scholarly journals Simultaneous identification of viruses and SARS-CoV-2 variants with programmable DNA nanobait

2021 ◽  
Author(s):  
Filip Boskovic ◽  
Jinbo Zhu ◽  
Ran Tivony ◽  
Alexander Ohmann ◽  
Kaikai Chen ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Target Selection ◽  
Respiratory Viruses ◽  
Rna Molecules ◽  
Rna Targets ◽  
Diagnostic Approaches ◽  
Syncytial Virus ◽  
Nucleotide Resolution ◽  
Simultaneous Identification ◽  
Multiple Pathogens

Respiratory infections are the major cause of death from infectious disease worldwide. The clinical presentation of many respiratory viruses is indistinguishable; therefore, diagnostic approaches that can identify multiple pathogens are essential for patient management. We aimed to address this challenge with self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid read-out via nanopore sensing. Here, we show this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from SARS-CoV-2, respiratory syncytial virus (RSV), rhinovirus, influenza, and parainfluenza. Our nanobait could be reprogrammed to discriminate viral variants, and we identified several key SARS-CoV-2 variants with single-nucleotide resolution. We increased assay specificity with bespoke nanobait that could identify numerous short RNA targets in the same viral sample in a complex background of the human transcriptome. Notably, we found that the sequence position in the viral RNA secondary structure is critical for nanobait design. Lastly, we show that nanobait could discriminate between samples extracted from oropharyngeal swabs from negative and positive SARS-CoV-2 patients using programmable target cleavage without pre-amplification. Our system allows for multiplexed identification of native RNA molecules, providing a new scalable approach for diagnostics of multiple respiratory viruses in a single assay.

scholarly journals Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1084
Author(s):  
Ho-Jae Lim ◽  
Jung-Eun Park ◽  
Min-Young Park ◽  
Joo-Hwan Baek ◽  
Sunkyung Jung ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Simultaneous Detection ◽  
Respiratory Viruses ◽  
Analytical Performance ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Significant Difference ◽  
Z Scores ◽  
Syncytial Virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

scholarly journals The Burden of Respiratory Viruses and Their Prevalence in Different Geographical Regions of India: 1970–2020

2021 ◽  
Vol 12 ◽  
Author(s):  
Rushabh Waghmode ◽  
Sushama Jadhav ◽  
Vijay Nema
Keyword(s):  
Influenza Virus ◽  
Disease Burden ◽  
Respiratory Infections ◽  
Seasonal Pattern ◽  
Respiratory Viruses ◽  
Geographical Regions ◽  
Severe Acute Respiratory Infection ◽  
Causes Of Mortality ◽  
Syncytial Virus ◽  
Global Population

As per the 2019 report of the National Health Portal of India, 41,996,260 cases and 3,740 deaths from respiratory infections were recorded across India in 2018. India contributes to 18% of the global population, with severe acute respiratory infection (SARI) as one of the prominent causes of mortality in children >5 years of age. Measures in terms of the diagnosis and surveillance of respiratory infections are taken up globally to discover their circulating types, detect outbreaks, and estimate the disease burden. Similarly, the purpose of this review was to determine the prevalence of respiratory infections in various regions of India through published reports. Understanding the pattern and prevalence of various viral entities responsible for infections and outbreaks can help in designing better strategies to combat the problem. The associated pathogens comprise respiratory syncytial virus (RSV), rhinovirus, influenza virus, parainfluenza virus, adenovirus, etc. Identification of these respiratory viruses was not given high priority until now, but the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has sensitized our system to be alert about the burden of existing infections and to have proper checks for emerging ones. Most of the studies reported to date have worked on the influenza virus as a priority. However, the data describing the prevalence of other respiratory viruses with their seasonal pattern have significant epidemiological value. A comprehensive literature search was done to gather data from all geographical regions of India comprising all states of India from 1970 to 2020. The same has been compared with the global scenario and is being presented here.

scholarly journals Interactions among common non-SARS-CoV-2 respiratory viruses and influence of the COVID-19 pandemic on their circulation in New York City

2021 ◽  
Author(s):  
Haokun Yuan ◽  
Alice Yeung ◽  
Wan Yang
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Cumulative Incidence ◽  
Respiratory Infections ◽  
Moving Average ◽  
Vaccination Campaign ◽  
Respiratory Viruses ◽  
Syncytial Virus ◽  
The Impact

Background Non-pharmaceutical interventions (NPIs) and voluntary behavioral changes during the COVID-19 pandemic have influenced the circulation of non-SARS-CoV-2 respiratory infections. We aimed to examine interactions among common non-SARS-CoV-2 respiratory virus and further estimate the impact of the COVID-19 pandemic on these viruses. Methods We analyzed incidence data for seven groups of respiratory viruses in New York City (NYC) during Oct 2015 - May 2021 (i.e., before and during the COVID-19 pandemic). We first used elastic net regression to identify potential virus interactions and further examined the robustness of the found interactions by comparing the performance of Auto Regressive Integrated Moving Average (ARIMA) models with and without the interactions. We then used the models to compute counterfactual estimates of cumulative incidence and estimate the reduction during the COVID-19 pandemic period from March 2020 to May 2021, for each virus. Results We identified potential interactions for three endemic human coronaviruses (CoV-NL63, CoV-HKU, and CoV-OC43), parainfluenza (PIV)-1, rhinovirus, and respiratory syncytial virus (RSV). We found significant reductions (by ~70-90%) in cumulative incidence of CoV-OC43, CoV-229E, human metapneumovirus, PIV-2, PIV-4, RSV, and influenza virus during the COVID-19 pandemic. In contrast, the circulation of adenovirus and rhinovirus was less affected. Conclusions Circulation of several respiratory viruses has been low during the COVID-19 pandemic, which may lead to increased population susceptibility. It is thus important to enhance monitoring of these viruses and promptly enact measures to mitigate their health impacts (e.g., influenza vaccination campaign and hospital infection prevention) in the coming months.

TOPICAL ISSUES OF INFECTIOUS RESPIRATORY PATHOLOGY IN CHILDREN

2020 ◽  
Vol 99 (6) ◽  
pp. 8-14
Author(s):  
A.V. Gorelov ◽  
◽  
S.V. Nikolaeva ◽  
◽  
Keyword(s):  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Acute Respiratory Infections ◽  
Present Stage ◽  
Pediatric Pathology ◽  
Parainfluenza Viruses ◽  
Serious Infection ◽  
Causative Agents ◽  
Respiratory Pathology ◽  
Syncytial Virus

Acute respiratory infections (ARI) are still topical, holding the first place in the structure of infectious pediatric pathology. The most common causative agents of ARI are viruses. Currently, about 200 respiratory viruses are known, among which the most significant are influenza and parainfluenza viruses, rhinoviruses, respiratory syncytial virus, adenoviruses. Relatively recently, previously unknown serotypes of coronaviruses (SARS-CoV, MERS-CoV, NL63 and HKU), bocaviruses and metapneumovirus were described, and at the end of 2019 a new coronavirus SARS-CoV-2 was discovered, which causes COVID-19 infection. Pneumotropic bacteria Streptococcus pneumoniae, Mycoplasma pneumoniae, Haemophilus influenzae, etc. contributed to the incidence of respiratory infections. Pertussis remains a serious infection for young children, which in recent years, despite the typical clinical picture, presents certain difficulties for diagnosis. The ability of ARI to provoke the development of secondary bacterial complications (bronchitis, bronchiolitis and pneumonia) often dictates the unjustified prescription of antibiotic therapy, which has led in recent years to an increase in antibiotic resistance. Thus, the relevance of ARI at the present stage is not in doubt, and the above problems dictate the need for an individual approach to each patient.

Survey of WU and KI polyomaviruses, coronaviruses, respiratory syncytial virus and parechovirus in children under 5 years of age in Tehran, Iran

2020 ◽  
Author(s):  
Fahimeh Sadat Aghamirmohammadali ◽  
Kaveh Sadeghi ◽  
Nazanin Zahra Shafiei-Jandaghi ◽  
Zahra Khoban ◽  
Talat Mokhtari-Azad ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Infections ◽  
Virus Detection ◽  
Respiratory Viruses ◽  
Hospitalized Children ◽  
Acute Respiratory Infections ◽  
Older Children ◽  
Viral Pathogen ◽  
Syncytial Virus ◽  
Tract Infections

Background and Objectives: Severe acute respiratory infections (SARI) remain an important cause for childhood morbid- ity worldwide. We designed a research with the objective of finding the frequency of respiratory viruses, particularly WU and KI polyomaviruses (WUPyV & KIPyV), human coronaviruses (HCoVs), human respiratory syncytial virus (HRSV) and human parechovirus (HPeV) in hospitalized children who were influenza negative. Materials and Methods: Throat swabs were collected from children younger than 5 years who have been hospitalized for SARI and screened for WUPyV, KIPyV, HCoVs, HRSV and HPeV using Real time PCR. Results: A viral pathogen was identified in 23 (11.16%) of 206 hospitalized children with SARI. The rate of virus detection was considerably greater in infants <12 months (78.2%) than in older children (21.8%). The most frequently detected vi- ruses were HCoVs with 7.76% of positive cases followed by KIPyV (2%) and WUPyV (1.5%). No HPeV and HRSV were detected in this study. Conclusion: This research shown respiratory viruses as causes of childhood acute respiratory infections, while as most of mentioned viruses usually causes mild respiratory diseases, their frequency might be higher in outpatient children. Mean- while as HRSV is really sensitive to inactivation due to environmental situations and its genome maybe degraded, then for future studies, we need to use fresh samples for HRSV detection. These findings addressed a need for more studies on viral respiratory tract infections to help public health.

scholarly journals Seasonal Variations in Clostridium difficile Infections Are Associated with Influenza and Respiratory Syncytial Virus Activity Independently of Antibiotic Prescriptions: a Time Series Analysis in Québec, Canada

2011 ◽  
Vol 56 (2) ◽  
pp. 639-646 ◽  
Author(s):  
Rodica Gilca ◽  
Élise Fortin ◽  
Charles Frenette ◽  
Yves Longtin ◽  
Marie Gourdeau
Keyword(s):  
Time Series ◽  
Influenza Virus ◽  
Respiratory Syncytial Virus ◽  
Clostridium Difficile ◽  
Seasonal Variations ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Temporal Variations ◽  
Average Delay ◽  
Syncytial Virus

ABSTRACTSeasonal variations inClostridium difficile-associated diarrhea (CDAD), with a higher incidence occurring during winter months, have been reported. Although winter epidemics of respiratory viruses may be temporally associated with an increase in CDAD morbidity, we hypothesized that this association is mainly due to increased antibiotic use for respiratory infections. The objective of this study was to evaluate the effect of the two most frequent respiratory viruses (influenza virus and respiratory syncytial virus [RSV]) and antibiotics prescribed for respiratory infections (fluoroquinolones and macrolides) on the CDAD incidence in hospitals in the province of Québec, Canada. A multivariable Box-Jenkins transfer function model was built to relate monthly CDAD incidence to the monthly percentage of positive tests for influenza virus and RSV and monthly fluoroquinolone and macrolide prescriptions over a 4-year period (January 2005 to December 2008). Analysis showed that temporal variations in CDAD incidence followed temporal variations for influenza virus (P= 0.043), RSV (P= 0.004), and macrolide prescription (P= 0.05) time series with an average delay of 1 month and fluoroquinolone prescription time series with an average delay of 2 months (P= 0.01). We conclude that influenza virus and RSV circulation is independently associated with CDAD incidence after controlling for fluoroquinolone and macrolide use. This association was observed at an aggregated level and may be indicative of other phenomena occurring during wintertime.

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

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Neli Korsun ◽  
Svetla Angelova ◽  
Ivelina Trifonova ◽  
Silvia Voleva ◽  
Iliana Grigorova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Respiratory Infections ◽  
Single Agent ◽  
Respiratory Viruses ◽  
Acute Respiratory Infections ◽  
Vp2 Gene ◽  
Genetic Characteristics ◽  
Influenza A H1n1 ◽  
Syncytial Virus

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.

scholarly journals The rapid reemergence of seasonal respiratory viruses in Houston, Texas, after relaxing COVID-19 restrictions

2021 ◽  
Author(s):  
Parsa Hodjat ◽  
Paul Christensen ◽  
Sishir Subedi ◽  
Randall James Olsen ◽  
David W Bernard ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Infections ◽  
State Level ◽  
Complete Removal ◽  
Respiratory Viruses ◽  
Rapid Decrease ◽  
The State ◽  
Respiratory Pathogens ◽  
Containment Measures ◽  
Syncytial Virus

Implementation of measures to limit the spread of the SARS-CoV-2 virus at the start of the COVID-19 pandemic resulted in a rapid decrease in all other respiratory pathogens. As COVID-19 containment measures were relaxed, the first non-COVID respiratory viruses to return to prepandemic levels were members of the rhinovirus/enterovirus, followed by the rapid return of seasonal coronaviruses, parainfluenza, and respiratory syncytial virus after the complete removal of COVID-19 precautions at the state level, including an end to mask mandates. Inasmuch as COVID-19 has dominated the landscape of respiratory infections since early 2020, it is important for clinicians to recognize the return of non-COVID respiratory pathogens may be rapid and significant when COVID-19 containment measures are removed.

scholarly journals Contribution of Nanotechnologies to Vaccine Development and Drug Delivery against Respiratory Viruses

PPAR Research ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-28
Author(s):  
Mahdi Ftouh ◽  
Nesrine Kalboussi ◽  
Nabil Abid ◽  
Souad Sfar ◽  
Nathalie Mignet ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Vaccine Development ◽  
Respiratory Infections ◽  
Antiviral Drug ◽  
Respiratory Illness ◽  
Short Review ◽  
Respiratory Viruses ◽  
Control And Prevention ◽  
Viral Illness ◽  
Syncytial Virus

According to the Center for Disease Control and Prevention (CDC), the coronavirus disease 2019, a respiratory viral illness linked to significant morbidity, mortality, production loss, and severe economic depression, was the third-largest cause of death in 2020. Respiratory viruses such as influenza, respiratory syncytial virus, SARS-CoV-2, and adenovirus, are among the most common causes of respiratory illness in humans, spreading as pandemics or epidemics throughout all continents. Nanotechnologies are particles in the nanometer range made from various compositions. They can be lipid-based, polymer-based, protein-based, or inorganic in nature, but they are all bioinspired and virus-like. In this review, we aimed to present a short review of the different nanoparticles currently studied, in particular those which led to publications in the field of respiratory viruses. We evaluated those which could be beneficial for respiratory disease-based viruses; those which already have contributed, such as lipid nanoparticles in the context of COVID-19; and those which will contribute in the future either as vaccines or antiviral drug delivery systems. We present a short assessment based on a critical selection of evidence indicating nanotechnology’s promise in the prevention and treatment of respiratory infections.

scholarly journals Impact of hygienic and social distancing measures against SARS-CoV-2 on respiratory infections caused by other viruses

2021 ◽  
Author(s):  
Jordi Reina ◽  
◽  
Ricardo M. Arcay ◽  
María Busquets ◽  
Herminia Machado
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Contact Material ◽  
Rt Pcr ◽  
Social Distancing ◽  
Syncytial Virus ◽  
The Impact

Introduction. To control the pandemic caused by SARS-CoV-2, the implementation of social and hygienic confinement measures was determined in all countries. These measures reduce the circulation of most respiratory viruses that are transmitted preferentially by air and contact. Material and methods. The impact of these measures on non-Covid respiratory viruses during the period August-December 2020 and 2019 has been comparatively analyzed. To all nasopharyngeal aspirates that were negative against SARS-CoV-2 by RT-PCR and the suspicion of acute respiratory infection persisted, were subjected to a new RT-PCR that simultaneously and differentially amplifies 21 different respiratory viruses. Results. In the year of the pandemic, a 36.6% decrease was detected in the number of respiratory samples studied and 66% in their positivity in relation to 2019. All viruses showed reduction percentages of between 40-100%. The only viruses that circulated during and after national lockdown were rhinovirus (74.1%), adenovirus (10.1%), and enterovirus (9.6%). Conclusion. The measures used to control the SARS-CoV-2 infection have also affected the community circulation of most respiratory viruses including influenza and respiratory syncytial virus.

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