scholarly journals Wastewater Virus Detection Complements Clinical COVID-19 Testing to Limit Spread of Infection at Kenyon College

2021 ◽  
Author(s):  
Daniel Barich ◽  
Joan L. Slonczewski
Keyword(s):  
Virus Detection ◽  
Population Management ◽  
College Instruction ◽  
Clinical Testing ◽  
Rna Detection ◽  
Case Identification ◽  
Virus Prevalence ◽  
Virus Surveillance ◽  
Spread Of Infection ◽  
The Village

ABSTRACTIn-person college instruction during the 2020 pandemic required effective and economical monitoring of COVID-19 prevalence. Kenyon College and the Village of Gambier conducted measurement of SARS-CoV-2 RNA from the village wastewater plant and from an on-campus sewer line. Wastewater RNA detection revealed virus prevalence leading to individual testing and case identification. Wastewater surveillance also showed when case rates had subsided, thus limiting the need for individual clinical testing. Overall, wastewater virus surveillance allows more targeted use of individual testing and increases community confidence in student population management.

scholarly journals Detection ofC. trachomatisin the Serum of the Patients with Urogenital Chlamydiosis

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Naylia A. Zigangirova ◽  
Yulia P. Rumyantseva ◽  
Elena Y. Morgunova ◽  
Lidia N. Kapotina ◽  
Lubov V. Didenko ◽  
...  
Keyword(s):  
Bacterial Load ◽  
Cell Monolayer ◽  
Immunogold Electron Microscopy ◽  
Rna Detection ◽  
Systemic Spread ◽  
Anatomical Localization ◽  
Taqman Pcr ◽  
Spread Of Infection ◽  
First Time

Extragenital chlamydial complications may be associated with systemic spread of infection, but haematogenous route forC. trachomatisdissemination has not been clearly demonstrated. Here we report that serum specimens obtained from patients with chlamydiosis contain elementary bodies ofC. trachomatisshown by culture and immunogold electron microscopy. We have found that 31 of the 52 patients had serum precipitates which were infective to McCoy cells. Immunostaining revealed very small inclusions resembling those reported during persistentC. trachomatisinfectionin vitro. DNA specimens from 49 (out of 52) patients with chlamydiosis gave positive PCR readings. The viability of the pathogen present in the sera was confirmed by chlamydial RNA detection in the cell monolayer inoculated by the serum precipitates. By using DNA isolation protocol from 1 mL of serum and quantitative TaqMan PCR, it was estimated that bacterial load in patients’ sera was2×102–103 GE/mL. These findings for the first time demonstrated thatC. trachomatiscan be disseminated directly by the plasma, independently from blood cell, which may represent a new possible pathway of the chronic infection development. Therefore, new methodological approaches for detection ofC. trachomatisin the serum of patients with complicated and chronic chlamydiosis could be important in the diagnosis of the infection regardless of its anatomical localization.

scholarly journals ESwab challenges influenza virus propagation in cell cultures

2014 ◽  
Vol 19 (50) ◽  
Author(s):  
R Trebbien ◽  
B Andersen ◽  
J Rønn ◽  
J McCauley ◽  
T Kølsen Fischer
Keyword(s):  
Influenza Virus ◽  
Virus Detection ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Virus Propagation ◽  
Rna Detection ◽  
Viral Propagation ◽  
Influenza Virus Detection ◽  
Polymerase Chain ◽  
Darby Canine Kidney

Although the ESwab kit (Copan, Brescia, Italy) is intended for sampling bacteria for culture, this kit is increasingly also used for virus sampling. The effect of ESwab medium on influenza virus detection by real-time reverse transcription-polymerase chain reaction (RT-PCR) or virus propagation in Madin-Darby canine kidney (MDCK) cell culture was investigated. The ESwab medium was suitable for viral RNA detection but not for viral propagation due to cytotoxicity. Sampling influenza viruses with ESwab challenges influenza surveillance by strongly limiting the possibility of antigenic characterisation.

scholarly journals Influenza Virus Detection Following Administration of Live-Attenuated Intranasal Influenza Vaccine in Children With Cystic Fibrosis and Their Healthy Siblings

2016 ◽  
Vol 3 (4) ◽  
Author(s):  
Constantina Boikos ◽  
Lawrence Joseph ◽  
Christine Martineau ◽  
Jesse Papenburg ◽  
David Scheifele ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Small Sample Size ◽  
Virus Detection ◽  
Credible Interval ◽  
Small Sample ◽  
Influenza Viruses ◽  
Study Cohort ◽  
Rt Pcr ◽  
Rna Detection

Abstract Background.  We aimed to explore the detection profile of influenza viruses following live-attenuated intranasal influenza vaccination (LAIV) in children aged 2–19 years with and without cystic fibrosis (CF). Methods.  Before the 2013–2014 influenza season, flocked nasal swabs were obtained before vaccination and 4 times in the week of follow-up from 76 participants (nCF: 57; nhealthy: 19). Influenza was detected by reverse transcription polymerase chain reaction (RT-PCR) assays. A Bayesian hierarchical logistic regression model was used to estimate the effect of CF status and age on influenza detection. Results.  Overall, 69% of the study cohort shed influenza RNA during follow-up. The mean duration of RT-PCR detection was 2.09 days (95% credible interval [CrI]: 1.73–2.48). The odds of influenza RNA detection on day 1 following vaccination decreased with age in years (odds ratio [OR]: 0.82 per year; 95% CrI: 0.70–0.95), and subjects with CF had higher odds of influenza RNA detection on day 1 of follow-up (OR: 5.09; 95% CrI: 1.02–29.9). Conclusion.  Despite the small sample size, our results indicate that LAIV vaccine strains are detectable during the week after LAIV, mainly in younger individuals and vaccinees with CF. It remains unclear whether recommendations for avoiding contact with severely immunocompromised patients should differ for these groups.

scholarly journals Respiratory virus surveillance in Canada during the COVID-19 pandemic: An epidemiological analysis of the effectiveness of pandemic-related public health measures in reducing seasonal respiratory viruses test positivity

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253451
Author(s):  
Kyu Young Park ◽  
Sumin Seo ◽  
Junhee Han ◽  
Ji Young Park
Keyword(s):  
Public Health ◽  
Respiratory Virus ◽  
Influenza Season ◽  
National Level ◽  
Virus Detection ◽  
Respiratory Viruses ◽  
Surveillance Data ◽  
Time Series Regression ◽  
Health Measures ◽  
Virus Surveillance

Background Various public health measures have been implemented globally to counter the coronavirus disease 2019 (COVID-19) pandemic. The purpose of this study was to evaluate respiratory virus surveillance data to determine the effectiveness of such interventions in reducing transmission of seasonal respiratory viruses. Method We retrospectively analysed data from the Respiratory Virus Detection Surveillance System in Canada, before and during the COVID-19 pandemic, by interrupted time series regression. Results The national level of infection with seasonal respiratory viruses, which generally does not necessitate quarantine or contact screening, was greatly reduced after Canada imposed physical distancing and other quarantine measures. The 2019–2020 influenza season ended earlier than it did in the previous year. The influenza virus was replaced by rhinovirus/enterovirus or parainfluenza virus in the previous year, with the overall test positivity remaining at approximately 35%. However, during the 2019–2020 post-influenza period, the overall test positivity of respiratory viruses during the COVID-19 was still low (7.2%). Moreover, the 2020–2021 influenza season had not occurred by the end of February 2021. Conclusion Respiratory virus surveillance data may provide real-world evidence of the effectiveness of implemented public health interventions during the current and future pandemics.

scholarly journals Sex hormones as an emerging weapon to combat COVID-19

2021 ◽  
Vol 5 (2) ◽  
pp. 01-03
Author(s):  
Dattatreya Mukherjee
Keyword(s):  
Close Contact ◽  
Virus Detection ◽  
World Health ◽  
Rapid Screening ◽  
Global Level ◽  
Rna Detection ◽  
Highly Pathogenic ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Respiratory Droplets

Coronavirus disease 2019 (COVID-19) started as an epidemic in Wuhan in 2019 and was declared pandemic by WHO in March 2020. The virus has been identified and named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This novel coronavirus strain is the causative agent of COVID-19, and continues to rapidly spread worldwide. SARS-CoV-2 is a highly pathogenic and transmissible coronavirus that spreads through respiratory droplets and unprotected close contact. “COVID‑19 outbreak, which has caused >95 million confirmed infections and >2 million coronavirus related deaths, is one of the most disastrous worldwide crises in recent years. Several methods have been used to examine SARS-CoV-2 infections.” i.e. RT-qPCR for viral RNA detection, and rapid screening procedures for antibody or virus detection. COVID-19 shows an incubation period of 3–7 days globally. Approximately 80% of the cases remain mild or asymptomatic, 15% are severe and 5% infectious cases turn to critical, requiring ventilation [2]. Several clinical trials have been proposed for its treatment and management with supportive aim of mortality reduction [1]. By glancing a view on fig 1, it can be evidently seen that COVID-19 cases have started to rise significantly since last few months. Furthermore, as per World Health Organization (WHO), there have been 131,020,967 confirmed cases of COVID-19 at a global level recently.

scholarly journals Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

2015 ◽  
Vol 43 (13) ◽  
pp. 6191-6206 ◽  
Author(s):  
Eric Roberto Guimarães Rocha Aguiar ◽  
Roenick Proveti Olmo ◽  
Simona Paro ◽  
Flavia Viana Ferreira ◽  
Isaque João da Silva de Faria ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Large Scale ◽  
Virus Detection ◽  
Virus Surveillance ◽  
Size Profile ◽  
Reference Databases ◽  
Similarity Searches ◽  
Viral Sequences

Abstract Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.

scholarly journals Streptococcal infections among children in a residential home: IV. Outbreaks of infection

1958 ◽  
Vol 56 (2) ◽  
pp. 211-237 ◽  
Author(s):  
Margaret C. Holmes ◽  
R. E. O. Williams ◽  
C. V. Bloom ◽  
Ann Hirch ◽  
Ann Lermit ◽  
...  
Keyword(s):  
Attack Rate ◽  
Single Case ◽  
Healthy Person ◽  
Carrier State ◽  
School Age Children ◽  
Residential Home ◽  
Carrier Rate ◽  
Primary Case ◽  
Spread Of Infection ◽  
The Village

In a residential home for children, 367 cases of streptococcal illness were observed in a period of 30 months. The children lived in groups of about twelve in separate cottages. There were 194 occasions on which a streptococcus was thought to have been newly introduced into and produced illness in a cottage; on 132 of these 194 occasions there were no secondary cases of illness. The remaining 62 cottage introductions were followed by one or more secondary cases.In 27% of the 194 introductions, the primary case of illness seemed to have been infected from a healthy person in the cottage. In all, 30% of introductions of a new streptococcus into a cottage could be attributed to recognized contacts with one or more known infected children.The most important factor determining spread within the cottage seemed to be the carrier state of the primary case, spread following more often when the primary case had streptococci in the nose either on admission to hospital, or in convalescence.There was no evidence that spread within cottage bedrooms was of great importance.In about 35% of the incidents with spread, the initial spread to secondary cases seemed to be from the incubation-stage carriage of the introducer; in 42% it was from his or her convalescent carriage.The carrier rate in the healthy cottage-contacts was generally higher in cottages experiencing clinical spread of infection than in those that had single-case introductions. There was a strong correlation between the carrier rate in the first week after an introduction and the final bacteriological attack rate, and a weaker correlation with the final clinical attack rate.Continued spread of infection in a cottage was commonly due to the arrival of new children and was almost always associated with the presence of nasal carriers of streptococci.The 194 cottage introductions could be grouped into sixty-three overlapping Village epidemics, each apparently derving from a new importation of the particular type into the Village, although the evidence for this was often merely the absence of known infections within the previous few months. Only 13% of the introductions resulted in more than 10 cases, and some 80% had 5 or fewer. Introductions were more frequent in the cottages receiving children new to the homes than in those for the more permanent residents.The principal factor found as determining the spread from the first cottage to others was the attack rate in the first cottage. Introductions in cottages for school-age children, and especially those in which a child attending the school in the Village grounds was the first to be attacked, also seemed to lead to spread more often than others.The interval between successive Village introductions of one type did not appear to affect the extent of spread at the second; but the number of cases occurring in the first of two introductions had a notable effect: in no case did two successive introductions both result in a large number of cases of illness.

Building-level wastewater surveillance using tampon swabs and RT-LAMP for rapid SARS-CoV-2 RNA detection

2021 ◽  
Author(s):  
Aaron Bivins ◽  
Megan Lott ◽  
Marlee Shaffer ◽  
Zhenyu Wu ◽  
Devin North ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Community Level ◽  
Clinical Testing ◽  
Rna Detection ◽  
Building Level

Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has demonstrated useful correlation with both coronavirus disease 2019 (COVID-19) cases and clinical testing positivity at the community level....

scholarly journals Wastewater SARS-CoV-2 Concentration and Loading Variability from Grab and 24-Hour Composite Samples

2020 ◽  
Author(s):  
Kyle Curtis ◽  
David Keeling ◽  
Kathleen Yetka ◽  
Allison Larson ◽  
Raul Gonzalez
Keyword(s):  
Mean Deviation ◽  
Clinical Testing ◽  
Public Health Response ◽  
Composite Sampling ◽  
Catchment Population ◽  
Sampling Schemes ◽  
Grab Sample ◽  
Health Response ◽  
Spread Of Infection ◽  
Composite Samples

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a significant, coordinated public health response. Assessing case density and spread of infection is critical and relies largely on clinical testing data. However, clinical testing suffers from known limitations, including test availability and a bias towards enumerating only symptomatic individuals. Wastewater-based epidemiology (WBE) has gained widespread support as a potential complement to clinical testing for assessing COVID-19 infections at the community scale. The efficacy of WBE hinges on the ability to accurately characterize SARS-CoV-2 concentrations in wastewater. To date, a variety of sampling schemes have been used without consensus around the appropriateness of grab or composite sampling. Here we address a key WBE knowledge gap by examining the variability of SARS-CoV-2 concentrations in wastewater grab samples collected every 2 hours for 72 hours compared with corresponding 24-hour flow-weighted composite samples. Results show relatively low variability (mean for all assays = 741 copies 100 mL-1, standard deviation = 508 copies 100 mL-1) for grab sample concentrations, and good agreement between most grab samples and their respective composite (mean deviation from composite = 159 copies 100 mL-1). When SARS-CoV-2 concentrations are used to calculate viral load, the discrepancy between grabs (log10 difference = 12.0) or a grab and its associated composite (log10 difference = 11.8) are amplified. A similar effect is seen when estimating carrier prevalence in a catchment population with median estimates based on grabs ranging 62-1853 carriers. Findings suggest that grab samples may be sufficient to characterize SARS-CoV-2 concentrations, but additional calculations using these data may be sensitive to grab sample variability and warrant the use of flow-weighted composite sampling. These data inform future WBE work by helping determine the most appropriate sampling scheme and facilitate sharing of datasets between studies via consistent methodology.

scholarly journals Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

2018 ◽  
Vol 56 (12) ◽  
Author(s):  
Kristine M. Wylie ◽  
Todd N. Wylie ◽  
Richard Buller ◽  
Brandi Herter ◽  
Maria T. Cannella ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antiviral Drug ◽  
Virus Detection ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Clinical Testing ◽  
Taxonomic Assignment ◽  
Sequence Capture ◽  
Antiviral Drug Resistance ◽  
Targeted Sequence Capture

ABSTRACTMetagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.

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