Computational approaches in viral ecology.
TLDR
A review of computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data can be found in this paper, where the authors focus on the challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes.Abstract:
Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.read more
Citations
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An Overview on SARS-CoV-2 (COVID-19) and Other Human Coronaviruses and Their Detection Capability via Amplification Assay, Chemical Sensing, Biosensing, Immunosensing, and Clinical Assays
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Bacteriophage ecology in biological wastewater treatment systems
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Journal ArticleDOI
Seasonal regime shift in the viral communities of a permafrost thaw lake
TL;DR: The results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada are presented and 351 viral populations (vOTUs) in the surface waters of this lake are uncovered.
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Unravelling the ecological complexity of soil viromes: Challenges and opportunities
TL;DR: In this article , the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil virus.
References
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