Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

Mee, Edward T.; Preston, Mark D.; Minor, Philip D.; Schepelmann, Silke; Huang, Xue-Ning; Nguyen, Jenny; Wall, David S.; Hargrove, Stacey; Fu, Thomas C.; Xu, George; Li, Li; Côté, Colette; Delwart, Eric; Li, Linlin; Hewlett, Indira; Simonyan, Vahan; Ragupathy, Viswanath; Alin, Voskanian-Kordi; Mermod, Nicolas; Hill, Christiane; Ottenwälder, Birgit; Richter, Daniel C.; Tehrani, Arman; Weber-Lehmann, Jacqueline; Cassart, Jean-Pol; Letellier, Carine; Vandeputte, Olivier M.; Ruelle, Jean-Louis; Deyati, Avisek; Neve, Fabio La; Modena, Chiara; Éloit, Marc; Muth, Erika; Lamamy, Arnaud; Jagorel, F.; Cheval, Justine; Anscombe, Catherine; Misra, Raju; Wooldridge, David; Gharbia, Saheer E.; Rose, Graham; Ng, Serena; Charlebois, Robert L.; Gisonni-Lex, Lucy; Mallet, Laurent; Dorange, Fabien; Chiu, Charles Y.; Naccache, Samia N.; Kellam, Paul; Hoek, Lia van der; Cotten, Matt; Mitchell, Christine; Baier, Brian S.; Wen-ping, Sun; Malicki, Heather D

doi:10.1016/j.vaccine.2015.12.020

Cited by 35 publications

(46 citation statements)

References 35 publications

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“…At an influenza A virus concentration of over 10 5 copies/ml, this dropped to just 0.5%, and at a reovirus concentration of 10 3 -10 4 copies/ml, no viral reads were detected 24 . With our method, whole genomes were obtained for those with the highest viral loads, and for minority viral targets, there was a correlation between ostensible quantity and coverage, including for two viruses undetectable by the panel distributor 42 , a result superior to that recently obtained from influenza in clinical respiratory samples 65 . Again, the presence of high quantities of one or more target is likely to have inhibited the representation of the minority species such that if tested individually, superior depths and coverages would seem likely.…”

Section: Discussionmentioning

confidence: 83%

“…The members of the multi-FASTA reference file for the BBV Panel were obtained by submitting FASTQ sets from the rRNA-depleted sample with the highest virus concentrations to the SPAdes-HMMER-mapping approach described in the previous paragraph. VMR Panel references were derived from sequences obtained from GenBank using accession numbers from Mee et al 42 . Additionally, the complete genome sequence of a human pegivirus (HPgV) present in the plasma diluent was discovered in the SPAdes contigs file.…”

Section: Discussionmentioning

confidence: 99%

“…A reagent comprising a suspension in PBS of 18 RNA viruses with different genomic and structural characteristics was provided by the National Institute for Biological Standards and Controls (NIBSC, Potters Bar, UK). Each viral component and its approximate relative concentrations is given in Mee et al 42 . Prior to extraction, the panel was mixed 1:1 with NHP.…”

Section: Sample Sets Blood-borne Virus (Bbv) Panelmentioning

confidence: 99%

“…No reads from either of the three samples mapped to either of the two norovirus genomes, coronavirus 229E or influenza B virus. By the panel distributor's qPCR 42 , the Threshold Cycle (C t ) of the coronavirus was >36 and the other three were not detected, hence these four targets were excluded from further analysis. Notwithstanding influenza virus A H3N2 and parainfluenza virus type 3 also not being detected by the qPCR, we recovered reads from both, with genome coverages ranging from 2.7% to 21.6%.…”

Section: Recovery Of Partial and Complete Genomes Of Diverse Virus Tymentioning

confidence: 99%

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Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

Manso

Bibby

Mbisa

2017

Sci Rep

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RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.

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Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Sample Sets Blood-borne Virus (Bbv) Panelmentioning

confidence: 99%

Section: Recovery Of Partial and Complete Genomes Of Diverse Virus Tymentioning

confidence: 99%

See 2 more Smart Citations

Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

Manso

Bibby

Mbisa

2017

Sci Rep

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“…However, the reasonable high values that could be detected using qPCR, indicated that the initial extraction was successful. Noroviruses have previously been documented to be difficult to detect using metagenomics [51,52] possibly because of the small genome, robust nucleocapsid, or inhibitory RNA secondary structures [53]. Virus species specific extraction efficiency biases are well documented in viral metagenomics [54] and should always be considered when interpreting the results.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

et al. 2017

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Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.

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Microbial Dynamics and Quality Monitoring in Biopharmaceutical Production

Pashang,

Gilbride,

Wenk

2024

ChemBioEng Reviews

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Prokaryotic cells are pivotal in meeting the global demand for biopharmaceuticals. However, challenges such as the absence of advanced technology for real‐time monitoring, standardized testing methodologies, and quality risk assessment of microbial activity have led to increased production costs, delays, and shortages of biopharmaceutical products. A thorough understanding of how biomolecule production interacts with microbial population structure and function is vital for improving continuous manufacturing and process automation. In this review, we discuss the current microbiological techniques that meet good manufacturing practice requirements in industrial settings, explore the advantages of monitoring and measuring biomass growth efficiency and turnover rates beyond regulatory criteria for product release, and provide a critical assessment of the current state of knowledge on bioassays and engineering tools for biomolecule yield measurement and monitoring. Furthermore, we identify areas for future development, potential applications, and the need for interdisciplinary innovation to drive future research, including advancing bioassays for biopharmaceutical wastewater risk.

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Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

Cited by 35 publications

References 35 publications

Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

Microbial Dynamics and Quality Monitoring in Biopharmaceutical Production

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