scholarly journals Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France

2021 ◽  
Author(s):  
Lisandru Capai ◽  
Géraldine Piorkowski ◽  
Oscar Maestrini ◽  
François Casabianca ◽  
Shirley Masse ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Enteric Viruses ◽  
Porcine Kobuvirus ◽  
P Value ◽  
Local Circulation ◽  
Rna Detection ◽  
Detection Rates ◽  
Consensus Sequences ◽  
Porcine Astrovirus ◽  
Pig Farms

AbstractMany enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT–qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7–65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5–48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8–10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e–13 for PAstV-1; 2.4e–12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e–6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were obtained This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.ImportanceThis study provides important information in the comprehension of the epidemiology of different viruses circulating in swine farms. We have shown the great diversity of viruses that could be present in extensive farms. Moreover, to our knowledge, this is the first detection of these different viruses in France. So far, this study has to be considered as a first step in the study of enteric viruses in Corsican pig farms.

scholarly journals Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0260161
Author(s):  
Lisandru Capai ◽  
Géraldine Piorkowski ◽  
Oscar Maestrini ◽  
François Casabianca ◽  
Shirley Masse ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Enteric Viruses ◽  
Porcine Kobuvirus ◽  
P Value ◽  
Local Circulation ◽  
Rna Detection ◽  
Detection Rates ◽  
Consensus Sequences ◽  
Porcine Astrovirus ◽  
Pig Farms

Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT–qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7–65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5–48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8–10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e–13 for PAstV-1; 2.4e–12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e–6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were detected. This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.

scholarly journals Diagnostic yield and appropriate indication of upper endoscopy in Jordanian children

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Eyad Altamimi ◽  
Yousef Odeh ◽  
Tuka Al-quraan ◽  
Elmi Mohamed ◽  
Naif Rawabdeh
Keyword(s):  
Abdominal Pain ◽  
Diagnostic Yield ◽  
Failure To Thrive ◽  
University Hospital ◽  
P Value ◽  
Upper Endoscopy ◽  
Detection Rates ◽  
Common Indication ◽  
Histopathological Findings ◽  
Endoscopic Findings

Abstract Background Upper endoscopy is an essential tool for diagnosing pediatric gastrointestinal issues. This study aimed to assess the indications, diagnostic yields, concordance between histopathological and endoscopic findings and suitability of upper endoscopies performed at a tertiary university hospital in Jordan. Methods Hospital records of children who underwent upper endoscopy were retrospectively reviewed. Demographics, endoscopic details (e.g., indications, findings and any complications), and histopathological findings were collected. The relationship between endoscopic findings and histopathological abnormalities was reported. Results The study included 778 patients (age, 92.5 ± 54.5 months; 380 girls, 48.8%). The most common age group was children younger than 60 months (273 patients, 34.3%). The most common indication for endoscopy was abdominal pain, followed by vomiting and failure to thrive or weight loss. Normal upper endoscopy was reported in 411 patients (52.8%). Age below 60 months, abdominal pain, dysphagia/odynophagia, and heartburn were predictive of abnormal endoscopy in multivariate analysis with p-value 0.000, 0.048, 0.001 and 0.01 respectively. Abnormal endoscopy showed 67.3% sensitivity and 69.9% specificity to predict histopathological abnormalities. Of those performed, 13.6% endoscopies were described as inappropriate indication. The suitability of the procedure was a sensitive predictor for abnormal endoscopic and histopathological findings. Conclusions Abdominal pain is the most common indication for upper endoscopy in our population. It is associated with a higher chance of abnormal endoscopy. Concordance between endoscopic and histopathological findings is not high. Normal endoscopic findings shouldn`t discourage the endoscopist from obtaining tissue biopsies. Considering more biopsies may improve pathological detection rates. Compliance with established endoscopy guidelines may reduce unnecessary procedures.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

scholarly journals Effect of multiple freeze-thaw cycles on detection of anti-SARS-CoV-2 IgG antibodies

2021 ◽  
Author(s):  
Farah M. Shurrab ◽  
Duaa W. Al-Sadeq ◽  
Fathima Amanullah ◽  
Salma N. Younes ◽  
Hadeel Al-Jighefee ◽  
...  
Keyword(s):  
Random Effect ◽  
Elisa Test ◽  
Antibody Detection ◽  
P Value ◽  
Elisa Assay ◽  
Igg Antibodies ◽  
Rna Detection ◽  
Freeze Thaw ◽  
Significant Difference ◽  
Number Of Cycles

AbstractSeveral studies have investigated the effect of repeated freeze-thaw (F/T) cycles on RNA detection for SARS-CoV-2. However, no data is available regarding the effect of repeated F/T cycles on SARS-CoV-2 antibody detection in serum. We investigated the effect of multiple F/T cycles on anti-SARS-CoV-2 IgG detection using an ELISA test targeting the nucleocapsid antibodies. Ten positive and one negative SARS-CoV-2 IgG sera from 11 participants, in replicates of five were subjected to a total of 16 F/T cycles and stored at 4°C until tested by ELISA. Statistical analysis was done to test for F/T cycle effect. Non-of the 10 positive sera turned into negative after 16 F/T cycles. There was no significant difference in the OD average reading between the first and last F/T cycles, except for one serum with a minimal decline in the OD. The random-effect linear regression of log (OD) on the number of cycles showed no significant trend with a slope consistent with zero (B=-0.0001; 95% CI −0.0008; 0.0006; p-value=0.781). These results suggest that multiple F/T cycles had no effect on the ability of the ELISA assay to detect the SARS-CoV-2 IgG antibodies.

Digital Droplet PCR (ddPCR) for Detection and Quantitation of Hepatitis Delt Virus

2021 ◽  
Author(s):  
Ling Xu ◽  
Xiangying Zhang ◽  
Yaling Cao ◽  
Zihao Fan ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Liver Failure ◽  
Lower Limit ◽  
Limit Of Detection ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Rna Detection ◽  
Detection Rates ◽  
Digital Droplet Pcr ◽  
Droplet Pcr ◽  
Hdv Infection

Abstract Background & Aims The prevalence of hepatitis delt virus (HDV) far exceeds our expected level, there remains a lack of reliable quantitative assays for HDV RNA detection. We sought to develop a new method based on digital droplet PCR (ddPCR) for HDV RNA quantitative detection. Methods With plasmid (pMD19T) containing HDV full-genome, we determined the method for ddPCR-based HDV RNA quantification. To compare various assays for HDV detection, 30 cases diagnosed hepatitis D and 14 controls were examined by ELISA, RT-PCR and ddPCR. 728 HBV-related patients including 182 chronic hepatitis B (CHB), 182 liver cirrhosis (LC), 182 hepatocellular carcinoma (HCC) and 182 liver failure (LF) were screened for HDV infection. Results The limit of detection of ddPCR for HDV is significantly low, which lower limit of detection (LLoD) and lower limit of quantitation (LLoQ) to be 5.51 copies/reaction (95% CI: 1.15–6.4*105) and 0.18 copies/reaction (95% CI: 0.0012151- 0.76436), respectively. Among the 44 samples, ELISA detected 30 cases positive for anti-HDV, ddPCR reported 24 samples and RT-PCR reported 10 samples positive for HDV RNA. Moreover, the positive rates of anti-HDV IgG were 1.1%, 3.3%, 2.7% and 7.1% in patients with CHB, LC, HCC, and LF; the detection rates of RT-PCR in HDV RNA were 0%, 16.67%, 15.4% and 20%, however, the detection rates of ddPCR were 0%, 33.33%, 30.77% and 60%. Conclusion We establish a high sensitivity and high specificity quantitative HDV RNA detection method based on ddPCR compared to RT-PCR. HBV-related end-stage liver disease, especially liver failure, are associated with a remarkably high rate of HDV infection.

scholarly journals Difference in the Mortality Between Weekend and Non-Weekend Coronary Artery Disease Admissions

2017 ◽  
Vol 02 (01) ◽  
pp. 036-041
Author(s):  
M. Sandeep ◽  
K. Satish
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Mortality Rate ◽  
Hospital Mortality ◽  
Risk Score ◽  
Wide Spectrum ◽  
P Value ◽  
Coronary Artery Diseases ◽  
Coronary Syndrome ◽  
Artery Disease

AbstractBackground: Acute coronary syndrome requires urgent diagnostic and therapeutic procedures, which may not be uniformly available throughout the week. So, we sought to examine the effects of admission on clinical outcomes in patients with wide spectrum coronary artery diseases.Methods: A retrospective analysis of ICCU Inpatient sample database of 17 months from 2015 to 2016 used to compare differences in in-hospital mortality between patients admitted on a non-weekday versus weekend for wide spectrum ACS which include STEMI, NSTEMI and unstable angina and patients with cardiogenic shock. Out of these 75% had higher TIMI risk score (5-7).Results: Total 2700 patients with ACS were included in the present study with wide spectrum coronary artery diseases. Out of that 20 % (n=541) were admitted in weekends and 79.9% (n=2159) were admitted in non-weekends. Total 804 females admitted on non-weekend had a mean age of 61.05±12 years and 162 females admitted on weekend had mean age 58.5±13.3 years (p value=0.025). Out of 2159 admitted on non-weekend, 1355 were males with mean age of 57.65±15.55 years and 379 were males admitted on weekend out of 541 patients with mean age of 56.85±13.1 years (p value =0.314). In-hospital mortality rate of these patients admitted on non-weekends was 9.4% (n=204) and those admitted on weekends was 5.9% (n=32) with statistically significant difference (95% CI; p= 0.003). The mortality rate of ACS without STEMI in non-weekend group was 8.6% (n=170) which was statistically significant (p = 0.006) with mortality of weekend group 5.3% (n=26).Conclusion: Our study shows that there is no added mortality in patients with coronary artery disease on weekend days compared with non-weekend days. As the patients admitted during non-weekend were elder and sicker than the weekend admissions (having the high risk score), the in-hospital mortality is higher on non-weekends. Efforts to improve health care system should ensure comparable outcomes for patients irrespective of time of hospital admission.

scholarly journals Virtual embryoscope for detection of structural abnormalities in first trimester pregnancy

2017 ◽  
Vol 6 (5) ◽  
pp. 1924
Author(s):  
Sumesh Choudhary ◽  
Vineet Mishra ◽  
Rohina Aggarwal
Keyword(s):  
First Trimester ◽  
3D Ultrasound ◽  
P Value ◽  
Detection Rates ◽  
Significant Difference ◽  
Structural Abnormalities ◽  
Innovative Tool ◽  
2D Ultrasound ◽  
Additional Value ◽  
A Prospective Study

Background: To determine whether there is an additional value of virtual embryoscopy with 3Dimensional (3D) ultrasound above (2D) ultrasound regarding detection rates of structural abnormalities in first trimester pregnancy.Methods: This was a prospective study consisting of 52 pregnant women with gestational age ranging from 6 to 12 weeks. 2D and 3D ultrasound scan was performed using GE voluson E8 transvaginal probe. All scans were evaluated by ten gynecologists trained in USG. The observations were noted and compared for anatomical details and detection of structural defects.Results: It was found that images were seen well with 3D (virtual embryoscope). i.e. maximum count 19 in the table and there is statistically significant difference between 3D and 2D images with a p-value <0.01 at 95% confidence interval (CI).Conclusions: Virtual embryoscope is an innovative tool for evaluation of developing embryo and early foetal morphology. The advantages are the ability to reconstruct 3D images with the stored scanned volume and examine without having to rescan the patient.

scholarly journals SARS-CoV-2 Detection in Different Respiratory Sites: A Systematic Review and Meta-Analysis

2020 ◽  
Author(s):  
Abbas Mohammadi ◽  
Elmira Esmaeilzadeh ◽  
Yijia Li ◽  
Ronald J Bosch ◽  
Jonathan Li
Keyword(s):  
Systematic Review ◽  
Symptom Onset ◽  
Meta Analysis ◽  
Nasopharyngeal Swab ◽  
Inclusion Criteria ◽  
Rna Detection ◽  
Timely Initiation ◽  
Detection Rates ◽  
Diverse Range ◽  
Oropharyngeal Swab

Background: The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and the timely initiation of treatment for COVID-19. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty as to the optimal sampling strategy for COVID-19 diagnosis and monitoring. Methods: We performed a systematic review and meta-analysis of studies comparing respiratory sampling strategies for the detection of SARS-CoV-2 RNA. The inclusion criteria were studies that assessed at least two respiratory sampling sites (oropharyngeal swab, nasopharyngeal swab, and sputum) in participants with COVID-19. The percentage positive tests were compared between sampling modalities by constructing a Z-test assuming independence and using the standard errors obtained from the random effects meta-analysis. Findings: From 1039 total studies, we identified 11 studies that met our inclusion criteria, with SARS-CoV-2 testing results from a total of 3442 respiratory tract specimens. Compared to nasopharyngeal swab sampling, sputum testing resulted in significantly higher rates of SARS-CoV-2 RNA detection while oropharyngeal swab testing had lower rates of viral RNA detection. Earlier sampling after symptom onset was associated with improved detection rates, but the differences in SARS-CoV-2 RNA detection by sampling method was consistent regardless of the duration of symptoms. Interpretation: The results support sputum sampling as a primary method of COVID-19 diagnosis and monitoring, and highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis.

scholarly journals Detection of Enteric Viruses and Bacterial Indicators in a Sewage Treatment Center and Shallow Water Bay

2020 ◽  
Vol 17 (18) ◽  
pp. 6483
Author(s):  
Essam M. Janahi ◽  
Sakina Mustafa ◽  
Saba F. D. Parkar ◽  
Humood A. Naser ◽  
Zaki M. Eisa
Keyword(s):  
Public Health ◽  
Hepatitis A Virus ◽  
Treatment Plant ◽  
Enteric Viruses ◽  
Treated Wastewater ◽  
Treatment Center ◽  
High Concentration ◽  
Salmonella Spp ◽  
Detection Rates ◽  
E Coli

The incidence of enteric viruses in treated wastewater and their potential release into the environment or use for agriculture are very critical matters in public health. In our study, PCR (polymerase chain reaction) analysis of enteric viruses was performed on 59 samples of influents and effluents collected from Tubli wastewater treatment plant (Water Pollution Control Center (WPCC)) and Tubli Bay, where the effluents were discharged, in Kingdom of Bahrain during two sampling periods. Four clinically essential waterborne enteric viruses were examined: enterovirus (EV), hepatitis A virus (HAV), astroviruses (AV), and rotaviruses (RV) and compared to standard bacterial and bacteriophages indicators of fecal pollution. Detection rates of EV, AV, HAV, and RV in the influent samples were 100%, 75%, 12.5%, and 12.5%, respectively, while 50% of the effluent samples from Tubli WPCC contained only EV RNA. None of the tested enteric viruses could be detected in any of the samples collected directly from Tubli Bay. Effluent samples from Tubli plant did not show significant seasonal differences. Since detection of enteric viruses genome does not necessarily indicate infectivity, the infectivity of these viruses was evaluated through isolation and growth of indictor bacteria and bacteriophages. High concentration of fecal bacteriological indicators was detected in all effluents samples (100%): 3.20 × 103 cfu/mL for E. coli, 1.32 × 103 cfu/mL for Salmonella spp., and 1.92 × 103 cfu/mL for Shigella spp. E. coli and Salmonella specific bacteriophages were also detected in the effluent samples in high titers. The combined results of PCR and bacterial enumeration point to a probable public health risk via the use of these wastewaters in agriculture or their discharge into the sea. Continuous surveillance of viral and bacterial prevalence and their resistance to sewage disinfection procedures could contribute to a better control of risks associated with the recycling of effluent wastewater and its release into the environment.

scholarly journals Comparison of the detection rates for retinopathy of prematurity (ROP) of the 2013 Philippine Academy of Ophthalmology (PAO) Revised Philippine Guidelines and the 2005 PAO-Philippine Pediatric Society (PPS) Guidelines for ROP screening in the Philippine General Hospital: a 5-year review

2020 ◽  
Vol 5 (1) ◽  
pp. e000448
Author(s):  
Jose Antonio Tan Paulino ◽  
Alvina Pauline Dy Santiago ◽  
Darby Espiritu Santiago
Keyword(s):  
General Hospital ◽  
Retinopathy Of Prematurity ◽  
Hyaline Membrane Disease ◽  
P Value ◽  
Cross Sectional ◽  
Detection Rates ◽  
Screening Guidelines ◽  
Pediatric Society ◽  
Department Of Ophthalmology ◽  
Rop Screening

ObjectivesCompare the detection rates of the 2013 Philippine Academy of Ophthalmology (PAO) guidelines for retinopathy of prematurity (ROP) screening and the 2005 PAO-Philippine Pediatric Society guidelines in identifying infants who develop ROP in the 5-year study period in the Philippine General Hospital (PGH). Secondary objectives include determination of ROP prevalence; correlation of gestational age (GA), birth weight (BW) and other risk factors to ROP; and identification of the most common intervention.Methods and analysisRetrospective cross-sectional study of ROP records between 1 December 2013 and 30 November 2018 from the Medical Retina Service of the Department of Ophthalmology and Visual Sciences of the institution was studied. Variables with p value <0.05 were considered significant. STATA V.14 was used for all analysis.ResultsOnly 851 of 898 infants screened for ROP were included in the study. Of these 698 would have been screened based on 2005 guidelines. All 118 infants with ROP were identified by both guidelines. Detection rate was higher using the 2005 than the 2013 guidelines (16.9% vs 13.3%, p value=0.0496). ROP prevalence was 9.7%. Among those with ROP, 70% have at least one identified risk factor, topped by sepsis, pneumonia, hyaline membrane disease, blood transfusion and oxygen supplementation. Only 8% required intervention consisting of laser, anti-vascular endothelial growth factor injection, surgery or in combination.ConclusionIn PGH, no infants with ROP were missed using the 2005 recommendations. There was no added benefit of increasing threshold for BW and GA as recommended by the 2013 PAO guidelines. Screening guidelines should, however, be tailored to institutional needs, requirements and experience.

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