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Parida P, N S, E R S, Jagadesh A, Marate S, Govindakaranavar A. The emergence of human metapneumovirus G gene duplication in hospitalized patients with respiratory tract infection, India, 2016-2018. Mol Biol Rep 2023; 50:1109-1116. [PMID: 36399244 PMCID: PMC9889522 DOI: 10.1007/s11033-022-08092-8] [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: 05/27/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Human metapneumovirus (HMPV) belongs to the family Pneumoviridae. It is one of the emerging respiratory viruses causing both upper and lower respiratory tract illnesses. HMPV has two genotypes: A and B. These genotypes are classified into lineage A1, A2, B1 and B2. Lineage-A2 is further classified as A2a, A2b and A2c. Similarly, B2 is classified as B2a and B2b. Studies have shown the circulation of A2b, B1 and B2 lineages in India. However, a limited amount of data is available on the current circulating genotypes of HMPV in India. METHODS Throat swab samples positive for HMPV by real-time RT- PCR, archived at Manipal Institute of Virology as a part of a hospital-based acute febrile illness surveillance study, was used from April 2016 to August 2018 by purposive sampling method. We performed the conventional reverse transcriptase-polymerase chain reaction for twenty samples targeting the G gene and then subjected them to sequencing. Phylogenetic analysis was done using MEGA X software by the Maximum Likelihood method. RESULTS All the twenty sequences belonged to the A2c subgroup. Phylogenetic analysis showed that strains from the study have genetic relation with circulating strains in Japan, China and Croatia. Seven out of the twenty sequences showed 180-nucleotide duplication and eleven sequences showed 111-nucleotide duplication. Two sequences did not show any duplications. CONCLUSION In the current study, we report that A2c is the sub-lineage in India from April 2016 to August 2018. This study is the first retrospective study reporting the circulation of the A2c sub-lineage among adults in India with 180- and 111-nucleotide duplications in the G gene of human metapneumovirus.
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Affiliation(s)
- Preetiparna Parida
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Sudheesh N
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
| | - Sanjay E R
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Anitha Jagadesh
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Srilatha Marate
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Arunkumar Govindakaranavar
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- , 2-49, Vaikathu, Maratithota Road, MooduAthradi, Athradi PO, Udupi, Karnataka, 576107, India.
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Kafintu-Kwashie AA, Nii-Trebi NI, Obodai E, Neizer M, Adiku TK, Odoom JK. Molecular epidemiological surveillance of viral agents of acute lower respiratory tract infections in children in Accra, Ghana. BMC Pediatr 2022; 22:364. [PMID: 35751110 PMCID: PMC9229459 DOI: 10.1186/s12887-022-03419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute lower respiratory tract infection (ALRTI) in children under 5 years is known to be predominantly caused by respiratory syncytial virus (RSV). In recent times, however, human metapneumovirus (HMPV) has also been implicated. This study sought to investigate and genotype respiratory syncytial virus and human metapneumovirus in children presenting with ALRTIs infection at the Princess Marie Louis Children's Hospital in Accra, Ghana. METHODS Children below 5 years who were clinically diagnosed of ALRTI and on admission at the study site were recruited between September 2015 and November 2016 for this study. Demographic data information was obtained by means of a standardized questionnaire; and relevant clinical information was obtained from medical records. Nasopharyngeal swabs were collected from 176 children recruited for the study. Ribonucleic acid was extracted from swabs and cDNA syntheses were performed by RT-PCR. RSV-positive amplicons were sequenced and analyzed for genotype assignment. RESULTS RSV and HMPV prevalence among the sampled subjects were 11.4 and 1.7% respectively. Of the RSV positives, 8/20 (40%) were RSV-A and 12/20 (60%) were RSV-B. The highest prevalence was observed in children less than 12 months old. Phylogenetic analysis of the second hypervariable region of the RSV G-gene revealed that all RSV group A viruses belonged to the "novel" ON1 genotype containing the 72-nucleotide duplication; and RSV group B viruses belong to the BA IX genotype. CONCLUSION RSV is frequently detected in children aged under 5 years admitted with ALRTI in Ghana. Continued surveillance of viral aetiological agents is warranted to elucidate the prevalence and transmission patterns of viral pathogens that cause respiratory tract infections among children. This will help inform appropriate intervention approaches.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Theophilus Korku Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
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Refay ASE, Shehata MA, Sherif LS, Nady HGE, Kholoussi N, Kholoussi S, Baroudy NRE, Gomma MR, Mahmoud SH, Shama NMA, Bagato O, Taweel AE, kandeil A, Ali MA. Prevalence of viral pathogens in a sample of hospitalized Egyptian children with acute lower respiratory tract infections: a two-year prospective study. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:103. [PMID: 35431533 PMCID: PMC9006499 DOI: 10.1186/s42269-022-00790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Viral pneumonias are a major cause of childhood mortality. Proper management needs early and accurate diagnosis. This study objective is to investigate the viral etiologies of pneumonia in children. RESULTS This prospective study enrolled 158 and 101 patients in the first and second year, respectively, and their mean age was 4.72 ± 2.89. Nasopharyngeal swabs were collected and subjected to virus diagnosis by reverse transcription polymerase chain reaction (RT-PCR). Viral etiologies of pneumonia were evidenced in 59.5% of the samples in the first year, all of them were affirmative for influenza A, 2 samples were affirmative for Human coronavirus NL63, and one for Human coronavirus HKU1. In the second year, 87% of patients had a viral illness. The most prevalent agents are human metapneumovirus which was detected in 44 patients (43.6%) followed by human rhinovirus in 35 patients (34.7%) and then parainfluenza-3 viruses in 33 patients (32.7%), while 14 patients had a confirmed diagnosis for both Pan coronavirus and Flu-B virus. CONCLUSIONS Viral infection is prevalent in the childhood period; however, the real magnitude of viral pneumonia in children is underestimated. The reverse transcriptase polymerase chain reaction has to be a vital tool for epidemiological research and is able to clear the gaps in-between clinical pictures and final diagnoses.
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Affiliation(s)
- Amira S. El Refay
- Child Health Department, National Research Centre, 33 El-Bohouth Street (Former El Tahrir St.), PO Box 12622, Dokki, Giza, Egypt
| | - Manal A. Shehata
- Child Health Department, National Research Centre, 33 El-Bohouth Street (Former El Tahrir St.), PO Box 12622, Dokki, Giza, Egypt
| | - Lobna S. Sherif
- Child Health Department, National Research Centre, 33 El-Bohouth Street (Former El Tahrir St.), PO Box 12622, Dokki, Giza, Egypt
| | - Hala G. El Nady
- Child Health Department, National Research Centre, 33 El-Bohouth Street (Former El Tahrir St.), PO Box 12622, Dokki, Giza, Egypt
| | - Naglaa Kholoussi
- Immunogenetics Department, National Research Centre, Dokki, Egypt
| | - Shams Kholoussi
- Immunogenetics Department, National Research Centre, Dokki, Egypt
| | | | - Mokhtar R. Gomma
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Noura M. Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Ola Bagato
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Ahmed El Taweel
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Ahmed kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed A. Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, Egypt
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Malekshahi SS, Yavarian J, Shafiei-Jandaghi NZ, Mokhtari-Azad T, Farahmand M. Prevalence of Human Metapneumovirus Infections in Iran: A Systematic Review and Meta-Analysis. Fetal Pediatr Pathol 2021; 40:663-673. [PMID: 32081050 DOI: 10.1080/15513815.2020.1725939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BackgroundWe sought to systematically review the literature and perform a meta-analysis by assessing the prevalence of human metapneumovirus (hMPV) infections from a number of studies conducted in Iran. Methods: Entire studies addressing epidemiology of hMPV in Iran using data from PubMed, Scopus, Science Direct, Web of science, Google Scholar, Embase, and national Persian databases up to June 2019 were included. Results: The estimated prevalence of hMPV was 8.9% (95% CI 5.4-14.2) in different regions in Iran. Compared to the global rate, in Iran hMPV infection presented an intermediate prevalence rate. The majority of hMPV positive patients were pediatric populations with pooled prevalence of 7.6% (I2 = 95%, 95% CI 3.5-15.6). Conclusion: This first comprehensive review covering researches over the last 11 years expanded our knowledge about hMPV circulating in Iran. Future large epidemiological studies are needed for the evaluation of hMPV prevalence and genotype distribution in different unanalyzed regions in Iran.
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Affiliation(s)
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farahmand
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Epidemiology of Human Metapneumovirus-associated Lower Respiratory Tract Infections in African Children: Systematic Review and Meta-analysis. Pediatr Infect Dis J 2021; 40:479-485. [PMID: 33480663 DOI: 10.1097/inf.0000000000003041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Human metapneumovirus (hMPV) has been associated with upper and lower respiratory tract infections (LRTI) in children and adults. This systematic review evaluated the epidemiology of hMPV-associated LRTI, including severe acute respiratory infection (SARI) hospitalization or clinically diagnosed severe pneumonia, in African children under 5 years of age. METHODS We searched Science Direct, PubMed, Cochrane Central, Scopus, and WHO regional databases using the terms "("Human metapneumovirus" AND "Africa") OR ("hMPV" AND "Africa")" up to September 17, 2020. Other sources included ClinicalTrials.gov to obtain unpublished data. Studies were included if children were less than 5 years of age and hospitalized with hMPV-associated LRTI, SARI or if clinically diagnosed with severe pneumonia in the community. The main outcomes were prevalence of hMPV identified among children with hospitalized LRTI or SARI. We further calculated odds ratios for hMPV in cases with LRTI compared with non-LRTI controls. Pooled results were calculated using a random-effects model. RESULTS Thirty studies were eligible for inclusion in the review. The prevalence of hMPV-LRTI/SARI among hospitalized and severe pneumonia cases was 4.7% [95% confidence interval (CI): 3.9-5.6, I2 = 95.0]. The case-control studies indicated that hMPV was 2.0-fold (95% CI: 0.9-4.4) more likely to be identified in LRTI cases (10.3%) than controls (6.0%). Three of 5 studies reported hMPV-associated LRTI case fatality risk, with a pooled estimate of 1.3% (95% CI: 0.3-2.9; I2 = 49). CONCLUSIONS hMPV was associated with approximately 5% of LRTI/SARI hospitalizations or severe pneumonia cases in Africa.
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Rodriguez PE, Frutos MC, Adamo MP, Cuffini C, Cámara JA, Paglini MG, Moreno L, Cámara A. Human Metapneumovirus: Epidemiology and genotype diversity in children and adult patients with respiratory infection in Córdoba, Argentina. PLoS One 2020; 15:e0244093. [PMID: 33370354 PMCID: PMC7769284 DOI: 10.1371/journal.pone.0244093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Human Metapneumovirus (hMPV) is responsible for acute respiratory infections in humans, with clinical and epidemiological relevance in pediatric, elderly, and immunocompromised populations. These features are largely unknown in Córdoba, Argentina and in adults in general. Hence, our goal was to broadly characterize hMPV infection in patients of all ages hospitalized with acute respiratory infections in Córdoba, Argentina, including epidemiology, clinical features and genetic diversity. Nasopharyngeal secretions were obtained from 795 patients during 2011-2013, 621 patients were 0-25 years old and 174 were 26-85 years old. HMPV was assayed by RT-PCR and other respiratory viruses by indirect immunofluorescence. Local strains were identified by sequence analysis. Human Metapneumovirus was detected in 20.3% (161/795) patients, 13.1% as single infections and 7.2% in co-infections, more frequently with Respiratory Syncytial Virus. HMPV circulated during late winter and spring in all age patients, but mainly in children under 4 years old in 71.4% (115/161) and adults between 26 and 59 years old in 12.4% (20/161). The most prevalent diagnosis was mild acute respiratory infection in 59.6% (96/161) and bronchiolitis in 9.3% (15/161). Local strains were clustered within A2 subtype; they presented 73-100% identities among them, showing a high degree of homology compared to isolations from neighboring countries. We demonstrate that hMPV circulated among all age patients with respiratory infection during 2011-2013 in Córdoba, contributing to the understanding of this virus, its diagnosis and patient handling in local health-care centers.
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Affiliation(s)
- Pamela Elizabeth Rodriguez
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
- * E-mail:
| | - María Celia Frutos
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
| | - María Pilar Adamo
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
| | - Cecilia Cuffini
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
| | - Jorge Augusto Cámara
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
| | - María Gabriela Paglini
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
- Instituto de Investigaciones Médicas Mercedes y Martín Ferreyra, INIMEC- CONICET, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
| | - Laura Moreno
- Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Hospital de Niños “Santísima Trinidad de Córdoba”, Córdoba Capital, Córdoba, Argentina
| | - Alicia Cámara
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba Capital, Córdoba, Argentina
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Jallow MM, Fall A, Kiori D, Sy S, Goudiaby D, Barry MA, Fall M, Niang MN, Dia N. Epidemiological, clinical and genotypic features of human Metapneumovirus in patients with influenza-like illness in Senegal, 2012 to 2016. BMC Infect Dis 2019; 19:457. [PMID: 31117983 PMCID: PMC6532257 DOI: 10.1186/s12879-019-4096-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
Background Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. Methods This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. Results In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July–September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. Conclusion In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.
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Affiliation(s)
- Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Davy Kiori
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Déborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, Dakar, Sénégal
| | - Malick Fall
- Département de Biologie, Animale Faculté des Sciences et Techniques Université Cheikh Anta DIOP de Dakar, Dakar, Sénégal
| | - Mbayame Ndiaye Niang
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal.
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Rahman MZ, Sumiya M, Sahabuddin M, Pell LG, Gubbay JB, Rahman R, Momtaz F, Azmuda N, Shanta SS, Jahan I, Rahman M, Mahmud AA, Roth DE, Morris SK. Genetic characterization of human metapneumovirus identified through community and facility-based surveillance of infants in Dhaka, Bangladesh. J Med Virol 2018; 91:549-554. [PMID: 30372530 DOI: 10.1002/jmv.25351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
Abstract
BACKGROUND Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children in low and middle-income countries. Human metapneumovirus (hMPV) is one of the most common viral etiological agents for ARIs in children. OBJECTIVES In this study, we explored the genotypic diversity and the epidemiology of hMPV among infants in Dhaka, Bangladesh. STUDY DESIGN Between December 2014 and August 2016, a total of 3810 mid-turbinate nasal swab samples were collected from infants (0 to 6 months of age) who met clinical ARI criteria, as a part of a prospective ARI cohort study. hMPV was detected using polymerase chain reaction, and genotyped by sequencing and phylogenetic analysis. RESULTS hMPV was identified in 206 (5.4%) nasal swab specimens. One-tenth of the hMPV-positive swabs (n = 19) were also positive for other respiratory viruses. hMPV activity peaked in January and September in 2015; however, no seasonal pattern of hMPV infection was detected. Phylogenetic analyses of the N and F gene-fragments revealed that the hMPV strains circulating in Dhaka, Bangladesh, belonged to three genotypes: A2b, A2c, and B1. Genotype A (57%) was the predominant hMPV genotype circulating in Bangladesh during the study period. CONCLUSION This study describes both the epidemiology of hMPV infection and its genotypic strain diversity in Dhaka, Bangladesh.
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Affiliation(s)
| | - Mariya Sumiya
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | | | - Lisa G Pell
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan B Gubbay
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada.,Public Health Ontario, Toronto, Ontario, Canada
| | - Rajibur Rahman
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | - Farhana Momtaz
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Shaila S Shanta
- Nutrition and Clinical Services Division (NCSD), icddr,b, Dhaka, Bangladesh
| | - Ishrat Jahan
- Maternal and Child Health Training Institute (MCHTI), Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | | | - Abdullah A Mahmud
- Nutrition and Clinical Services Division (NCSD), icddr,b, Dhaka, Bangladesh
| | - Daniel E Roth
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Shaun K Morris
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
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Kenmoe S, Bigna JJ, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis. Influenza Other Respir Viruses 2018; 12:793-803. [PMID: 29908103 PMCID: PMC6185896 DOI: 10.1111/irv.12584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2018] [Indexed: 12/31/2022] Open
Abstract
AIM The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa. METHOD We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352. RESULTS A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2 = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality. CONCLUSION This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.
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Affiliation(s)
- Sebastien Kenmoe
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
| | - Jean Joel Bigna
- Department of Epidemiology and Public HealthNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
- School of Public HealthFaculty of MedicineUniversity of Paris SudLe Kremlin‐BicêtreFrance
| | | | - Fredy Brice N. Simo
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Véronique B. Penlap
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Astrid Vabret
- Normandie UniversitéCaenFrance
- Groupe de Recherche sur l'Adaptation Microbienne (GRAM)Université de CaenCaenFrance
- Laboratoire de VirologieCentre Hospitalo‐Universitaire de CaenCaenFrance
| | - Richard Njouom
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
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Bigna JJ, Kenmoe S, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017). Data Brief 2018; 20:940-947. [PMID: 30225305 PMCID: PMC6138983 DOI: 10.1016/j.dib.2018.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/24/2018] [Accepted: 08/15/2018] [Indexed: 11/28/2022] Open
Abstract
Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.
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Affiliation(s)
- Jean Joel Bigna
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Sebastien Kenmoe
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Estelle Amandine Well
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box 1364, Yaoundé, Cameroon
| | - Fredy Brice N. Simo
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Véronique B. Penlap
- Department of Biochemistry, Faculty of Sciences, University of Yaoundé 1, P.O. Box 337, Yaoundé, Cameroon
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France
- Université de Caen, Groupe de Recherche sur l’Adaptation Microbienne (GRAM), F-14000 Caen, France
- Laboratoire de Virologie, Centre Hospitalo-Universitaire de Caen, F-14033 Caen, France
| | - Richard Njouom
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
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Hassan DA, Rachid SK, Ziebuhr J. A Single-Center Study of Viral Respiratory Tract Infections in Hospitalized Children From the Kurdistan Region of Iraq. Glob Pediatr Health 2018; 5:2333794X18784996. [PMID: 30014009 PMCID: PMC6042015 DOI: 10.1177/2333794x18784996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022] Open
Abstract
Viral respiratory infections are among the most common causes of disease in humans, particularly in young children, and remain a major public health problem worldwide. For many geographic regions, there is limited epidemiological information on the main causative agents of these diseases. In this article, we investigated, in a prospective study, the viral agents leading to acute respiratory disease in children younger than 15 years of age who were admitted to the pediatric emergency unit of a major teaching hospital in Erbil City, capital of the Kurdistan region, Iraq. Nasopharyngeal samples obtained from 269 hospitalized children were analyzed for viral respiratory pathogens using the xTAG Respiratory Virus Panel Fast assay, and the data were correlated with the clinical and demographic information available for these patients. One or more respiratory virus(es) were detected in 203 out of 269 (75.5%) samples. The most frequent viruses were enterovirus/rhinovirus (n = 88; 32.7%), respiratory syncytial virus (n = 55; 20.4%), and human metapneumovirus (n = 36; 13.4%). In 42 samples (15.6%), coinfections with 2 or more respiratory viruses were detected, with enterovirus/rhinovirus, respiratory syncytial virus, human metapneumovirus, and adenovirus being identified as the most common agents in viral coinfections in these patients.
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Affiliation(s)
- Dlshad A Hassan
- Public Health Laboratory Management, Virology Unit, Hawler, Kurdistan Region, Erbil, Iraq
| | | | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
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Jagušić M, Slović A, Ljubin-Sternak S, Mlinarić-Galinović G, Forčić D. Genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in Croatia. J Med Virol 2017. [DOI: 10.1002/jmv.24884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maja Jagušić
- Centre for Research and Knowledge Transfer in Biotechnology; University of Zagreb; Zagreb Croatia
- Centre of Excellence for Viral Immunology and Vaccines; CERVirVac; Croatia
| | - Anamarija Slović
- Centre for Research and Knowledge Transfer in Biotechnology; University of Zagreb; Zagreb Croatia
- Centre of Excellence for Viral Immunology and Vaccines; CERVirVac; Croatia
| | - Sunčanica Ljubin-Sternak
- Teaching Institute of Public Health “Dr. Andrija Štampar,” Zagreb; Croatia
- School of Medicine, University of Zagreb; Zagreb Croatia
| | | | - Dubravko Forčić
- Centre for Research and Knowledge Transfer in Biotechnology; University of Zagreb; Zagreb Croatia
- Centre of Excellence for Viral Immunology and Vaccines; CERVirVac; Croatia
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Horton KC, Dueger EL, Kandeel A, Abdallat M, El-Kholy A, Al-Awaidy S, Kohlani AH, Amer H, El-Khal AL, Said M, House B, Pimentel G, Talaat M. Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014. PLoS One 2017; 12:e0180954. [PMID: 28704440 PMCID: PMC5509236 DOI: 10.1371/journal.pone.0180954] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/23/2017] [Indexed: 11/19/2022] Open
Abstract
Introduction Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. Methods Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1–3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. Results At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens–influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. Conclusions Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest.
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Affiliation(s)
- Katherine C. Horton
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
- * E-mail:
| | - Erica L. Dueger
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
- Global Disease Detection Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Mohamed Abdallat
- Communicable Disease Department, Ministry of Health, Amman, Jordan
| | - Amani El-Kholy
- Clinical Pathology Department, Cairo University Hospitals, Cairo, Egypt
| | - Salah Al-Awaidy
- Communicable Disease Department, Ministry of Health, Muscat, Oman
| | | | - Hanaa Amer
- Clinical Pathology Department, Ain Shams University, Cairo, Egypt
| | | | - Mayar Said
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Brent House
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Guillermo Pimentel
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Maha Talaat
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
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Amer HM. Molecular Epidemiology of Human Metapneumovirus in Riyadh Province, Saudi Arabia. J Mol Microbiol Biotechnol 2016; 26:414-421. [DOI: 10.1159/000448374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/12/2016] [Indexed: 11/19/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important cause of respiratory tract illness in children. Two HMPV subgroups, A and B, and four genotypes, A1, A2, B1 and B2, have been identified. Concurrent circulation of the different genotypes in yearly epidemics has been recorded globally, but not in Saudi Arabia. The current report was designed to study HMPV epidemiology in Saudi children and to analyze the genetic diversity and circulation patterns. Nasopharyngeal aspirates (n = 174) were collected from hospitalized children in Riyadh (2008-2009). The screening of samples using real-time RT-PCR identified 19 HMPV strains. The majority of the strains belonged to subgroup B, while all strains of subgroup A were members of genotype A2. In 2008, only subgroup B was recognized, whereas in 2009 both subgroups were identified to be cocirculating at similar rates. The full-length attachment (G) gene and a partial sequence of the fusion (F) gene of positive samples were sequenced. The G gene showed a high degree of genetic diversity and exhibited a variable number of positively selected sites in different lineages. In contrast, the F gene demonstrated an extensive genetic stability with a higher tendency toward purifying selection. This is the first report on HMPV genotype circulation in Saudi Arabia; however, the exact circulation kinetics requires further retrospective and prospective study.
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Abstract
BACKGROUND Human metapneumovirus (HMPV) is a leading cause of acute respiratory tract infection in young children. Our objectives were to define HMPV epidemiology and circulating strains and determine markers of severe disease in Jordanian children. METHODS We conducted a prospective study from March 16, 2010 to March 31, 2013 using quantitative reverse transcription-polymerase chain reaction to determine the frequency of HMPV infection among children <2 years old admitted with fever and/or acute respiratory illness to a major government hospital in Amman, Jordan. RESULTS HMPV was present in 273 of 3168 (8.6%) of children presenting with acute respiratory tract infection. HMPV A2, B1 and B2, but not A1, were detected during the 3-year period. HMPV-infected children were older and more likely to be diagnosed with bronchopneumonia than HMPV-negative children. HMPV-infected children with lower respiratory tract infection had higher rates of cough and shortness of breath than children with lower respiratory tract infection infected with other or no identifiable viruses. Symptoms and severity were not different between children with HMPV only compared with HMPV coinfection. Children with HMPV subgroup A infection were more likely to require supplemental oxygen. In a multivariate analysis, HMPV subgroup A and age <6 months were independently associated with supplemental oxygen requirement. CONCLUSIONS HMPV is a leading cause of acute respiratory tract disease in Jordanian children <2 years old. HMPV A and young age were associated with severe disease. Ninety percent of HMPV-infected hospitalized children were full term and otherwise healthy, in contrast to high-income nations; thus, factors contributing to disease severity likely vary depending on geographic and resource differences.
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Reiche J, Jacobsen S, Neubauer K, Hafemann S, Nitsche A, Milde J, Wolff T, Schweiger B. Human metapneumovirus: insights from a ten-year molecular and epidemiological analysis in Germany. PLoS One 2014; 9:e88342. [PMID: 24505479 PMCID: PMC3914980 DOI: 10.1371/journal.pone.0088342] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/13/2014] [Indexed: 11/19/2022] Open
Abstract
Human metapneumovirus (HMPV) is a cause of respiratory tract illness at all ages. In this study the epidemiological and molecular diversity among patients of different ages was investigated. Between 2000-2001 and 2009-2010, HMPV was detected in 3% (138/4,549) of samples from outpatients with influenza-like illness with a new, sensitive real-time RT-PCR assay. Several hundred (797) clinical specimens from hospitalized children below the age of 4 years with acute respiratory illness were investigated and HMPV was detected in 11.9% of them. Investigation of outpatients revealed that HMPV infections occurred in individuals of all ages but were most prevalent in children (0-4 years) and the elderly (>60 years). The most present clinical features of HMPV infections were cough, bronchitis, fever/shivers and pneumonia. About two thirds of HMPV-positive samples were detected in February and March throughout the study period. Molecular characterization of HMPV revealed a complex cyclic pattern of group dominance where HMPV subgroup A and B viruses predominated in general for three consecutive seasons. German HMPV represented all genetic lineages including A1, A2, B1, B2, sub-clusters A2a and A2b. For Germany, not only time-dependent circulation of lineages and sub-clusters was observed but also co-circulation of two or three predominant lineages. Two newly emerging amino acid substitutions (positions 223 and 280) of lineage B2 were detected in seven German HMPV sequences. Our study gives new insights into the molecular epidemiology of HMPV in in- and outpatients over a time period of 10 years for the first time. It is one of only few long-term surveillance studies in Europe, and allows comparative molecular analyses of HMPV circulating worldwide.
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Affiliation(s)
- Janine Reiche
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Sonja Jacobsen
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Katrin Neubauer
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Susi Hafemann
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Robert Koch Institute, Berlin, Germany
| | - Jeanette Milde
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Thorsten Wolff
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
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