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Background:
Diarrhea is a major source of morbidity and mortality among young children in low-income and middle-income countries. Human adenoviruses (HAdV), particular HAdV species F (40, 41) has been recognized as important causal pathogens, however limited data exist on molecular epidemiology of other HAdV associated with acute gastroenteritis....
Context in source publication
Context 1
... qPCR positive samples were then retested by nested PCR and sequencing for serotyping as described in a previous study [16] The nested PCR was conducted using Premix Taq™ (TaKaRa Taq™ Version 2.0 plus dye) (Takara, Dalian, China) in a PCR Amplifier (Thermo Electron Corp., Vantaa, Finland) according to the manufacturer's instructions. The primers/probes used in this study are listed in Table 1. ...
Similar publications
Background:
Human adenoviruses are common causes of community-acquired respiratory tract and enteric infections. Severe disseminated infections with high mortality rates may be seen in immunocompromised individuals. An accurate and cost-effective quantitative assay is essential not only for laboratory diagnosis of adenoviral infections, but also f...
Citations
... This 236 is the first applicaSon of the adenovirus part of the RespiCov method to stool samples for 237 genotyping enteric viral infecSons. Previous studies from China, Tunisia, Kenya and Brazil have 238 reported detecSon of non-F HAdVs similar to our findings 3,7,9,10,12,19,20 . Non-F types such as 239 B3, C1, C2, C5 and C6 have been associated with increased risk of diarrhoea but direct 240 causaSon is not yet clear 3,10 . ...
... Previous studies from China, Tunisia, Kenya and Brazil have 238 reported detecSon of non-F HAdVs similar to our findings 3,7,9,10,12,19,20 . Non-F types such as 239 B3, C1, C2, C5 and C6 have been associated with increased risk of diarrhoea but direct 240 causaSon is not yet clear 3,10 . In this study, we did not detect HAdV B3 but detected the HAdV 241 types C1 and C5; although we cannot conclude that they were the main cause of diarrhoea in 242 these individuals. ...
Background
Although seven human adenovirus (HAdV) species are known to exist, only F (types 40 and 41) and G, are identified as diarrhoeal disease agents. The role of other HAdV species in diarrhoeal disease remains unclear and data of their prevalence is limited. We describe HAdV species and types in hospitalised children with diarrhoea in coastal Kenya.
Methods
329 stool samples collected between June 2022 and August 2023 from children aged <13-years were screened for HAdV using quantitative polymerase chain reaction (qPCR). Positive HAdV cases were genotyped by adenovirus primers from the RespiCoV panel by amplification, next generation sequencing followed by phylogenetic analysis.
Results
65 samples (20%) tested HadV positive from which five HAdV species were identified. Other than HAdV F, other species included A, B, C and D; these were detected as either mono-detections or coinfections. Six HAdV F identified by NGS had been missed by our q PCR typing method. This appeared to be as a result of a 133-nucleotide deletion in the long fiber protein which abrogated a primer and probe binding site. Based on VESIKARI scores grading of diarrhoeal disease severity, 93% of the HAdV cases presented with severe disease. One child with an HAdV F infection died.
Conclusion
Our study shows the enormous diversity and clinical characteristics of HAdV species in children with diarrhoea in coastal Kenya. These data offers an opportunity to improve current diagnostic assays, increase knowledge of HAdV in Africa for control of outbreaks in the future.
... HAdV was found in 32% of the stool samples from children with acute gastroenteritis in Ethiopia, with types 40/41 accounting for 21.5% of those cases [44]. In China, HAdV was found in the stool samples of 28.9% of children with diarrhea, with types 40/41 accounting for 56.9% [45]. In Thailand, HAdV positivity was found in 7.2% of the pediatric gastroenteritis stool samples, of which 28.5% were types 40/41 [46]. ...
... Among non-type 40/41 HAdVs, species B, type 3 (B/3), species C, type 2 (C/2), and species A, type 31 (A/31) are the most frequent found in stool [14,[44][45][46][47][48][49]. There is debate concerning their possible contribution to childhood gastroenteritis in immunocompetent children. ...
Objective:
We determined the molecular prevalence and genotype distribution of human adenovirus (HAdV) among children under five years of age with gastroenteritis in Iran.
Methods:
One hundred stool samples from children hospitalized were tested by PCR for adenovirus, and some of the positive samples were sequenced to determine the specific genotype.
Results:
HAdV DNA was found in 15 samples (15%). The highest and the lowest prevalence of HAdV was observed in the age groups 24-60 months (n = 6; 40%) and 7-12 months (n = 2; 13.3%), respectively (p = 0.01). Nine HAdV-positive samples were sequenced, of which four isolates were HAdV type 2 and five isolates were HAdV type 41.
Conclusion:
HAdV was most common in the 24-60-month-old children. Of the samples sequenced, we found only types 2 and 41. Our results show that in addition to HAdV types 40 and 41, HAdV type 2 may also play a role in causing gastroenteritis in children.
... HAdV-F41, is one of the two enteric types of species HAdV-F. Like type F40, it is highly endemic globally, circulates year-round and causes gastroenteritis in children [19][20][21]. Considerable intratypic genetic variability has been described for HAdV-F41 with two major clades identifiable by phylogenetic analysis of whole or partial genomic sequences [22]. ...
Adenovirus (HAdV) F41 is a common cause of gastroenteritis and has rarely been reported associated with disseminated disease. In this report, an adult patient with a history of ulcerative colitis, cryptogenic cirrhosis, stage III adenocarcinoma, high-grade diffuse large B-cell lymphoma on chemotherapy was diagnosed with disseminated adenovirus infection. HAdV DNA was quantified in stool, plasma, and urine with viral loads of 7, 4, and 3 log10 copies/mL, respectively. The patient’s course was rapidly progressive and he passed away 2 days after initiation of antiviral therapy. The patient’s infecting virus was characterized as HAdV-F41 by whole genome sequencing.
... Most studies have been limited to hospitalized patients, children, or a single pathogen. Case-control studies of adults and children with diarrhea have identified pathogens with known respiratory manifestations such as adenovirus [6] and bocavirus [7] as causes of GI symptoms. There is a need for communitybased sampling across age groups with broad pathogen testing and detailed symptomatic data collection to better understand the burden of GI symptoms in patients with respiratory infections. ...
Background
Gastrointestinal (GI) symptoms are recognized sequelae of acute respiratory illness (ARI), but their prevalence is not well documented. Our study aim was to assess the incidence of GI symptoms in community ARI cases for persons of all ages and their association with clinical outcomes.
Methods
We collected mid-nasal swabs, clinical, and symptom data from Seattle-area individuals during the 2018–2019 winter season as part of a large-scale prospective community surveillance study. Swabs were tested by polymerase chain reaction (PCR) for 26 respiratory pathogens. Likelihood of GI symptoms given demographic, clinical, and microbiological covariates were analyzed with Fisher’s exact, Wilcoxon-rank-sum, and t-tests and multivariable logistic regression.
Results
In 3183 ARI episodes, 29.4% had GI symptoms (n = 937). GI symptoms were significantly associated with pathogen detection, illness interfering with daily life, seeking care for the illness, and greater symptom burden (all p < 0.05). Controlling for age, > 3 symptoms, and month, influenza (p < 0.001), human metapneumovirus (p = 0.004), and enterovirus D68 (p = 0.05) were significantly more likely to be associated with GI symptoms than episodes with no pathogen detected. Seasonal coronaviruses (p = 0.005) and rhinovirus (p = 0.04) were significantly less likely to be associated with GI symptoms.
Conclusion
In this community-surveillance study of ARI, GI symptoms were common and associated with illness severity and respiratory pathogen detection. GI symptoms did not track with known GI tropism, suggesting GI symptoms may be nonspecific rather than pathogen-mediated. Patients presenting with GI and respiratory symptoms should have respiratory virus testing, even if the respiratory symptom is not the primary concern.
... Transfer learning has been shown to enhance the performance of deep learning models in various domains. In the field of load forecasting in buildings, a building-to-building transfer learning framework was proposed to overcome the challenge of limited historical data [1] [2] . This approach improved the forecasting accuracy by 56.8% compared to training from scratch, using a transformer model that outperformed other sequential deep learning models such as LSTM and RNN [3] . ...
Transfer learning, a technique in machine learning, has emerged as a powerful approach to enhance the performance of deep learning models by leveraging knowledge gained from one task or domain to improve learning in another. This paper provides an overview of transfer learning in the context of deep learning, exploring its principles, methods, and applications. We discuss the benefits and challenges of transfer learning, highlighting its capacity to expedite model training, improve generalization, and facilitate the adaptation of deep learning models to new tasks and domains. Furthermore, we examine various strategies for transfer learning, including fine-tuning, feature extraction, and domain adaptation, along with practical considerations and best practices. Through real-world examples and case studies, we illustrate the effectiveness of transfer learning across diverse domains, including computer vision, natural language processing, and healthcare. Finally, we address current trends, open challenges, and future directions in harnessing the power of transfer learning to advance the capabilities of deep learning models.
... In our study, SaV was more prevalent than NoV, which contradicts those studies that detected NoV at a higher rate of infection (Grytdal et al., 2016;Gelaw et al., 2019;Oliveira-Tozetto et al., 2021;Rossouw et al., 2021). The overall rate of HAdV infection in children with diarrhea observed in this study was 6.67%, similar to those reported in other countries such as Thailand (7.2%) (Kumthip et al., 2020), Korea (6.5%) (Kim et al., 2017), the Republic of Congo (10.5%) (Medkour et al., 2020), India (11.8%) (Banerjee et al., 2017), and Bangladesh (10.7%) (Afrad et al., 2018), but there are also reports from other regions with higher prevalence rates, such as China (28.94%) (Qiu et al., 2018), Ethiopia (32%) (Gelaw et al., 2019), and Gabon (19.6%) (Lekana-Douki et al., 2015). The risk factors associated with the presence of AdV and SaV in children were the "type of drinking water" for both and the "presence of animals in the home" for SaV; importantly, children who drank bottled water were less infected. ...
Introduction
Diarrheal disease is a major cause of infant mortality and morbidity in Africa and results primarily from contaminated food and water sources, but its prevalence predictors in Cape Verde are not completely known. For this reason, this study aimed to identify the etiological agents of diarrhea in Cape Verdean children and assess its associated risk factors.
Methods
A survey questionnaire was used, and a total of 105 stool samples from children with diarrhea aged 0–12 years at the Central Hospital of Praia (Santiago, Cape Verde) were analyzed. The analyses were carried out using Biofire FilmArray Gastrointestinal Panels. Possible risk factors for these pathogens were analyzed using logistic regression, chi-square tests, or Fisher’s exact test.
Results
Among the bacteria, enteroaggregative Escherichia coli (45.71%; 95% CI: 36.71–56.70), enteropathogenic E. coli (40%; 95% CI: 30.56–50.02), Shigella/enteroinvasive E. coli (29.52%; 95% CI: 21.02–39.22), E. coli enterotoxigenic (12.38%; 95% CI: 6.76–20.24), Campylobacter sp. (10.48%; 95% CI: 5.35–1.97), Vibrio sp. (4.76%; 95% CI: 1.56–10.76), Clostridioides difficile (3.81%; 95% CI: 1.05–9.47), Vibrio cholerae (2.86%; 0.59–8.12), Shiga-like toxin-producing E. coli (2.86%; 0.59–8.12) and Salmonella sp. (0.95%; 0.02–5.19) were identified; four viruses, Rotavirus A (28.57%; 95% CI: 20.18–38.21), Sapovirus I. II. IV and V (11.43%; 95% CI: 6.05–19.11), Norovirus GI.GII (6.67%; 95% CI: 2.72–13.25) and Adenovirus F 40.41 (6.67%; 95% CI: 2.72–13.25) were also observed. All the pathogens detected in this study were found in coinfections. Significant associations with risk factors were found; specifically, having a bathroom at home reduced the risk of Campylobacter sp., having animals at home increased the risk of Shigella /EIEC infection, and drinking bottled water reduced the risk of Sapovirus infection.
Discussion
From the findings of this study, it can be concluded that, in Cape Verde, there is a high prevalence and diversity of pathogens among children. Our results could help to establish an adequate diagnosis and effective treatments for diarrheal disease.
... Similarly, in case-control studies carried out by Fan-Zhou and co-authors [13], a group of children hospitalized due to gastroenteritis caused by the HAdV found that 91.14% of patients were under three years of age. Our patients with respiratory tract symptoms were substantively significantly younger than patients with symptoms concerning the digestive tract. ...
... It also confirms the observation that the course of viral infections in small children is often accompanied by nonspecific symptoms from different organs regardless of the primary tropism of the HAdV serotype. In a case-control study carried out by Fang-zhou Qiu and co-authors [13], HAdV3 genetic material was found in stool samples of patients who presented with diarrhea, which is classically believed to cause respiratory system infections. ...
Objective:
A restrospective analysis of the clinical picture (inflammatory markers, characteristics of fever, comorbidities) in different clinical manifestations of human adenovirus (HAdV) infections confirmed using point-of-care testing in a group of hospitalized children.
Material and methods:
A total of 135 children with confirmed HAdV infections were divided into three groups according to their clinical symptoms: Group A-respiratory (n = 57), Group B-gastrointestinal (n = 40), and Griup C-mixed (n = 38).
Results:
Respiratory and mixed HAdV-infected patients, as compared with gastrointestinal HAdV-infected patients, were younger (median value (Me) and interquartile range (IQR) (months): 17 (12-30) and 17 (12-27) vs. 30 (16-50), p = 0.04), had a longer duration of fever (days): 3 (1-5) and 3 (1-4) vs. 1 (1-2), p = 0.01), and had higher C-reactive protein values (mg/L): 29.2 (10.4-69.1) and 28.7 (10.8-49.1) vs. <5 (<5-20.6), p < 0.001). There were no correlations between CRP levels and patient's age, fever duration, the occurrence of acute otitis media and lower respiratory tract infection, and antibiotic treatment before admission.
Conclusions:
Patients with respiratory HAdV infections have fevers more often, the duration of the fever prior to admission is longer, and CRP levels are higher.
... Following is a list of acronyms used in this manuscript: In genetics, case/control studies for humans, animals, and different species [1][2][3][4][5][6][7] are of great importance for the diagnosis of a particular disease in organisms. Genotype data available for genetic analysis can significantly improve the final results [8]. ...
Background
For some understudied populations, genotype data is minimal for genotype-phenotype prediction. However, we can use the data of some other large populations to learn about the disease-causing SNPs and use that knowledge for the genotype-phenotype prediction of small populations. This manuscript illustrated that transfer learning is applicable for genotype data and genotype-phenotype prediction.
Results
Using HAPGEN2 and PhenotypeSimulator, we generated eight phenotypes for 500 cases/500 controls (CEU, large population) and 100 cases/100 controls (YRI, small populations). We considered 5 (4 phenotypes) and 10 (4 phenotypes) different risk SNPs for each phenotype to evaluate the proposed method. The improved accuracy with transfer learning for eight different phenotypes was between 2 and 14.2 percent. The two-tailed p-value between the classification accuracies for all phenotypes without transfer learning and with transfer learning was 0.0306 for five risk SNPs phenotypes and 0.0478 for ten risk SNPs phenotypes.
Conclusion
The proposed pipeline is used to transfer knowledge for the case/control classification of the small population. In addition, we argue that this method can also be used in the realm of endangered species and personalized medicine. If the large population data is extensive compared to small population data, expect transfer learning results to improve significantly. We show that Transfer learning is capable to create powerful models for genotype-phenotype predictions in large, well-studied populations and fine-tune these models to populations were data is sparse.
... In our study it was found that only 33% of the aEPEC strains belonged to classical subtype, may be our serotyping was unable to diagnose the classical aEPEC subtype. Serotyping is a popular procedure used in many countries including China 22 . aEPEC strains that were identified in Mexico reported high antibiotic resistance. ...
Background: Diarrhea is known as one of the highly infectious diseases affecting the world population around the globe especially the children community. It is associated with the highest mortality and morbidity rates in children. Objective: The study was carried out to find the characteristic features of diarrheagenic Escherichia coli among children with acute diarrhea under the age of 5 years. Study design: It is a prospective based study conducted for the duration of the one year from September 2021 to August 2022. Material and Methods: There were 130 patients that participated in this study. The samples were collected from each patient. The clinical symptoms and demographic features of each patient were recorded. The SPSS was used for statistical analysis. Results: Some of the features that were commonly observed among children were nausea (n=23), vomiting (n=32), abdominal pain (n=60) and fever (n=12). There were 27% patients that reported diarrhea in spring, 26% in autumn, 33% and 12% in summer and winter respectively. It was found that the isolate rate was decreasing in the order from EPEC, EAEC, ETEC, STEC and EIEC in age group 0-11. Conclusion: This study reported that EPEC is an important phenotype present among children under the age of 5 who are suffering from DEC infection. The drug resistance cases are increasing in DEC strains with time. The antibiotic resistance was shown for ampicillin in both DEC strains and the aEPEC subtype. The data can be used to study the antimicrobial investigation against these strains. Keywords: Escherichia coli.
... Adenoviruses B and C are the most common respiratory infections, with Adenoviruses species A impacting the respiratory system in immunocompromised patients, and Adenoviruses F, including types 40 and 41, have been identified as one of the principal viruses causing infantile gastroenteritis [7]. Epidemiological investigations of HAdV undertaken in numerous countries throughout the world, including India, Bangladesh, Brazil, Korea, and China, revealed that the virus infected 2% to 10% of diarrheic patients, with the virus mostly infecting infants under the age of two [8][9][10][11]. In Egypt, just a few studies show the incidence of enteric adenovirus infections in children [12][13][14][15]. ...
... Human adenoviruses, after rotaviruses, are the second most common cause of diarrhea in infants in Egypt [10,11]. Adenovirus infections account for 2% to 10% of diarrheal cases [27]. ...
Human adenoviruses (HAdV) are a prevalent cause of diarrhea in children all over the world. Adenoviral infections are responsible for 2% to 10% of diarrheic cases. A long-term investigation was required to gain better knowledge about the incidence of HAdV in Egypt. Herein, we conducted 5 years of detection, isolation, and genotyping of HAdV in fecal and sewage samples from 2016 to 2020, in Cairo, Egypt using molecular and cell culture assays. Human adenoviruses were identified in 35 of 447 fecal samples (7.8%), but only 53.3% (64/120) of the sewage samples. Children under the age of two had the highest positive rate for HAdV infection (77.1%). Species F of HAdV was the most common prevalent genotype in fecal and sewage samples, at 88.5% and 85.9%, respectively. The most prevalent genotypes detected in fecal samples were HAdV-41 (71.2%), HAdV-40 (17.2%), HAdV-6 (5.7%), and HAdV-1 (5.7%). In contrast, the most common genotypes in sewage samples were HAdV-41 (64%), HAdVs-40 (21.8%), HAdV-6 (7.8%), HAdV-1 (4.7%), and HAdV-2 (1.6%). HAdV was detected in all months of the year, with a peak period for clinical samples from December to February (p < 0.001), which matched Egypt’s rainy season, while the monthly distribution of HAdV in sewage samples remained consistent throughout the year, with no statistically significant peak period. Interestingly, the HAdV-type 41 genotype was the most common genotype during all of the years of this study. Throughout a 5-year period, our work revealed the infection rate, seasonal distribution, virus isolates, and genetic diversity of HAdV infections in environmental and clinical samples in Cairo, Egypt. Non-enteric adenovirus types (1, 2 and 6), as well as enteric adenovirus (41 and 40), may play a key role in gastroenteritis in Egypt.
