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A Multicenter Study of Viral Aetiology of Community-Acquired Pneumonia in Hospitalized Children in Chinese Mainland. Virol Sin 2021; 36:1543-1553. [PMID: 34523109 PMCID: PMC8440149 DOI: 10.1007/s12250-021-00437-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
Community-acquired pneumonia (CAP) is one of the leading causes of morbidity and mortality in children worldwide. In this study, we aimed to describe the aetiology of viral infection of pediatric CAP in Chinese mainland. During November 2014 to June 2016, the prospective study was conducted in 13 hospitals. The hospitalized children under 18 years old who met the criteria for CAP were enrolled. The throat swabs or nasopharyngeal aspirates (NPAs) were collected which were then screened 18 respiratory viruses using multiplex PCR assay. Viral pathogens were present in 56.6% (1539/2721) of the enrolled cases, with the detection rate of single virus in 39.8% of the cases and multiple viruses in 16.8% of the cases. The most frequently detected virus was respiratory syncytial virus (RSV) (15.2%, 414/2721). The highest detection rate of virus was in < 6-month-age group (70.7%, 292/413). RSV, human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs) and influenza B virus (Flu B) showed the similar prevalence patterns both in north and south China, but HPIVs, Flu A, human bocavirus (HBoV), human adenovirus (HAdV) and human coronaviruses (HCoVs) showed the distinct circulating patterns in north and south China. Human enterovirus/human rhinovirus (HEV/HRV) (27.6%, 27/98), HBoV (18.4%, 18/98), RSV (16.3%, 16/98) and HMPV (14.3%, 14/98) were the most commonly detected viruses in severe pneumonia cases with single virus infection. In conclusion, viral pathogens are frequently detected in pediatric CAP cases and may therefore play a vital role in the aetiology of CAP. RSV was the most important virus in hospitalized children with CAP in Chinese mainland.
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Ljubin-Sternak S, Meštrović T, Lukšić I, Mijač M, Vraneš J. Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot. Front Public Health 2021; 9:691163. [PMID: 34291031 PMCID: PMC8287126 DOI: 10.3389/fpubh.2021.691163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/04/2021] [Indexed: 02/02/2023] Open
Abstract
Respiratory viral infections are the leading cause of morbidity and mortality in the world; however, there are several groups of viruses that are insufficiently routinely sought for, and can thus be considered neglected from a diagnostic and clinical standpoint. Timely detection of seasonality of certain respiratory viruses (e.g., enveloped viruses such as seasonal coronaviruses) in the local context can aid substantially in targeted and cost-effective utilization of viral diagnostic approaches. For the other, non-enveloped and year-round viruses (i.e., rhinovirus, adenovirus, and bocavirus), a continuous virological diagnosis needs to be implemented in clinical laboratories to more effectively address the aetiology of respiratory infections, and assess the overall impact of these viruses on disease burden. While the coronavirus disease 2019 (COVID-19) pandemic is still actively unfolding, we aimed to emphasize the persistent role of seasonal coronaviruses, rhinoviruses, adenoviruses and bocaviruses in the aetiology of respiratory infections. Consequently, this paper concentrates on the burden and epidemiological trends of aforementioned viral groups on a global level, but also provides a snapshot of their prevalence patterns in Croatia in order to underscore the potential implications of viral seasonality. An overall global prevalence in respiratory tract infections was found to be between 0.5 and 18.4% for seasonal coronaviruses, between 13 and 59% for rhinoviruses, between 1 and 36% for human adenoviruses, and between 1 and 56.8% for human bocaviruses. A Croatian dataset on patients with respiratory tract infection and younger than 18 years of age has revealed a fairly high prevalence of rhinoviruses (33.4%), with much lower prevalence of adenoviruses (15.6%), seasonal coronaviruses (7.1%), and bocaviruses (5.3%). These insights represent a relevant discussion point in the context of the COVID-19 pandemic where the testing of non-SARS-CoV-2 viruses has been limited in many settings, making the monitoring of disease burden associated with other respiratory viruses rather difficult.
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Affiliation(s)
- Sunčanica Ljubin-Sternak
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tomislav Meštrović
- Clinical Microbiology and Parasitology Unit, Zora Profozić Polyclinic, Zagreb, Croatia.,University Centre Varaždin, University North, Varaždin, Croatia
| | - Ivana Lukšić
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
| | - Maja Mijač
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jasmina Vraneš
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
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Haddadin Z, Rankin DA, Lipworth L, Suh M, McHenry R, Blozinski A, George SS, Fernandez KN, Varjabedian R, Spieker AJ, Shepard DS, Halasa NB. Respiratory Virus Surveillance in Infants across Different Clinical Settings. J Pediatr 2021; 234:164-171.e2. [PMID: 33774057 DOI: 10.1016/j.jpeds.2021.03.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES We aimed to evaluate the distribution, clinical presentations and severity of common acute respiratory infections (ARI) viruses in infants across 3 clinical settings. STUDY DESIGN In a prospective virus surveillance study, infants under 1 year with fever and/or respiratory symptoms were enrolled from outpatient, emergency department, and inpatient settings from December 16, 2019 through April 30, 2020. Demographic and clinical characteristics were collected through parent/guardian interviews, medical chart abstractions, and follow-up surveys. Nasal swabs were collected and tested for viruses using quantitative reverse-transcription polymerase chain reaction. RESULTS We enrolled 366 infants and tested nasal swabs on 360 (98%); median age was 6.3 months, 50% male. In total, 295 (82%) had at least 1 virus detected; rhinovirus/enterovirus (RV/EV; 42%), respiratory syncytial virus (RSV; 34%), and influenza (15%) were the most common. RSV was the most frequently detected virus in the inpatient (63%) and emergency department (37%) settings, and RV/EV was most frequently detected virus in the outpatient setting (54%). RSV-positive infants had a lower median age (4.9 months) and were more likely to have respiratory distress, and RV/EV-positive infants were less likely to have respiratory distress. Influenza-positive infants had a higher median age (8 months) and were more likely to have systemic symptoms. RSV infection and younger age were associated with higher odds of hospitalization in multivariable logistic regression. CONCLUSIONS Across 3 clinical settings, and combining virologic, patient, and health-system information, our results highlight the burden of viral ARI among infants. Overall, RSV, RV/EV, and influenza were most commonly detected, with RSV having the highest disease severity.
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Affiliation(s)
- Zaid Haddadin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.
| | - Danielle A Rankin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Nashville, TN
| | - Loren Lipworth
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN
| | | | - Rendie McHenry
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Anna Blozinski
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Kailee N Fernandez
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Donald S Shepard
- Heller School for Social Policy and Management, Brandeis University, Waltham, MA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
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Widhidewi NW, Wiyatno A, Dewantari AK, Paramasatiari L, Aryastuti SA, Artika IN, Setiawan WD, Soebandrio A, Aye Myint KS, safari D. Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia. Access Microbiol 2020; 2:acmi000120. [PMID: 32974585 PMCID: PMC7494194 DOI: 10.1099/acmi.0.000120] [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: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 12/04/2022] Open
Abstract
Acute respiratory tract infection (ARTI) is the most common infectious disease in humans worldwide. The morbidity and mortality rates are high, especially in developing countries from Southeast Asia and Africa. While ARTI is commonly associated with viruses, there is limited data on the spectrum of viruses causing ARTI in developing countries, including Indonesia. This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In total, 98 out of 200 samples (49.0 %) tested positive for viruses. Our study confirmed 64.3 % viral etiology in children and 12.2 % in adults. Viruses that were detected were Herpesviridae (15.0 %) followed by enteroviruses (12.0 %), influenza A virus (11.5 %), respiratory syncytial virus (8.0 %), Adenoviridae (6.5 %), human metapneumovirus (3.5 %), Paramyxoviridae (2.0 %), bocavirus (1.0 %) and Coronaviridae (0.5 %). The study sheds light on the viral spectrum of ARTI in children and adults in Tabanan, Bali, Indonesia.
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Affiliation(s)
- Ni Wayan Widhidewi
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Ageng Wiyatno
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | | | - Lila Paramasatiari
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Sri Agung Aryastuti
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - I Nengah Artika
- Tabanan General Hospital, Jl. Pahlawan, Tabanan, Bali, Indonesia
| | | | - Amin Soebandrio
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Khin Saw Aye Myint
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Dodi safari
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
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Ljubin-Sternak S, Meštrović T, Ivković-Jureković I, Kolarić B, Slović A, Forčić D, Tot T, Mijač M, Vraneš J. The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children - Clinical and Molecular Epidemiological Study From Croatia, 2017-2019. Front Microbiol 2019; 10:2737. [PMID: 31849887 PMCID: PMC6901631 DOI: 10.3389/fmicb.2019.02737] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/11/2019] [Indexed: 01/06/2023] Open
Abstract
Rhinoviruses (RVs) are increasingly implicated not only in mild upper respiratory tract infections, but also in more severe lower respiratory tract infections; however, little is known about species diversity and viral epidemiology of RVs among the infected children. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. For respiratory virus detection, nasopharyngeal and pharyngeal flocked swabs were taken from each patient and subsequently analyzed with multiplex RT-PCR. To determine the RV species in a subset of positive children, 5'UTR in RV-positive samples has been sequenced. Nucleotide sequences of referent RV strains were retrieved by searching the database with Basic Local Alignment Tool, and used to construct alignments and phylogenetic trees using MAFFT multiple sequence alignment tool and the maximum likelihood method, respectively. In our study population RV was the most frequently detected virus, diagnosed in 197 patients (33.4%), of which 60.4% was detected as a monoinfection. Median age of RV-infected children was 2.25 years, and more than half of children infected with RV (55.8%) presented with lower respiratory tract infections. Most RV cases were detected from September to December, and all three species co-circulated during the analyzed period (2017-2019). Sequence analysis based on 5'UTR region yielded 69 distinct strains; the most prevalent was RV-C (47.4%) followed by RV-A (44.7%) and RV-B (7.9%). Most of RV-A sequences formed a distinct phylogenetic group; only strains RI/HR409-18 (along with a reference strain MF978777) clustered with RV-C strains. Strains belonging to the group C were the most diverse (41.6% identity among strains), while group B was the most conserved (71.5% identity among strains). Despite such differences in strain groups (hitherto undescribed in Croatia), clinical presentation of infected children was rather similar. Our results are consistent with newer studies that investigated the etiology of acute respiratory infections, especially those focused on children with lower respiratory tract infections, where RVs should always be considered as potentially serious pathogens.
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Affiliation(s)
- Sunčanica Ljubin-Sternak
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
- Medical Microbiology Department, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Tomislav Meštrović
- Clinical Microbiology and Parasitology Unit, Polyclinic “Dr. Zora Profozić”, Zagreb, Croatia
- University Centre Varaždin, University North, Varaždin, Croatia
| | - Irena Ivković-Jureković
- Department of Pulmonology, Allergy, Immunology and Rheumatology, Children’s Hospital Zagreb, Zagreb, Croatia
- Faculty for Dental Medicine and Healthcare/School of Medicine, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Branko Kolarić
- Department of Epidemiology, Dr. Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
- Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Anamarija Slović
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Dubravko Forčić
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Tatjana Tot
- Department of Microbiology, General Hospital Karlovac, Karlovac, Croatia
| | - Maja Mijač
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
- Medical Microbiology Department, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Jasmina Vraneš
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
- Medical Microbiology Department, School of Medicine, University of Zagreb, Zagreb, Croatia
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Civljak R, Kosutic-Gulija T, Slovic A, Huljev E, Turcic N, Mestrovic T, Vranes J, Ljubin-Sternak S. An Outbreak of Human Parainfluenza Virus 3 (Phylogenetic Subcluster C5) Infection among Adults at a Residential Care Facility for the Disabled in Croatia, 2018. Intervirology 2019; 62:174-181. [PMID: 31661701 DOI: 10.1159/000503630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Although highly pertinent for children, outbreaks of human parainfluenza virus (HPIV) may cause up to 15% of all respiratory illnesses in adults and predispose them to serious adverse outcomes, with HPIV serotype 3 (HPIV3) being the most common. This study represents the first report of an HPIV3 outbreak among adults at a long-term health-care facility in Croatia. METHODS A retrospective study was conducted to investigate an outbreak of acute respiratory infection (ARI) at a single residential care facility for the disabled in Croatia. Demographic, epidemiological, and clinical data were collected for all residents, while hospitalized patients were appraised in detail by laboratory/radiological methods. Multiplex PCR for respiratory viruses and sequencing was performed. Partial HPIV3 HN 581 nt sequences were aligned with HPIV3 sequences from the GenBank database to conduct a phylogenetic analysis, where different bioinformatic approaches were employed. RESULTS In late June 2018, 5 of the 10 units at the facility were affected by the outbreak. Among the 106 residents, 23 (21.7%) developed ARI, and 6 (26.1%) of them were hospitalized. HPIV3 was identified in 18 (73%) of the residents and 5 (83%) of the hospitalized individuals. Isolated HPIV3 strains were classified within the phylogenetic subcluster C5 but grouped on 2 separate branches of the phylogenetic tree. During the entire outbreak period, none of the institution's employees reported symptoms of ARI. CONCLUSIONS Our study has shown that this health care-associated outbreak of HPIV3 infection could have been linked to multiple importation events. Preventive measures in curbing such incidents should be enforced vigorously.
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Affiliation(s)
- Rok Civljak
- Department of Respiratory Tract Infections,Dr. Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tanja Kosutic-Gulija
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Anamarija Slovic
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Eva Huljev
- Department of Respiratory Tract Infections,Dr. Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nikolina Turcic
- Department of Epidemiology, Zagreb County Institute of Public Health, Dugo Selo Branch, Dugo Selo, Croatia
| | - Tomislav Mestrovic
- Clinical Microbiology and Parasitology Unit, Dr. Zora Profozic Polyclinic, Zagreb, Croatia.,University Centre Varaždin, University North, Varaždin, Croatia
| | - Jasmina Vranes
- Clinical Microbiology Department, Dr. Andrija Stampar Teaching Institute of Public Health, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Suncanica Ljubin-Sternak
- Clinical Microbiology Department, Dr. Andrija Stampar Teaching Institute of Public Health, University of Zagreb School of Medicine, Zagreb, Croatia,
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Halaji M, Hashempour T, Moayedi J, Pouladfar GR, Khansarinejad B, Khashei R, Moattari A, Musavi Z, Ghassabi F, Pirbonyeh N. Viral etiology of acute respiratory infections in children in Southern Iran. Rev Soc Bras Med Trop 2019; 52:e20180249. [PMID: 31365620 DOI: 10.1590/0037-8682-0249-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/20/2018] [Indexed: 01/20/2023] Open
Abstract
INTRODUCTION Prevalence of influenza A virus (Flu-A), respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) was assessed in children with acute respiratory infections (ARIs). METHODS Nasopharyngeal aspirates and throat swabs were subjected to real-time polymerase chain reaction (PCR) to detect RSV and Flu-A and to conventional PCR to detect hMPV. RESULTS Of the 156 children assessed, 93 (59.6%) carried at least one virus, with 35.9% positive for RSV, 14.1% for hMPV, and 9.6% for Flu-A. The prevalence of co-infections was 2.6%. CONCLUSIONS The high detection rate may reflect increased sensitivity of real-time PCR compared to traditional PCR and viral culture.
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Affiliation(s)
- Mehrdad Halaji
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tayebeh Hashempour
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholam Reza Pouladfar
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Khansarinejad
- Department of Microbiology & Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Reza Khashei
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Musavi
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzaneh Ghassabi
- Clinical Microbiology Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Zhong P, Zhang H, Chen X, Lv F. Clinical characteristics of the lower respiratory tract infection caused by a single infection or coinfection of the human parainfluenza virus in children. J Med Virol 2019; 91:1625-1632. [PMID: 31066075 PMCID: PMC7166436 DOI: 10.1002/jmv.25499] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Human parainfluenza virus (HPIV), usually combined with other pathogens, causes lower respiratory tract infection (LRTI) in children. However, clinical characteristics of HPIV coinfection with other pathogens were unclear. This study aimed to investigate the viral and atypical bacterial etiology of LRTI in children and compare the clinical characteristics of HPIV single infection with those of coinfection. METHODS This study included 1335 patients, aged between 1 to 71 months, diagnosed with LRTI in Yuying Children's Hospital, Zhejiang, China, from December 2013 to June 2015. Nasopharyngeal secretions were collected, and respiratory pathogens were detected using Multiplex polymerase chain reaction. The clinical data of patients were collected and analyzed. RESULTS At least 1 pathogen was detected in 1181/1335 (88.5%) patients. The pathogens identified most frequently were respiratory syncytial virus, human rhinovirus, HPIV, adenovirus, and human metapneumovirus. The coinfection rate was 24.8%. HPIV coinfection with other viruses was more associated with running nose, shortness of breath, and oxygen support compared with HPIV single infection. Moreover, HPIV coinfection with atypical bacteria was more related to running nose, moist rales, and longer hospital duration compared with HPIV single infection, and also to longer hospital duration compared with coinfection with other viruses. CONCLUSIONS This study demonstrated that viral infections were highly associated with LRTI and the rate of coinfection was high. HPIV single infection was milder than coinfection with other viruses. Moreover, HPIV coinfection with atypical bacteria was more serious than HPIV single infection and coinfection with other viruses.
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Affiliation(s)
- Peipei Zhong
- Department of Children's Respiration Disease, The Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hailin Zhang
- Department of Children's Respiration Disease, The Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaofang Chen
- Department of Children's Respiration Disease, The Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fangfang Lv
- Department of Children's Respiration Disease, The Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
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A 3-Year Retrospective Study of the Epidemiology of Acute Respiratory Viral Infections in Pediatric Patients With Cancer Undergoing Chemotherapy. J Pediatr Hematol Oncol 2019; 41:e242-e246. [PMID: 30688827 DOI: 10.1097/mph.0000000000001418] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Acute viral respiratory infections are common causes of febrile episodes in children. There are still limited data about distribution of acute viral respiratory infections in children with cancer. OBJECTIVE The first aim of this study was to evaluate the viral etiology and seasonality of acute viral respiratory infection in pediatric patients with cancer in a 3-year study. Our second aim was to evaluate the impact of viral infections on delaying the patients' chemotherapy or radiotherapy. MATERIALS AND METHODS This cross-sectional study was conducted from January 2014 to July 2017. Nasopharyngeal aspirates were analyzed in patients younger than 21 years with acute respiratory infections. Patients were treated in the Pediatric Hematology and Oncology Department of Dr. Behçet Uz Children's Hospital with real-time multiplex polymerase chain reaction. Data were analyzed to determine the frequency and seasonality of infections. The χ or the Fisher exact tests were used. RESULTS A total of 219 samples of nasopharyngeal aspirates and blood were analyzed. The mean patient age was 76.8±59.3 months, with 46.3% female and 53.7% male children in a total of 108 patients. Of this total, 55% (60/108 cases) had multiple acute respiratory infections. Acute lymphoblastic leukemia (48.1%) was the most prevalent disease. The 3 most prevalent viruses were human rhinovirus (HRV) (33.1%), parainfluenza (PI) (18.7%), and coronavirus (CoV) (14.8%). In terms of the seasonal distribution of viruses, PI was most common in winter 2014, HRV in spring 2014, HRV in fall 2014, PI in winter 2015 and summer 2015, CoV in spring 2015, HRV in fall 2015, both influenza and HRV in winter 2016, both human metapneumovirus and bocavirus in spring 2016, HRV in summer 2016, both HRV and PI in fall 2016, both respiratory syncytial virus and influenza in winter 2017, HRV in spring 2017, and both HRV and adenovirus in summer 2017. The mean duration of neutropenia for patients with viral respiratory infection was 17.1±13.8 (range: 2 to 90) days. The mean duration of symptoms of viral respiratory infection was 6.8±4.2 (range: 2 to 31) days. A delay in chemotherapy treatment owing to viral respiratory infection was detected in 73 (33.3%) patients. The mean duration of delay in chemotherapy treatment was 9.6±5.4 (range: 3 to 31) days. CONCLUSIONS In conclusion, we report our 3-year experience about the frequency and seasonality of respiratory viruses in children with cancer.
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Civljak R, Tot T, Falsey AR, Huljev E, Vranes J, Ljubin-Sternak S. Viral pathogens associated with acute respiratory illness in hospitalized adults and elderly from Zagreb, Croatia, 2016 to 2018. J Med Virol 2019; 91:1202-1209. [PMID: 30801727 PMCID: PMC7166480 DOI: 10.1002/jmv.25437] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
Aims To investigate the viral etiology of acute respiratory infection (ARI) in hospitalized adults and elderly patients in Croatia, compare the prevalence of detected viruses, and to determine clinical characteristics and seasonal occurrence of investigated infections. Methods From January 2016 to June 2018, a total of 182 adult patients presented with symptoms of ARI and admitted to the hospital were tested for 15 respiratory viruses by multiplex reverse‐transcription polymerase chain reaction. Clinical data were collected by retrospective analysis of the patient's chart. Results A virus was identified in 106 (58.5%) of the patients. The most commonly detected virus was influenza virus (41.5%), followed by respiratory syncytial virus (13.8%), human metapneumovirus (13.0%), parainfluenza viruses (12.2%), rhinoviruses (11.4%), adenovirus and coronaviruses with equal frequencies (3.3%), and enterovirus (1.6%). The serum level of C‐reactive protein and white blood cell count were significantly lower in patients with respiratory viruses identified when compared with those in whom no virus was detected (P < 0.001 and
P = 0.007, respectively). There were no differences in clinical symptoms according to the type of the detected virus, except for more frequent illness exposure recall for influenza infection (
P = 0.010). Influenza, parainfluenza, and pneumoviruses were detected mostly in winter months, while rhinoviruses in autumn and spring. Conclusions In addition to influenza, pneumoviruses, rhinoviruses, and parainfluenza viruses play an important role in etiology of ARIs in adults. Fast and accurate laboratory diagnosis for respiratory viruses in routine practice is needed for clinicians optimally manage patients with ARI and potentially avoid the unnecessary use of antimicrobial drugs.
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Affiliation(s)
- Rok Civljak
- Department of Respiratory Tract Infections, Dr Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tatjana Tot
- Department of Microbiology, General Hospital Karlovac, Karlovac, Croatia
| | - Ann R Falsey
- Department of Medicine, Rochester General Hospital and University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Eva Huljev
- Department of Respiratory Tract Infections, Dr Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jasmina Vranes
- Department of Clinical Microbiology, Dr Andrija Stampar Teaching Institute of Public Health, Zagreb, Croatia.,Department of Medical Microbiology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Suncanica Ljubin-Sternak
- Department of Clinical Microbiology, Dr Andrija Stampar Teaching Institute of Public Health, Zagreb, Croatia.,Department of Medical Microbiology, University of Zagreb School of Medicine, Zagreb, Croatia
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11
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De Conto F, Conversano F, Medici MC, Ferraglia F, Pinardi F, Arcangeletti MC, Chezzi C, Calderaro A. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy. Diagn Microbiol Infect Dis 2019; 94:260-267. [PMID: 30745224 PMCID: PMC7126416 DOI: 10.1016/j.diagmicrobio.2019.01.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/13/2022]
Abstract
Acute respiratory tract infections (ARTIs) are among the leading causes of morbidity and mortality in children. The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. Respiratory viruses were detected in 1299 cases (50.44%); 1037 (79.83%) were single infections and 262 (20.17%) mixed infections. The highest infection incidence was in children aged >6 months to ≤3 years (57.36%). Human respiratory syncytial virus (27.12%) and human adenovirus (23.58%) were the most common viruses identified. The virus detection rate decreased significantly between the first and third epidemic season (53.9% vs. 43.05%, P < 0.0001). The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Respiratory viruses were assessed in children from October 2012 to September 2015. Viruses were detected using antigen and molecular assays, and cell culture. Respiratory syncytial virus and adenovirus were the most common viruses detected. Influenza virus and respiratory syncytial virus detection showed seasonal variation. Respiratory virus detection was highest in children aged >6 months to ≤3 years.
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Affiliation(s)
- Flora De Conto
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy.
| | - Francesca Conversano
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
| | - Maria Cristina Medici
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
| | - Francesca Ferraglia
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
| | - Federica Pinardi
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
| | | | - Carlo Chezzi
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
| | - Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy
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12
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Ayegbusi OT, Ajagbe OA, Afowowe TO, Aransi AT, Olusola BA, Awogbindin IO, Ogunsemowo OO, Faneye AO, Odaibo GN, Olaleye DO. Virus genes and host correlates of pathology are markedly reduced during respiratory syncytial and influenza virus co-infection in BALB/c mice. Heliyon 2019; 5:e01094. [PMID: 30623128 PMCID: PMC6319304 DOI: 10.1016/j.heliyon.2018.e01094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/14/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
Globally, influenza A virus (IAV) and respiratory syncytial virus (RSV) infection remain very high. There is also a high burden of IAV and RSV co-infection in developing countries. To develop universally protective vaccines against these infections, it is imperative that viral genes and immune correlates of pathology are elucidated. As such, we profiled virus genes expressions, histopathology and immunological responses of BALB/c mice infected with RSV and/or IAV in this study. RSV A2 and/or influenza A/H3N2/Perth/16/09 (Pr/H3N2) were induced over a seven-day period in BALB/c mice. Anaesthetized BALB/c mice (12-14 g) were divided into six groups (15-20 mice per group), inoculated with 32 μl each of 3LD50 Pr/H3N2 and/or 100 TCID50 RSV. Two groups (R or I) received RSV or Pr/H3N2 intranasally. Prior infection with either RSV or Pr/H3N2 was followed with a second challenge of the other virus 24 hours post inoculation in RI and IR groups. Another set was exposed to the two viruses simultaneously (I + R group) while the last group served as healthy controls. Five to seven mice per group were euthanized at days 2, 4 and 7. Lung and spleen organs were harvested for virus genes quantitation and immune cells phenotyping respectively. I + R group showed progressive downregulation of RSV F, G, NS1 and NS2 genes. IAV PB2 and M genes had high fold increase on day 2 and 4 post infections. However, by day 7 post infection, M and PB2 fold increase was lower. Also, increased proportions of NKT and T cell subsets were observed throughout the period in I + R group. Conversely, I group was characterized by reduced NKT cell counts and enhanced CD8 T cells levels while R group only showed an increased proportion of CD8 T cells towards the peak of infection. This study shows that RSV and IAV co-infection lead to reduced virulence and pathology compared to single infections. This information is very useful in combinatorial RSV/IAV vaccine design and development.
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Affiliation(s)
- Olaitan T. Ayegbusi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluwaseyi A. Ajagbe
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tosin O. Afowowe
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Abideen T. Aransi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Babatunde A. Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | | | - Adedayo O. Faneye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Georgina N. Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - David O. Olaleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
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13
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The 5' Untranslated Region of Human Bocavirus Capsid Transcripts Regulates Viral mRNA Biogenesis and Alternative Translation. J Virol 2018; 92:JVI.00443-18. [PMID: 30111560 PMCID: PMC6189511 DOI: 10.1128/jvi.00443-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 12/22/2022] Open
Abstract
Alternative translation of HBoV1 capsid mRNAs is vital for the viral life cycle, as capsid proteins perform essential functions in genome packaging, assembly, and antigenicity. The 5′ untranslated regions (UTRs) of capsid mRNAs are generated by alternative splicing, and they contain different exons. Our study shows that the 5′ UTR not only modulates mRNA abundance but also regulates capsid expression. Two upstream ATGs (uATGs) that were upstream of the capsid translation initiation site in the 5′ UTR were found to affect viral capsid mRNA polyadenylation, alternative translation, and progeny virus production. The results reveal that uATGs play an important role in the viral life cycle and represent a new layer to regulate HBoV1 RNA processing, which could be a target for gene therapy. The capsid mRNA transcripts of human bocavirus 1 (HBoV1) can be generated by alternative splicing from the mRNA precursor transcribed from the P5 promoter. However, the alternative translation regulation mechanism of capsid mRNA transcripts is largely unknown. Here we report that the polycistronic capsid mRNA transcripts encode VP1, VP2, and VP3 in vitro and in vivo. The 5′ untranslated regions (UTRs) of capsid mRNA transcripts, which consist of exons, affected not only the abundance of mRNA but also the translation pattern of capsid proteins. Further study showed that exons 2 and 3 were critical for the abundance of mRNA, while exon 4 regulated capsid translation. Alternative translation of capsid mRNA involved a leaky scan mechanism. Mutating the upstream ATGs (uATGs) located in exon 4 resulted in more mRNA transcripts polyadenylated at the proximal polyadenylation [(pA)p] site, leading to increased capsid mRNA transcripts. Moreover, uATG mutations induced more VP1 expression, while VP3 expression was decreased, which resulted in less progeny virus production. Our data show that the 5′ UTR of HBoV1 plays a critical role in the modulation of mRNA abundance, alternative RNA processing, alternative translation, and progeny virus production. IMPORTANCE Alternative translation of HBoV1 capsid mRNAs is vital for the viral life cycle, as capsid proteins perform essential functions in genome packaging, assembly, and antigenicity. The 5′ untranslated regions (UTRs) of capsid mRNAs are generated by alternative splicing, and they contain different exons. Our study shows that the 5′ UTR not only modulates mRNA abundance but also regulates capsid expression. Two upstream ATGs (uATGs) that were upstream of the capsid translation initiation site in the 5′ UTR were found to affect viral capsid mRNA polyadenylation, alternative translation, and progeny virus production. The results reveal that uATGs play an important role in the viral life cycle and represent a new layer to regulate HBoV1 RNA processing, which could be a target for gene therapy.
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14
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Pellegrinelli L, Bubba L, Galli C, Anselmi G, Primache V, Binda S, Pariani E. Epidemiology and molecular characterization of influenza viruses, human parechoviruses and enteroviruses in children up to 5 years with influenza-like illness in Northern Italy during seven consecutive winter seasons (2010–2017). J Gen Virol 2017; 98:2699-2711. [DOI: 10.1099/jgv.0.000937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Giovanni Anselmi
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Via Carlo Pascal, 36 - 20133 Milan, Italy
- Department of Health Sciences, CIRI-IT, University of Genoa, Via Antonio Pastore, 1 - 16132 Genoa, Italy
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15
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Košutić-Gulija T, Slovic A, Ljubin-Sternak S, Mlinarić-Galinović G, Forčić D. Genetic analysis of human parainfluenza virus type 3 obtained in Croatia, 2011-2015. J Med Microbiol 2017; 66:502-510. [PMID: 28463659 DOI: 10.1099/jmm.0.000459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE This study investigated the HPIV3 circulating strains in Croatia and whether the other parts of HPIV3 genome (F gene and HN 582 nucleotides fragment) could be equally suitable for genetic and phylogenetic analysis. METHODOLOGY Clinical materials were collected in period 2011-2015 from children suffering from respiratory illnesses. In positive HPIV3 samples viral genome was partially amplified and sequenced for HN and F genes. Obtained sequences were analysed by phylogenetic analysis and genetic characterization was performed. RESULTS All samples from this study belonged to subcluster C and over a short period of time, genetic lineage C3a gained prevalence over the other C genetic lineages, from 39 % in 2011 to more than 90 % in 2013 and 2014. Phylogenetic classifications of HPIV3 based on the entire HN gene, HN 582 nt fragment and entire fusion (F) gene showed identical classification results for Croatian strains and the reference strains. Molecular analysis of the F and HN glycoproteins, showed their similar nucleotide diversity (Fcds P=0.0244 and HNcds P=0.0231) and similar Ka/Ks ratios (F Ka/Ks=0.0553 and HN Ka/Ks=0.0428). Potential N-glycosylation sites, cysteine residues and antigenic sites are generally strongly conserved in HPIV3 glycoproteins from both our and the reference samples. CONCLUSION The HPIV3 subclaster C3 (genetic lineage C3a) became the most detected circulating HPIV3 strain in Croatia. The results indicated that the HN 582 nt and the entire F gene sequences were as good for phylogenetic analysis as the entire HN gene sequence.
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Affiliation(s)
- Tanja Košutić-Gulija
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Anamarija Slovic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Sunčanica Ljubin-Sternak
- Andrija Stampar Teaching Institute of Public Health, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Gordana Mlinarić-Galinović
- Department of Virology, Croatian National Institute of Public Health, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Dubravko Forčić
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
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