scholarly journals The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 960
Author(s):  
Nguyen Thi Kha Tu ◽  
Nguyen Thi Thu Hong ◽  
Nguyen Thi Han Ny ◽  
Tran My Phuc ◽  
Pham Thi Thanh Tam ◽  
...  
Keyword(s):  
At Risk ◽  
Influenza A ◽  
Respiratory Diseases ◽  
Respiratory Pathogens ◽  
The Novel ◽  
Rt Pcr ◽  
Pcr Screening ◽  
Zoonotic Infections ◽  
Acute Respiratory Diseases ◽  
Syncytial Virus

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.

scholarly journals Application of RT-PCR for diagnosis of respiratory syncytial virus and human metapneumovirus infections in Bulgaria, 2006-7 and 2007-8

2009 ◽  
Vol 14 (23) ◽  
Author(s):  
S Pavlova ◽  
T Hadzhiolova ◽  
P Abadjieva ◽  
R Kotseva
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Diseases ◽  
National Laboratory ◽  
Human Metapneumovirus ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Acute Respiratory Diseases ◽  
Polymerase Chain ◽  
Syncytial Virus

We describe here the results of respiratory syncytial virus (RSV) detection by reverse transcription polymerase chain reaction (RT-PCR) during two consecutive seasons, from December 2006 to February 2007 and from October 2007 to March 2008, performed in the National Laboratory of Influenza and Acute Respiratory Diseases, Bulgaria. A total number of 278 nasopharyngeal samples obtained from hospitalised children up to the age of five years were investigated for these two seasons. During the first season, the aetiological role of RSV was confirmed in 56 of 148 samples (37.8%) compared to 11 of 130 samples (8.5%) during the second season. Since the beginning of January 2008, RT-PCR for the detection of the recently identified human metapneumovirus (HMPV) has also been introduced in Bulgaria. This virus has been demonstrated as the aetiological agent in 13 out of 81 samples (16%) from children of the same age group. The use of RT-PCR allows the detection of a broader spectrum of viruses causing respiratory diseases, as well as better discrimination of the aetiological agents in clinically similar cases.

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 A Machine Learning Model Incorporating Laboratory Blood Tests Discriminates Between SARS-CoV-2 and Influenza Infections at Emergency Department Visit

2021 ◽  
Author(s):  
Junyi Liu ◽  
Lars F Westblade ◽  
Amy Chadburn ◽  
Richard Fideli ◽  
Arryn Craney ◽  
...  
Keyword(s):  
Emergency Department ◽  
Laboratory Test ◽  
Calcium Level ◽  
Influenza A ◽  
Respiratory Pathogens ◽  
Rt Pcr ◽  
Blood Tests ◽  
Laboratory Test Results ◽  
Presentation Methods ◽  
The Impact

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus are contagious respiratory pathogens with similar symptoms but require different treatment and management strategies. This study investigated whether laboratory blood tests can discriminate between SARS-CoV-2 and influenza infections at emergency department (ED) presentation. Methods: 723 influenza A/B positive (2018/1/1 to 2020/3/15) and 1,281 SARS-CoV-2 positive (2020/3/11 to 2020/6/30) ED patients were retrospectively analyzed. Laboratory test results completed within 48 hours prior to reporting of virus RT-PCR results, as well as patient demographics were included to train and validate a random forest (RF) model. The dataset was randomly divided into training (2/3) and testing (1/3) sets with the same SARS-CoV-2/influenza ratio. The Shapley Additive Explanations technique was employed to visualize the impact of each laboratory test on the differentiation. Results: The RF model incorporating results from 15 laboratory tests and demographic characteristics discriminated SARS-CoV-2 and influenza infections, with an area under the ROC curve value 0.90 in the independent testing set. The overall agreement with the RT-PCR results was 83% (95% CI: 80-86%). The test with the greatest impact on the differentiation was serum total calcium level. Further, the model achieved an AUC of 0.82 in a new dataset including 519 SARS-CoV-2 ED patients (2020/12/1 to 2021/2/28) and the previous 723 influenza positive patients. Serum calcium level remained the most impactful feature on the differentiation. Conclusion: We identified characteristic laboratory test profiles differentiating SARS-CoV-2 and influenza infections, which may be useful for the preparedness of overlapping COVID-19 resurgence and future seasonal influenza.

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 Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

2020 ◽  
Vol 59 (1) ◽  
pp. e02142-20
Author(s):  
Ahmed Babiker ◽  
Heath L. Bradley ◽  
Victoria D. Stittleburg ◽  
Jessica M. Ingersoll ◽  
Autum Key ◽  
...  
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Human Metapneumovirus ◽  
Molecular Testing ◽  
Metagenomic Sequencing ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
Testing Algorithms ◽  
Syncytial Virus

ABSTRACTBroad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.

scholarly journals Molecular Detection of a Novel Human Influenza (H1N1) of Pandemic Potential by Conventional and Real-Time Quantitative RT-PCR Assays

2009 ◽  
Vol 55 (8) ◽  
pp. 1555-1558 ◽  
Author(s):  
Leo L M Poon ◽  
K H Chan ◽  
G J Smith ◽  
C S W Leung ◽  
Y Guan ◽  
...  
Keyword(s):  
Real Time ◽  
Influenza A ◽  
H1n1 Virus ◽  
Influenza Viruses ◽  
The Novel ◽  
Human Influenza ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Recent Emergence ◽  
Human H5n1

Abstract Background: Influenza A viruses are medically important viral pathogens that cause significant mortality and morbidity throughout the world. The recent emergence of a novel human influenza A virus (H1N1) poses a serious health threat. Molecular tests for rapid detection of this virus are urgently needed. Methods: We developed a conventional 1-step RT-PCR assay and a 1-step quantitative real-time RT-PCR assay to detect the novel H1N1 virus, but not the seasonal H1N1 viruses. We also developed an additional real-time RT-PCR that can discriminate the novel H1N1 from other swine and human H1 subtype viruses. Results: All of the assays had detection limits for the positive control in the range of 1.0 × 10−4 to 2.0 × 10−3 of the median tissue culture infective dose. Assay specificities were high, and for the conventional and real-time assays, all negative control samples were negative, including 7 human seasonal H1N1 viruses, 1 human H2N2 virus, 2 human seasonal H3N2 viruses, 1 human H5N1 virus, 7 avian influenza viruses (HA subtypes 4, 5, 7, 8, 9, and 10), and 48 nasopharyngeal aspirates (NPAs) from patients with noninfluenza respiratory diseases; for the assay that discriminates the novel H1N1 from other swine and human H1 subtype viruses, all negative controls were also negative, including 20 control NPAs, 2 seasonal human H1N1 viruses, 2 seasonal human H3N2 viruses, and 2 human H5N1 viruses. Conclusions: These assays appear useful for the rapid diagnosis of cases with the novel H1N1 virus, thereby allowing better pandemic preparedness.

scholarly journals Etiological characteristics of acute respiratory diseases in servicemen of the Western military district in 2014-2019

2020 ◽  
Vol 22 (1) ◽  
pp. 81-86
Author(s):  
A N Gorenchuk ◽  
P V Kulikov ◽  
S D Zhogolev ◽  
R M Aminev ◽  
A A Kuzin ◽  
...  
Keyword(s):  
Environmental Sustainability ◽  
Respiratory Diseases ◽  
Respiratory Infections ◽  
Genetic Material ◽  
Influenza Viruses ◽  
Respiratory Pathogens ◽  
Acute Respiratory Diseases ◽  
Socio Demographic Factors ◽  
Comparison Of The Results ◽  
Active Implementation

The species affiliation of respiratory pathogens isolated from patients and carriers in the military units of the Western Military District in 2014-2019 was studied. The analysis of long-term and seasonal dynamics of their circulation is carried out. It was found that S. pneumoniae and adenoviruses are more often detected in acute respiratory diseases in conscripts. The genetic material of adenoviruses was found in 31,9% of samples, influenza viruses in 13,3%, rhinoviruses in 11,2%, respiratory syncytial viruses in 1,7%, metapneumoviruses in 0,9%, parainfluenza viruses 0,7%, bocaviruses0,5%, coronaviruses 0,1%, S. pneumoniae 33,9%, H. influenzae 13%, M. pneumoniae 9%, C. pneumoniae - in 3,3%, N. meningitidis - in 16%. Comparison of the results of work with studies carried out by domestic research groups among the civilian population in the same period showed that the circulation of various respiratory viruses depends on the year, season, and is also influenced by socio-demographic factors. A direct high functional correlation was found between the dynamics of circulation of adenovirus and S. pneumoniae in different years and epidemic seasons. Evidence has been obtained of the active implementation of the process of self-maintenance of the reservoir of infections and the multifactorial nature of the overall environmental sustainability of the system in organized military teams. In the etiological structure of respiratory infections, the proportion of pathogens varies depending on the season in different years, the characteristics of the formation and composition of organized groups, as well as epidemic periods.

scholarly journals Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens

2018 ◽  
Vol 56 (8) ◽  
Author(s):  
Soya S. Sam ◽  
Angela M. Caliendo ◽  
Jessica Ingersoll ◽  
Deborah Abdul-Ali ◽  
Charles E. Hill ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Positive Result ◽  
Lower Respiratory Tract ◽  
Influenza A ◽  
Performance Characteristics ◽  
Influenza B Virus ◽  
Influenza B ◽  
Respiratory Pathogens ◽  
Percent Agreement ◽  
Syncytial Virus

ABSTRACT Accurate and rapid diagnosis is needed for timely intervention and clinical management of acute respiratory infections. This study evaluated performance characteristics of the Panther Fusion assay for the detection of influenza A virus (Flu A), influenza B virus (Flu B), respiratory syncytial virus (RSV), parainfluenza viruses 1 to 3 (Para 1 to 3), human metapneumovirus (hMPV), rhinovirus (RV), and adenovirus (Adeno) targets in comparison to those of the eSensor and Lyra assays using 395 nasopharyngeal (NP) and 104 lower respiratory tract (LRT) specimens. Based on the consensus positive result established (positive result in 2 of the 3 assays), the NP specimens for the Fusion and eSensor assays had 100% positive percent agreement (PPA) for all the analytes and the Lyra assays had 100% PPA for Flu A and Adeno analytes. A 100% negative percent agreement (NPA) was observed for all the Lyra analytes, whereas those for the Fusion targets ranged from 98.4 to 100% and those for the eSensor ranged from 99.4 to 100% for all the analytes except RV. For the LRT specimens, Fusion had 100% PPA and 100% NPA for all the targets except hMPV. There was a 100% PPA for eSensor analytes; the NPA ranged from 98 to 100%, except for RV. For the Lyra assays, the PPA ranged between 50 and 100%, while the NPA was 100% for all the targets except Adeno. The Fusion assay performed similarly to the eSensor assay for majority of the targets tested and provides laboratories with a fully automated random-access system to test for a broad array of viral respiratory pathogens.

scholarly journals Co-detection of respiratory pathogens in patients hospitalized with Coronavirus viral disease-2019 pneumonia

2020 ◽  
Author(s):  
María Luisa Blasco ◽  
Javier Buesa ◽  
Javier Colomina ◽  
María José Forner ◽  
María José Galindo ◽  
...  
Keyword(s):  
Positive Result ◽  
Clinical Laboratory ◽  
Viral Disease ◽  
Respiratory Pathogens ◽  
Rt Pcr ◽  
Laboratory Findings ◽  
Routine Testing ◽  
Multiplexed Pcr ◽  
Co Detection ◽  
Syncytial Virus

ABSTRACTThere is scarce information on the frequency of co-detection of respiratory pathogens (RP) in patients with Covid-19. Documentation of coinfections in Covid-19 pneumonia patients may be relevant for appropriate clinical and therapeutic management of patients. Between March 4th and March 28th, 2020, a total of 183 adult patients testing positive by SARS CoV-2 RT-PCR on respiratory specimens were hospitalized with interstitial pneumonia at our center, of whom 103 were tested for other RP by a multiplexed PCR assay. Three patients had a positive result for either one (n=2; Coronavirus HKU1 or Mycoplasma pneumoniae) or two targets (n=1; Influenza virus A (H3) and Respiratory syncytial virus B). Twenty-three patients testing negative by SARS CoV-2 RT-PCR and presentig with clinical, laboratory findings and imaging compatibe with Covid-19 pneumonia underwent RP screening. Of these, 6 (26%) had a positive result for a single RP. Our data indicate that despite the apparent rarity of coinfections in patients with Covid-19 pneumonia, routine testing for RP should be advised, since agents for which specific therapy can be prescribed may be detected.

scholarly journals Coinfection with Respiratory Pathogens in COVID-19 in Korea

2020 ◽  
Author(s):  
Kyoung Ho Roh ◽  
Yu Kyung Kim ◽  
Shin-Woo Kim ◽  
Eun-Rim Kang ◽  
Yong-Jin Yang ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Diagnostic Value ◽  
Respiratory Pathogens ◽  
Respiratory Specimen ◽  
Upper Respiratory ◽  
Viral Coinfection ◽  
Syncytial Virus ◽  
Respiratory Specimens

AbstractDetection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) were investigated. From the study subjects (N = 258) retrospectively enrolled when confirmed as SARS-CoV-2 positive, nasopharyngeal (NPS), oropharyngeal swabs (OPS), and sputum specimens were restored for retesting SARS-CoV-2 and detecting respiratory pathogens. Majority of the study subjects (95.7%, N = 247) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens, suggesting that the upper respiratory specimen is most valuable in detecting SARS-CoV-2. Coinfection rates in COVID-19 patients (N = 258) with respiratory pathogens were 9.7% (N = 25); 8.5% (N = 22) respiratory viruses and 1.2% (N = 3) Mycoplasma pneumoniae, an atypical bacterium. Of the respiratory virus coinfection cases (N = 22), 20 (90.9%) were co-infected with a single respiratory virus and 2 (0.8%) (metapneumovirus/adenovirus and rhinovirus/bocavirus 1/2/3/4) with two viruses. Respiratory viruses in single viral coinfection cases with SARS-CoV-2 were as follows: non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.9%), rhinovirus (N = 4, 1.6%), metapneumovirus (N = 3, 1.2%), influenza A (N = 3, 1.2%), respiratory syncytial virus A and B (N = 3, 1.2%), and adenovirus (N = 2, 0.8%). No mixed coinfections with respiratory viruses and M. pneumoniae were found. In conclusion, the diagnostic value of utilizing NPS/OPS specimen is excellent, and, as the first report in Korea, coinfection with respiratory pathogens were detected at a rate of 9.7% in patients with COVID-19.

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