scholarly journals Epidemiology and molecular diagnosis of canine coronavirus in Egypt: evaluation of different tests used for its diagnosis

2020 ◽  
Vol 23 (4) ◽  
pp. 467-477
Author(s):  
R. Awad ◽  
S. Ali Hassan ◽  
A. Attallah ◽  
W. Khalil

This work aimed to study the epidemiology and molecular detection of existing canine coronavirus (CCoV) strain circulating in Egypt. A total number of 86 dogs with clinical signs suggestive for CCoV infection was subjected to clinical examination and quick immunochromatography (IC) on faecal swabs to detect viral antigen. To identify CCoV viral RNA and S protein gene in blood and faeces, conventional PCR and quantitative RT-PCR were used. All examined dogs showed clinical signs suggestive of CCoV infection. Only 32 out of 86 dogs were positive for IC. Of all samples, 36 showed positive results in PCR and the amplification products from these 36 samples were confirmed as CCoV-S protein partial gene by the analysis of nucleotide sequence. However, the qRT-PCR analysis detected 45 positive samples e.g. more than those of IC or conventional polymerase chain reaction. Statistical evaluation of IC and conventional PCR to the results of qRT-PCR performance showed sensitivity, specificity, accuracy, positive and negative predictive values of 71%, 100%, 84.9%, 100%, 75.9% for IC and 80%, 100%, 89.5%, 100%, 82% for PCR, respectively. Sex and age had no effects on IC and PCR results. The prevalence of CCoV infection among the population of this study was 52.3%. Sequence analysis results proved that CCoV strain 59/08 was the strain, circulating in Egypt among dog populations. PCR products of the CCoV cDNA were closely identical to published CCoV-S partial gene. The NCBI Genbank accession number of sequence of the studied gene (CCoV-S partial gene) in this study was KY655745.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mitnala Sasikala ◽  
Yelamanchili Sadhana ◽  
Ketavarapu Vijayasarathy ◽  
Anand Gupta ◽  
Sarala Kumari Daram ◽  
...  

Abstract Background A considerable amount of evidence demonstrates the potential of saliva in the diagnosis of COVID-19. Our aim was to determine the sensitivity of saliva versus swabs collected by healthcare workers (HCWs) and patients themselves to assess whether saliva detection can be offered as a cost-effective, risk-free method of SARS-CoV-2 detection. Methods This study was conducted in a hospital involving outpatients and hospitalized patients. A total of 3018 outpatients were tested. Of these, 200 qRT-PCR-confirmed SARS-CoV-2-positive patients were recruited for further study. In addition, 101 SARS-CoV-2-positive hospitalized patients with symptoms were also enrolled in the study. From outpatients, HCWs collected nasopharyngeal swabs (NPS), saliva were obtained. From inpatients, HCWs collected swabs, patient-collected swabs, and saliva were obtained. qRT-PCR was performed to detect SARS-CoV-2 by TAQPATH assay to determine the sensitivity of saliva detection. Sensitivity, specificity and positive/negative predictive values (PPV, NPV) of detecting SARS-CoV-2 were calculated using MedCalc. Results Of 3018 outpatients (asymptomatic: 2683, symptomatic: 335) tested by qRT-PCR, 200 were positive (males: 140, females: 60; aged 37.9 ± 12.8 years; (81 asymptomatic, 119 symptomatic). Of these, saliva was positive in 128 (64%); 39 of 81 asymptomatic (47%),89 of 119 symptomatic patients (74.8%). Sensitivity of detection was 60.9% (55.4–66.3%, CI 95%), with a negative predictive value of 36%(32.9–39.2%, CI 95%).Among 101 hospitalized patients (males:65, females: 36; aged 53.48 ± 15.6 years), with HCW collected NPS as comparator, sensitivity of saliva was 56.1% (47.5–64.5, CI 95%), specificity 63.5%(50.4–75.3, CI95%) with PPV of 77.2% and NPV of 39.6% and that of self-swab was 52.3%(44–60.5%, CI95%), specificity 56.6% (42.3–70.2%, CI95%) with PPV 77.2% and NPV29.7%. Comparison of positivity with the onset of symptoms revealed highest detection in saliva on day 3 after onset of symptoms. Additionally, only saliva was positive in 13 (12.8%) hospitalized patients. Conclusion Saliva which is easier to collect than nasopharyngeal swab is a viable alternate to detect SARS-COV-2 in symptomatic patients in the early stage of onset of symptoms. Although saliva is currently not recommended for screening asymptomatic patients, optimization of collection and uniform timing of sampling might improve the sensitivity enabling its use as a screening tool at community level.


2016 ◽  
Vol 45 (2) ◽  
pp. 76
Author(s):  
Suprawita Sari ◽  
Supriatmo Supriatmo ◽  
S L Margaretha ◽  
S Nafianti ◽  
B Hasibuan ◽  
...  

Objective To evaluate the diagnostic accuracy and agreementbetween the 1980 and 1990 WHO criteria for determining the de-gree of dehydration in children with acute diarrhea.Methods This prospective study was conducted in two hospitalsfrom October 2002 to February 2003. Clinical signs of dehydrationall patients were recorded. The degree of dehydration based onthe 1980 and 1990 WHO criteria was determined and comparedwith fluid deficit measured by the difference of body weight on ad-mission and on discharge. Chi-square test and kappa value analy-ses were performed. Sensitivity, specificity, predictive values, andaccuracy of each WHO criteria were assessed. The prevalence ofdehydration was also determined.Results Sixty-five patients, comprising 40 boys and 25 girls, werestudied. There was a significant difference between the two WHOcriteria in differentiating between dehydration and non-dehydra-tion (P<0.05). Based on the 1980 WHO criteria the prevalence ofdehydration was 62.2%. Its sensitivity, specificity, and accuracy indiagnosing dehydration were 100.0%, 55.5%, and 86.2%, respec-tively. Based on the 1990 WHO criteria, the prevalence of dehy-dration was 60.0%. Its sensitivity, specificity, and accuracy in diag-nosing dehydration were 94.9%, 46.1%, and 75.4%, respectively.There was also a significant difference between both criteria indetermining severe dehydration (P<0.05). Based on the 1980 cri-teria, the prevalence of severe dehydration was 15.4%. Its sensi-tivity, specificity, and accuracy in diagnosing severe dehydrationwere 30.0%, 94.5%, and 84.6%, respectively. Based on the 1990criteria, these results were 40.0%, 94.5%, and 86.2%, respectively.The prevalence was 15.4%. Kappa value comparing the two WHOcriteria was 0.852 in diagnosing dehydration and 0.915 in diag-nosing severe dehydration. There was no significant differencebetween the two criteria in their sensitivity and specificity (P>0.05).Conclusion Both WHO criteria can be applied to determine de-hydration in patients with acute diarrhea, although we feel that the1990 criteria is simpler


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3888-3888
Author(s):  
Francesca R Mauro ◽  
Mara Riminucci ◽  
Davide Rossi ◽  
Francesca Paoloni ◽  
Luca Laurenti ◽  
...  

Abstract Abstract 3888 Chronic lymphocytic leukemia (CLL) is a heterogeneous leukemia with a very variable outcome. The occurrence of a second malignancy (SM) or of a disease transformation (DT) may complicate the course of the disease. An aggressive diffuse large B-cell lymphoma (DLBCL) and, less frequently, a Hodgkin's lymphoma (HL) are the most commonly observed forms of DT, defined as Richter's syndrome (RS). Since the presence of enlarged “bulky nodes”, as well as the observation of extra-nodal lesions, can lead both to the suspicion of a CLL progression and to the possibility of a DT or of a SM, a biopsy of the involved tissue is the only appropriate approach for a correct diagnosis. Positron emission tomography/computed tomography (PET/CT) is currently used for the initial staging and restaging of HL and DLBCL, as well as for the identification of other malignancies. In a previous report by Bruzzi et al. (JNM, 2006), PET/CT showed a high predictive value in demonstrating or excluding DT. The same finding has been observed in single case reports, where in patients with CLL a high 18F-FDG uptake was associated with the presence of a DLBCL. With the aim of discriminating the presence of a DT or a SM malignancy, between June 2008 and June 2012, a PET/CT exam followed by the biopsy of the involved tissue was performed in CLL patients from 4 Italian centers. Patients included in this study showed disease progression requiring treatment according to the 2008 revised IWCLL criteria and clinical signs suggestive of the presence of a more aggressive disease, such as rapidly enlarging or bulky lymph nodes (diameter ≥5 cm) and/or extra-nodal lesions associated with at least one additional sign including B systemic symptoms, increased serum lactate dehydrogenase (LDH), increased β2 microglobulin (B2M). The 18F-FDG uptake was correlated with the histologic findings and, for the purpose of this study, a maximum standardized uptake value (SUVmax) ≥5 was considered highly suggestive of a more aggressive disease. Data on 64 CLL patients (median age, 66 years, range, 35–85) were retrospectively analyzed. At the time of PET/CT, the median follow-up from CLL diagnosis was 73 months (range, 3– 227 months) and a Binet C stage was observed in 16 cases (25%). Twenty-three (36%) patients were treatment-naïve and 41 (64%) had been previously treated (median number of prior treatments, 2; range, 1–4), including 14 (22%) refractory cases. Systemic symptoms were recorded in 25% of cases, LDH was increased in 41% and B2M in 72%. The majority of patients (61%) were IGVH unmutated, 45% CD38 positive and 56% ZAP-70 positive. Bulky lymph nodes (diameter ≥5 cm) and/or marked splenomegaly (longitudinal diameter ≥17 cm) were observed in 30 cases (47%). Evidence of extra-nodal disease was recorded in 8 cases (12.5%): thyroid, 2 cases; uterine fundus, 1; gastric,1; bone, 1; nasopharynx, 1; skin infiltrates, 2. The biopsy confirmed a SLL/CLL diagnosis in 44 cases, a DT in 15 (DLBCL, 10; HL, 5) and SM in 5 (thyroid cancer + SLL/CLL, 2 cases; lymph node metastasis of carcynoid + SLL/CLL, 1; lymph-node metastasis of a squamous cancer, 1; lejomioma of the uterine fundus,1). Sites of abnormal 18F-FDG uptake having a SUVmax ≥5 were recorded in a total number of 30 cases, in 13/44 cases (30%) with a SLL/CLL histology, in 13/15 with DT (87%), including 9/10 (90%) cases of DLBCL and 4/5 (80%) HL. An abnormal uptake was recorded also in 4/5 patients with SM. Based on these results, for the diagnosis of a DT or SM, PET/CTPET/CT showed an overall sensitivity, specificity, positive and negative predictive values of 85% 70%, 57% and 91%, respectively, while for the diagnosis of a DT (DLBCL+HL) the sensitivity, specificity, positive and negative predictive values were 87%, 65%, 43% and 94%, respectively. The cases with a SLL/CLL histology having a SUVmax ≥5 were characterized by a higher Ki-67% expression (p=0.0001) suggesting a high rate of cell turnover. Our results show that a PET/CT performed in CLL patients at the time of disease progression can detect cases with a high likelihood of DT or SM, representing therefore a very helpful imaging technique in guiding the appropriate site that should be considered for biopsy. Disclosures: No relevant conflicts of interest to declare.


Author(s):  
Maria Fernanda F. de Lima e Costa ◽  
Roberto S. Rocha ◽  
Daniel Colley ◽  
Giovanni Gazzenelli ◽  
Naftale Katz

Sensitivity, specificity and positive predictive values of selected clinical signs and symptoms in the diagnosis of Schistosoma mansoni infection were evaluated in 403 individuals (69% of inhabitants over 1 year of age) in an endemic area in Brazil (Divino). Highest sensitivity (13%) was found for blood in stools. Specificity over 90% was found for blood in stools, palpable liver with normal consistency and palpable hardened liver at middle clavicular (MCL) or middle sternal lines (MSL). Hardened liver at MSL (83%) or MCL (75%), and blood in stools (78%) presented higher positive predictive values for S. mansoni infection, while palpable liver with normal consistency at MCL (45%) or MSL (48%) presented smaller values. Enlarged liver without specification of its consistency has been traditionally used as an indicator of the infection in areas where malaria or Kalazar are not endemic. Our results demonstrate that the probability that a person with blood in stools or hardened palpable liver is infected is higher than among those with palpable liver with normal consistency.


CoDAS ◽  
2015 ◽  
Vol 27 (2) ◽  
pp. 186-192 ◽  
Author(s):  
Lenice de Fatima da Silva-Munhoz ◽  
Karina Elena Bernardis Bühler ◽  
Suelly Cecilia Olivan Limongi

Purpose: To verify the accuracy of clinical evaluation compared with videofluoroscopic swallowing studies in the detection of isolated laryngeal penetration and laryngeal aspiration in children with suspected dysphagia; to identify clinical signs and symptoms associated with isolated laryngeal penetration and laryngeal aspiration; and to determine the sensitivity and specificity of the clinical signs and symptoms identified. Methods: Retrospective analysis of data from clinical and videofluoroscopic evaluations carried out in 55 children from 1 month to 7 years and 11 months old. For clinical assessment, the Protocol for Clinical Assessment of Pediatric Dysphagia was used. The sensitivity, specificity, and positive and negative predictive values of clinical evaluation were analyzed. For statistical analysis, the Fisher's exact and χ2 tests were used. Results: Clinical evaluation showed, in general, a sensitivity of 86% and a specificity of 32%. For isolated laryngeal penetration, clinical evaluation showed a sensitivity of 88%. For laryngeal aspiration, clinical evaluation showed a sensitivity of 86%. However, the specificity values were low for both alterations. There was no association between clinical evaluation and videofluoroscopic findings. Choking was the only clinical sign associated with isolated laryngeal penetration thin fluid and showed a sensitivity of 53% and a specificity of 77%. Conclusions: Clinical evaluation was sensible to detect isolated laryngeal penetration and laryngeal aspiration in children with suspected dysphagia. However, it showed a low specificity. Choking was the only clinical sign associated with isolated laryngeal penetration of thin fluid. More prospective studies are needed to confirm these findings in this population.


2016 ◽  
Vol 25 (2) ◽  
pp. 172-178 ◽  
Author(s):  
Juliana Gottlieb ◽  
Marcos Rogério André ◽  
João Fábio Soares ◽  
Luiz Ricardo Gonçalves ◽  
Mateus Tonial de Oliveira ◽  
...  

Abstract Pathogens transmitted by ticks are an emerging problem worldwide, this study aimed to diagnose the causal agents of infection in dogs presenting suspected hemoparasitoses. Fifty-eight dogs with clinical signs such as depression, hemorrhagic diathesis and fever were evaluated regarding clinical presentation, hemogram, blood smears and serological tests, using the indirect immunofluorescence method for the agents Babesia vogeli and Ehrlichia canis and conventional PCR for Babesia spp. (gene 18S rRNA), Rangelia vitalii (gene 18S rRNA) and Ehrlichia spp. (gene dsb). Five (8.6%) of the 58 dogs were serologically positive for Babesia spp. and three (5.1%) for E. canis. Four dogs (6.8%) were positive for R. vitalii through the molecular diagnosis. The PCR products were sequenced and the DNA from R. vitalii was found to be 99% genetically identical to samples of R. vitalii that had been isolated in Brazil. No presence of Babesia spp. or E. canis was observed through PCR on the dogs evaluated here. The results indicate the presence of R. vitalii and exposure to Babesia spp. and Ehrlichia spp. among the dogs analyzed.


2020 ◽  
Author(s):  
Mitnala Sasikala ◽  
Yelamanchili Sadhana ◽  
Ketavarapu Vijayasarathy ◽  
Anand Gupta ◽  
Sarala kumari Daram ◽  
...  

Abstract Background: A considerable amount of evidence demonstrates the potential of saliva in the diagnosis of COVID-19. Our aim was to determine the sensitivity of saliva versus swabs collected by healthcare workers (HCWs) and patients themselves to assess whether saliva detection can be offered as a cost-effective, risk-free method of SARS-CoV-2 detection.Methods: This study was conducted in a hospital involving outpatients and hospitalized patients. A total of 3018 outpatients (asymptomatic: 2683, symptomatic: 335) were screened. Of these, 200 qRT-PCR-confirmed SARS-CoV-2-positive patients were recruited (81 asymptomatic, 119 symptomatic). In addition, 101 SARS-CoV-2-positive hospitalized patients with symptoms were also enrolled in the study. From outpatients, HCWs collected nasopharyngeal swabs (NPS), saliva were obtained. From inpatients, HCWs collected swabs, patient-collected swabs, and saliva were obtained. qRT-PCR was performed to detect SARS-CoV-2 by TAQPATH assay to determine the sensitivity of saliva detection. Sensitivity, specificity and positive/negative predictive values (PPV, NPV) of detecting SARS-CoV-2 were calculated using MedCalc.Results: Of 3018 outpatient swabs tested by qRT-PCR, 200 were positive (males: 140, females: 60; aged 37.85±12.76 years). Of these, saliva was positive in 128 (64%); 39 of 81 asymptomatic (47%),89 of 119 symptomatic patients (74.78%). Sensitivity of detection was 60.9% (55.4-66.3%, CI 95%), with a negative predictive value of 36%(32.9-39.2%, CI 95%).Among 101 hospitalized patients (males:65, females: 36; aged 53.43±15.58 years), with HCW collected NPS as comparator, sensitivity of saliva was 56.1% (47.5-64.5, CI 95%), specificity 63.5%(50.4-75.3, CI95%) with PPV of 77.2% and NPV of 39.6% and that of self-swab was 52.3%(44-60.5%, CI95%), specificity 56.6% (42.3-70.2%, CI95%) with PPV 77.2% and NPV29.7%. Comparison of positivity with the onset of symptoms revealed highest detection in saliva on day 3 after onset of symptoms. Additionally, only saliva was positive in 13 (12.8%) hospitalized patients.Conclusion: Our results demonstrate the use of saliva to detect SARS-COV-2 in symptomatic patients early after the onset of symptoms. Additionally, these results suggest that saliva may not be recommended as a screening tool at the community level due to the lower detection rate than that for swabs. Saliva testing in symptomatic patients whose nasopharyngeal swab does not detect SARS-CoV-2 reduces false negativity.


Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2080
Author(s):  
Julia Walter-Weingärtner ◽  
Michèle Bergmann ◽  
Karin Weber ◽  
Uwe Truyen ◽  
Cosmin Muresan ◽  
...  

A real-time polymerase chain reaction (qPCR) is considered the gold standard for the laboratory diagnosis of canine parvovirus (CPV) infection but can only be performed in specialized laboratories. Several point-of-care tests (POCT), detecting CPV antigens in faeces within minutes, are commercially available. The aim of this study was to evaluate eight POCT in comparison with qPCR. Faecal samples of 150 dogs from three groups (H: 50 client-owned, healthy dogs, not vaccinated within the last four weeks; S: 50 shelter dogs, healthy, not vaccinated within the last four weeks; p = 50 dogs with clinical signs of CPV infection) were tested with eight POCT and qPCR. Practicability, sensitivity, specificity, positive (PPV) and negative predictive values (NPV), as well as overall accuracy were determined. To assess the differences between and agreement among POCT, McNemar’s test and Cohen’s Kappa statistic were performed. Specificity and PPV were 100.0% in all POCT. Sensitivity varied from 22.9–34.3% overall and from 32.7–49.0% in group P. VetexpertRapidTestCPVAg® had the highest sensitivity (34.3% overall, 49.0% group P) and differed significantly from the 3 POCT with the lowest sensitivities (Fassisi®Parvo (27.7% overall, 36.7% group P), Primagnost®ParvoH+K (24.3% overall, 34.7% group P), FASTest®PARVOCard (22.9% overall, 32.7% group P)). The agreement among all POCT was at least substantial (kappa >0.80). A positive POCT result confirmed the infection with CPV in unvaccinated dogs, whereas a negative POCT result did not definitely exclude CPV infection due to the low sensitivity of all POCT.


Author(s):  
Kathrine Kronberg Jakobsen ◽  
Jakob Schmidt Jensen ◽  
Tobias Todsen ◽  
Freddy Lippert ◽  
Cyril Jean-Marie Martel ◽  
...  

AbstractBackgroundRapid and accurate detection of SARS-CoV-2 infection is essential in limiting the spread of infection during the ongoing COVID-19 pandemic. The aim of this study was to determine the accuracy of the STANDARD Q COVID-19 Ag test (SD BIOSENSOR) by comparison with RT-PCR in a public setting.MethodIndividuals aged 18 years or older who had booked an appointment for a RT-PCR test on December 26-31, 2020 at a public test center in Copenhagen, Denmark, were invited to participate. An oropharyngeal swab was collected for RT-PCR analysis, immediately followed by a nasopharyngeal swab examined by the STANDARD Q COVID-19 Ag test (SD BIOSENSOR). Sensitivity, specificity, positive and negative predictive values of the antigen test were calculated with test results from RT-PCR as reference.ResultsOverall, 4697 individuals were included (female n=2456, 53.3%; mean age: 44.7 years, SD: 16.9 years); 196 individuals were tested twice or more. Among 4811 paired conclusive test results from the RT-PCR and antigen tests, 221 (4.6%) RT-PCR tests were positive. The overall sensitivity and specificity of the antigen test were 69.7% and 99.5%, the positive and negative predictive values were 87.0% and 98.5%. Ct values were significantly higher among individuals with false negative antigen tests compared to true positives.ConclusionThe sensitivity, specificity, and predictive values found indicate that the STANDARD Q COVID-19 Ag is a good supplement to RT-PCR testing.


2020 ◽  
Vol 51 (4) ◽  
pp. 1220-1225
Author(s):  
Faraj & Al- Amery

Ascaridiosis is a very important parasitic disease of birds, it is caused by Ascaridia. This study was conducted to identify the Ascaridia species by microscopic and molecular assay in Baghdad city. One hundred and sixty fecal samples were collected from domestic pigeons during the period from 1/1/ 2019 to 31/3/ 2019.  Results showed that the rate of infection for Ascaridia spp. 15.62% by microscopic examination.  Significant difference was observed in infection rates between males and females pigeons. Fifty samples randomly selected and subjected to molecular diagnosis of Ascaridia  spp.. Molecular examination results, the total infection rate showed 16%(8/50). The eight  positive PCR products were sequenced and deposited in Gene bank data base, phylogenic analysis demonstrated that 4 sequences belongs to Ascaridia galli ( MK918635.1, MK918636.1, MK918847.1, MK919081.1), while 2 (MK919199.1, MK919200.1) belong to  Ascaridia nymphii and 2 (MK919207.1, MK919264.1)  belong to Ascaridia numidae. It is the first study in Iraq to diagnosis of  Ascaridia nymphii and Ascaridia numidae  in domesticed pigeons by using conventional PCR.


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