stem cell Transplant Unit, "Aghia Sophia" Children's Hospital Athens Greece
| | - Evgenios Goussetis
- Stem cell Transplant Unit, "Aghia Sophia" Children's Hospital Athens Greece
| | - Stelios Graphakos
- Stem cell Transplant Unit, "Aghia Sophia" Children's Hospital Athens Greece
| | | | - Elina Horefti
- Public Health Laboratories, Hellenic Pasteur Institute Athens Greece
| | - Andreas Mentis
- Public Health Laboratories, Hellenic Pasteur Institute Athens Greece
| | - Ioannis Elefsiniotis
- Department of Internal Medicine, Faculty of Nursing Athens General and Oncology Hospital "Agii Anargyri", National and Kapodistrian University of Athens Athens Greece
| | - Ioanna D. Pavlopoulou
- Faculty of Nursing Pediatric Clinic, "P & A Kyriakou" Children's Hospital, National and Kapodistrian University of Athens Athens Greece
- Pediatric Research Laboratory, Faculty of Nursing National and Kapodistrian University of Athens Athens Greece
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Antalis E, Oikonomopoulou Z, Kottaridi C, Kossyvakis A, Spathis A, Magkana M, Katsouli A, Tsagris V, Papaevangelou V, Mentis A, Tsiodras S. Mixed viral infections of the respiratory tract; an epidemiological study during consecutive winter seasons. J Med Virol 2018; 90:663-670. [PMID: 29244214 PMCID: PMC7167177 DOI: 10.1002/jmv.25006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
Abstract
The current study aimed to describe the molecular epidemiology of mixed respiratory viral infections during consecutive winter seasons in a tertiary care hospital. Patients with symptoms of respiratory tract infection were evaluated during the 2009‐2011 and 2013‐15 winter seasons. A clinical microarray technique was used for viral detection. Clinical and epidemiological data were correlated with mixed viral detection and the need for hospitalization. In 332 out of 604 (54.4%) evaluated patients (17.6% children) a respiratory virus was identified. Mixed viral infections were diagnosed in 68/332 (20.5%) patients with virus detection (66.2% mixed Influenza‐RSV infections). Mixed viral infections were more commonly detected in children (OR 3.7; 95%CI 1.9‐5.6, P < 0.01) and patients with comorbidities. In logistic regression analyses, mixed viral infections were associated with younger age (mean age 30.4 years vs. 41.8 years, P ≤ 0.001) and increased rates of fever (OR: 2.7; 95%CI 1.04‐7.2, P < 0.05) but no adverse outcomes or increased rates of hospitalization. High rates of mixed viral infections were noted during all winter seasons (especially Influenza and RSV) and were more common in younger patients. The clinical significance of mixed respiratory viral infection needs further elucidation.
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Affiliation(s)
- Emmanouil Antalis
- 4th Department of Internal Medicine, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Zacharoula Oikonomopoulou
- 4th Department of Internal Medicine, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Christine Kottaridi
- Department of Cytopathology, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | | | - Aris Spathis
- Department of Cytopathology, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Magkana
- Department of Cytopathology, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Aikaterini Katsouli
- 4th Department of Internal Medicine, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Vassileios Tsagris
- 3rd Department of Pediatrics, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Vassiliki Papaevangelou
- 3rd Department of Pediatrics, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | | | - Sotirios Tsiodras
- 4th Department of Internal Medicine, University Hospital Attikon, National and Kapodistrian University of Athens Medical School, Athens, Greece
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Tafalla M, Buijssen M, Geets R, Vonk Noordegraaf-Schouten M. A comprehensive review of the epidemiology and disease burden of Influenza B in 9 European countries. Hum Vaccin Immunother 2016; 12:993-1002. [PMID: 26890005 PMCID: PMC4962970 DOI: 10.1080/21645515.2015.1111494] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/28/2015] [Accepted: 10/17/2015] [Indexed: 12/15/2022] Open
Abstract
This review was undertaken to consolidate information on the epidemiology and burden of influenza B, as well as the circulation patterns of influenza B lineage in 9 European countries. Following a comprehensive search of peer-reviewed and gray literature sources, we found that published data on influenza B epidemiology and burden are scarce. Surveillance data show frequent co-circulation of both influenza B lineages during influenza seasons, but little is known about its impact, especially in adults and the clinical burden of influenza B remains unknown. Mismatch between the circulating influenza B lineage and vaccine recommendations has been seen in at least one influenza season in every country. Such observations could impact the effectiveness of seasonal influenza vaccination programs using trivalent vaccines, which contain only one influenza B lineage (B/Yamagata or B/Victoria) and highlight the need for local studies to better understand the epidemiology and burden of influenza B in these countries.
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Dupouey J, Ninove L, Ferrier V, Py O, Gazin C, Thirion-Perrier L, de Lamballerie X. Molecular detection of human rhinoviruses in respiratory samples: a comparison of Taqman probe-, SYBR green I- and BOXTO-based real-time PCR assays. Virol J 2014; 11:31. [PMID: 24548758 PMCID: PMC3936951 DOI: 10.1186/1743-422x-11-31] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 02/11/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human Rhinoviruses (HRV) are major causative agents of acute respiratory tract infections in all age group and important contributing factors of childhood morbidity and mortality. Clinical presentation is poorly specific and the great antigenic and genetic variability of HRVs renders the biological diagnosis complex. Here, we have evaluated several molecular diagnostic protocols, including Taqman probe-based and intercalating agent-based RT-PCR assays. METHODS 5,627 respiratory samples sent to the laboratory of Virology of the University Hospitals of Marseille, France, from March 2011 to February 2012, were tested using a real-time RT-PCR assay in the 5'NCR of the rhinoviral genome that associated a Taqman probe and the detection of DNA-BOXTO-dye complexes. A sample of 500 BOXTO-positive samples were further tested using the same probe assay (without BOXTO), and a SYBR Green assay (using the same amplification primers). The specific amplification of HRV sequences was assessed by NGS amplicon sequencing. RESULTS The Taqman probe RT-PCR assay identified 696/5,627 samples (12,4%) as HRV-positive. BOXTO-positive samples included all probe-positive samples and 1,913 additional samples, of which only 24.3% were confirmed by sequencing. The SYBR Green assay was more specific (16/550 samples were probe-negative/SYBR Green-positive, all confirmed by 5'NCR sequencing), but 3/500 samples were probe-positive/SYBR Green-negative. CONCLUSIONS Our results highlight the difficulty in detecting HRVs in clinical samples using a single molecular detection system. Amongst the 3 systems tested, the best compromise was obtained with the SYBR Green assay, which, by comparison with our probe-based assay provided an improved sensitivity without altering the detection specificity. Interestingly, a majority of probe-negative/BOXTO- or SYBR Green-positive samples were not associated with mutations in the sequence targeted by the probe. Sequence-based modifications of the secondary structure of the HRV 5'NCR may be associated with a limited access to the probe hybridisation region. Further investigations may identify a test combining a probe based- and an intercalating agent-based detection, which will significantly improve the diagnosis of HRV infections.
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Affiliation(s)
- Julien Dupouey
- IRD French Institute of Research for Development, EHESP French School of Public Health, Aix Marseille Univ, UMR_D 190 "Emergence des Pathologies Virales", Marseille 13005, France.
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Pogka V, Moutousi A, Kossyvakis A, Kalliaropoulos A, Sgouras DN, Giannaki M, Mentis AF. Genetic variability of human metapneumo- and bocaviruses in children with respiratory tract infections. Influenza Other Respir Viruses 2013; 8:107-15. [PMID: 24373295 PMCID: PMC4177804 DOI: 10.1111/irv.12185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2013] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES The genotypic analysis of human metapneumo-(HMPV) and boca-(HBoV) viruses circulating in Greece and their comparison to reference and other clinical strains. DESIGN Genetic analysis of representative strains over three consecutive winter seasons of the years 2005-2008. SETTING Representative positive specimens for HMPV and HBoV from paediatric patients of healthcare units and hospitals in Southern Greece with influenza-like illness or other respiratory tract infections. SAMPLE Seven to ten positive specimens for either HMPV or HBoV from each winter period. In total, 24 specimens positive for HMPV and 26 for HBoV, respectively. MAIN OUTCOME MEASURES Sequence diversity of HMPV and HBoV strains by sequencing the complete G and VP1/VP2 genes, respectively. RESULTS In total, 24 HMPV strains were found to have a 92-100% nucleotide and a 85.9-100% amino acid identity. Phylogenetic analysis based on the number of amino acid differences, revealed circulation of 4 different subclusters belonging to genetic lineage B2. Similarly, analysis of 26 HBoV strains indicated that 22 clustered within genotype St2, 2 into genotype St1 and the remaining 2 formed a third cluster derived from potential recombination between different St1 genotype strains. St2 HBoV genotype was observed throughout the whole observation period whereas St1 only during the second and the third winter period. Higher levels of heterogeneity were observed between HMPV compared to HBoV strains. CONCLUSIONS Phylogenetic analysis revealed circulation of one single lineage (B2) for HMPV viruses and predominance of St2 genotype for HBoV viruses. A possible recombination between St1 genotype strains of HBoV was observed.
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Affiliation(s)
- Vasiliki Pogka
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, Athens, Greece
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Clinical characteristics and genetic variability of human rhinovirus in Mexico. Viruses 2012; 4:200-10. [PMID: 22470832 PMCID: PMC3315212 DOI: 10.3390/v4020200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/17/2012] [Accepted: 01/17/2012] [Indexed: 12/19/2022] Open
Abstract
Human rhinovirus (HRV) is a leading cause of acute respiratory infection (ARI) in young children and infants worldwide and has a high impact on morbidity and mortality in this population. Initially, HRV was classified into two species: HRV-A and HRV-B. Recently, a species called HRV-C and possibly another species, HRV-D, were identified. In Mexico, there is little information about the role of HRV as a cause of ARI, and the presence and importance of species such as HRV-C are not known. The aim of this study was to determine the clinical characteristics and genetic variability of HRV in Mexican children. Genetic characterization was carried out by phylogenetic analysis of the 5'-nontranslated region (5'-NTR) of the HRV genome. The results show that the newly identified HRV-C is circulating in Mexican children more frequently than HRV-B but not as frequently as HRV-A, which was the most frequent species. Most of the cases of the three species of HRV were in children under 2 years of age, and all species were associated with very mild and moderate ARI.
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