Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing

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

doi:10.1016/j.biologicals.2014.10.004

Cited by 8 publications

(8 citation statements)

References 37 publications

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“…Besides the development of metagenomics as a diagnostic tool in clinical virology [26,27], this methodology was applied to viral safety for biotechnological and biological products [28,29]. Using metagenomics, it is then possible to provide manufacturers the exhaustive viral bioburden of raw materials [30][31][32][33][34] and to detect adventitious viruses in live-attenuated vaccines [35].…”

Section: Introductionmentioning

confidence: 99%

Viral metagenomics and blood safety

Sauvage

Éloit

2016

Transfusion Clinique et Biologique

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The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.

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Section: Introductionmentioning

confidence: 99%

Viral metagenomics and blood safety

Sauvage

Éloit

2016

Transfusion Clinique et Biologique

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“…To describe the viral burden associated with this raw material, researchers performed HTS on mucus samples collected from European pigs and destined for heparin manufacture They identified Circoviridae and Parvoviridae family members as the most prevalent contaminating viruses, together with viruses from the Adenoviridae, Anelloviridae, Astroviridae, Birnaviridae, Caliciviridae, Picornaviridae, and Reoviridae families. These investigations indicated the effectiveness of HTS and related bioinformatics in improving biosafety and both animal and human health (87).…”

Section: Hts-based Investigations Into the Composition And Quality Ofmentioning

confidence: 92%

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine

Granberg

Bálint

Belák

2016

Rev. Sci. Tech. OIE

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Next-generation sequencing (NGS), also referred to as deep, high-throughput or massively parallel sequencing, is a powerful new tool that can be used for the complex diagnosis and intensive monitoring of infectious disease in veterinary medicine. NGS technologies are also being increasingly used to study the aetiology, genomics, evolution and epidemiology of infectious disease, as well as host-pathogen interactions and other aspects of infection biology. This review briefly summarises recent progress and achievements in this field by first introducing a range of novel techniques and then presenting examples of NGS applications in veterinary infection biology. Various work steps and processes for sampling and sample preparation, sequence analysis and comparative genomics, and improving the accuracy of genomic prediction are discussed, as are bioinformatics requirements. Examples of sequencing-based applications and comparative genomics in veterinary medicine are then provided. This review is based on novel references selected from the literature and on experiences of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.

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“…The porcine RNA viruses identified included kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. Other reports similarly attest to the diversity of the swine virome, including the presence of previously undescribed viruses (Lager et al, 2012Zhang et al, 2014Dumarest, et al, 2015). Against this vast, diverse and dynamic backdrop of viral evolution in pigs, the emergence of 3 highly pathogenic viruses over 25 years can be considered extremely rare events, but probably provides a reasonable estimate of what we should anticipate into the future.…”

Section: Continuing An Unhappy Tradition: Emergence and Evolution Of mentioning

confidence: 94%

The dilemma of rare events: Porcine epidemic diarrhea virus in North America

Davies

2015

Preventive Veterinary Medicine

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Porcine epidemic diarrhea virus (PEDV) has been recognized as a swine pathogen for 40 years, but until 2013 had not been detected in the Western Hemisphere. From originally causing a relatively mild and sporadic disease, PEDV has been more recently associated with severe outbreaks of diarrheal disease in Asia, and subsequently North America. PEDV shares some important characteristics with two major pandemic viruses (porcine reproductive and respiratory virus; porcine circovirus type 2) of pigs that have high rates of mutation and high host specificity, and appear to have been present in the swine virome for decades prior to emerging to cause severe clinical disease. A unique feature of the PEDV in North America has been the implication of feed as a vehicle for transmission, with particular concerns related to ingredients of porcine origin. The importance of relatively rare events in contributing to both the emergence and transmission of PEDV is discussed in relation to approaches for managing the associated risks.

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Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing

Cited by 8 publications

References 37 publications

Viral metagenomics and blood safety

Viral metagenomics and blood safety

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine

The dilemma of rare events: Porcine epidemic diarrhea virus in North America

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