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Valiant WG, Borman J, Cai K, Vallone PM. Efficient extraction of adventitious virus nucleic acid using commercially available methods. Biologicals 2024; 85:101741. [PMID: 38157678 DOI: 10.1016/j.biologicals.2023.101741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 04/16/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024] Open
Abstract
An essential step in pharmaceutical product development is screening for contamination with adventitious agents, and there is desire to develop highly sensitive assays to detect adventitious viral nucleic acid. This study sought to examine the nucleic acid extraction efficiency of three viral candidates in relevant background matrices using four different extraction methods. Three model adventitious viruses, Minute virus of Mice, Porcine Circovirus, and Feline Leukemia Virus, were diluted within a variety of background matrices relevant to pharmaceutical production methods. Upon extraction, the nucleic acid was quantified using droplet digital PCR methods. Four nucleic acid extraction methods were assessed, including commercially available kits and manual extraction methods. Each method recovered nucleic acid post-extraction for each of the model viruses within the tested background matrices. The silica-column based method recovered a greater amount of viral nucleic acid, compared to the other methods tested. Similar trends were observed when model virus was diluted in bioreactor supernatant, which replicates industry testing conditions and provides details on which extraction methods might be used in Next Generation Sequencing and PCR methods for detecting contamination within pharmaceutical products.
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Affiliation(s)
- William G Valiant
- Biomolecular Measurement Division, Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jon Borman
- Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Kang Cai
- Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Peter M Vallone
- Biomolecular Measurement Division, Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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Nagy A, Chakrabarti L, Kurasawa J, Mulagapati SHR, Devine P, Therres J, Chen Z, Schmelzer AE. Engineered CHO cells as a novel AAV production platform for gene therapy delivery. Sci Rep 2023; 13:19210. [PMID: 37932360 PMCID: PMC10628118 DOI: 10.1038/s41598-023-46298-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
The Herpes simplex virus (HSV)-based platform for production of recombinant adeno-associated viral vectors (rAAVs) yields higher titers and increased percentage of full capsids when compared to the triple transient transfection (TTT) method. However, this platform currently faces two major challenges. The first challenge is the reliance on commercial media, sometimes supplemented with serum, leading to costly manufacturing and a high risk for introduction of adventitious agents. The second challenge is that the production of HSV-1 relies on adherent complementing Vero cells (V27), making it difficult to scale up. We engineered serum-free-adapted CHO cells expressing key HSV-1 entry receptors, HVEM and/or Nectin-1 to address the first challenge. Using high-throughput cloning methods, we successfully selected a HVEM receptor-expressing clone (CHO-HV-C1) that yields 1.62 × 109, 2.51 × 109, and 4.07 × 109 viral genome copies/mL with rAAV6.2-GFP, rAAV8-GFP, and rAAV9-GFP vectors respectively, within 24 h post rHSV-1 co-infection. Moreover, CHO-HV-C1-derived rAAVs had comparable in vitro transduction, infectivity, and biodistribution titers to those produced by TTT. The second challenge was addressed via engineering CHO-HV-C1 cells to express HSV-1 CP27. These cells successfully produced rHSV-1 vectors, but with significantly lower titers than V27 cells. Taken together, the CHO/HSV system provides a novel, scalable, reduced cost, serum-free AAV manufacturing platform.
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Affiliation(s)
- Abdou Nagy
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA.
| | - Lina Chakrabarti
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - James Kurasawa
- Biologics Engineering, R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Sri Hari Raju Mulagapati
- Analytical Science, Biopharmaceutical Development, Biopharma R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Paul Devine
- Analytical Science, Biopharmaceutical Development, Biopharma R&D, AstraZeneca, Milstein Building, Granta Park, Cambridge, CB216GH, UK
| | - Jamy Therres
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Zhongying Chen
- Clinical Pharmacology and Safety Sciences, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Albert E Schmelzer
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA.
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Wei F, Hua Q, Liang J, Yue M, Xu D, Tian W, Yu L, Feng Z. Cell line derived from muscle of Gymnocypris przewalskii, a species of Schizothoracinae in Qinghai Lake, Qinghai-Tibet Plateau. In Vitro Cell Dev Biol Anim 2022; 58:970-978. [PMID: 36287296 DOI: 10.1007/s11626-022-00729-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/17/2022] [Indexed: 12/27/2022]
Abstract
Gymnocypris przewalskii (naked carp), a native teleost, plays an important role in the ecosystem of Qinghai Lake (altitude, 3.2 km) on the Qinghai-Tibet Plateau in China. We developed a new cell line from the muscle of G. przewalskii using the explant technique and named the cell line GPM. This cell line was maintained in DMEM medium (high glucose) supplemented with 15% fetal bovine serum (FBS). The cell line was successfully subcultured up to 32 passages and was authenticated by immunofluorescence assay, sequencing the mitochondrial cytochrome C oxidase subunit I (COI) and 16S rRNA genes, and by chromosome analysis. In the medium containing 15% FBS, the cell line could be passaged stably at 25 °C. The GPM cell line could express green fluorescent protein (GFP) with a CMV promoter with about 5% transfection efficiency. MTT tests showed that Clostridium botulinum toxin (BTX) was toxic to the cell line. The cell line could be successfully cryopreserved in liquid nitrogen with a revival efficiency of over 70%. This study demonstrated that the GPM cell line can be used as an important tool for understanding the physiological characteristics of G. przewalskii, and it can provide a resource for studying gene function and toxicological reactions in vitro.
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Affiliation(s)
- Fulei Wei
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China.
| | - Miao Yue
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China
| | - Dingfan Xu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China
| | - Wengen Tian
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
| | - Luxian Yu
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
| | - Zhaohui Feng
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
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Pilgrim CR, McCahill KA, Rops JG, Dufour JM, Russell KA, Koch TG. A Review of Fetal Bovine Serum in the Culture of Mesenchymal Stromal Cells and Potential Alternatives for Veterinary Medicine. Front Vet Sci 2022; 9:859025. [PMID: 35591873 PMCID: PMC9111178 DOI: 10.3389/fvets.2022.859025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Fetal bovine serum (FBS) remains widely used as a supplement in cell culture media used in the isolation and expansion of mesenchymal stromal cells (MSC) despite longstanding practical, clinical, and ethical concerns over its use. As a result, research on alternative culture media supplement solutions that conserve crucial MSC characteristics has become increasingly relevant. Species-specific supplements and serum-free media such as platelet lysate or chemically defined media have been assessed for their effect in MSC cultures regarding proliferation, differentiation, and immunomodulatory capacity. While none of the alternatives offer a complete solution in replacing traditional FBS supplemented media for culturing MSCs for all species, short-term or transitional use of FBS-free media can perform equally well and could address some of the concerns over the use of FBS.
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Affiliation(s)
| | | | | | | | | | - Thomas G. Koch
- Department of Biomedical Science, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products. Viruses 2021; 13:v13122425. [PMID: 34960693 PMCID: PMC8705701 DOI: 10.3390/v13122425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies’ established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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Water-soluble tetra-cationic porphyrins display virucidal activity against Bovine adenovirus and Bovine alphaherpesvirus 1. Photodiagnosis Photodyn Ther 2020; 31:101947. [PMID: 32768587 DOI: 10.1016/j.pdpdt.2020.101947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 11/21/2022]
Abstract
Porphyrins are photoactive compounds that can absorb the energy of light and transfer it to oxygen molecules, producing reactive oxygen species (ROS). Once produced, ROS may alter biological molecules and cellular mechanisms, leading to cell apoptosis or inactivation of microorganisms, such as bacteria, fungi, and viruses. Therefore, the objective of this study was to evaluate the in vitro virucidal activity of six tetra-cationic porphyrins against two bovine viruses (Bovine alphaherpesvirus 1, BoHV-1, enveloped; and Bovine adenovirus, BAV, non-enveloped). For this, viral suspensions were incubated with each porphyrin (H2TMeP, ZnTMeP, and CuTMeP at 4.0 μM, NiTMeP at 5.0 μM, and CoClTMeP and MnClTMeP at 1.0 μM) and exposed to white-light irradiation for 0, 60, 120, and 180 min (BAV) or 0, 30, 60, 90, and 120 min (BoHV-1). Then, the remaining viral titers were determined by limiting dilution and compared with the control (virus + porphyrins without light exposition). The porphyrins H2TMeP and ZnTMeP showed the highest virucidal activity against both viruses. ZnTMeP inactivated BoHV-1 after 30 min of photoactivation and H2TMeP after 60 min. The BAV was photo-inactivated by both porphyrins at 180 min of white-light exposition. CuTMeP, NiTMeP, and CoClTMeP porphyrins had weak virucidal activity against BoHV-1 and MnClTMeP showed no virucidal activity against both viruses. These results indicated that free-base H2TMeP and ZnTMeP porphyrins present virucidal activity against non-enveloped and enveloped viruses, opening the possibility for their use to inactivate viruses on surfaces, biological substrates, and solutions.
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Identification of a novel bovine copiparvovirus in pooled fetal bovine serum. Virus Genes 2020; 56:522-526. [PMID: 32306155 PMCID: PMC7329774 DOI: 10.1007/s11262-020-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/03/2020] [Indexed: 01/12/2023]
Abstract
A novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~ 50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to the Copiparvovirus genus, being most closely related to bovine parvovirus 2 (BPV2) with 41% identity with the non-structural protein NS1 and 47% identity with the virus capsid protein of BPV2. A screen of individual and pooled bovine sera identified a closely related variant of the novel virus in a second serum pool. For classification purposes, the novel virus has been designated bovine copiparvovirus species 3 isolate JB9 (bocopivirus 3-JB9).
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Jiménez-Meléndez A, Fernández-Álvarez M, Calle A, Ramírez MÁ, Diezma-Díaz C, Vázquez-Arbaizar P, Ortega-Mora LM, Álvarez-García G. Lytic cycle of Besnoitia besnoiti tachyzoites displays similar features in primary bovine endothelial cells and fibroblasts. Parasit Vectors 2019; 12:517. [PMID: 31685001 PMCID: PMC6829937 DOI: 10.1186/s13071-019-3777-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bovine besnoitiosis, caused by the cyst-forming apicomplexan parasite Besnoitia besnoiti, is a chronic and debilitating cattle disease that continues to spread in Europe in the absence of control tools. In this scenario, in vitro culture systems are valuable tools to carry out drug screenings and to unravel host-parasite interactions. However, studies performed in bovine target cells are scarce. METHODS The objective of the present study was to obtain primary bovine aortic endothelial cells (BAECs) and fibroblast cell cultures, target cells during the acute and the chronic stage of the disease, respectively, from healthy bovine donors. Afterwards, expression of surface (CD31, CD34 and CD44) and intracellular markers (vimentin and cytokeratin) was studied to characterize cell populations by flow cytometry. Next, the lytic cycle of B. besnoiti tachyzoites was studied in both target cells. Invasion rates (IRs) were determined by immunofluorescence at several time points post-infection, and proliferation kinetics were studied by quantitative PCR (qPCR). Finally, the influence of bovine viral diarrhea virus (BVDV) co-infection on the host cell machinery, and consequently on B. besnoiti invasion and proliferation, was investigated in BAECs. RESULTS Morphology and cytometry results confirmed the endothelial and fibroblast origins. CD31 was the surface marker that best discriminated between BAECs and fibroblasts, since fibroblasts lacked CD31 labelling. Expression of CD34 was weak in low-passage BAECs and absent in high-passage BAECs and fibroblasts. Positive labelling for CD44, vimentin and cytokeratin was observed in both BAECs and fibroblasts. Regarding the lytic cycle of the parasite, although low invasion rates (approximately 3-4%) were found in both cell culture systems, more invasion was observed in BAECs at 24 and 72 hpi. The proliferation kinetics did not differ between BAECs and fibroblasts. BVDV infection favoured early Besnoitia invasion but there was no difference in tachyzoite yields observed in BVDV-BAECs compared to BAECs. CONCLUSIONS We have generated and characterized two novel standardized in vitro models for Besnoitia besnoiti infection based on bovine primary target BAECs and fibroblasts, and have shown the relevance of BVDV coinfections, which should be considered in further studies with other cattle pathogens.
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Affiliation(s)
- Alejandro Jiménez-Meléndez
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - María Fernández-Álvarez
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Alexandra Calle
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Avenida Puerta de Hierro 12, local 10, 28040 Madrid, Spain
| | - Miguel Ángel Ramírez
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Avenida Puerta de Hierro 12, local 10, 28040 Madrid, Spain
| | - Carlos Diezma-Díaz
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Patricia Vázquez-Arbaizar
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Luis Miguel Ortega-Mora
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Gema Álvarez-García
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Zhai SL, Lu SS, Wei WK, Lv DH, Wen XH, Zhai Q, Chen QL, Sun YW, Xi Y. Reservoirs of Porcine Circoviruses: A Mini Review. Front Vet Sci 2019; 6:319. [PMID: 31616677 PMCID: PMC6763682 DOI: 10.3389/fvets.2019.00319] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023] Open
Abstract
Porcine circovirus (PCV) is one of the smallest known DNA viruses in mammals. At present, PCVs are divided into three species, PCV1, PCV2, and PCV3. PCV1 and PCV2 were found in the 1970s and the 1990s, respectively, whereas PCV3 was discovered recently in 2016. PCV1 does not cause diseases in pigs. However, PCV3, similar to PCV2, is reported to be associated with several swine diseases, including porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCVs are very common in domestic pigs as well as wild boars. However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. PCVs are also abundant in the environment, including water samples and air samples. Interestingly, PCV1 and/or PCV2 antibody or antigen has also been detected in sera, stool samples and respiratory swab samples of human, revealing zoonotic potential of PCVs. Thus, PCVs inhabit many types of reservoirs. In this review, we summarize the reservoirs of PCVs, and this information would be helpful in understanding the natural circulating status and possible cross-species transmission of PCVs.
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Affiliation(s)
- Shao-Lun Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Shou-Sheng Lu
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Wen-Kang Wei
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Dian-Hong Lv
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Xiao-Hui Wen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qi Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qin-Ling Chen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Yan-Wei Sun
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Yun Xi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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11
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Basso G, Cargnelutti JF, Oliveira AL, Acunha TV, Weiblen R, Flores EF, Iglesias BA. Photodynamic inactivation of selected bovine viruses by isomeric cationic tetra-platinated porphyrins. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619500767] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Porphyrin-based photodynamic processes have been used for the inactivation of microorganisms and treatment of tumors. The virucidal activity of porphyrins 3-PtTPyP and 4-PtTPyP was investigated against bovine viruses representative of the main structural groups (enveloped/non-enveloped, DNA/RNA: BVDV, BoHV-1, BAV and BEV), and against two epitheliotropic viruses (VSV and VACV). Viral suspensions were incubated at 0.91 [Formula: see text]mol [Formula: see text] L[Formula: see text] and exposed to a white-light LED array source (25 mW [Formula: see text] cm[Formula: see text]; 90 J [Formula: see text] cm[Formula: see text] for 0, 15, 30 and 60 min followed by determination of the remaining virus titers. Porphyrin 3-PtTPyP reduced almost 6 log of VSV and 3.5 log of BVDV titers after 15 min and complete virus photoinactivation was achieved after 30 min. 4-PtTPyP at 0.91 [Formula: see text]mol [Formula: see text] L[Formula: see text] produced reduction of titers of all enveloped virus depending on the time of light irradiation. No virucidal activity of any of the porphyrins was observed for non-enveloped viruses and these results showed the potential of porphyrins to inactivate viruses in premises.
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Affiliation(s)
- Giovana Basso
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Juliana F. Cargnelutti
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Amanda L. Oliveira
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
- Programa de Residência Multiprofissional em Área Profissional de Saúde/Medicina Veterinária, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Thiago V. Acunha
- Departamento de Química, Laboratório de Bioinorgânica e Materiais Porfirínicos, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Rudi Weiblen
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Eduardo F. Flores
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
| | - Bernardo A. Iglesias
- Departamento de Química, Laboratório de Bioinorgânica e Materiais Porfirínicos, Universidade Federal de Santa Maria, Av. Roraima 1000, Santa Maria, Rio Grande do Sul, Brazil. CEP 97105-900, Brazil
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12
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Application of next generation sequencing technology on contamination monitoring in microbiology laboratory. BIOSAFETY AND HEALTH 2019; 1:25-31. [PMID: 32501441 PMCID: PMC7148601 DOI: 10.1016/j.bsheal.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.
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13
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Haddad-Boubaker S, Joffret ML, Pérot P, Bessaud M, Meddeb Z, Touzi H, Delpeyroux F, Triki H, Eloit M. Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia. Arch Virol 2019; 164:747-755. [DOI: 10.1007/s00705-018-04141-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/29/2018] [Indexed: 01/24/2023]
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14
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Bergner LM, Orton RJ, da Silva Filipe A, Shaw AE, Becker DJ, Tello C, Biek R, Streicker DG. Using noninvasive metagenomics to characterize viral communities from wildlife. Mol Ecol Resour 2018; 19:128-143. [PMID: 30240114 PMCID: PMC6378809 DOI: 10.1111/1755-0998.12946] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022]
Abstract
Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.
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Affiliation(s)
- Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Andrew E Shaw
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Daniel J Becker
- Odum School of Ecology, University of Georgia, Athens, Georgia.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia.,Department of Microbiology and Immunology, Montana State University, Bozeman, Montana
| | - Carlos Tello
- Association for the Conservation, Development of Natural Resources, Lima, Peru.,Yunkawasi, Lima, Peru
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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15
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Whitmer SLM, Yadav PD, Sarkale P, Chaubal GY, Francis A, Klena J, Nichol ST, Ströher U, Mourya DT. Characterization of Unknown Orthobunya-Like Viruses from India. Viruses 2018; 10:v10090451. [PMID: 30149496 PMCID: PMC6165560 DOI: 10.3390/v10090451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.
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Affiliation(s)
- Shannon L M Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | | | | | | | - Alicia Francis
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30322, USA.
| | - John Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Ute Ströher
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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16
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Piletz JE, Drivon J, Eisenga J, Buck W, Yen S, McLin M, Meruvia W, Amaral C, Brue K. Human Cells Grown With or Without Substitutes for Fetal Bovine Serum. CELL MEDICINE 2018; 10:2155179018755140. [PMID: 32634183 PMCID: PMC6172986 DOI: 10.1177/2155179018755140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022]
Abstract
Safety concerns over cell-derived pharmaceutical products being manufactured in
supplements of fetal bovine serum (FBS) have ignited pleas to replace FBS. Herein, four
newly marketed alternatives to FBS were compared: a xeno-free product called Cell-Ess®, a
human platelet lysate marketed as GroPro®, and two mixtures of adult bovine serum varying
in their proportions of neonatal growth factors, called Liporo® and FetalGro®. An
endothelial cell line (C2BBe1) and a neuronal cell line (SHSY5Y) near confluency in media
with 10% FBS were selectively scraped and taken through a 25-day step-wise algorithm to
replace FBS, and another human endothelial cell line (HRA-19) was studied to replicate
C2BBe1. Cells were stained, counted, and compared for viability, migration, and spheroids.
The C2BBe1 and HRA-19 cell lines failed to proliferate in 10% Cell-Ess® but grew in 10%
GroPro® or 10% FetalGro® reasonably well compared to reference 10% FBS. With SH-SY5Y, only
FetalGro® approached FBS's efficacy. These were all inferior to 11 different branded lots
of FBS (positive controls), but five days into switching just amongst the FBS brands, 4 of
11 supported less proliferation than reference FBS in endothelial HRA-19
(p < 0.004). Moreover, neurospheres were enriched in two branded
lots of FBS and FetalGro® (each p < 0.004), neurospheres being an
unwanted phenotype for any neuronal cell application. Because platelet-derived GroPro®
stood out amongst the non-FBS growth supplements to allow proliferation without inducing
spheroids, it seems the best (mindful that the cells still grew slower in it compared to
FBS). While no perfect replacement was found amongst the alternatives to FBS, the
algorithm for switching should be useful in future testing of new alternatives to FBS as
the need arises to switch from FBS and expand pharmaceutical products with safety for
human use.
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Affiliation(s)
- John E Piletz
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Jennifer Drivon
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - John Eisenga
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Will Buck
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Sabrina Yen
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Megan McLin
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - William Meruvia
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Carolina Amaral
- Department of Biology, Mississippi College, Clinton, MS, USA
| | - Kellie Brue
- Department of Biology, Mississippi College, Clinton, MS, USA
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17
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Aetiology of acute meningoencephalitis in Cambodian children, 2010-2013. Emerg Microbes Infect 2017; 6:e35. [PMID: 28536430 PMCID: PMC5520480 DOI: 10.1038/emi.2017.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 01/09/2023]
Abstract
Acute meningoencephalitis (AME) is associated with considerable morbidity and mortality in children in developing countries. Clinical specimens were collected from children presenting with AME at two Cambodian paediatric hospitals to determine the major aetiologies associated with AME in the country. Cerebrospinal fluid (CSF) and blood samples were screened by molecular and cell culture methods for a range of pathogens previously associated with AME in the region. CSF and serum (acute and convalescent) were screened for antibodies to arboviruses such as Japanese encephalitis virus (JEV), dengue virus (DENV), and chikungunya virus (CHIKV). From July 2010 through December 2013, 1160 children (one month to 15 years of age) presenting with AME to two major paediatric hospitals were enroled into the study. Pathogens associated with AME were identified using molecular diagnostics, cell culture and serology. According to a diagnostic algorithm, a confirmed or highly probable aetiologic agent was detected in 35.0% (n=406) of AME cases, with a further 9.2% (total: 44.2%, n=513) aetiologies defined as suspected. JEV (24.4%, n=283) was the most commonly identified pathogen followed by Orientia tsutsugamushi (4.7%, n=55), DENV (4.6%, n=53), enteroviruses (3.5%, n=41), CHIKV (2.0%, n=23) and Streptococcus pneumoniae (1.6%, n=19). The majority of aetiologies identified for paediatric AME in Cambodia were vaccine preventable and/or treatable with appropriate antimicrobials.
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18
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Toohey-Kurth K, Sibley SD, Goldberg TL. Metagenomic assessment of adventitious viruses in commercial bovine sera. Biologicals 2017; 47:64-68. [PMID: 28366627 DOI: 10.1016/j.biologicals.2016.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/29/2022] Open
Abstract
Animal serum is an essential supplement for cell culture media. Contamination of animal serum with adventitious viruses has led to major regulatory action and product recalls. We used metagenomic methods to detect and characterize viral contaminants in 26 bovine serum samples from 12 manufacturers. Across samples, we detected sequences with homology to 20 viruses at depths of up to 50,000 viral reads per million. The viruses detected represented nine viral families plus four taxonomically unassigned viruses and had both RNA genomes and DNA genomes. Sequences ranged from 28% to 96% similar at the amino acid level to viruses in the GenBank database. The number of viruses varied from zero to 11 among samples and from one to 11 among suppliers, with only one product from one supplier being entirely "clean." For one common adventitious virus, bovine viral diarrhea virus (BVDV), abundance estimates calculated from metagenomic data (viral reads per million) closely corresponded to Ct values from quantitative real-time reverse transcription polymerase chain reaction (rtq-PCR), with metagenomics being approximately as sensitive as rtq-PCR. Metagenomics is useful for detecting taxonomically and genetically diverse adventitious viruses in commercial serum products, and it provides sensitive and quantitative information.
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Affiliation(s)
- Kathy Toohey-Kurth
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; Wisconsin Veterinary Diagnostic Laboratory, 445 Easterday Lane, Madison, WI 53706, USA
| | - Samuel D Sibley
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA
| | - Tony L Goldberg
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; University of Wisconsin-Madison Global Health Institute, 1300 University Avenue, Madison, WI 53706, USA.
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19
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Sadeghi M, Kapusinszky B, Yugo DM, Phan TG, Deng X, Kanevsky I, Opriessnig T, Woolums AR, Hurley DJ, Meng XJ, Delwart E. Virome of US bovine calf serum. Biologicals 2017; 46:64-67. [PMID: 28100412 DOI: 10.1016/j.biologicals.2016.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/02/2016] [Accepted: 12/29/2016] [Indexed: 01/23/2023] Open
Abstract
Using viral metagenomics we analyzed four bovine serum pools assembled from 715 calves in the United States. Two parvoviruses, bovine parvovirus 2 (BPV2) and a previously uncharacterized parvovirus designated as bosavirus (BosaV), were detected in 3 and 4 pools respectively and their complete coding sequences generated. Based on NS1 protein identity, bosavirus qualifies as a member of a new species in the copiparvovirus genus. Also detected were low number of reads matching ungulate tetraparvovirus 2, bovine hepacivirus, and several papillomaviruses. This study further characterizes the diversity of viruses in calf serum with the potential to infect fetuses and through fetal bovine serum contaminate cell cultures.
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Affiliation(s)
- Mohammadreza Sadeghi
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Virology, University of Helsinki, Finland
| | - Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Danielle M Yugo
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Isis Kanevsky
- Department of Dairy Science, College of Agriculture and Life Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Tanja Opriessnig
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, Scotland, UK
| | - Amelia R Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, MS, USA
| | - David J Hurley
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
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20
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Klug B, Robertson JS, Condit RC, Seligman SJ, Laderoute MP, Sheets R, Williamson AL, Chapman L, Carbery B, Mac LM, Chen RT. Adventitious agents and live viral vectored vaccines: Considerations for archiving samples of biological materials for retrospective analysis. Vaccine 2016; 34:6617-6625. [PMID: 27317264 PMCID: PMC5130882 DOI: 10.1016/j.vaccine.2016.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 11/25/2022]
Abstract
Vaccines are one of the most effective public health medicinal products with an excellent safety record. As vaccines are produced using biological materials, there is a need to safeguard against potential contamination with adventitious agents. Adventitious agents could be inadvertently introduced into a vaccine through starting materials used for production. Therefore, extensive testing has been recommended at specific stages of vaccine manufacture to demonstrate the absence of adventitious agents. Additionally, the incorporation of viral clearance steps in the manufacturing process can aid in reducing the risk of adventitious agent contamination. However, for live viral vaccines, aside from possible purification of the virus or vector, extensive adventitious agent clearance may not be feasible. In the event that an adventitious agent is detected in a vaccine, it is important to determine its origin, evaluate its potential for human infection and pathology, and discern which batches of vaccine may have been affected in order to take risk mitigation action. To achieve this, it is necessary to have archived samples of the vaccine and ancillary components, ideally from developmental through to current batches, as well as samples of the biological materials used in the manufacture of the vaccine, since these are the most likely sources of an adventitious agent. The need for formal guidance on such vaccine sample archiving has been recognized but not fulfilled. We summarize in this paper several prior major cases of vaccine contamination with adventitious agents and provide points for consideration on sample archiving of live recombinant viral vector vaccines for use in humans.
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Affiliation(s)
- Bettina Klug
- Divison Immunology Paul-Ehrlich-Institut, D-63225 Langen, Germany
| | - James S. Robertson
- Independent Adviser (formerly of National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK)
| | - Richard C. Condit
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610
| | - Stephen J. Seligman
- Department of Microbiology and Immunology, New York Medical College Valhalla, NY 10595, USA
| | - Marian P. Laderoute
- Immune System Management Inc., Ottawa, Ontario, Canada, K1S 5R5 (formerly of Blood Safety Contribution Program, Public Health Agency of Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Rebecca Sheets
- Independent Adviser (formerly of NIAID, NIH, Bethesda, MD 20893, USA)
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
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21
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Duong V, Mey C, Eloit M, Zhu H, Danet L, Huang Z, Zou G, Tarantola A, Cheval J, Perot P, Laurent D, Richner B, Ky S, Heng S, Touch S, Sovann L, van Doorn R, Tan Tran T, Farrar JJ, Wentworth DE, Das SR, Stockwell TB, Manuguerra JC, Delpeyroux F, Guan Y, Altmeyer R, Buchy P. Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia. Emerg Microbes Infect 2016; 5:e104. [PMID: 27651091 PMCID: PMC5113052 DOI: 10.1038/emi.2016.101] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/03/2016] [Accepted: 07/25/2016] [Indexed: 02/08/2023]
Abstract
Human enterovirus 71 (EV-A71) causes hand, foot and mouth disease (HFMD). EV-A71 circulates in many countries and has caused large epidemics, especially in the Asia-Pacific region, since 1997. In April 2012, an undiagnosed fatal disease with neurological involvement and respiratory distress occurred in young children admitted to the Kantha Bopha Children's Hospital in Phnom Penh, Cambodia. Most died within a day of hospital admission, causing public panic and international concern. In this study, we describe the enterovirus (EV) genotypes that were isolated during the outbreak in 2012 and the following year. From June 2012 to November 2013, 312 specimens were collected from hospitalized and ambulatory patients and tested by generic EV and specific EV-A71 reverse transcription PCR. EV-A71 was detected in 208 clinical specimens while other EVs were found in 32 patients. The VP1 gene and/or the complete genome were generated. Our phylogenetic sequencing analysis demonstrated that 80 EV-A71 strains belonged to the C4a subgenotype and 3 EV-A71 strains belonged to the B5 genotype. Furthermore, some lineages of EV-A71 were found to have appeared in Cambodia following separate introductions from neighboring countries. Nineteen EV A (CV-A6 and CV-A16), 9 EV B (EV-B83, CV-B3, CV-B2, CV-A9, E-31, E-2 and EV-B80) and 4 EV C (EV-C116, EV-C96, CV-A20 and Vaccine-related PV-3) strains were also detected. We found no molecular markers of disease severity. We report here that EV-A71 genotype C4 was the main etiological agent of a large outbreak of HFMD and particularly of severe forms associated with central nervous system infections. The role played by other EVs in the epidemic could not be clearly established.
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MESH Headings
- Adolescent
- Adult
- Cambodia/epidemiology
- Child
- Child, Preschool
- Disease Outbreaks
- Enterovirus A, Human/classification
- Enterovirus A, Human/genetics
- Enterovirus A, Human/isolation & purification
- Enterovirus A, Human/pathogenicity
- Epidemics
- Female
- Genome, Viral
- Genotype
- Hand, Foot and Mouth Disease/epidemiology
- Hand, Foot and Mouth Disease/mortality
- Hand, Foot and Mouth Disease/virology
- Hospitalization
- Humans
- Infant
- Male
- Phylogeny
- RNA, Viral/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Young Adult
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Affiliation(s)
- Veasna Duong
- Pasteur Institute in Cambodia, Phnom Penh 12000, Cambodia
| | - Channa Mey
- Pasteur Institute in Cambodia, Phnom Penh 12000, Cambodia
| | | | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Lucie Danet
- Pasteur Institute in Cambodia, Phnom Penh 12000, Cambodia
| | - Zhong Huang
- Institut Pasteur in Shanghai, Shanghai 200025, China
| | - Gang Zou
- Institut Pasteur in Shanghai, Shanghai 200025, China
| | | | | | | | | | - Beat Richner
- Kantha Bopha Hospital, Phnom Penh 12000, Cambodia
| | - Santy Ky
- Kantha Bopha Hospital, Phnom Penh 12000, Cambodia
| | - Sothy Heng
- Kantha Bopha Hospital, Phnom Penh 12000, Cambodia
| | - Sok Touch
- Ministry of Health, Phnom Penh 12000, Cambodia
| | - Ly Sovann
- Ministry of Health, Phnom Penh 12000, Cambodia
| | - Rogier van Doorn
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh P1Q5, Vietnam
| | - Thanh Tan Tran
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh P1Q5, Vietnam
| | - Jeremy J Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh P1Q5, Vietnam
| | | | - Suman R Das
- J. Craig Venter Institute, Rockville, MD 92037, USA
| | | | | | - Francis Delpeyroux
- Pasteur Institute, Paris 75724, France
- National Institute for Health and Medical Research, INSERM U994, Paris 75000, France
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Ralf Altmeyer
- Institut Pasteur in Shanghai, Shanghai 200025, China
| | - Philippe Buchy
- Pasteur Institute in Cambodia, Phnom Penh 12000, Cambodia
- GlaxoSmithKline Vaccines R&D, Singapore 189720, Singapore
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22
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Johnson SA, Brown MR, Lute SC, Brorson KA. Adapting viral safety assurance strategies to continuous processing of biological products. Biotechnol Bioeng 2016; 114:21-32. [DOI: 10.1002/bit.26060] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Sarah A. Johnson
- DBRRII, Office of Biotechnology Products, Office of Pharmaceutical Quality; Center for Drug Evaluation and Research, Food and Drug Administration; Silver Spring Maryland 20993
| | - Matthew R. Brown
- DBRRII, Office of Biotechnology Products, Office of Pharmaceutical Quality; Center for Drug Evaluation and Research, Food and Drug Administration; Silver Spring Maryland 20993
| | - Scott C. Lute
- DBRRII, Office of Biotechnology Products, Office of Pharmaceutical Quality; Center for Drug Evaluation and Research, Food and Drug Administration; Silver Spring Maryland 20993
| | - Kurt A. Brorson
- DBRRII, Office of Biotechnology Products, Office of Pharmaceutical Quality; Center for Drug Evaluation and Research, Food and Drug Administration; Silver Spring Maryland 20993
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23
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Viral metagenomics applied to blood donors and recipients at high risk for blood-borne infections. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 14:400-7. [PMID: 27136432 DOI: 10.2450/2016.0160-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/18/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Characterisation of human-associated viral communities is essential for epidemiological surveillance and to be able to anticipate new potential threats for blood transfusion safety. In high-resource countries, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) is currently considered to be under control. However, other unknown or unsuspected viruses may be transmitted to recipients by blood-derived products. To investigate this, the virome of plasma from individuals at high risk for parenterally and sexually transmitted infections was analysed by high throughput sequencing (HTS). MATERIALS AND METHODS Purified nucleic acids from two pools of 50 samples from recipients of multiple transfusions, and three pools containing seven plasma samples from either HBV-, HCV- or HIV-infected blood donors, were submitted to HTS. RESULTS Sequences from resident anelloviruses and HPgV were evidenced in all pools. HBV and HCV sequences were detected in pools containing 3.8×10(3) IU/mL of HBV-DNA and 1.7×10(5) IU/mL of HCV-RNA, respectively, whereas no HIV sequence was found in a pool of 150 copies/mL of HIV-RNA. This suggests a lack of sensitivity in HTS performance in detecting low levels of virus. In addition, this study identified other issues, including laboratory contaminants and the uncertainty of taxonomic assignment of short sequence. No sequence suggestive of a new viral species was identified. DISCUSSION This study did not identify any new blood-borne virus in high-risk individuals. However, rare and/or viruses present at very low titre could have escaped our protocol. Our results demonstrate the positive contribution of HTS in the detection of viral sequences in blood donations.
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24
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Abstract
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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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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25
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Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Vaccine 2015; 34:2035-43. [PMID: 26709640 PMCID: PMC4823300 DOI: 10.1016/j.vaccine.2015.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/30/2015] [Accepted: 12/05/2015] [Indexed: 02/05/2023]
Abstract
Deep sequencing has potential as an improved adventitious virus screening method. 15 laboratories sequenced a common reagent containing 25 target viruses. 6 viruses were detected by all lab, the remainder were detected by 4–14 labs. A wide range of sample preparation and bioinformatics methods is currently used. A common reference material is essential to enable results to be compared.
Background Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. Methods A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. Results Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. Conclusion The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories.
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26
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Postel A, Cavalleri JMV, Pfaender S, Walter S, Steinmann E, Fischer N, Feige K, Haas L, Becher P. Frequent presence of hepaci and pegiviruses in commercial equine serum pools. Vet Microbiol 2015; 182:8-14. [PMID: 26711022 DOI: 10.1016/j.vetmic.2015.10.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/28/2022]
Abstract
Novel viruses belonging to the genera Hepacivirus and Pegivirus have recently been discovered in horses and other animal species. Viral genomes of non-primate hepaciviruses (NPHV), equine pegivirus 1 (EPgV 1) and Theiler's disease associated virus (TDAV) were detected in a horse serum routinely used for cell culture propagation in our laboratory. Therefore, a study was carried out to further investigate the presence of these human Hepatitis C virus (HCV) related viruses in equine serum based products used in veterinary medicine and for research and to characterize the viral genomes. Without exception all commercially available equine sera purchased for cell culture propagation (n=6) were tested positive for NPHV, EPgV 1 or TDAV genomes by qRT-PCR. Molecular analyses of one single commercial horse serum from Europe confirmed multiple viral genomes, including two TDAV genomes significantly different from the only published TDAV sequence. Furthermore, multiple batches of horse serum pools (n=35) collected for manufacturing of biological products turned out to be positive for NPHV and EPgV 1 genomes. Nevertheless, the final commercial products (n=9) were exclusively tested qRT-PCR negative. Field samples (n=119) obtained from two premises located in the same region as the donor horses were analyzed, demonstrating the frequent presence of NPHV and EPgV 1, but the absence of TDAV genomes. The presence of NPHV, EPgV 1 and TDAV in commercial equine sera and serum based products could have considerable consequences for biosecurity and may also bias the outcome of research studies conducted with related viruses.
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Affiliation(s)
- Alexander Postel
- Institute for Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Germany
| | | | - Stephanie Pfaender
- Institute for Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Stephanie Walter
- Institute for Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Eike Steinmann
- Institute for Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| | - Karsten Feige
- Clinic for Horses, University of Veterinary Medicine Hannover, Germany
| | - Ludwig Haas
- Institute for Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Germany
| | - Paul Becher
- Institute for Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Germany.
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27
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Silveira S, Weber MN, Mósena ACS, da Silva MS, Streck AF, Pescador CA, Flores EF, Weiblen R, Driemeier D, Ridpath JF, Canal CW. Genetic Diversity of Brazilian Bovine Pestiviruses Detected Between 1995 and 2014. Transbound Emerg Dis 2015; 64:613-623. [DOI: 10.1111/tbed.12427] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Indexed: 12/30/2022]
Affiliation(s)
- S. Silveira
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - M. N. Weber
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - A. C. S. Mósena
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - M. S. da Silva
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - A. F. Streck
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - C. A. Pescador
- Laboratório de Patologia Veterinária; Universidade Federal de Mato Grosso (UFMT); Cuiabá Brazil
| | - E. F. Flores
- Setor de Virologia; Centro de Ciências Rurais; Universidade Federal de Santa Maria (UFSM); Santa Maria Brazil
| | - R. Weiblen
- Setor de Virologia; Centro de Ciências Rurais; Universidade Federal de Santa Maria (UFSM); Santa Maria Brazil
| | - D. Driemeier
- Setor de Patologia Veterinária; Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - J. F. Ridpath
- Ruminant Diseases and Immunology Research Unit; National Animal Disease Center; United States Department of Agriculture (USDA); Ames IA USA
| | - C. W. Canal
- Laboratório de Virologia, Faculdade de Veterinária; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
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28
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Denesvre C, Dumarest M, Rémy S, Gourichon D, Eloit M. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin. Virus Genes 2015. [PMID: 26223320 DOI: 10.1007/s11262-015-1231-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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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Affiliation(s)
- Caroline Denesvre
- INRA, UMR1282, Infectious Diseases and Public Health, ISP, BIOlogy of Avian Viruses Team, 37380, Nouzilly, France.
| | - Marine Dumarest
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, 75015, Paris, France
| | - Sylvie Rémy
- INRA, UMR1282, Infectious Diseases and Public Health, ISP, BIOlogy of Avian Viruses Team, 37380, Nouzilly, France
| | - David Gourichon
- INRA, Pôle d'expérimentation avicole de Tours, 37380, Nouzilly, France
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, 75015, Paris, France. .,PathoQuest, Paris, 25 rue du Dr Roux, 75015, Paris, France.
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29
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Identification of a Novel Hepacivirus in Domestic Cattle from Germany. J Virol 2015; 89:7007-15. [PMID: 25926652 DOI: 10.1128/jvi.00534-15] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED 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% (n = 5) of 158 investigated cattle herds in Germany were positive for bovine hepacivirus. Repeated reverse transcription-PCR (RT-PCR) analyses of animals from one dairy herd proved that a substantial percentage of cows were infected, with some of them being viremic for over 6 months. Clinical and postmortem examination revealed no signs of disease, including liver damage. Interestingly, quantitative RT-PCR from different organs and tissues, together with the presence of an miR-122 binding site in the viral genome, strongly suggests a liver tropism for bovine hepacivirus, making this novel virus a promising animal model for HCV infections in humans. IMPORTANCE Livestock animals act as important sources for emerging pathogens. In particular, their large herd size and the existence of multiple ways of direct and food-borne infection routes emphasize their role as virus reservoirs. Apart from the search for novel viruses, detailed characterization of these pathogens is indispensable in the context of risk analysis. Here, we describe the identification of a novel HCV-like virus in cattle. In addition, determination of the prevalence and of the course of infection in cattle herds provides valuable insights into the biology of this novel virus. The results presented here form a basis for future studies targeting viral pathogenesis of bovine hepaciviruses and their potential to establish zoonotic infections.
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30
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Dumarest M, Muth E, Cheval J, Gratigny M, Hébert C, Gagnieur L, Eloit M. Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing. Biologicals 2014; 43:31-6. [PMID: 25466699 PMCID: PMC7172073 DOI: 10.1016/j.biologicals.2014.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022] Open
Abstract
Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picornaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination.
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Affiliation(s)
- Marine Dumarest
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Erika Muth
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Justine Cheval
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Marlène Gratigny
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Charles Hébert
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Léa Gagnieur
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Marc Eloit
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France; PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France; Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie ENVA, INRA, ANSES, 7 Avenue Général de Gaulle, F-94704 Maisons Alfort, France.
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