Near-Complete Genome Sequences of Five Siciniviruses from North America

Goraichuk, Iryna V.; Davis, James F.; Parris, Darren J.; Kariithi, Henry M.; Afonso, Claudio L.; Suarez, David L.

doi:10.1128/mra.00364-21

Cited by 3 publications

(3 citation statements)

References 17 publications

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“…The present metagenomics study further confirmed the circulation of two recently discovered uncultivable intestinal poultry viruses in Belgium. Sicinivirus was discovered as a new picornavirus with unknown clinical manifestation of poultry in 2012 in Ireland [ 66 ] and currently has a worldwide documented distribution [ 67 – 70 ], while a retrospective metagenomic analysis showed its presence in samples dating back to 2003 [ 71 ]. Our study identified a significant normalized Sicinivirus read count in a pool of respiratory and intestinal tissue samples, suggesting a relatively high viral load.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples

et al. 2021

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Infectious bronchitis virus (IBV, genus Gammacoronavirus ) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity. Supplementary Information The online version contains supplementary material available at 10.1007/s11262-021-01872-7.

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Section: Discussionmentioning

confidence: 99%

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples

et al. 2021

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“…Goraichuk. Collaborators discovered five novel siciniviruses from poultry samples from North America [ 42 ]. In a different case, a 15-year-old sample confirmed the circulation of the GA08-like strain and complete genomes of avian coronavirus 4 years before its first reported outbreak [ 43 ].…”

Section: Short-read Sequencing On Poultry and Avian Speciesmentioning

confidence: 99%

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Afonso,

Afonso

2023

Veterinary Sciences

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Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of “semi-quantitative” information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

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“…In recent years, untargeted next-generation sequencing (NGS) technology has been increasingly employed for the detection and characterization of RNA viruses, particularly in the context of avian diseases ( Chen et al, 2013 ; Tang et al, 2015 ; Goraichuk et al, 2016 , 2017 , 2019 , 2021a , b ; Croville et al, 2018 ; Ferreri et al, 2019 ; Tal et al, 2019 ; Patzina-Mehling et al, 2020 ; Crossley et al, 2021 ; Chrzastek et al, 2022 ; Damir et al, 2023 ; Ip et al, 2023 ; Kariithi et al, 2023 ; Techera et al, 2023 ). Avian viruses, including highly pathogenic avian influenza virus (AIV) and Newcastle disease virus (NDV), pose significant threats to poultry populations and public health ( Alexander, 1998 ; Suarez, 2017 ; Swayne et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing

Goraichuk,

Harden,

Spackman

et al. 2024

Front. Microbiol.

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Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.

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Near-Complete Genome Sequences of Five Siciniviruses from North America

Cited by 3 publications

References 17 publications

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing

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