High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Fitzpatrick, Amy; Rupnik, Agnieszka; O’Shea, Helen; Crispie, Fiona; Keaveney, Sinéad; Cotter, Paul D.

doi:10.3389/fmicb.2021.621719

Cited by 43 publications

(49 citation statements)

References 172 publications

(132 reference statements)

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“…2 c). Sequencing technologies are now capable of identifying both DNA and RNA viruses [104] , [43] . Nonetheless, the diversity of capsid architectures among viruses different than tailed phages is smaller [89] .…”

Section: Discussionmentioning

confidence: 99%

Predicting the capsid architecture of phages from metagenomic data

Lee

Bartels

McNair

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Discussionmentioning

confidence: 99%

Predicting the capsid architecture of phages from metagenomic data

Lee

Bartels

McNair

et al. 2022

Computational and Structural Biotechnology Journal

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“…Enrichment strategies are often needed to increase the sensitivity of NGS approaches ( Lewandowski et al. 2019 ; Fitzpatrick et al. 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing

Cassidy¹,

Schuele

Lizarazo-Forero

et al. 2022

Virus Evolution

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Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10−3 substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient.

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“…Additionally, rotaviral opportunities for inter and intra-viral family recombination are enhanced through environmental persistence, factors that promote the emergence of genetic variants with increased capacity to cause large scale outbreaks. 147 When in air and on fomites under the conditions of high humidity, studies have shown that they can persist for hours without losing their infectivity. 148 Although RV diseases are universally distributed, the epidemiological characteristics vary in different climatic regions.…”

Section: Survival and Factors Influencing Viral Persistence In The Aq...mentioning

confidence: 99%

Epidemiological significance of the occurrence and persistence of rotaviruses in water and sewage: a critical review and proposal for routine microbiological monitoring

Omatola

Olaniran

2022

Environ. Sci.: Processes Impacts

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High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Cited by 43 publications

References 172 publications

Predicting the capsid architecture of phages from metagenomic data

Predicting the capsid architecture of phages from metagenomic data

Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing

Epidemiological significance of the occurrence and persistence of rotaviruses in water and sewage: a critical review and proposal for routine microbiological monitoring

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