scholarly journals Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
My V. T. Phan ◽  
Charles N. Agoti ◽  
Patrick K. Munywoki ◽  
Grieven P. Otieno ◽  
Mwanajuma Ngama ◽  
...  
Keyword(s):  
Parvovirus B19 ◽  
Respiratory Pathogens ◽  
Metagenomic Sequencing ◽  
Viral Pathogens ◽  
Mortality And Morbidity ◽  
Local Standard ◽  
Virus Diagnostics ◽  
Diagnostic Panel ◽  
Syncytial Virus ◽  
Ngs Data

AbstractPneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.

scholarly journals Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

2017 ◽  
Author(s):  
C Langelier ◽  
MS Zinter ◽  
K Kalantar ◽  
GA Yanik ◽  
S Christenson ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Respiratory Infections ◽  
Human Herpesvirus ◽  
Microbial Pathogens ◽  
Respiratory Pathogens ◽  
Metagenomic Sequencing ◽  
Respiratory Illnesses ◽  
Standard Testing ◽  
Syncytial Virus ◽  
Tract Infections

ABSTRACTRATIONALECurrent microbiologic diagnostics often fail to identify the etiology of lower respiratory tract infections (LRTI) in hematopoietic cellular transplant recipients (HCT), which precludes the implementation of targeted therapies.OBJECTIVESTo address the need for improved LRTI diagnostics, we evaluated the utility of metagenomic next generation sequencing (mNGS) of bronchoalveolar lavage (BAL) to detect microbial pathogens in HCT patients with acute respiratory illnesses.METHODSWe enrolled 22 post-HCT adults ages 19-69 years with acute respiratory illnesses who underwent BAL at the University of Michigan between January 2012 and May 2013. mNGS was performed on BAL fluid to detect microbes and simultaneously assess the host transcriptional response. Results were compared against conventional microbiologic assays.MEASUREMENTS & MAIN RESULTSmNGS demonstrated 100% sensitivity for detecting respiratory microbes (human metapneumovirus, respiratory syncytial virus,Stenotrophomonas maltophilia, human herpesvirus 6 and cytomegalovirus) when compared to standard testing. Previously unrecognized LRTI pathogens were identified in six patients for whom standard testing was negative (human coronavirus 229E, human rhinovirus A,Corynebacterium propinquumandStreptococcus mitis); findings were confirmed by independent PCR and 16S rRNA sequencing. Relative to patients without infection, patients with infection had increased expression of immunity related genes (p=0.022) and significantly lower diversity of their respiratory microbiome (p=0.017).CONCLUSIONSCompared to conventional diagnostics, mNGS enhanced detection of pathogens in BAL fluid from HCT patients. Furthermore, our results suggest that combining unbiased microbial pathogen detection with assessment of host gene biomarkers of immune response may hold promise for enhancing the diagnosis of post-HCT respiratory infections.

scholarly journals Acute respiratory viral infections in children in Rio de Janeiro and Teresópolis, Brazil

2012 ◽  
Vol 54 (5) ◽  
pp. 249-255 ◽  
Author(s):  
Maria Carolina M. Albuquerque ◽  
Rafael B. Varella ◽  
Norma Santos
Keyword(s):  
Rio De Janeiro ◽  
Influenza A ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Nasal Swabs ◽  
Syncytial Virus ◽  
Viral Respiratory Infections

The frequency of viral pathogens causing respiratory infections in children in the cities of Rio de Janeiro and Teresópolis was investigated. Nasal swabs from children with acute respiratory illnesses were collected between March 2006 and October 2007. Specimens were tested for viral detection by conventional (RT)-PCR and/or real time PCR. Of the 205 nasal swabs tested, 64 (31.2%) were positive for at least one of the viral pathogens. Single infections were detected in 56 samples, 50 of those were caused by RNA viruses: 33 samples tested positive for rhinovirus, five for influenza A, five for metapneumovirus, four for coronavirus and, three for respiratory syncytial virus. For the DNA viruses, five samples were positive for bocavirus and one for adenovirus. Co-infections with these viruses were detected in eight samples. Our data demonstrate a high frequency of viral respiratory infections, emphasizing the need for a more accurate diagnosis particularly for the emerging respiratory viruses. The fact that the emerging respiratory viruses were present in 9.2% of the tested samples suggests that these viruses could be important respiratory pathogens in the country.

Other Respiratory Viruses as a Cause of Community-Acquired Pneumonia

2020 ◽  
Vol 41 (04) ◽  
pp. 579-591
Author(s):  
James M. Walter
Keyword(s):  
Pneumococcal Vaccination ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Nucleic Acid Amplification ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Vaccination Programs ◽  
Syncytial Virus ◽  
Human Parainfluenza Virus ◽  
Immunocompetent Patients

AbstractCommunity-acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. There is growing appreciation of the burden of noninfluenza viral pathogens in CAP. Due to multiple factors including pneumococcal vaccination programs, declining rates of cigarette smoking, an aging population, and increasingly sensitive diagnostic tests, respiratory viruses are now the most common pathogens detected in CAP, outpacing Streptococcus pneumoniae. Noninfluenza respiratory pathogens are widely accepted as causal pathogens in CAP including in immunocompetent patients. This review provides an overview of five noninfluenza respiratory viral pathogens commonly implicated in CAP pathogenesis: rhinovirus, human metapneumovirus, respiratory syncytial virus, human parainfluenza virus, and human adenoviruses. Nucleic acid amplification testing platforms and their impact on antimicrobial stewardship efforts are also considered.

scholarly journals Influenza, RSV, and Other Respiratory Infections among Children in Qatar

2020 ◽  
Author(s):  
Maria K. Smatti ◽  
Hamad E. Al-Romaihi ◽  
Hebah A. Al-Khatib ◽  
Peter V. Coyle ◽  
Asmaa A Al Thani ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Control Strategies ◽  
Age Groups ◽  
Influenza Viruses ◽  
Respiratory Pathogen ◽  
Infection Prevention And Control ◽  
Respiratory Pathogens ◽  
Gulf Region ◽  
Mortality And Morbidity ◽  
Syncytial Virus

Background: Acute respiratory infections (ARIs) lead to high rates of mortality and morbidity among children. However, studies on the etiology of respiratory infections among children in Qatar and surrounding countries are still limited. Objectives: To describe the prevalence and seasonality of RSV, influenza, and other respiratory pathogens among children in Qatar. Methods: We retrospectively collected data of 33,404 patients <15 years old presented with Influenza-like illness (ILI) from 2012 to 2017. All samples were tested for influenza viruses, while 30,946 were tested for a complete panel of 21 respiratory pathogens. Results: At least one respiratory pathogen was detected in 26,138 (78%) of patients. Together, human rhinoviruses (HRV), respiratory syncytial virus (RSV), and influenza viruses comprised nearly two-thirds of all ILI cases, detected in 24%, 19.7%, and 18.5%, respectively. A detection rate of 5-10% was recorded for adenovirus, human parainfluenza viruses (HPIVs), bocavirus (HboV), and human coronaviruses (HCoVs). Other pathogens such as human metapneumovirus (HMPV), enteroviruses, mycoplasma pneumonia, and parechovirus had prevalence rates below 5%. ILI positive cases were detected throughout the year. RSV, influenza, HMPV exhibited strong seasonal activity in the winter, while HRV was primarily active during low RSV and influenza activity. The burden of RSV exceeds that of influenza among young age groups (<5 years), affecting 17-30% of ILI cases. Prevalence of influenza, on the other hand, correlated positively with age, ranging from 23% to 32% in age groups above five years. Further, male patients had higher rates of HRV (26%) and adenovirus (9%), whereas females showed a higher prevalence of influenza (22%), and RSV (20%) infections. Conclusion: This comprehensive report provides insights into the etiology of ILI among children in Qatar, which represents the Gulf region. Our results reinforce the significance of active surveillance of respiratory pathogens to improve infection prevention and control strategies, particularly among children.

scholarly journals Bacterial and Viral Coinfections with the Human Respiratory Syncytial Virus

2021 ◽  
Vol 9 (6) ◽  
pp. 1293
Author(s):  
Gaspar A. Pacheco ◽  
Nicolás M. S. Gálvez ◽  
Jorge A. Soto ◽  
Catalina A. Andrade ◽  
Alexis M. Kalergis
Keyword(s):  
Respiratory Syncytial Virus ◽  
Influenza A ◽  
Human Respiratory Syncytial Virus ◽  
Respiratory Pathogens ◽  
Parainfluenza Viruses ◽  
Starting Point ◽  
The Social ◽  
Syncytial Virus ◽  
Tract Infections ◽  
Polymicrobial Infections

The human respiratory syncytial virus (hRSV) is one of the leading causes of acute lower respiratory tract infections in children under five years old. Notably, hRSV infections can give way to pneumonia and predispose to other respiratory complications later in life, such as asthma. Even though the social and economic burden associated with hRSV infections is tremendous, there are no approved vaccines to date to prevent the disease caused by this pathogen. Recently, coinfections and superinfections have turned into an active field of study, and interactions between many viral and bacterial pathogens have been studied. hRSV is not an exception since polymicrobial infections involving this virus are common, especially when illness has evolved into pneumonia. Here, we review the epidemiology and recent findings regarding the main polymicrobial infections involving hRSV and several prevalent bacterial and viral respiratory pathogens, such as Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae, human rhinoviruses, influenza A virus, human metapneumovirus, and human parainfluenza viruses. As reports of most polymicrobial infections involving hRSV lack a molecular basis explaining the interaction between hRSV and these pathogens, we believe this review article can serve as a starting point to interesting and very much needed research in this area.

scholarly journals Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

2021 ◽  
Author(s):  
Jutte J.C. de Vries ◽  
Julianne R. Brown ◽  
Nicole Fischer ◽  
Igor A. Sidorov ◽  
Sofia Morfopoulou ◽  
...  
Keyword(s):  
De Novo ◽  
Respiratory Infections ◽  
Limit Of Detection ◽  
Bioinformatic Analysis ◽  
Clinical Samples ◽  
Mixed Infections ◽  
Metagenomic Sequencing ◽  
User Friendliness ◽  
Viral Pathogens ◽  
Clinical Diagnostic

Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. Methods Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analysed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analysed. Results Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. Conclusion A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.

scholarly journals Circulation of Respiratory Viruses in Hospitalized Adults before and during the COVID-19 Pandemic in Brescia, Italy: A Retrospective Study

2021 ◽  
Vol 18 (18) ◽  
pp. 9525
Author(s):  
Maria Antonia De Francesco ◽  
Caterina Pollara ◽  
Franco Gargiulo ◽  
Mauro Giacomelli ◽  
Arnaldo Caruso
Keyword(s):  
Respiratory Syncytial Virus ◽  
Influenza A ◽  
Statistical Significance ◽  
Respiratory Viruses ◽  
Influenza Viruses ◽  
Contact Tracing ◽  
Nucleic Acid Detection ◽  
Respiratory Pathogens ◽  
Syncytial Virus ◽  
Human Coronaviruses

Different preventive public health measures were adopted globally to limit the spread of SARS-CoV-2, such as hand hygiene and the use of masks, travel restrictions, social distance actions such as the closure of schools and workplaces, case and contact tracing, quarantine and lockdown. These measures, in particular physical distancing and the use of masks, might have contributed to containing the spread of other respiratory viruses that occurs principally by contact and droplet routes. The aim of this study was to evaluate the prevalence of different respiratory viruses (influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, 3 and 4, rhinovirus, adenovirus, metapneumovirus and human coronaviruses) after one year of the pandemic. Furthermore, another aim was to evaluate the possible impact of these non-pharmaceutical measures on the circulation of seasonal respiratory viruses. This single center study was conducted between January 2017–February 2020 (pre-pandemic period) and March 2020–May 2021 (pandemic period). All adults >18 years with respiratory symptoms and tested for respiratory pathogens were included in the study. Nucleic acid detection of all respiratory viruses was performed by multiplex real time PCR. Our results show that the test positivity for influenza A and B, metapneumovirus, parainfluenza virus, respiratory syncytial virus and human coronaviruses decreased with statistical significance during the pandemic. Contrary to this, for adenovirus the decrease was not statistically significant. Conversely, a statistically significant increase was detected for rhinovirus. Coinfections between different respiratory viruses were observed during the pre-pandemic period, while the only coinfection detected during pandemic was between SARS-CoV-2 and rhinovirus. To understand how the preventive strategies against SARS-CoV-2 might alter the transmission dynamics and epidemic patterns of respiratory viruses is fundamental to guide future preventive recommendations.

scholarly journals Antibiotic Minocycline Prevents Respiratory Syncytial Virus Infection

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 739 ◽  
Author(s):  
Swapnil S. Bawage ◽  
Pooja M. Tiwari ◽  
Shreekumar Pillai ◽  
Vida A. Dennis ◽  
Shree R. Singh
Keyword(s):  
Respiratory Syncytial Virus ◽  
Specific Activity ◽  
The Body ◽  
Effective Vaccine ◽  
Mortality And Morbidity ◽  
Viral Activity ◽  
Immunodeficiency Virus ◽  
Rsv Infection ◽  
Syncytial Virus ◽  
Common Respiratory Virus

Treatment drugs, besides their specific activity, often have multiple effects on the body. The undesired effect of the drug may be repurposed as therapeutics, saving significant investigative time and effort. Minocycline has anti-cancer, anti-oxidant, anti-inflammatory, and anti-apoptotic properties. Presently, minocycline is also known to show anti-viral activity against Influenza virus, Japanese encephalitis virus, Simian immunodeficiency virus, Human immunodeficiency virus and West Nile virus. Here, we investigate the effect of minocycline on Respiratory syncytial virus (RSV), a common respiratory virus that causes severe mortality and morbidity in infants, children, and older adult populations. Currently, there is no effective vaccine or treatment for RSV infection; hence, there is a critical need for alternative and effective drug choices. Our study shows that minocycline reduces the RSV-mediated cytopathic effect and prevents RSV infection. This is the first study demonstrating the anti-viral activity of minocycline against RSV.

Incidence of respiratory pathogens in persons hospitalized with pneumonia in two provinces in Thailand

2010 ◽  
Vol 138 (12) ◽  
pp. 1811-1822 ◽  
Author(s):  
S. J. OLSEN ◽  
S. THAMTHITIWAT ◽  
S. CHANTRA ◽  
M. CHITTAGANPITCH ◽  
A. M. FRY ◽  
...  
Keyword(s):  
Nasopharyngeal Swab ◽  
Respiratory Pathogens ◽  
Middle Income ◽  
Viral Pathogen ◽  
Effective Prevention ◽  
Middle Income Countries ◽  
Viral Culture ◽  
Comprehensive Information ◽  
Rsv Infection ◽  
Syncytial Virus

SUMMARYAlthough pneumonia is a leading cause of death from infectious disease worldwide, comprehensive information about its causes and incidence in low- and middle-income countries is lacking. Active surveillance of hospitalized patients with pneumonia is ongoing in Thailand. Consenting patients are tested for seven bacterial and 14 viral respiratory pathogens by PCR and viral culture on nasopharyngeal swab specimens, serology on acute/convalescent sera, sputum smears and antigen detection tests on urine. Between September 2003 and December 2005, there were 1730 episodes of radiographically confirmed pneumonia (34·6% in children aged <5 years); 66 patients (3·8%) died. A recognized pathogen was identified in 42·5% of episodes. Respiratory syncytial virus (RSV) infection was associated with 16·7% of all pneumonias, 41·2% in children. The viral pathogen with the highest incidence in children aged <5 years was RSV (417·1/100 000 per year) and in persons aged ⩾50 years, influenza virus A (38·8/100 000 per year). These data can help guide health policy towards effective prevention strategies.

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