Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture

Gagnieur, Léa; Cheval, Justine; Gratigny, Marlène; Hébert, Charles; Muth, Erika; Dumarest, Marine; Éloit, Marc

doi:10.1016/j.biologicals.2014.02.002

Cited by 37 publications

(35 citation statements)

References 38 publications

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“…Sequences were trimmed and filtered according to their quality score and the chicken genome sequence galGal4 (ICGSC Gallus_gallus-4.0 (GCA_000002315.2)) was subtracted. Finally, de novo assembly and taxonomic assignation of contigs were conducted as previously described [5]. We evidenced contigs corresponding to endogenous retroviruses (A: 299 reads in 20 contigs, B: 385 reads in 25 contigs), which confirm previous findings: defective and non-defective loci of endogenous retroviruses are present in chicken primary fibroblasts used for the production of vaccines.…”

supporting

confidence: 65%

Analysis by high throughput sequencing of Specific Pathogen Free eggs

Gagnieur

Cheval²,

Cochet

et al. 2014

Biologicals

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supporting

confidence: 65%

Analysis by high throughput sequencing of Specific Pathogen Free eggs

Gagnieur

Cheval²,

Cochet

et al. 2014

Biologicals

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“…After chicken genome sequence subtraction (Gallus gallus complete genome, galGal4, ICGSC Gallus_gallus-4.0, GCA_000002315.2) with Cushaw2 and BlastN, reads were assembled in contigs using CLC Genomics Assembly Workbench (Cambridge, USA), and contigs and singletons were assigned a given taxonomy using the Blast algorithm. Criteria for taxonomic assignation have been described previously [9]. Sequences of the main contigs are available upon request.…”

Section: Hts and Bioinformatic Analysismentioning

confidence: 99%

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin

Denesvre¹,

Dumarest

Rémy³

et al. 2015

Virus Genes

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Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

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“…Moreover, a great diversity of hepacivirus sequences was detected in rodents and bats from Europe, Africa, Asia, and Central America (10,11). In addition to HCV-like sequences, other viral genomes assigned to the proposed genus Pegivirus were identified, expanding the family Flaviviridae (11)(12)(13)(14)(15)(16).…”

mentioning

confidence: 99%

“…Some of these viruses have been discovered through unbiased high-throughput sequencing methods (next-generation sequencing [NGS]) (11,14,16). Recent examples from human as well as veterinary diagnostics nicely document the benefit of NGS approaches in the discovery of previously unknown viruses associated with specific diseases (17,18).…”

mentioning

confidence: 99%

Identification of a Novel Hepacivirus in Domestic Cattle from Germany

Baechlein

Fischer

Grundhoff

et al. 2015

J Virol

116

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Hepatitis C virus (HCV) continues to represent one of the most significant threats to human health. In recent years, HCV-related sequences have been found in bats, rodents, horses, and dogs, indicating a widespread distribution of hepaciviruses among animals. By applying unbiased high-throughput sequencing, a novel virus of the genus Hepacivirus was discovered in a bovine serum sample. De novo assembly yielded a nearly full-length genome coding for a polyprotein of 2,779 amino acids. Phylogenetic analysis confirmed that the virus represents a novel species within the genus Hepacivirus. Viral RNA screening determined that 1.6% (n ‫؍‬ 5) of 320 individual animals and 3.2% (

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Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture

Cited by 37 publications

References 38 publications

Analysis by high throughput sequencing of Specific Pathogen Free eggs

Analysis by high throughput sequencing of Specific Pathogen Free eggs

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin

Identification of a Novel Hepacivirus in Domestic Cattle from Germany

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