scholarly journals Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259859
Author(s):  
Sondes Haddad-Boubaker ◽  
Cherif Ben Hamda ◽  
Kais Ghedira ◽  
Khaoula Mefteh ◽  
Aida Bouafsoun ◽  
...  
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Genotypic Diversity ◽  
Evolutionary Analysis ◽  
Northern Tunisia ◽  
Severe Acute Respiratory Infection ◽  
Epidemic Period ◽  
The World

Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses’ dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.

scholarly journals High genotypic diversity of Rhinoviruses obtained from Tunisian children with severe acute respiratory infection

2021 ◽  
Vol 15 (05) ◽  
pp. 726-735
Author(s):  
Sondes Haddad-Boubaker ◽  
Khaoula Mefteh ◽  
Chaima Mejri ◽  
Aida Bouaffsoun ◽  
Awatef El Moussi ◽  
...  
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Pediatric Intensive Care ◽  
Extended Period ◽  
Genotypic Diversity ◽  
Genomic Region ◽  
Human Enterovirus ◽  
African Region ◽  
Severe Acute Respiratory Infection ◽  
High Prevalence

Introduction: Rhinoviruses (HRV) are among the leading causes of Severe Acute Respiratory Infection (SARI). Their burden and genetic diversity vary from one region to another and little is known in Northern African regions. This study describes epidemiological patterns and genotypic diversity of HRV in SARI cases during a two and half year’s study, in Northern Tunisia. Methodology: A total of 271 SARI cases, admitted into the Pediatric Intensive Care Unit of Bechir Hamza Children's Hospital in Tunis, were collected between September 2015 and December 2017. The investigation concerned 104 samples positive for HRV and/or HEV (Human Enterovirus) obtained among these cases. Specific HRV and HEV detections were assessed by real-time PCRs. The HRV molecular typing was based on the VP4-VP2 genomic region analyses. Results: Among the viral SARI cases, 33.5% and 12.3% were positive for HRV and HEV respectively. Molecular investigations showed high prevalence of HRV-A (63.3%) followed by HRV-C (30.6%) and HRV-B (6.1%) and high genotypic diversity with 27 types. HRV cases were mostly detected in toddlers younger than 6 months. A total of 16 cases (28%) were found with bacterial and/or viral co-infection. HRV-C infection and HRV-A with bacterial co-infection were associated with complicated infection. Some of the detected types showed a continuous circulation or turnover during an extended period. HRV-A101 and HRV-C45 were the most frequently detected types. Conclusions: This study revealed, for the first time, the high HRV diversity in Tunisia, a North-African region. Specific phylogenetic investigations may help to evaluate their diversity and to trace their spread and epidemiological origin.

Correct Execution of the Nasopharyngeal Swab: A Fundamental Method to Improve Diagnosis of SARS-CoV-2 Infection

2021 ◽  
pp. JDNP-D-20-00040
Author(s):  
Giacomo Spinato ◽  
Cristoforo Fabbris ◽  
Anna Menegaldo ◽  
Silvia Marciani ◽  
Piergiorgio Gaudioso ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Correct Diagnosis ◽  
Video Recording ◽  
Nasopharyngeal Swab ◽  
Severe Acute Respiratory Infection ◽  
The World ◽  
Correct Execution ◽  
Important Challenge

BackgroundSevere acute respiratory infection Coronavirus 2 (SARS-CoV-2) infection has spread all over the world since December 2019. Treatment of the syndrome represents an important challenge for all physicians. Spread prevention relies on a correct diagnosis which is performed with nasopharyngeal swabs.ObjectiveTo describe the proper execution of the swab with a few simple steps.MethodsFigures and video recording.Results:A few simple steps are presented within this paper in order to perform easily nasopharyngeal swab for SARS-Cov-2 diagnosis and for other possible infectious diseases of the airways tract.Conclusions and Implication for NursingNasopharyngeal swab may be performed in an easier way than usually thought. This method may also be used for any other microorganism detection. By following simple steps, a correct diagnosis can easily be obtained.

scholarly journals Etiologies of severe acute respiratory infection (SARI) and misdiagnosis of influenza in Indonesia, 2013‐2016

2020 ◽  
Vol 15 (1) ◽  
pp. 34-44
Author(s):  
Abu Tholib Aman ◽  
Tri Wibawa ◽  
Herman Kosasih ◽  
Rizka Humardewayanti Asdie ◽  
Ida Safitri ◽  
...  
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Severe Acute Respiratory Infection

scholarly journals Viral Infection in Adults With Severe Acute Respiratory Infection in Colombia

2015 ◽  
Vol 2 (suppl_1) ◽  
Author(s):  
Yuly Remolina ◽  
María Ulloa ◽  
Hernan Vargas ◽  
Jorge Cortes ◽  
Liliana Diaz ◽  
...  
Keyword(s):  
Viral Infection ◽  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Severe Acute Respiratory Infection

scholarly journals SARS-CoV-2 and influenza virus coinfection among patients with severe acute respiratory infection during the first wave of COVID-19 pandemic in Bangladesh: a hospital-based descriptive study

BMJ Open ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. e053768
Author(s):  
Zubair Akhtar ◽  
Md Ariful Islam ◽  
Mohammad Abdul Aleem ◽  
Syeda Mah-E-Muneer ◽  
M Kaousar Ahmmed ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Hospital Mortality ◽  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Descriptive Study ◽  
Tertiary Level ◽  
Future Studies ◽  
Severe Acute Respiratory Infection ◽  
Hospital Deaths ◽  
Secondary Outcomes

ObjectiveTo estimate the proportion of SARS-CoV-2 and influenza virus coinfection among severe acute respiratory infection (SARI) cases-patients during the first wave of COVID-19 pandemic in Bangladesh.DesignDescriptive study.SettingNine tertiary level hospitals across Bangladesh.ParticipantsPatients admitted as SARI (defined as cases with subjective or measured fever of ≥38 C° and cough with onset within the last 10 days and requiring hospital admission) case-patients.Primary and secondary outcomesProportion of SARS-CoV-2 and influenza virus coinfection and proportion of mortality among SARI case-patients.ResultsWe enrolled 1986 SARI case-patients with a median age: 28 years (IQR: 1.2–53 years), and 67.6% were male. Among them, 285 (14.3%) were infected with SARS-CoV-2; 175 (8.8%) were infected with the influenza virus, and five (0.3%) were coinfected with both viruses. There was a non-appearance of influenza during the usual peak season (May to July) in Bangladesh. SARS-CoV-2 infection was significantly more associated with diabetes (14.0% vs 5.9%, p<0.001) and hypertension (26.7% vs 11.5%, p<0.001). But influenza among SARI case-patients was significantly less associated with diabetes (4.0% vs 7.4%, p=0.047) and hypertension (5.7% vs 14.4%, p=0.001). The proportion of in-hospital deaths among SARS-CoV-2 infected SARI case-patients were higher (10.9% (n=31) vs 4.4% (n=75), p<0.001) than those without SARS-CoV-2 infection; the proportion of postdischarge deaths within 30 days was also higher (9.1% (n=25) vs 4.6% (n=74), p=0.001) among SARS-CoV-2 infected SARI case-patients than those without infection. No in-hospital mortality or postdischarge mortality was registered among the five coinfected SARI case-patients.ConclusionsOur findings suggest that coinfection with SARS-CoV-2 and influenza virus was not very common and had less disease severity considering mortality in Bangladesh. There was no circulating influenza virus during the influenza peak season during the COVID-19 pandemic in 2020. Future studies are warranted for further exploration.

scholarly journals Molecular typing and epidemiologic profiles of human metapneumovirus infection among children with severe acute respiratory infection in Huzhou, China

2021 ◽  
Author(s):  
Lei Ji ◽  
Liping Chen ◽  
Deshun Xu ◽  
Xiaofang Wu
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Epidemiological Data ◽  
Human Metapneumovirus ◽  
Respiratory Pathogen ◽  
Nasopharyngeal Swab ◽  
F Gene ◽  
Severe Acute Respiratory Infection ◽  
Hmpv Infection ◽  
High Incidence

Abstract Background Human metapneumovirus (hMPV) is one of the important pathogens in infant respiratory tract infection. However, the molecular epidemiology of hMPV among children < 14 years of age hospitalized with severe acute respiratory infection (SARI) is unclear. We investigated the hMPV infection status and genotypes of children hospitalized with SARI from January 2016 to December 2020 in Huzhou, China. Methods A nasopharyngeal flocked swab, nasal wash, or nasopharyngeal swab/or opharyngeal swab combination sample was collected from children with SARI in Huzhou from January 2016 to December 2020. Quantitative reverse transcription-polymerase chain reaction was performed to detect hMPV RNA. The hMPV F gene was amplified and sequenced, followed by analysis using MEGA software (ver. 7.0). Epidemiological data were analyzed using Microsoft Excel 2010 and SPSS (ver. 22.0) software. Results A total of 1133 children with SARI were recruited from 2016 to 2020. Among them, 56 (4.94%) were positive for hMPV-RNA. Children < 5 years of age accounted for 85.71% of the positive cases. The hMPV incidence was high in spring and winter, especially in December and January to March. Phylogenetic analysis of the F-gene sequences of 28 hMPV strains showed that the A1, B1, and B2 genotypes were prevalent in Huzhou, and the dominant hMPV genotype varied according to surveillance year. Conclusions HMPV is an important respiratory pathogen in children in Huzhou, with a high incidence in winter and spring in children < 5 years of age. In this study, genotypes A1, B1, and B2 were the most prevalent.

Sign in / Sign up

Export Citation Format

Share Document