Cross Sectional Study for Evaluation of Rapid Test and RT-PCR in Detection of BRV in Fecal Samples of Diarrhetic Calves in Egypt

Abstract Background: The COVID-19 pandemic is affecting people worldwide. In Spain, the first wave was especially severe. Objectives: This study aimed to identify sources and levels of distress among Spanish primary care physicians (PCPs) during the first wave of the pandemic (April 2020). Methods: A cross-sectional study was conducted using a survey that included sociodemographic data, a description of working conditions related to distress [such as gaps in training in protective measures, cleaning, and hygiene procedures in work setting, unavailability of personal protective equipments (PPEs) and COVID-19 RT-PCR test, and lack of staff due to be infected] and a validated scale, the ‘Self-applied Acute Stress Scale’ (EASE). The survey was answered by a non-probability sampling of PCPs working in family healthcare centres from different regions of Spain. Analysis of variance and multivariate linear regression analysis were performed. Results: In all, out of 518 PCP participants, 123 (23.7%) obtained high psychological distress scores. Only half of them had received information about the appropriate use of PPE. PCP characteristics associated with higher levels of distress include female gender [1.69; 95% confidence interval (CI) 0.54, 2.84]; lack of training in protective measures (1.96; 95% CI 0.94, 2.99); unavailable COVID-19 RT-PCR for health care workers after quarantine or COVID-19 treatment (−0.77 (−1.52, −0.02). Reinforcing disinfection of the work environment (P < 0.05), availability of PPEs (P < 0.05), and no healthcare professional was infected (P < 0.05) were related to the lowest distress score. Conclusions: A better understanding of the sources of distress among PCPs could prevent its effect on future outbreaks.

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Prevalence of Cryptosporidiosis in Crossbred Calves in Two Selected Areas of Bangladesh

Bangladesh Journal of Veterinary Medicine ◽

10.3329/bjvm.v12i2.21288 ◽

2014 ◽

Vol 12 (2) ◽

pp. 185-190

Author(s):

A Khair ◽

MM Alam ◽

AKMA Rahman ◽

M Shahiduzzaman ◽

MS Parvez ◽

...

Keyword(s):

Rapid Detection ◽

Clinical Status ◽

Cross Sectional Study ◽

Positive Control ◽

Age Group ◽

Sectional Study ◽

Chain Reaction ◽

Cross Sectional ◽

Fecal Samples ◽

Polymerase Chain

A cross-sectional study was conducted to determine the prevalence of bovine cryptosporidiosis using 110 fecal samples of crossbred diarrhoeic calves from two different areas (Muktagacha, Mymensingh and Shajadpur, Sirajgonj) in Bangladesh during April 2012 to September 2014. The fecal samples were screened by rapid detection kit and confirmed by Modified Ziehl- Neelsen staining, and polymerase chain reaction (PCR). The positive samples along with standard positive control yielded 1325bp band on PCR. The overall prevalence of cryptosporidiosis in crossbred calves was 28.18% (31/110) by rapid detection kit. The higher prevalence of cryptosporidiosis was found in the calves from Shajadpur (29.76%) than the calves from Muktagacha (23.08%).The prevalence of cryptosporidiosis was significantly (p<0.001) higher in calves between 1-2 months (70%) age group than less than one month age group (24.49%). Cryptosporidiosis was not observed in calves over two months age. The prevalence of cryptosporidiosis was higher in males (34.75%) than females (24.64%) although not significant statistically. It is evident that the prevalence of cryptosporidiosis in bovine in these areas is under diagnosed and the clinical status of infection is potentially high.DOI: http://dx.doi.org/10.3329/bjvm.v12i2.21288 Bangl. J. Vet. Med. (2014). 12 (2): 185-190

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Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study

F1000Research ◽

10.12688/f1000research.29991.2 ◽

2021 ◽

Vol 10 ◽

pp. 123

Author(s):

Maysaa El Sayed Zaki ◽

Raghdaa Shrief ◽

Rasha H. Hassan

Keyword(s):

Stool Sample ◽

Acute Gastroenteritis ◽

Rna Extraction ◽

Winter Season ◽

Molecular Study ◽

Cross Sectional Study ◽

Sectional Study ◽

Rt Pcr ◽

Cross Sectional ◽

Presenting Symptoms

Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there are insufficient data about the presence of this virus among children with acute gastroenteritis. The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis by reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: A cross-sectional study enrolled 100 children patients with acute gastroenteritis from outpatient clinics with excluded bacterial pathogens and parasitic infestation. A stool sample was collected from each child for laboratory examination. Each stool sample was subjected to study by direct microscopic examination, study for rotavirus by enzyme-linked immunoassay (ELISA) and the remaining sample was subjected to RNA extraction and RT- PCR for sapovirus. Results: The most frequently detected virus was rotavirus by ELISA (25%). RT-PCR detected sapovirus in 7% of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt (42.9%). The main presenting symptoms were fever (71.4%) and vomiting (57.1%). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in 5 patients (71.4%, P=0.01). There was an insignificant difference between symptoms of gastroenteritis in children with sapovirus and children with gastroenteritis without sapovirus as regards vomiting (P=0.7), fever (P=0.46), and abdominal pain (P=0.69). Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.

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Immunological and molecular detection of rotavirus genotype in calves with gastroenteritis in Diyala-Iraq

10.53346/wjbpr.2021.1.1.0013 ◽

2021 ◽

Vol 1 (1) ◽

pp. 001-013

Author(s):

Ammar Talib Nasser ◽

Abdulrazak Shafiq Hasan ◽

Amer Khazaal Saleh ◽

Mohammad Kassem Saleh

Keyword(s):

Molecular Detection ◽

Cross Sectional Study ◽

Sectional Study ◽

Rt Pcr ◽

Cross Sectional ◽

Reverse Transcription Pcr ◽

Group A ◽

Stool Antigen ◽

Stool Samples ◽

Age Range

Aim: To explore the prevalence of rotavirus infection along with the molecular detection and genotyping of group A rotavirus (RVA) among bovine calves up to 5 months old in Diyala province-Iraq. Methods: This is a cross sectional study conducted in Diyala province-Iraq during the period of 2019-2020. One hundred bovine calves with age range of 1-5 months were included in the study. All were suffering acute gastroenteritis. Serum anti-rotavirus IgM and IgG plus fecal rotavirus Ag were tested for using ELISA techniques. Stool samples positive for rotavirus Ag were submitted for reverse transcription PCR (RT-PCR) for G and P genes, followed by sequencing and genotyping thereafter. Statistical analysis was done using SPSS version 25 and P values ≤ 0.05 were considered significant. Results: The positivity rate of anti-rotavirus IgM was 80% (P = 0.0001), and that of anti-rotavirus IgG was 79% (P = 0.0001). The rotavirus stool antigen was detected in 68% of calves (P = 0.01). A total of 45 stool samples which were positive for rotavirus Ag were submitted for RT-PCR; 13 (28.9%) were positive and 32 (71.1%) were negative (P = 0.084). 10 PCR positive samples were used for sequencing and genotyping and indicated that all investigated strains belonged to G1P[8] genotype. Conclusion: The current strains analyzed belonged to the G1P[8] RVA genotypes, affirming that employment of VP7 gene polymorphism accurately yielded uniform phylogenetic distances amongst investigated rotavirus strains and that there were no noticeable assortment events between human and animal rotavirus strains in Diyala province.

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Evaluation of nine serological rapid tests for the detection of SARS-CoV-2

Revista Panamericana de Salud Pública ◽

10.26633/rpsp.2020.149 ◽

2020 ◽

Vol 44 ◽

pp. 1

Author(s):

Marcela Mercado ◽

Jeadran Malagón-Rojas ◽

Gabriela Delgado ◽

Vivian Vanesa Rubio ◽

Lida Muñoz Galindo ◽

...

Keyword(s):

Study Groups ◽

Cross Sectional Study ◽

Igg Antibodies ◽

Sectional Study ◽

Rt Pcr ◽

Serum Samples ◽

Serological Tests ◽

Cross Sectional ◽

Diagnostic Aid ◽

Rapid Tests

Objective. To evaluate the operative capacity of nine serological rapid tests to detect the IgM/IgG antibodies response in serum from patients with SARS-CoV-2 in different clinical stages. Methods. A cross-sectional study of serological rapid tests was designed to compare the performance of the evaluated immunochromatographic tests for the diagnosis of SARS-CoV-2. A total of 293 samples was used, including negatives, asymptomatic, and symptomatic serum samples. Results. The sensitivity of the evaluated tests was low and moderate in the groups of asymptomatic serum samples and the group of serums coming from patients with less than 11 days since the onset of the symptoms. The specificity for the anti-SARS-CoV-2 antibodies tests ranged between 86.5%-99% for IgM and 86.5%-99.5% for IgG. The sensitivity and the likelihood ratio were different according to the study groups. The usefulness of these tests is restricted to symptomatic patients and their sensitivity is greater than 85% after 11 days from the appearance of symptoms. Conclusions. Serological tests are not an adequate strategy for the identification of asymptomatic and pre-symptomatic patients. Serological rapid tests for the detection of specific anti-SARS-CoV-2 antibodies can be used as a diagnostic aid, but diagnosis must be confirmed by RT-PCR. Rapid tests should be reserved for patients with symptoms lasting more than 11 days.

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Comparison between CT and RT-PCR in a cohort of symptomatic patients with suspected COVID-19 pneumonia during the outbreak peak in Italy

10.21203/rs.3.rs-26275/v1 ◽

2020 ◽

Author(s):

Giulia Besutti ◽

Paolo Giorgi Rossi ◽

Valentina Iotti ◽

Lucia Spaggiari ◽

Riccardo Bonacini ◽

...

Keyword(s):

Cross Sectional Study ◽

Ground Glass ◽

Reference Standard ◽

Sectional Study ◽

Rt Pcr ◽

Cross Sectional ◽

Oxygen Saturation Level ◽

Blood Tests ◽

Cell Counts ◽

Italian Cohort

Abstract Objective: To assess sensitivity and specificity of CT vs RT-PCR for the diagnosis of COVID-19 pneumonia in a prospective Italian cohort of symptomatic patients during the outbreak peak.Methods: In this cross-sectional study we included all consecutive patients who presented to the ER between March 13th and 23rd for suspected COVID-19 and underwent both CT and RT-PCR within 3 days. Using a structured report, radiologists prospectively classified CTs in highly suggestive, suggestive, and non-suggestive of COVID-19 pneumonia. Ground-glass, consolidation, and visual extension of parenchymal changes were collected. Three different RT-PCR-based reference standard definitions were used. Oxygen saturation level, CRP, LDH, and blood cell counts were collected and compared between CT/RT-PCR classes.Results: The study included 696 patients (41.4% women; age 59±15.8 years): 423/454 (93%) patients with highly suggestive CT, 97/127 (76%) with suggestive CT, and 31/115 (27%) with non-suggestive CT had positive RT-PCR. CT sensitivity ranged from 73% to 77% and from 90% to 94% for high and low positivity threshold, respectively. Specificity ranged from 79% to 84% for high positivity threshold and was about 58% for low positivity threshold. PPV remained ≥90% in all cases. Ground-glass was more frequent in patients with positive RT-PCR in all CT classes. Blood tests were significantly associated with RT-PCR and CT classes. Leukocytes, lymphocytes, neutrophils, and platelets decreased, CRP and LDH increased from non-suggestive to suggestive CT classes.Conclusions: During the outbreak peak, CT presented high PPV and may be considered a good reference to recognize COVID-19 patients while waiting for RT-PCR confirmation.

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Sero-prevalence of anti-SARS-CoV-2 Antibodies in Addis Ababa, Ethiopia

10.1101/2020.10.13.337287 ◽

2020 ◽

Author(s):

Berhanu Nega Alemu ◽

Adamu Addissie ◽

Gemechis Mamo ◽

Negussie Deyessa ◽

Tamrat Abebe ◽

...

Keyword(s):

Serological Test ◽

Addis Ababa ◽

Rapid Test ◽

Cross Sectional Study ◽

Rt Pcr ◽

Serological Tests ◽

Cross Sectional ◽

History Of ◽

Community Transmission ◽

Pcr Test

AbstractBackgroundAnti-SARS-CoV-2 antibody tests are being increasingly used for sero-epidemiological purposes to provide better understanding of the extent of the infection in the community, and monitoring the progression of the COVID-19 epidemic. We conducted sero-prevalence study to estimate prior infection with with SARS-CoV-2 in Addis Ababa.MethodsA cross-sectional study was done from April 23 to 28, 2020 among 301 randomly selected residents of Addis Ababa; with no known history of contact with confirmed COVID-19 person. Interviews on socio demographic and behavioural risk factor followed by serological tests were performed for SARS-CoV-2 IgM, and IgG antibodies, using COVID-19 IgG/IgM Rapid Test Cassette. The test has sensitivity of 87·9% and specificity of 100% for lgM; and a sensitivity of 97·2% and specificity of 100% for IgG. RT-PCR test was also done on combined nasopharyngeal and oropharengeal swabs as an important public health consideration.FindingsThe unadjusted antibody-based crude SARS-CoV-2 prevalence was 7·6% and the adjusted true SARS-CoV-2 prevalence was estimated at 8·8% (95% CI 5·5%-11·6%) for the study population. Higher sero-prevalence were observed for males (9.0%), age below 50 years (8.2%), students and unemployed (15.6%), those with primary education (12.1%), smokers (7.8%), alcohol consumers (8.6%), chatt-chewers (13.6%) and shish smokers (18.8%). Seroprevalence was not significantly associated neither with socio-demographic not behavioral characteristics. According to the findings, possibly more individuals had been infected in Addis Ababa than what was being detected and reported by RT-PCR test suggestive of community transmission. The use of serological test for epidemiological estimation of the extent of SARS-CoV-2 epidemic gives a more precise estimate of magnitude which would be used for further monitoring and surveillance of the magnitude of the SARS CoV-2 infection.

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Association between RT-PCR Ct Values and COVID-19 New Daily Cases: A Multicenter Cross-Sectional Study

10.1101/2020.12.07.20245233 ◽

2020 ◽

Author(s):

Abdulkarim Abdulrahman ◽

Saad Mallah ◽

Abdulla Ismael AlAwadhi ◽

Simone Perna ◽

Essam Janahi ◽

...

Keyword(s):

Population Studies ◽

Population Level ◽

Female Gender ◽

Cross Sectional Study ◽

Newly Diagnosed ◽

Sectional Study ◽

Rt Pcr ◽

Cross Sectional ◽

Viral Loads ◽

Epidemiological Changes

Introduction: Proactive prediction of the epidemiologic dynamics of viral diseases and outbreaks of the likes of COVID-19 has remained a difficult pursuit for scientists, public health researchers, and policymakers. It is unclear whether RT-PCR Cycle Threshold (Ct) values of COVID-19 (or any other virus) as indicator of viral load, could represent a possible predictor for underlying epidemiological changes on a population level. Objectives: To investigate whether population-wide changes in SARS-CoV-2 RT-PCR Ct values over time are associated with the daily fraction of positive COVID-19 tests. In addition, this study analyses the factors that could influence the RT-PCR Ct values. Method: A retrospective cross-sectional study was conducted on 63,879 patients from May 4, 2020 to September 30, 2020, in all COVID-19 facilities in the Kingdom of Bahrain. Data collected included number of tests and newly diagnosed cases, as well as Ct values, age, gender nationality, and symptomatic status. Results: Ct values were found to be negatively and very weakly correlated with the fraction of daily positive cases in the population r = -0.06 (CI95%: -0.06; -0.05; p=0.001). The R-squared for the regression model (adjusting for age and number of daily tests) showed an accuracy of 45.3%. Ct Values showed an association with nationality (p=0.012). After the stratification, the association between Ct values and the fraction of daily positive cases was only maintained for the female gender and Bahraini-nationality. Symptomatic presentation was significantly associated with lower Ct values (higher viral loads). Ct values do not show any correlation with age (p=0.333) or gender (p=0.522). Conclusion: We report one of the first and largest studies to investigate the epidemiological associations of Ct values with COVID-19. Ct values offer a potentially simple and widely accessible tool to predict and model epidemiological dynamics on a population level. More population studies and predictive models from global cohorts are necessary.

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Detection of blaVIM and blaIMP Carbapenemase-Producing Pseudomonas aeruginosa from Clinical Samples in Iran

International Journal of Medical Laboratory ◽

10.18502/ijml.v8i3.7324 ◽

2021 ◽

Author(s):

Mohammad Reza Zolfaghari

Keyword(s):

Pseudomonas Aeruginosa ◽

Cross Sectional Study ◽

Clinical Samples ◽

Sectional Study ◽

Rt Pcr ◽

Chain Reaction ◽

Cross Sectional ◽

High Prevalence ◽

Polymerase Chain ◽

High Level

Background and Aims: The prevalence of carbapenemase-producing Pseudomonas aeruginosa (P. aeruginosa) strains has been recently reported worldwide. Therefore, accurate and rapid detection of carbapenemase-producing isolates is essential. So, this study aimed to detect blaVIM and blaIMP carbapenemase-producing strains using the modified Hodge test (MHT) and reverse transcription-polymerase chain reaction (RT-PCR). Materials and Methods: In this cross-sectional study, P. aeruginosa strains were collected from clinical samples (blood, urine, wound, and other liquids body) in Firoozgar and Shahid Motahari Hospitals in Tehran and Velayat Hospital in Rasht Province, from May to December 2018. After identifying the isolates using the standard microbial tests, carbapenemase-producing strains were isolated by the modified hodge test. After that, the detection of blaVIM and blaIMP genes was performed by RT-PCR technique. Results: One hundred P. aeruginosa were isolated from different clinical samples. Among these, 74 (74%) isolates were considered as carbapenemase positive using MHT. The frequencies of blaVIM and blaIMP genes were obtained as 83% and 11%, respectively. Conclusions: The results of this study indicate a high level of resistance to most of the antibiotics tested and a high prevalence of blaVIM gene in P. aeruginosa strains.

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Headache associated with COVID-19: Frequency, characteristics and association with anosmia and ageusia

Cephalalgia ◽

10.1177/0333102420966770 ◽

2020 ◽

Vol 40 (13) ◽

pp. 1443-1451 ◽

Cited By ~ 2

Author(s):

Pedro Augusto Sampaio Rocha-Filho ◽

João Eudes Magalhães

Keyword(s):

Polymerase Chain Reaction ◽

Cross Sectional Study ◽

Sectional Study ◽

Rt Pcr ◽

Chain Reaction ◽

Chi Square ◽

Cross Sectional ◽

Severe Intensity ◽

Chi Square Test ◽

Polymerase Chain

Objectives To assess the frequency and characteristics of headache in patients with COVID-19 and whether there is an association between headache and anosmia and ageusia. Methods This was a cross-sectional study. Consecutive patients admitted to hospital with COVID-19, confirmed by reverse transcription polymerase chain reaction (RT-PCR) technique, were assessed by neurologists. Results Seventy-three patients were included in the study, 63% were male; the median age was 58 years (IQR: 47–66). Forty-seven patients (64.4%) reported headaches, which had most frequently begun on the first day of symptoms, were bilateral (94%), presenting severe intensity (53%) and a migraine phenotype (51%). Twelve patients (16.4%) presented with headache triggered by coughing. Eleven (15%) patients reported a continuous headache. Twenty-eight patients (38.4%) presented with anosmia and 29 (39.7%) with ageusia. Patients who reported hyposmia/anosmia and/or hypogeusia/ageusia experienced headache more frequently than those without these symptoms (OR: 5.39; 95% CI:1.66–17.45; logistic regression). Patients with anosmia and ageusia presented headache associated with phonophobia more often compared to those with headache without these complaints (Chi-square test; p < 0.05). Headache associated with COVID-19 presented a migraine phenotype more frequently in those experiencing previous migraine ( p < 0.05). Conclusion Headaches associated with COVID-19 are frequent, are generally severe, diffuse, present a migraine phenotype and are associated with anosmia and ageusia.

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