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1.
Gastroenterology ; 162(7):S-652-S-653, 2022.
Article in English | EMBASE | ID: covidwho-1967354

ABSTRACT

SARS-CoV-2 has had a profound impact on the human population in the last 24 months. This includes dramatic changes in lifestyle, hygiene, and altered food sources/consumption patterns, which could directly impact the small bowel microbiome on an individual and perhaps even at a population level. To date, this has not been examined. Here, we compare small bowel microbial profiles in subjects before SARS-CoV-2 and intra-pandemic. Methods: The REIMAGINE study is a large-scale study using validated methods for duodenal aspirate collection and microbiome sequencing in subjects undergoing upper endoscopy. Subjects were divided into 2 groups: pre-pandemic, from February 2019 to March 2020;and intrapandemic, from April 2021 to September 2021. Groups were matched for gender, age, and BMI. Duodenal aspirates were collected, and microbial DNA was isolated using the MagAttract PowerSoilDNA Kit. V3 and V4 libraries were sequenced on a MiSeq. Reference-based Operational Taxonomic Unit clustering was performed using SILVA v132 database. Taxonomic analysis was performed with CLC Microbial Genomics Module v.2.5 and MicrobiomeAnalyst, and duodenal microbial alpha- and beta-diversity indices were calculated. Significance was determined by Wilcox test. Results: In total 94 subjects were included in the analysis. The overall duodenal microbiome profile (beta-diversity) of intra-pandemic subjects (n=38, mean age= 51 ± 18, mean BMI =23.9 ± 4.7) was significantly different from pre-pandemic subjects (n=56, mean age= 51 ± 15, mean BMI = 25.24 ± 4.9)(p<0.002, Fig1A), with no significant changes in duodenal microbial alpha diversity between groups (Fig1B). Significant duodenal microbial taxonomic differences were identified between groups, including changes in the relative abundance (RA) of 2 phyla, 3 classes, 6 orders, 4 families and 23 genera (Fig2A). At the phylum level, Actinobacteria RA was significantly decreased in the intra vs. the pre group (FC=-1.99, P=9.83E-8, Fig2B). Additionally, at the genus level, RA of Rothia (P= 6.85E-7), Pseudomonas (P=0.0376), and Escherichia (P=0.0092) were significantly decreased in the intra group (Fig2A). Of note, the phylum Deinococcus (P=0.0016) was increased in the intra vs. the pre group (Fig2B). Conclusion: In this first study examining the effect of the COVID-19 pandemic on the small bowel microbiome, we show substantial changes in microbial profiles intra-pandemic as compared to pre-pandemic. The duodenal microbiome of intra-pandemic subjects was associated with less disrupter bacteria (Escherichia and Pseudomonas), commonly associated with GI disorders. In contrast, Deinococcus phylum was increased intra-pandemic. This phylum includes organisms resistant to sanitation and increased in the nasal passage of people during the pandemic. The short and long term impact of these changes on human health require further study.(Figure Presented)

2.
Journal of the Academy of Consultation-Liaison Psychiatry ; 63:S108, 2022.
Article in English | EMBASE | ID: covidwho-1966678

ABSTRACT

Background: Within the general hospital setting, Consultation-Liaison (C-L) Psychiatry services are critical for managing patients with behaviors that frequently result in behavioral emergencies, including agitation, verbal aggression, physical aggression, and demanding behavior (Pestka et al., 2012). To most effectively manage these difficult patient behaviors, early consultation to C-L Psychiatry may prevent behavior from escalating to the level of a behavioral emergency. Yet, data is limited regarding the effectiveness of C-L Psychiatry in impacting the occurrence and reoccurrence of behavioral emergencies. Method: Data on all behavioral emergencies that occurred at the University of Virginia Medical Center from January 2020 to December 2020 were collected. Variables collected include patient demographic information, frequency of behavioral emergency, type of behavioral emergency, factors contributing to behavioral emergency, and whether the C-L Psychiatry service had been consulted. Patients who received a C-L Psychiatry consult prior to a behavioral emergency will be compared on the above variables to patients who did not receive this consult to identify differences between the two groups. Results: Preliminary data indicates that UVA Medical Center had an average of 61.2 (range 38-82) behavioral emergencies per month between January 2020 and December 2020. These fell into five categories consistent with previous pilot data: physical aggression, leaving the unit, verbal aggression, agitation, and non-compliance (Yost & Smith, 2020). Factors contributing to behavioral emergencies were identified as delirium, dementia, personality disorder, substance withdrawal, frustration, and TBI. Data will be further analyzed to determine how frequently patients who exhibit behavioral emergencies had received C-L Psychiatry services prior to the behavioral emergency or had not received this service during their hospitalization. Additional analyses will be conducted to determine differences between these two groups on type of behavioral emergency and factors contributing to behavioral emergency. Discussion: This data will inform how patients with challenging behavior are identified early in their hospitalization and how C-L Psychiatry can proactively intervene to decrease behavioral emergencies. Further, this project suggests a need to create process for identifying patients at risk for behavioral emergencies. Future directions will be discussed. Conclusions/Implications: The findings from this quality improvement project have important clinical implications concerning how C-L Psychiatry manages patients with challenging behavior and how frontline staff identify and utilize C-L Psychiatry. References: 1. Pestka EL, Hatteberg DA, Larson LA, Zwygart AM, Cox DL, Borgen EE Jr. Enhancing safety in behavioral emergency situations. Medsurg Nurs. 2012;21(6):335-41. 2. Yost, JS & Smith, JB. A taxonomy of behavioral emergencies in the general hospital: A comparison of behavioral emergencies pre-covid-19 and during the covid-19 outbreak. Brief oral presentation delivered at the 2020 Annual Meeting of the Academy of Consultation-Liaison Psychiatry.

3.
DETUROPE ; 14(1):147-163, 2022.
Article in English | Scopus | ID: covidwho-1965097

ABSTRACT

The need to take action to mitigate the effects of climate change is widely recognized by governments and economic actors around the world. Likewise, an awareness of a more holistic approach to financing policy goals, so that all social, economic, and environmental aspects receive adequate consideration, has been on the rise, too. The UN sustainable development goals (SDGs) combined with the European Green Deal objectives have themselves induced a major funding challenge, which is now aggravated by the COVID crisis and the war in Ukraine. Development finance and investment are strongly needed. In the public finance sector, besides European institutions and national governments, national development banks (NDBs) play an important role in providing funds and implementing development and investment programmes. By using public and private funds, they are actively involved in financing infrastructure projects as well as they are acting as holding fund managers or financial intermediaries for different financial instruments such as investment platforms or EU funded financial instruments. The paper assesses the compliance of European national development banks with sustainability requirements by exploring their strategic objectives and investment activities. The aim of the paper is to examine whether and how the contradiction between stimulating growth and maintaining a sustainable fiscal strategy can be resolved. The new obligations stemming from the EU Taxonomy rules and the weight of national development banks in investments and specifically in infrastructure finance gives particular relevance to the enquiry. European National Development Banks satisfy a wide range of specific missions to address market failures. They can be clustered based on the basis of the duration of their operations, the financial market situation and level of economic development in their country as well as the sustainable development index. The level of commitment the government makes to green growth and of the influence it holds over the bank has been observed to correlate with bank’s contribution to sustainable finance. The results of the analysis of their various management and investment areas show that the investments they currently finance are to a large extent harmonized with the sustainable finance requirements and regulations of the European taxonomy. Meanwhile, their mandates and the wider context of national development strategies continue to provide strong incentives for sustainable finance. © 2022. DETUROPE.All Rights Reserved

4.
Biomedica ; 42(Suppl. 2), 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-1957852

ABSTRACT

Introduction: The severe acute respiratory syndrome of the new coronavirus (SARS-CoV-2) is the causal agent of the health emergency due to the COVID-19 pandemic. Although humans are the main susceptible host, experimental studies and reported cases of natural infection have evidenced scenarios of SARS-CoV-2 reverse zoonosis in animals.

5.
Journal of Sensors ; 2022, 2022.
Article in English | ProQuest Central | ID: covidwho-1950369

ABSTRACT

There is a massive transformation in the traditional healthcare system from the specialist-centric approach to the patient-centric approach by adopting modern and intelligent healthcare solutions to build a smart healthcare system. It permits patients to directly share their medical data with the specialist for remote diagnosis without any human intervention. Furthermore, the remote monitoring of patients utilizing wearable sensors, Internet of Things (IoT) technologies, and artificial intelligence (AI) has made the treatment readily accessible and affordable. However, the advancement also brings several security and privacy concerns that poorly maneuvered the effective performance of the smart healthcare system. An attacker can exploit the IoT infrastructure, perform an adversarial attack on AI models, and proliferate resource starvation attacks in smart healthcare system. To overcome the aforementioned issues, in this survey, we extensively reviewed and created a comprehensive taxonomy of various smart healthcare technologies such as wearable devices, digital healthcare, and body area networks (BANs), along with their security aspects and solutions for the smart healthcare system. Moreover, we propose an AI-based architecture with the 6G network interface to secure the data exchange between patients and medical practitioners. We have examined our proposed architecture with the case study based on the COVID-19 pandemic by adopting unmanned aerial vehicles (UAVs) for data exchange. The performance of the proposed architecture is evaluated using various machine learning (ML) classification algorithms such as random forest (RF), naive Bayes (NB), logistic regression (LR), linear discriminant analysis (LDA), and perceptron. The RF classification algorithm outperforms the conventional algorithms in terms of accuracy, i.e., 98%. Finally, we present open issues and research challenges associated with smart healthcare technologies.

6.
IEEE Access ; : 1-1, 2022.
Article in English | Scopus | ID: covidwho-1948719

ABSTRACT

With the growing popularity of Android smart devices, and especially with the recent advances brought on by the COVID-19 pandemic on digital adoption and transformation, the importance of protecting these devices has grown, as they carry very sensitive data. Malicious attacks are targeting Android since it is open source and has the highest adoption rate among mobile platforms. Botnet attacks are one of the most often forgotten types of attacks. In addition, there is a lack of review papers that can clarify the state of knowledge and indicate research gaps in detecting android botnets. Therefore, in this paper, we conduct a literature review to highlight the contributions of several studies in the domain of Android Botnet detection. This study attempts to provide a comprehensive overview of the deployed AI apps for future academics interested in performing Android Botnet Detection studies. We focused on the applications of artificial intelligence and its two prominent subdomains, machine learning (ML) and deep learning (DL) techniques. The study presents available Android Botnet datasets suitable for detection using ML and DL algorithms. Moreover, this study provides an overview of the methodologies and tools utilized in APK analysis. The paper also serves as a comprehensive taxonomy of Android Botnet detection methods and highlights a number of challenges encountered while analyzing Android Botnet detection techniques. The research gaps indicated an absence of hybrid analysis research in the area, as well as a lack of an up-to-date dataset and a time-series dataset. The findings of this paper show valuable prospective directions for future research and development opportunities. Author

7.
Educ Inf Technol (Dordr) ; : 1-17, 2022 May 03.
Article in English | MEDLINE | ID: covidwho-1942146

ABSTRACT

Distance education has been the concern of educational institutions nowadays due to COVID 19 pandemic. The purpose of this study which was carried out during COVID-19 pandemic lockdown period in 2020 was to evaluate the effectiveness of webcast applications on teacher training. Since it was a sudden and an unpredicted transition from face-to-face education to webcast education, it was crucial to evaluate the outcome of teaching applications in order to compensate for the missing points in education. The evaluation framework in this study was based on Bloom's Digital Taxonomy. The participants' responses demonstrated that as a consequence of the webcast application in education, remembering, understanding, and analyzing skills were activated better than applying, evaluating, and creating thinking skills in the digital taxonomy. The findings would not be applicable to all webcast training but only to the course design that was delivered as an emergency remote course in a global pandemic.

8.
Bonplandia ; 31(2), 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-1934961

ABSTRACT

The normal management of plant germplasm conservation laboratories involves carrying out numerous and diverse activities, which were affected by the coronavirus pandemic (COVID-19). The objective of this publication was to review the evolution of the cassava in vitro germplasm bank at the FCA-UNNE and IBONE (CONICET-UNNE) and to tell about usual management practices and the procedures to preserve living plant material and the personnel's life involved in pre-pandemic and COVID-19 pandemic times. Teachers, researchers, undergraduate and graduate students carried out, for almost 40 years, the in vitro conservation of 56 cassava cultivars from different countries. Before March 2020, the bank management consisted mainly in scientific-technological activities for the conservation of the material and the search for parameters to establish an order of subcultures. Having decreed Social, Preventive and Compulsory Isolation in Argentina, conservation activities continued applying the usual practices by following political-institutional sanitary measures. To face the new sanitary scenarios, methodologies must be adjusted so that they are effective at maintaining viability of the plant material and at prolonging conservation time.

9.
Folia Oeconomica Stetinensia ; 22(1):191-218, 2022.
Article in English | ProQuest Central | ID: covidwho-1923987

ABSTRACT

Research background: This paper focuses on the preparers’ opinion on reporting in the European Single Electronic Format (ESEF).Purpose: The goal of the paper is to examine the preparers’ perception of adopting Inline XBRL as a fundamental technology to report annual consolidated financial statements under International Financial Reporting Standards (IFRS) within the ESEF framework.Research methodology: In the present work, Poland was considered as a case study. Using the survey, we obtained evidence from 25 issuers of securities listed on the Warsaw Stock Exchange, whose financial reports were complied with IFRS.Results: The questionnaires were completed in the majority by issuers with no previous experience in XBRL utilisation. One of the more significant findings to emerge from this study is that respondents could not be able to judge the appropriateness of Inline XBRL selection as a digital reporting format, or they disagreed with it. Furthermore, over half of them saw no need to extend this technology to other business reports, including non-financial reporting.Novelty: The paper can offer valuable pre-insights into preparers’ perception of introducing Inline XBRL in the context of ESEF reporting and ensure initial feedback to the policy-makers responsible for ongoing and forthcoming digital reporting standards initiatives in the European Union.

10.
Veteriner Hekimler Dernegi Dergisi / Journal of the Turkish Veterinary Medical Society ; 93(2):124-132, 2022.
Article in Turkish | CAB Abstracts | ID: covidwho-1924975

ABSTRACT

Coronaviruses in the family Coronaviridae cause digestive and respiratory system infections in humans and animals. There are two subtypes of canine coronaviruses (CCoV), which are included in the alfacoronavirus, as CCoV I and CCoV II. CCoV-II is divided into two genotypes, CCoV-IIa and IIb. Although CCoV affects dogs of all ages and all diets, newborn puppies can be particularly susceptible and severely affected. According to the literature research, no molecular studies have been found in our country for the detection of canine coronavirus, especially in lower respiratory tract infections. In this study, it was aimed to detect and molecular characterization of CCoV un shelter dogs with lower respiratory tract infection. For this purpose, Bronchoalveolar Lavage (BAL) fluids taken from 40 shelter dogs with lower respiratory tract infections were examined. CCoV was detected in 3 of the BAL fluids of 40 dogs tested. A phylogenetic tree was constructed with the sequences obtained after the sequence analysis. It was determined that 2 of the 3 positive samples in the phylogenetic tree were CCoV-I and one sample was CCoV-II. In conclusion, this study revealed that CCoV-I and CCoV-II may play a role in lower respiratory system disorders of shelter dogs. In addition, the detection of two different CCoVs in different animals in the same shelter has been considered as an important data, and the detection of both types in dogs housed in crowded environments such as shelter conditions shows that the possibility of new variants or subtypes that may occur in the future should not be ignored.

11.
Global Advances in Health and Medicine ; 11:23, 2022.
Article in English | EMBASE | ID: covidwho-1916556

ABSTRACT

Methods: This 2-phase study used a sequential, mixed methods design to explore changes made to study protocols, particularly clinical interventions, in response to the evolving pandemic. A structured REDCap questionnaire queried about emerging adaptations using the periodic reflections method across 3 timepoints. Following Phase 1 analysis, brief checklists and 3 setting-specific focus groups were completed with principal investigators and key staff via video-conference to elicit information about study adaptations. Focus group interview schedules and directed content analyses were guided by the Framework for Reporting Adaptations and Modifications-Expanded (FRAME) taxonomy. Results: Eleven PCTs completed questionnaires and 16 representatives from 10 PCTs joined focus groups. In periodic reflections, teams reported between 2 to 6 adaptations in the first 5 months of the pandemic. PCTs in the implementation stage reported delays in site/clinic onboarding, staff training, and/or patient recruitment, with 3 trials pausing intervention delivery. Intervention protocols were adapted with 6 PCTs adding/expanding virtual care. Trials testing manual therapies reported clinic closures and care restrictions. FRAME analyses of focus groups identified adaptation goals to increase trial feasibility, decrease patient/provider COVID exposures, and increasing patient engagement/retention. Context adaptations focused on virtual delivery while content adaptations included adding elements to enhance safety, tailoring/refining protocols for virtual delivery, and removing/skipping hands-on pain management interventions. Background: The COVID-19 pandemic changed the delivery of healthcare services and disrupted clinical research programs. This study evaluated adaptations made to 11 in-progress, pragmatic clinical trials (PCTs) of non-pharmacological pain management interventions in Department of Veterans Affairs and Department of Defense healthcare facilities. Conclusion: While core elements of trial interventions were retained, investigators were required to adapt study protocols for non-pharmacological pain management PCTs to address COVID-related disruptions and restrictions.

12.
Sustainability ; 14(12):7081, 2022.
Article in English | ProQuest Central | ID: covidwho-1911534

ABSTRACT

This article presents the first results of the project Architecture 360, which focuses on learning alternatives for developing working skills in higher education courses, and specifically construction competences for architecture students. The project aims to help teachers to choose the best learning solutions for their classes from numerous alternatives of strategies, dynamics and activities. The assistance is based on developing a new approach that combines several methods (strengths, weaknesses, opportunities and threats (SWOT);multi-criteria decision-making;Delphi;and the Knapsack problem) and draws from teachers’ experience, a panel of experts’ expertise, the revised Bloom Taxonomy and neuroscience for education. The new approach to assisting university teachers in choosing the best practical learning alternatives was successfully developed and validated for the case study of a course at Barcelona Architecture School. In general, the approach defined the main strengths, weaknesses, opportunities and threats of 26 learning alternatives. In the case study, the following optimized set of alternatives were identified: blended learning, challenge-based learning, reflective learning, videos of real cases, case studies, site visits, interactive simulation and gamification. Moreover, 23 activities were analysed. It was concluded, for instance, that active alternatives would improve implementation, including teachers’ available teaching materials and dedication outside class.

13.
Journal of Intelligent and Fuzzy Systems ; 43(2):1995-2004, 2022.
Article in English | Scopus | ID: covidwho-1910978

ABSTRACT

The World Health Organization has stated Covid-19 as a pandemic that has posture a current hazard to humanity. Covid-19 pandemic has magnificently forced global shutdown of several events, including educational activities. This has caused in tremendous crisis-response immigration of educational institutes with online smart learning helping as the educational platform. Smart learning targets at providing universal learning to students consuming modern technology to completely prepare them for a fast-changing world everywhere. In this research paper an evaluation system has been developed that is based on bloom taxonomy. A Neuro-fuzzy system for the training and testing of the data for smart and traditional learning outcomes has been applied on collected data. For this research work, we have selected students of the computing discipline and focus on core-computing subjects. The findings of this research work shows the importance of smart learning and its positive impact on student learning outcomes. The evaluation criteria are based on revised bloom taxonomy levels, such that all six levels have been covered. The students' performance are very much encouraging when compared with ground truth values and reported 91.2% overall accuracy of proposed model on collected samples. © 2022 - IOS Press. All rights reserved.

14.
Journal of Engineering, Design and Technology ; 20(4):861-865, 2022.
Article in English | ProQuest Central | ID: covidwho-1909128

ABSTRACT

Whilst there is a clear need for increased spending, embracing innovation, working smarter and collaboratively to enhance capability and capacity will also have a significant impact in bridging this gap and saving global economies valuable resources (Chen et al., 2018;World Economic Forum, 2019). [...]the topic of developing smart systems and technological advancements in facilitating, building and sustaining capacity and capability is of significance for infrastructure development and a necessity for the construction sector. [...]bibliometric and content analysis was used, and a taxonomy of risks associated to OSM was developed. [...]a novel deep CNN learning model was developed to maximise crack detection accuracy. [...]in article seven, Danquah et al. looked into the awareness of design requirements to enable future technology applications.

15.
International Conference on Tourism Research ; : 413-422,IX, 2022.
Article in English | ProQuest Central | ID: covidwho-1905320

ABSTRACT

Developing a course curricula is a complex and difficult task since it must reflect the fundamental technical competencies and skills, but also the soft skills that students must develop to practice a specific profession. In this sense, Higher Education Institutions have been struggling to find strategies and incorporate methodologies into their course curricula that will promote the balanced development of these technical and transversal competencies and skills. Therefore, this paper describes an exploratory study on how the competencies and skills dynamic is featured in the description of the learning outcomes of a 3-year Bachelor in Hospitality Management degree in Portugal. It analysed the forty learning outcomes of the different subjects of the degree and framed in the Reference Framework by The Council of the European Union. Moreover, it also analysed the application of the taxonomy of Bloom in describing the learning outcomes. The preliminary results show that there are some explicit learning outcomes outlined in the reference framework of the European Union but they still lack those related to soft skills development. Furthermore, the application of the taxonomy of Bloom is adequate and fully present in the learning outcomes. These results highlight the need of reviewing the description of the learning outcomes, mainly its alignment with the content and teaching and assessment methodologies adopted by the different subjects.

16.
Pakistan Journal of Zoology ; 54(4):1899-1904, 2022.
Article in English | CAB Abstracts | ID: covidwho-1904009

ABSTRACT

Coronavirus consists of single-stranded, enveloped and RNA virus, largest genome among all RNA viruses and has 4 proteins i.e. envelope, spike, nucleocapsid and membrane. Coronaviruses are classified into 4 genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Betacoronavirus most probably originated from bats and the virus may have jumped to avian species and evolved as Deltacoronavirus group. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavirus from Deltacoronavirus, while Betacoronavirus may have given rise to Alphacoronavirus. It is known that SARS-CoV-2 belongs to Betacoronavirus. This most similar virus is verified in bat and Malayan Pangolin. Analysis showed that SARS-CoV-2 most probably originated by recombination of both bat and pangolin viruses. Viral protein seroconversion and viral specific nucleotide positive documented in all COVID-19 patients tested provides confirmation of a link between the presence of this virus and the disease.

17.
Studies in Mycology ; 101:417-564, 2022.
Article in English | CAB Abstracts | ID: covidwho-1902874

ABSTRACT

This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names.

18.
NAVC Clinician's Brief ; 29, 2022.
Article in English | CAB Abstracts | ID: covidwho-1898327
19.
Zhongguo Yufang Shouyi Xuebao / Chinese Journal of Preventive Veterinary Medicine ; 44(3):320-324, 2022.
Article in English, Chinese | CAB Abstracts | ID: covidwho-1898320

ABSTRACT

Chicken infectious bronchitis (IB) is one of the epidemic diseases that cause severe economic loss to poultry industry and induced by the infection of infectious bronchitis virus (IBV). IBV was prone to mutation and recombination due to its genomic characteristics, resulting in new antigenic variants. In order to understand the prevalence and variation of IBV in Shanxi province and provide reference for IB epidemic prevention and control in this area, tissues of a broiler flock suspected of respiratory virus infection were collected in Jinzhong city, Shanxi province. Through PCR identification, chicken embryo inoculation, and sequencing verification, an IBV strain was isolated and named CK/Shanxi-01/2021. On the basis of S1 gene sequencing, the sequence was compared with those of the representative IBV strains of different genotypes deposited in NCBI database, and the phylogenetic tree was constructed. The results of genetic evolution analysis showed that the IBV strain isolated in this study was belonged to GI-19 genotype. The sequence alignment of CK/Shanxi-01/2021 with common IBV vaccine strains H120, M41, H52, 4/91, and LDT3-A showed that the nucleotide homology between the isolated strain and the current common vaccine strain was 78.1%-85.2%, and the amino acid homology was only 75.2%-78.4%. Compared with the sequences of GI-19 genotype strains, some new mutations, including V68I, S120A, A271T, N282T, and N291S, were identified in the S1 protein hypervariable region(HVR). Therefore, it is of great significance for the prevention and control of IB epidemic to strengthen the epidemiological monitoring of IBV and timely grasp the current epidemic IBV genotype and its variation characteristics.

20.
Genomics ; 114(4): 110414, 2022 Jun 17.
Article in English | MEDLINE | ID: covidwho-1895509

ABSTRACT

Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.

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