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Shen Q, Zhou YH, Zhou YQ. A prospects tool in virus research: Analyzing the applications of organoids in virus studies. Acta Trop 2024; 254:107182. [PMID: 38479469 DOI: 10.1016/j.actatropica.2024.107182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/28/2024]
Abstract
Organoids have emerged as a powerful tool for understanding the biology of the respiratory, digestive, nervous as well as urinary system, investigating infections, and developing new therapies. This article reviews recent progress in the development of organoid and advancements in virus research. The potential applications of these models in studying virul infections, pathogenesis, and antiviral drug discovery are discussed.
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Affiliation(s)
- Qi Shen
- Institute of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 20036, China; Institute of Microbiology Laboratory, Shanghai Institute of Preventive Medicine, Shanghai 20036, China
| | - Yu-Han Zhou
- College of Public Health, Jilin University, Changchun 130021, China
| | - Yan-Qiu Zhou
- Institute of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 20036, China; Institute of Microbiology Laboratory, Shanghai Institute of Preventive Medicine, Shanghai 20036, China.
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2
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Lee H, Kim SH, Cho SJ, Lee YU, Lee K, Lee YP, Seo J, Chung YS. Genetic Analysis of HPIV3 That Emerged during the SARS-CoV-2 Pandemic in Gwangju, South Korea. Viruses 2022; 14:v14071446. [PMID: 35891425 PMCID: PMC9317768 DOI: 10.3390/v14071446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Community mitigation measures taken owing to the COVID-19 pandemic have caused a decrease in the number of respiratory viruses, including the human parainfluenza virus type 3 (HPIV3), and a delay in their occurrence. HPIV3 was rarely detected as a consequence of monitoring respiratory viral pathogens in Gwangju, Korea, in 2020; however, it resurfaced as a delayed outbreak and peaked in September–October 2021. To understand the genetic characteristics of the reemerging virus, antigenic gene sequences and evolutionary analyses of the hemagglutinin-neuraminidase (HN) and fusion (F) genes were performed for 129 HPIV3 pathogens prevalent in Gwangju from 2018 to 2021. Unlike the prevalence of various HPIV3 strains in 2018-2019, the prevalence of HPIV3 by strains with reduced diversity was confirmed in 2021. It could be inferred that this decrease in genetic diversity was due to the restriction of inflow from other regions at home and abroad following the community mitigation measures and the spread within the region. The HPIV3 that emerged in 2021 consisted of HN coding regions that were 100% consistent with the sequence identified in Saitama, Japan, in 2018, and F coding regions exhibiting 99.6% homology to a sequence identified in India in 2017, among the ranks reported to the National Center for Biotechnology Information. The emergence of a new lineage in a community can lead to a mass outbreak by collapsing the collective immunity of the existing acquired area; therefore, continuous monitoring is necessary.
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Affiliation(s)
- Hongsu Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Sun-Hee Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
- Correspondence: (S.-H.K.); (Y.-S.C.)
| | - Sun-Ju Cho
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yeong-Un Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Kwangho Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yong-Pyo Lee
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Diseases Control and Prevention Agency, Gwangju 61947, Korea;
| | - Jinjong Seo
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yoon-Seok Chung
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Diseases Control and Prevention Agency, Gwangju 61947, Korea;
- Correspondence: (S.-H.K.); (Y.-S.C.)
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Kim HN, Yoon SY, Lim CS, Lee CK, Yoon J. Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea. J Clin Virol 2022; 153:105213. [DOI: 10.1016/j.jcv.2022.105213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
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Elusah J, Bulimo WD, Opanda SM, Symekher SL, Wamunyokoli F. Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene. PLoS One 2020; 15:e0229355. [PMID: 32155160 PMCID: PMC7064169 DOI: 10.1371/journal.pone.0229355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Human respirovirus type 3 (HRV3) is a leading etiology of lower respiratory tract infections in young children and ranks only second to the human respiratory syncytial virus (HRSV). Despite the public health importance of HRV3, there is limited information about the genetic characteristics and diversity of these viruses in Kenya. To begin to address this gap, we analyzed 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013. Viral RNA was extracted from the isolates, and the entire HN gene amplified by RT-PCR followed by nucleotide sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates grouped into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of isolates belonged to sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence analysis revealed high identities between the Kenyan isolates and the HRV3 prototype strain both at the amino acid (96.5-97.9%) and nucleotide (94.3-95.6%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection pressure analyses showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses revealed that the mean TMRCA for the HN sequence dataset was 1942 (95% HPD: 1928-1957), while the mean evolutionary rate was 4.65x10-4 nucleotide substitutions/site/year (95% HPD: 2.99x10-4 to 6.35x10-4). Overall, our results demonstrate the co-circulation of strains of cluster C HRV3 variants in Kenya during the study period. This is the first study to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene.
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Affiliation(s)
- Juliet Elusah
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Wallace Dimbuson Bulimo
- Department of Emerging infections, US Army Medical Directorate–Africa, Nairobi, Kenya
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | | | | | - Fred Wamunyokoli
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
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Farrag MA, Hamed ME, Amer HM, Almajhdi FN. Epidemiology of respiratory viruses in Saudi Arabia: toward a complete picture. Arch Virol 2019; 164:1981-1996. [PMID: 31139937 PMCID: PMC7087236 DOI: 10.1007/s00705-019-04300-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Acute lower respiratory tract infection is a major health problem that affects more than 15% of the total population of Saudi Arabia each year. Epidemiological studies conducted over the last three decades have indicated that viruses are responsible for the majority of these infections. The epidemiology of respiratory viruses in Saudi Arabia is proposed to be affected mainly by the presence and mobility of large numbers of foreign workers and the gathering of millions of Muslims in Mecca during the Hajj and Umrah seasons. Knowledge concerning the epidemiology, circulation pattern, and evolutionary kinetics of respiratory viruses in Saudi Arabia are scant, with the available literature being inconsistent. This review summarizes the available data on the epidemiology and evolution of respiratory viruses. The demographic features associated with Middle East respiratory syndrome-related coronavirus infections are specifically analyzed for a better understanding of the epidemiology of this virus. The data support the view that continuous entry and exit of pilgrims and foreign workers with different ethnicities and socioeconomic backgrounds in Saudi Arabia is the most likely vehicle for global dissemination of respiratory viruses and for the emergence of new viruses (or virus variants) capable of greater dissemination.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Maaweya E Hamed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia.
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Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018; 3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.
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Affiliation(s)
- Anna Smielewska
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Edward Emmott
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Department of Bioengineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Kyriaki Ranellou
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Ashley Popay
- Eastern Field Epidemiology Unit, Institute of Public Health, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Hamid Jalal
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
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Brini Khalifa I, Hannachi N, Guerrero A, Orth-Höller D, Bhiri S, Bougila J, Boughamoura L, Merchaoui SN, Sboui H, Mahdhaoui N, Schiela B, Laer DHV, Boukadida J, Stoiber H. Demographic and seasonal characteristics of respiratory pathogens in neonates and infants aged 0 to 12 months in the Central-East region of Tunisia. J Med Virol 2018; 91:570-581. [PMID: 30351487 PMCID: PMC6492255 DOI: 10.1002/jmv.25347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/17/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND This study aimed to characterize the epidemiology of pathogenic respiratory agents in patients aged 0 to 12 months and hospitalized for acute respiratory infections in Tunisia between 2013 and 2014. METHODS A total of 20 pathogens, including viruses, Mycoplasma pneumoniae, and Streptococcus pneumoniae, were detected using molecular sensitive assays, and their associations with the patient's demographic data and season were analyzed. RESULTS Viral infectious agents were found in 449 (87.2%) of 515 specimens. Dual and multiple infectious agents were detected in 31.4% and 18.6% of the samples, respectively. Viral infection was predominant in the pediatric environment (90.8%, P < 0.001), male patients (88.0%), and spring (93.8%). Rhinovirus was the most detected virus (51.8%) followed by respiratory syncytial virus A/B (34.4%), coronavirus group (18.5%), adenovirus (17.9%), and parainfluenza viruses 1-4 (10.9%). Respiratory Syncytial virus A/B was significantly associated with gender (38.0% male cases vs 28.3% female cases, P = 0.02). Infections by Adenovirus, Bocavirus, and Metapneumovirus A/B increased with increasing age of patients (predominated cases aged 6-12 months, P < 0.001). S. pneumoniae was detected in 30.9% of th tested samples. In 18.2% of the negative viral infections, only S. pneumoniae was identified. CONCLUSION A predominance of the rhinovirus infection was observed in this study. Coronavirus subtypes were described for the first time in Tunisia. The observed different pathogenic profiles across age groups could be helpful to avoid the misclassification of patients presenting with ARIs at the triage level when no standardized protocol is available. This study will provide clues for physicians informing decisions regarding preventive strategies and medication in Tunisia.
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Affiliation(s)
- Ines Brini Khalifa
- Department of Microbiology, Immunology, and Parasitology, Laboratory of Microbiology, Sousse Medical University, University of Sousse, Sousse, Tunisia.,Department of Microbiology, Research Unit for Genomic Characterization of Infectious Agents UR12SP34, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia.,Doctoral School of Biological Sciences, Biotechnology and Health, Higher Institute of Biotechnology of Monastir, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Division of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Naila Hannachi
- Department of Microbiology, Immunology, and Parasitology, Laboratory of Microbiology, Sousse Medical University, University of Sousse, Sousse, Tunisia.,Department of Microbiology, Research Unit for Genomic Characterization of Infectious Agents UR12SP34, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Aida Guerrero
- Division of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Sana Bhiri
- Department of Epidemiology and Medical Statistics, Division of Medical Statistics, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Jihene Bougila
- Pediatric Ward, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Lamia Boughamoura
- Pediatric Ward, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | | | - Hassen Sboui
- Neonatology Ward, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Nabiha Mahdhaoui
- Neonatology Ward, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Britta Schiela
- Division of Virology, Innsbruck Medical University, Innsbruck, Austria
| | | | - Jalel Boukadida
- Department of Microbiology, Immunology, and Parasitology, Laboratory of Microbiology, Sousse Medical University, University of Sousse, Sousse, Tunisia.,Department of Microbiology, Research Unit for Genomic Characterization of Infectious Agents UR12SP34, University-Hospital of Farhat Hached of Sousse, Sousse, Tunisia
| | - Heribert Stoiber
- Division of Virology, Innsbruck Medical University, Innsbruck, Austria
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Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018; 3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 10/05/2023] Open
Abstract
Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.
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Affiliation(s)
- Anna Smielewska
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Edward Emmott
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Department of Bioengineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Kyriaki Ranellou
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Ashley Popay
- Eastern Field Epidemiology Unit, Institute of Public Health, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Hamid Jalal
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
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Jornist I, Muhsen K, Ram D, Lustig Y, Levy V, Orzitser S, Azar R, Weil M, Indenbaum V, Sofer D, Mendelson E, Mandelboim M, Hindiyeh M. Characterization of human parainfluenza virus-3 circulating in Israel, 2012-2015. J Clin Virol 2018; 107:19-24. [PMID: 30114677 DOI: 10.1016/j.jcv.2018.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Human parainfluenza virus 3 (hPIV-3) causes respiratory tract infection. OBJECTIVES The objective of this study was to describe the epidemiology of hPIV-3 infection among hospitalized patients and characterize the circulating strains. STUDY DESIGN A cross-sectional study was conducted using respiratory samples of 15,946 hospitalized patients with respiratory symptoms in 2012-2015 in Israel. All samples were subjected to q-PCR and q-RT-PCR to determine the presence of hPIV-3 and other respiratory viruses. Samples positive for hPIV-3 were subjected to molecular typing and phylogenetic analysis. RESULTS Overall, 547 samples 3.4% (95% CI 3.2-3.7) were positive for hPIV-3. Of these 87 (15.9%) were mixed infections; 41.4% with adenovirus, 40.2% with RSV (40.2%) and 19.5% influenza A viruses. The prevalence of hPIV-3 was highest (5.1%) in children aged 0-4 years. Hospitalization in oncology department was associated with increased likelihood of hPIV-3 infection: adjusted odds ratio [aOR] 2.29 (95% confidence intervals [CI] 1.78-2.96), as well as hospitalization in organ transplantation department: aOR 3.65 (95% CI 2.80-4.76). The predominant lineages were C3c (62.3%) and C1b (24.6%), followed by sub-lineages C5 (8.7%) and C3b (2.9%). A new sub-lineage emerged in our analysis, named C1d, which was 17 (1.5%) nucleotide different from C1a, 25 (2.2%) nucleotide different from C1b and 24 (2.1%) nucleotide different from C1c. DISCUSSION Young children and immunocompromised patients are likely the risk groups for severe respiratory infections with hPIV-3. Strains belonging to lineages C3c and C1b, which are present worldwide, should be targeted in vaccine development. The emergence of new lineage might have public health implications and on vaccine development.
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Affiliation(s)
- Irina Jornist
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Microbiology and Immunology, Tel-Aviv University, Tel-Aviv, Israel
| | - Khitam Muhsen
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Daniela Ram
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Virginia Levy
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Sara Orzitser
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Merav Weil
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Viki Indenbaum
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Musa Hindiyeh
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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Godoy C, Peremiquel-Trillas P, Andrés C, Gimferrer L, Uriona SM, Codina MG, Armadans L, Martín MDC, Fuentes F, Esperalba J, Campins M, Pumarola T, Antón A. A molecular epidemiological study of human parainfluenza virus type 3 at a tertiary university hospital during 2013-2015 in Catalonia, Spain. Diagn Microbiol Infect Dis 2016; 86:153-9. [PMID: 27524509 PMCID: PMC7127006 DOI: 10.1016/j.diagmicrobio.2016.07.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 01/13/2023]
Abstract
Human parainfluenza virus type 3 (HPIV-3) is one of the most common respiratory viruses particularly among young children and immunocompromised patients. The seasonality, prevalence and genetic diversity of HPIV-3 at a Spanish tertiary-hospital from 2013 to 2015 are reported. HPIV-3 infection was laboratory-confirmed in 102 patients (76%, under 5 years of age). Among <5 years-old patients, 9 (11.5%) were under any degree of immunosuppression, whereas this percentage was significantly higher (19; 79.2%) among patients older than 5 years. HPIV-3 was detected at varying levels, but mainly during spring and summer. All characterized HN/F sequences fell within C1b, C5 and in other two closely C3a-related groups. Furthermore, a new genetic lineage (C1c) was described. Genetic similarity and epidemiological data confirmed some nosocomial infections, highlighting the importance of the HPIV-3 surveillance, particularly in high-risk patients. This study provides valuable information on HPIV-3 diversity due to the scarce information in Europe. Children and immunosuppressed adults showed a great susceptibility to infection. Valuable information about the current genetic diversity in Europe is provided. Different lineages, including a first described, were locally circulating. Genetic similarity and epidemiological data confirmed some nosocomial infections. The present study highlights the importance of the HPIV-3 surveillance.
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Affiliation(s)
- Cristina Godoy
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Laura Gimferrer
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Sonia María Uriona
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - María Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Lluis Armadans
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - María Del Carmen Martín
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Francisco Fuentes
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Magda Campins
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.
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11
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Liu T, Li Z, Zhang S, Song S, Julong W, Lin Y, Guo N, Xing C, Xu A, Bi Z, Wang X. Viral Etiology of acute respiratory tract infections in hospitalized children and adults in Shandong Province, China. Virol J 2015; 12:168. [PMID: 26467854 PMCID: PMC4606902 DOI: 10.1186/s12985-015-0388-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/20/2015] [Indexed: 11/17/2022] Open
Abstract
Background The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized patients. Improved etiological insight is needed to improve clinical management and prevention of ARIs. Methods Clinical and demographic information and throat swabs were collected from 607 patients from 2011 to 2013 in Shandong Province, China. Multiplex RT-PCR (SeeplexTM RV detection, Seegene) was performed to detected 12 respiratory viral pathogens. Results A total of 607 hospitalized patients were enrolled from 2011 to 2013. Viruses were identified in 35.75 % (217/607) of cases, including 78 influenza virus A and B (IVA and IVB), 47 para-influenza viruses (PIVs), 41 respiratory syncytial virus (RSV) and 38 adenovirus (ADV). For the children under 15 year old, the common detected viruses were influenza viruses, RSV, PIVS and ADV, while the principal respiratory viruses were human coronaviruses (HCoV), PIVs, influenza viruses for the old adults. Co-infections with multiple viruses were detected in 15.67 % of patients. Children under 5 years were more likely to have one or more detectable virus associated with their ARI. The peak of ARI caused by the respiratory viruses occurred in winter. Conclusion This study demonstrated respiratory viruses were the major cause of hospitalized ARI patients in Shandong Province, influenza virus was the most common detected, RSV was the highest incidence among the young children (≤5 years). These findings also gave a better understand of virus distribution among different age and seasons, which help to consider potential therapeutic approaches and develop effective prevention strategies for respiratory virus infection.
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Affiliation(s)
- Ti Liu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Zhong Li
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Shengyang Zhang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Shaoxia Song
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Wu Julong
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Yi Lin
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Nongjian Guo
- Jinan Central Hospital Affiliated to Shandong University, Jinan, 250014, Shandong, China.
| | - Chunyan Xing
- Jinan Central Hospital Affiliated to Shandong University, Jinan, 250014, Shandong, China.
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Zhenqiang Bi
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
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12
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Almajhdi FN. Hemagglutinin-neuraminidase gene sequence-based reclassification of human parainfluenza virus 3 variants. Intervirology 2015; 58:35-40. [PMID: 25592955 DOI: 10.1159/000369208] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/18/2014] [Indexed: 11/19/2022] Open
Abstract
The most comprehensive phylogenetic classification of human parainfluenza virus 3 (HPIV-3) was recently developed [PLoS One 2012;7:e43893]. This classification included three distinct clusters (A, B and C) with subdivision of cluster C into four subclusters (C1-4). In the present report, the classification of HPIV-3 was refined by inclusion of 27 overlooked beside newly characterized Saudi variants. The new phylogram was developed and included the same clusters described before, in which cluster A remained unchanged and cluster B contained more recent isolates. The organization of cluster C was altered through inclusion of a new subcluster (C5), subdivision of C1 into two lineages C1a and C1b and subdivision of C3 into three lineages C3a, C3b and C3c. The majority of Saudi variants were classified as members of subcluster C1b, whereas only one variant was placed in each of subclusters C2 and C5. This study illustrates an up-to-date phylogenetic classification of HPIV-3 variants.
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Affiliation(s)
- Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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13
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Zhang D, He Z, Xu L, Zhu X, Wu J, Wen W, Zheng Y, Deng Y, Chen J, Hu Y, Li M, Cao K. Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China. Int J Infect Dis 2014; 25:159-64. [PMID: 24927663 PMCID: PMC7110535 DOI: 10.1016/j.ijid.2014.02.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) ranks respiratory tract infection (RTI) as the second leading cause of death worldwide for children under 5 years of age. The aim of this work was to evaluate the epidemiology characteristics of respiratory viruses found in children and adults with RTI from July 2009 to June 2012 in southern China. Methods In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Results The demographic characteristics, viral prevalence, age distribution, seasonal distribution, and pathogen spectrum of the patients with RTIs were analyzed. Co-infection was observed in 483 specimens, but it was more common in male patients, inpatients, children, and young adults. It varied by season, being more prevalent in the spring and summer and less so in the winter. Human coronavirus and human bocavirus were the most common pathogens, tending to occur in co-infection with other respiratory viruses. Conclusions This work adds to our knowledge of the epidemiology characteristics of these seven common respiratory viruses among patients with RTI in southern China. The detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection, and might also provide data relevant to the development of prevention strategies.
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Affiliation(s)
- Dingmei Zhang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Zhenjian He
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Lin Xu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Xun Zhu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Jueheng Wu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Weitao Wen
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yun Zheng
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yu Deng
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Jieling Chen
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yiwen Hu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Mengfeng Li
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China.
| | - Kaiyuan Cao
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China.
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Sasaki M, Ishii A, Orba Y, Thomas Y, Hang'ombe BM, Moonga L, Mweene AS, Ogawa H, Nakamura I, Kimura T, Sawa H. Human parainfluenza virus type 3 in wild nonhuman primates, Zambia. Emerg Infect Dis 2014; 19. [PMID: 23968816 PMCID: PMC3810902 DOI: 10.3201/eid1909.121404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human parainfluenza virus type 3 (HPIV3) genome was detected in 4 baboons in Zambia. Antibody for HPIV3 was detected in 13 baboons and 6 vervet monkeys in 2 distinct areas in Zambia. Our findings suggest that wild nonhuman primates are susceptible to HPIV3 infection.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Hokkaido University, Research Center for Zoonosis Control, West 10 North 20, Kita-ku, Sapporo 001-0020, Japan
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Berrueco R, Antón A, Rives S, Català A, Toll T, Ruiz A, Camós M, Torrebadell M, Estella J, Muñoz-Almagro C. Multiplex real-time PCR for prompt diagnosis of an outbreak of human parainfluenza 3 virus in children with acute leukemia. Infection 2013; 41:1171-5. [PMID: 23821486 PMCID: PMC7100800 DOI: 10.1007/s15010-013-0498-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 06/18/2013] [Indexed: 01/22/2023]
Abstract
Introduction Human parainfluenza virus type 3 (HPIV-3) causes significant morbimortality in immunocompromised patients. Outbreaks of severe pneumonitis have been previously described in this setting. Materials and methods Retrospective observational study in children diagnosed with acute leukemia and a documented HPIV-3 infection in the context of a nosocomial outbreak occurred in a single center. Result During summer 2012, an HPIV-3 infection was detected in six hospitalized children with acute leukemia. All the patients had respiratory symptoms and one of them suffered from parotitis. Conclusion Early diagnoses using multiplex real-time polymerase chain reaction (PCR) let us control this outbreak. A phylogenetic analysis confirmed person-to-person transmission of a single HPIV-3 variant.
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Affiliation(s)
- R Berrueco
- Pediatric Hematology Department, Hospital Sant Joan de Déu, University of Barcelona, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Spain,
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