Analysis of Emerging Variants of Turkey Reovirus using Machine Learning

Avian reoviruses continue to cause disease in turkeys with varied pathogenicity and tissue tropism. Turkey enteric reovirus has been identified as a causative agent of enteritis or inapparent infections in turkeys. The new emerging variants of turkey reovirus, tentatively named turkey arthritis reov...

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Bibliographic Details
Published in:	Briefings in bioinformatics Vol. 25; no. 3
Main Authors:	KafiKang, Maryam, Abeysiriwardana, Chamudi, Singh, Vikash K, Young Koh, Chan, Prichard, Janet, Mor, Sunil K, Hendawi, Abdeltawab
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 27-03-2024
Subjects:	Animals Machine Learning Orthoreovirus, Avian - classification Orthoreovirus, Avian - genetics Orthoreovirus, Avian - pathogenicity Phylogeny Poultry Diseases - virology Problem Solving Protocol Reoviridae Infections - virology Turkeys - virology reovirus classification double-stranded RNA machine learning Reovirus analysis
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Summary:	Avian reoviruses continue to cause disease in turkeys with varied pathogenicity and tissue tropism. Turkey enteric reovirus has been identified as a causative agent of enteritis or inapparent infections in turkeys. The new emerging variants of turkey reovirus, tentatively named turkey arthritis reovirus (TARV) and turkey hepatitis reovirus (THRV), are linked to tenosynovitis/arthritis and hepatitis, respectively. Turkey arthritis and hepatitis reoviruses are causing significant economic losses to the turkey industry. These infections can lead to poor weight gain, uneven growth, poor feed conversion, increased morbidity and mortality and reduced marketability of commercial turkeys. To combat these issues, detecting and classifying the types of reoviruses in turkey populations is essential. This research aims to employ clustering methods, specifically K-means and Hierarchical clustering, to differentiate three types of turkey reoviruses and identify novel emerging variants. Additionally, it focuses on classifying variants of turkey reoviruses by leveraging various machine learning algorithms such as Support Vector Machines, Naive Bayes, Random Forest, Decision Tree, and deep learning algorithms, including convolutional neural networks (CNNs). The experiments use real turkey reovirus sequence data, allowing for robust analysis and evaluation of the proposed methods. The results indicate that machine learning methods achieve an average accuracy of 92%, F1-Macro of 93% and F1-Weighted of 92% scores in classifying reovirus types. In contrast, the CNN model demonstrates an average accuracy of 85%, F1-Macro of 71% and F1-Weighted of 84% scores in the same classification task. The superior performance of the machine learning classifiers provides valuable insights into reovirus evolution and mutation, aiding in detecting emerging variants of pathogenic TARVs and THRVs.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1467-5463 1477-4054
DOI:	10.1093/bib/bbae224