Metagenomic identification of viral sequences in laboratory reagents

Porter, Ashleigh F.; Cobbin, Joanna C. A.; Li, Cixiu; Eden, John-Sebastian; Holmes, Edward C.

doi:10.1101/2021.09.10.459871

Cited by 10 publications

(7 citation statements)

References 55 publications

(84 reference statements)

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“…Circoviridae and Genomoviridae contigs, as well as a complete pneumovirus genome detected in our sequencing libraries, were considered likely reagent‐associated contaminants (Porter et al., 2021) and not analyzed in this study. Notably, the majority of nr hits for circovirus sequences were to viruses from an environmental source, and a phylogenetic analysis of putative mammalian sequences revealed that all were likely reagent contaminants.…”

Section: Methodsmentioning

confidence: 99%

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats

Brussel

Wang

Shī

et al. 2022

Transbounding Emerging Dis

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Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta‐transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV‐cases) and 36 age‐matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV‐cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV‐cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV‐cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV‐cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV‐cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co‐infections on clinical disease severity in cats with FPL.

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Section: Methodsmentioning

confidence: 99%

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats

Brussel

Wang

Shī

et al. 2022

Transbounding Emerging Dis

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“…Another probable contaminant was detected in the Miseq generated datasets, i.e., in the datasets of the healthy piglets and the piglets with signs of splay leg; reads and contigs classified as Equine infectious anemia. The common discovery of reads and contigs classified as Equine infectious anemia virus in datasets produced by metagenomic next-generation sequencing has recently been attributed to a reagent contaminant, a novel reagent-associated lenti-like virus [33]. Phylogenetic analysis of this novel reagent-associated lenti-like virus shows that it is closely related to and clusters with several known sequences of Equine infectious anemia virus, making it a recurrent classification and alignment error in datasets [33].…”

Section: Discussionmentioning

confidence: 99%

“…A few viral contigs were detected in all samples, but after blast validation almost all of them turned out to be from the Sus scrofa genome. One contig classified as Equine infectious anemia virus was detected in all samples and could be blast validated as Equine infectious anemia viru and thus most likely a reagent contaminant [33]…”

Section: Healthy Piglets (Miseq)mentioning

confidence: 99%

“…There were reads classified as viral by Kraken, but once the reads were extracted and submitted for a BLAST search only reads classified as Equine infectious anemia virus generated hits in BLAST. Virus classified as Equine infectious anemia virus is assumed to be a reagent contaminant commonly detected in metagenomic datasets [33]. The other reads classified as viral reads by Kraken did not generate viral hits when blasted but mainly hits from the pig genome.…”

Section: Piglets With Signs Of Splay Leg (Miseq and Novaseq)mentioning

confidence: 99%

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Congenital tremor and splay leg in piglets – insights into the virome, local cytokine response, and histology

et al. 2022

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Background Atypical porcine pestivirus (APPV) is a neurotropic virus associated with congenital tremor type A-II. A few experimental studies also indicate an association between APPV and splay leg. The overarching aim of the present study was to provide insights into the virome, local cytokine response, and histology of the CNS in piglets with signs of congenital tremor or splay leg. Results Characterization of the cytokine profile and virome of the brain in piglets with signs of congenital tremor revealed an APPV-associated upregulation of Stimulator of interferon genes (STING). The upregulation of STING was associated with an increased expression of the gene encoding IFN-α but no differential expression was recorded for the genes encoding CXCL8, IFN-β, IFN-γ, IL-1β, IL-6, or IL-10. No viral agents or cytokine upregulation could be detected in the spinal cord of piglets with signs of splay leg or in the brain of piglets without an APPV-infection. The histopathological examination showed no lesions in the CNS that could be attributed to the APPV-infection, as no difference between sick and healthy piglets could be seen. Conclusion The results from this study provide evidence of an APPV-induced antiviral cytokine response but found no lesions related to the infection nor any support for a common causative agent.

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“…Accordingly, these viruses were removed from the bird libraries and excluded from all analyses. Additionally, any viruses that fell into the same clades as those found in blank libraries were conservatively assumed to be contaminants [46] and similarly removed. As a result of this screen one circo-like virus in Circoviridae (single-strand DNA viruses) was removed from the data set.…”

Section: Methodsmentioning

confidence: 99%

Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand

French

Filion

Niebuhr

et al. 2022

Preprint

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New Zealand has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has received little research attention. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior undersampling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were found only in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance is needed in New Zealand avifauna, particularly in Turdus populations and endemic species.

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Metagenomic identification of viral sequences in laboratory reagents

Cited by 10 publications

References 55 publications

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats

Congenital tremor and splay leg in piglets – insights into the virome, local cytokine response, and histology

Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand

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