Prevalence and Genetic Characteristics of Human Bocaviruses Detected in Patients with Acute Respiratory Infections in Bulgaria

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Neli Korsun ◽  
Svetla Angelova ◽  
Ivelina Trifonova ◽  
Silvia Voleva ◽  
Iliana Grigorova ◽  

Нuman bocaviruses (hBoVs) are often associated with acute respiratory infections (ARIs). Information on the distribution and molecular epidemiology of hBoVs in Bulgaria is currently limited. The objectives of this study were to investigate the prevalence and genetic characteristics of hBoVs detected in patients with ARIs in Bulgaria. From October 2016 to September 2019, nasopharyngeal/oropharyngeal swabs were prospectively collected from 1842 patients of all ages and tested for 12 common respiratory viruses using a real-time RT-PCR. Phylogenetic and amino acid analyses of the hBoV VP1/VP2 gene/protein were performed. HBoV was identified in 98 (5.3%) patients and was the 6th most prevalent virus after respiratory-syncytial virus (20.4%), influenza A(H1N1)pdm09 (11.1%), A(H3N2) (10.5%), rhinoviruses (9.9%), and adenoviruses (6.8%). Coinfections with other respiratory viruses were detected in 51% of the hBoV-positive patients. Significant differences in the prevalence of hBoVs were found during the different study periods and in patients of different age groups. The detection rate of hBoV was the highest in patients aged 0–4 years (6.9%). In this age group, hBoV was the only identified virus in 9.7%, 5.8%, and 1.1% of the children diagnosed with laryngotracheitis, bronchiolitis, and pneumonia, respectively. Among patients aged ≥5 years, hBoV was detected as a single agent in 2.2% of cases of pneumonia. Phylogenetic analysis showed that all Bulgarian hBoV strains belonged to the hBoV1 genotype. A few amino acid substitutions were identified compared to the St1 prototype strain. This first study amongst an all-age population in Bulgaria showed a significant rate of hBoV detection in some serious respiratory illnesses in early childhood, year-to-year changes in the hBoV prevalence, and low genetic variability in the circulating strains.

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Asmae Lamrani Hanchi ◽  
Morad Guennouni ◽  
Meriem Rachidi ◽  
Toufik Benhoumich ◽  
Hind Bennani ◽  

Sever acute respiratory infections (SARIs) are a public health issue that are common in children and are associated with an important morbidity and mortality rate worldwide. Although SARI are mainly caused by viruses, they are still a cause of antibiotic overuse. The use of molecular methods especially real-time multiplex PCR allowed to detect a wide range of respiratory viruses and their subtype as well as some atypical bacteria. The aim of this study was to investigate the epidemiology of respiratory pathogens detected in children admitted with SARI and to highlight the role of real-time multiplex PCR in the rapid diagnosis of viral and bacterial SARI. This work is a descriptive observational study from January 2018 to December 2019 including nasopharyngeal secretions collected from 534 children hospitalised in paediatric department. The detection of respiratory viruses and bacteria was performed by the FilmArray® Respiratory Panel. A total of 387 (72.5%) children were tested positive for at least one respiratory pathogen, and 23.3% of them were coinfected with more than one pathogen. Viral aetiology was found in 91.2% (n = 340). The most common viruses detected were HRV (n = 201) and RSV (n = 124), followed by PIV (n = 35) influenza A (n = 29) and human metapneumovirus (n = 27). Bacteria was found in 8.8% (n = 47), and Bordetella pertussis was the most detected. Respiratory syncytial virus and Bordetella pertussis were significantly higher in infants less than 6 months old. The detection of RSV and influenza A presented a pic in winter, and HMPV was statistically significant in spring ( p < 0.01 ). This study described the epidemiology of respiratory pathogens involved in severe respiratory infections in children that were affected by several factors such as season and age group. It also highlighted the importance of multiplex PCR in confirming viral origin, thus avoiding irrational prescription of antibiotics in paediatric settings.

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Shirley Masse ◽  
Lisandru Capai ◽  
Alessandra Falchi

Background. The current study aims to describe the demographical and clinical characteristics of elderly nursing home (NH) residents with acute respiratory infections (ARIs) during four winter seasons (2013/2014–2016/2017), as well as the microbiological etiology of these infections. Methods. Seventeen NHs with at least one ARI resident in Corsica, France, were included. An ARI resident was defined as a resident developing a sudden onset of any constitutional symptoms in addition to any respiratory signs. Nasopharyngeal swabs from ARI residents were screened for the presence of 21 respiratory agents, including seasonal influenza viruses. Results. Of the 107 ARI residents enrolled from NHs, 61 (57%) were positive for at least one of the 21 respiratory pathogens. Forty-one (38.3%) of the 107 ARI residents had influenza: 38 (92%) were positive for influenza A (100% A(H3N2)) and three (8%) for influenza B/Victoria. Axillary fever (≥38°C) was significantly more common among patients infected with influenza A(H3N2). Conclusion. The circulation of seasonal respiratory viruses other than influenza A(H3N2) seems to be sporadic among elderly NH residents. Investigating the circulation of respiratory viruses in nonwinter seasons seems to be important in order to understand better the dynamic of their year-round circulation in NHs.

2019 ◽  
Vol 11 (3) ◽  
pp. 38-45
S. A. Khmilevskaya ◽  
N. I. Zryachkin ◽  
V. E. Mikhailova

The aim: to study the etiological structure of acute respiratory infections in children aged 3 to 12 hospitalized in the early stages of the disease in the department of respiratory infections of the children’s hospital, and to reveal the features of their clinical course and the timing of DNA / RNA elimination of respiratory viruses from nasal secretions, depending on the method of therapy. Materials and methods: 100 children with acute respiratory infections aged 3 to 12 years were monitored. The nasal secrets on the DNA / RNA of respiratory viruses were studied by PCR. Depending on the method of therapy, patients were divided into 2 groups: patients of group 1 (comparison) received basic treatment (without the use of antiviral drugs), in patients of the 2nd group (main), along with basal therapy, the drug was used umifenovir in a 5-day course at the ageappropriate dosage. Results: In the etiologic structure of ARVI in children from 3 to 12 years, the leading place was taken by rhinovirus, influenza and metapneumovirus infections (isolated – 18%, 19% and 20% respectively, in the form of a mixed infection – 11%). The main syndromic diagnosis at the height of the disease was rhinopharyngitis. Complications were observed in 42% of cases, as often as possible with flu – 53% of cases. Features of metapneumovirus infection in children of this age group were: predominance of non-severe forms of the disease in the form of acute fever with symptoms of rhinopharyngitis, as well as a small incidence of lower respiratory tract infections. The use of the drug umiphenovir in children with acute respiratory viral infections of various etiologies contributed to significantly faster elimination of viral DNA / RNA from the nasal secretion, which was accompanied by a ecrease in the duration of the main clinical and hematological symptoms of the disease, a decrease in the incidence of complications, and reduced the duration of stay in hospital. Conclusion: application of modern molecular genetic methods of diagnostics made it possible to identify the leading role of influenza, metapneumovirus and rhinovirus infections in the etiology of acute respiratory viral infection in patients aged 3 to 12 years, and to determine a number of clinical features characteristic of this age group. The results of the study testify to the effectiveness of umiphenovir in the treatment of children with acute respiratory viral infections of various etiologies and allow us to recommend this drug as an effective and safe etiotropic agent.

Iman S. Naga ◽  
Gamal Eldin Elsawaf ◽  
Mahmoud Elzalabany ◽  
Mohamed Youssef Eltalkhawy ◽  
Ola Kader

Abstract Respiratory infections have a significant impact on health worldwide. Viruses are major causes of acute respiratory infections among children. Limited information regarding its prevalence in Egypt is available. This study investigated prevalence of 10 respiratory viruses; Adenovirus, influenza A, B, respiratory syncytial virus (RSV), Parainfluenza virus (PIV)type 1-4, enterovirus, and human coronavirus OC43 (HCoV-OC43) among children in Alexandria, Egypt presenting with acute lower respiratory tract infections. The study was conducted on children <14 years of age selected from ElShatby Pediatric Hospital, Alexandria University, Egypt. One hundred children presenting during winter season with influenza-like illness were eligible for the study. Oropharyngeal swabs were collected and subjected to viral RNA and DNA extraction followed by polymerase chain reaction. Viral infections were detected in 44% of cases. Adenovirus was the most common, it was found in 19% of the patients. Prevalence of PIV (3 and 4) and enterovirus was 7% each. Prevalence of RSV and HCoV-OC43 was 5% and 3% respectively. Two percentage were Influenza A positive and 1% positive for influenza B. Mixed viral infection was observed in 7%. To the best of our knowledge, this is the first report of the isolation of HCoV-OC43 from respiratory infections in Alexandria, Egypt.

Aleksandr V. Alimov ◽  
Svetlana S. Smirnova ◽  
Evgenia V. Lelenkova ◽  
Aleksandr Yu. Markaryan ◽  
Ivan V. Vyalykh ◽  

Objective. To study the role of influenza viruses in the development of severe acute respiratory infections (SARI) in patients admitted to Yekaterinburg hospitals during 2017-2018 epidemic season.Materials and Methods. A retrospective epidemiological analysis of influenza incidence in Yekaterinburg was conducted, 403 influenza and acute respiratory viral infections case sheets were studied, and PCR analysis of clinical samples from the patients for respiratory viral infections was performed.Results. During the epidemic period a total 27.0% of the Yekaterinburg population were reported with influenza and other SARI, with 1.8% patients hospitalized. 5.6% of the total number of patients admitted with influenza and SARI in Yekaterinburg hospitals were included in the study. The rate of the detection of influenza A and B viruses RNA in the clinical samples from the patients with SARI was 28.3%. The rates of the detection in PCR of influenza B/Yamagata, A(H1N1)pdm09 and A(H3N2) were 46.5, 20.2 and 10.5%, respectively.Conclusion. The study results indicated that influenza viruses remain significant pathogens of respiratory infections that required hospitalization. Among patients with SARI the highest incidence was observed in children of a younger age group and was mainly associated with influenza B virus of Yamagata lineage and influenza A virus (H1N1)pdm09. According to the results of a molecular genetic study, influenza A (H1N1) pdm09 viruses belonged to clade 6B.1, carried characteristic amino acid substitutions in hemagglutinin S84N, S162N (with the acquisition of a potential glycosylation site) and I216T and were similar to the A/Michigan/45/2015 vaccine strain. The influenza B viruses studied belonged to the Yamagata lineage, clade 3. The influenza B/Ekaterinburg /RII-4723S/2018 virus differed from the reference strain B/Phuket/3073/2013 by two amino acid substitutions in the hemagglutinin gene M251V and L172Q.

2021 ◽  
Vol 21 (3) ◽  
pp. 123-126
Evgeniya Viktorovna Lelenkova ◽  
Alexandr Yurievich Markaryan

BACKGROUND: Acute respiratory viral infections are ubiquitous. Part of the cases are severe and require hospital treatment. AIM: Studying the etiology of severe acute respiratory infections in patients of Ekaterinburg hospitals in different epidemic seasons (from 2017 to 2020). MATERIALS AND METHODS: 1,132 cases of severe acute respiratory infection were assessed. The structure of laboratory-confirmed cases was determined. RESULTS: In the assessed seasons, the proportion of respiratory viruses in the etiological structure of severe acute respiratory infections was 56.0% on average. B/Yamagata lineage of influenza viruses was predominant in the season of 2017/2018 (23.9% from the total number of respiratory viruses), influenza А (H1N1)pdm09 viruses were predominant in the season of 2018/2019 (27.7%), and influenza A and B viruses were identified in 2019/2020 (39.4% and 31.7%, respectively). СONCLUSIONS: The obtained results confirm a key role of influenza viruses in the etiology of severe acute respiratory infections among the hospital patients in different epidemic seasons.

2021 ◽  
Vol 11 (4) ◽  
pp. 413-425
Anna Sominina ◽  
Daria Danilenko ◽  
Andrey Komissarov ◽  
Maria Pisareva ◽  
Tamila Musaeva ◽  

AbstractThe expansion and standardization of clinical trials, as well as the use of sensitive and specific molecular diagnostics methods, provide new information on the age-specific roles of influenza and other respiratory viruses in development of severe acute respiratory infections (SARI). Here, we present the results of the multicenter hospital-based study aimed to detect age-specific impact of influenza and other respiratory viruses (ORV). The 2018–2019 influenza season in Russia was characterized by co-circulation of influenza A(H1N1)pdm09 and A(H3N2) virus subtypes which were detected among hospitalized patients with SARI in 19.3% and 16.4%, respectively. RSV dominated among ORV (15.1% of total cases and 26.8% in infants aged ≤ 2 years). The most significant SARI agents in intensive care units were RSV and influenza A(H1N1)pdm09 virus, (37.3% and 25.4%, respectively, of PCR-positive cases). Hyperthermia was the most frequently registered symptom for influenza cases. In contrast, hypoxia, decreased blood O2 concentration, and dyspnea were registered more often in RSV, rhinovirus, and metapneumovirus infection in young children. Influenza vaccine effectiveness (IVE) against hospitalization of patients with PCR-confirmed influenza was evaluated using test-negative case–control design. IVE for children and adults was estimated to be 57.0% and 62.0%, respectively. Subtype specific IVE was higher against influenza A(H1N1)pdm09, compared to influenza A(H3N2) (60.3% and 45.8%, respectively). This correlates with delayed antigenic drift of the influenza A(H1N1)pdm09 virus and genetic heterogeneity of the influenza A(H3N2) population. These studies demonstrate the need to improve seasonal influenza prevention and control in all countries as states by the WHO Global Influenza Strategy for 2019–2030 initiative.

Intervirology ◽  
2021 ◽  
pp. 1-9
Neli S. Korsun ◽  
Svetla G. Angelova ◽  
Ivelina T. Trifonova ◽  
Silvia E. Voleva ◽  
Iliana G. Grigorova ◽  

<b><i>Introduction:</i></b> We investigated the prevalence of human metapneumovirus (hMPV) among patients with acute respiratory infections in Bulgaria, and performed genetic characterization of the F gene of these strains. <b><i>Methods:</i></b> Nasopharyngeal swabs collected from patients of a range of ages were tested by using real-time PCR for 12 respiratory viruses. The F gene was sequenced, and phylogenetic and amino acid analyses of the F gene/protein were performed. <b><i>Results:</i></b> A total of 1,842 patients were examined during a 3-year period; 1,229 patients (66.7%) were positive for at least one respiratory virus. hMPV was identified in 83 (4.5%) patient samples. Eleven (13%) of hMPV-positive patients were coinfected with another respiratory virus. The hMPV incidence rate in the 2016/2017, 2017/2018, and 2018/2019 winter seasons was 5.4, 5.4, and 3.1%, respectively. hMPV was mainly detected in specimens collected between January and May (89.2% of cases). The incidence of hMPV infection was highest (5.1%) among the youngest age-group (0–4 years), where hMPV was a causative agent in 8.1 and 4.8% of bronchiolitis and pneumonia cases, respectively. Among the patients aged ≥5 years, hMPV was detected in 2.2 and 3.2% of cases of pneumonia and central nervous system infections, respectively. Phylogenetic analysis of the F gene showed that the sequenced hMPV strains belonged to the A2b, B1, and B2 genotypes. Numerous amino acid substitutions were identified compared with the NL00/1 prototype strain. <b><i>Conclusion:</i></b> This study revealed the significant role of hMPV as a causative agent of serious respiratory illnesses in early childhood, and also demonstrated year-to-year changes in hMPV prevalence and genetic diversity in circulating strains.

2021 ◽  
Nagarajan Muruganandam ◽  
Avijit Roy ◽  
Nimisha Sivanandan ◽  
Alwin Vins ◽  
Nisha Beniwal ◽  

Abstract Background: Acute respiratory infections (ARIs) and severe acute respiratory illness (SARI) are public health burdens globally. The percentage of non-SARS CoV-2 respiratory viruses among patients having ARI and SARI who visit Car Nicobar's hospital settings is undocumented. Changes in the epidemiology of other respiratory viruses during COVID19 pandemic is being reported worldwide.Methods: Inpatient and outpatient settings at BJR hospital, Car Nicobar Island, India, were used to conduct prospective monitoring for ARI and SARI among Nicobarese tribal members. The patients with ARI and SARI were enlisted in BJR hospital from June 2019 to May 2021. At the ICMR-NIV in Pune, duplex qRTPCR assays were used to test the presence of respiratory viruses. The prevalence of non- SARS CoV-2 respiratory viruses was measured by comparing here between pandemic and pre-pandemic periods.Results: During the COVID19 pandemic, Influenza A (H3N2) (55.7%), and rhinovirus (12.5%) were predominantly reported non-SARS CoV-2 respiratory viruses while Human metapneumovirus (48.1%) and influenza A (H1N1)pdm09 (18.5%) were most commonly reported in the prepandemic period. This result indicates the altered circulation of non-SARS CoV-2 during pandemic.Conclusions: A considerable proportion of respiratory infection was correlated with respiratory viruses. Prevalence of non-SARS CoV-2 respiratory viruses was high at the time of infection when compared with pre-pandemic period, at Car Nicobar Island. This study enlightened the change in circulation of other respiratory viruses among the indigenous Nicobarese tribes. Clinicians and allied medical staff should be more prudent of these respiratory infections.

2015 ◽  
Vol 87 (6) ◽  
pp. 917-924 ◽  
Juana del Valle Mendoza ◽  
Angela Cornejo-Tapia ◽  
Pablo Weilg ◽  
Eduardo Verne ◽  
Ronald Nazario-Fuertes ◽  

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