Comparative analysis of the performance of residual host cell DNA assays for viral vaccines produced in Vero cells
Open accessAbstract
Residual host cell DNA (rcDNA) from continuous cell lines used for manufacturing of biological medicinal products has been considered as safety risk. Historically, several analytical methods have been used for rcDNA quantitation including hybridization assay, Threshold® assay and quantitative polymerase chain reaction (qPCR). Sanofi Pasteur has a wealth of experience in the development of methods quantifying rcDNA in vaccines. Here, we compared the performance of our in-house assays for quantifying rcDNA in viral vaccines produced in Vero cells. Vero alpha-satellite sequence qPCR was compared with the hybridization and Threshold® assays in terms of specificity, sensitivity and precision. The impact of viral inactivation with β-propiolactone (BPL) on rcDNA, within the vaccine production process, was also assessed. We demonstrate that the quantity of rcDNA measured is influenced by the analytical method used. Vero cell DNA-specific qPCR assay was shown to be robust with a large dynamic range and no matrix interference on a range of products. The qPCR assay demonstrated greater sensitivity and specificity versus the hybridization and Threshold® methods. Vero alpha-satellite sequence qPCR is a specific and sensitive method for the assessment of the quantity of Vero rcDNA in the highly purified vaccines.
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Written from the paper’s full text.
TL;DR
This paper compares Sanofi Pasteur’s Vero alpha-satellite qPCR assay with hybridization and Threshold® assays for quantifying residual host cell DNA (rcDNA) in Vero-cell viral vaccines. The qPCR method was more sensitive, specific, and precise, and BPL inactivation reduced rcDNA content and larger DNA fragments.
Key findings
- Vero alpha-satellite qPCR had a much lower limit of quantitation than Threshold®: LOQ 0.40–0.60 pg/mL depending on vaccine, versus 230 pg/mL for Threshold® in IPV, about 400-fold lower.
- qPCR validation across three vaccines showed linear ranges of 0.40–1084 pg/mL (RMAO-free rabies), 0.50–652 pg/mL (dengue), and 0.60–1743 pg/mL (IPV), with recoveries of 77–90%, 83–104%, and 94–128%, respectively.
- In rabies vaccine benchmarking, qPCR measured higher rcDNA than Threshold® in 3 of 5 competitor vaccines and higher than hybridization in 4 of 5; one competitor vaccine had rcDNA fragments of 407 and 620 bp, while Sanofi Pasteur’s rabies vaccine had fragmented rcDNA of 59–240 bp, with 81% below 108 bp.
- BPL inactivation reduced rcDNA content by an average of 30% for VERORAB® and 46% for the RMAO-free rabies vaccine, with marked reduction of fragments ≥240 bp; in VERORAB® harvests H2 and H3, fragments ≥108 bp were reduced by more than 50%.
Methods
- Comparative analytical validation and benchmarking study using Sanofi Pasteur’s in-house assays: Vero alpha-satellite qPCR, Threshold® total DNA assay, and hybridization assay.
- Samples included three Vero-cell viral vaccines at drug substance stage (RMAO-free rabies vaccine, dengue vaccine, IPV), VERORAB® and RMAO-free rabies vaccine before/after BPL inactivation, and five competitor rabies vaccines compared with VERORAB®.
- qPCR validation followed ICH Q2(R1) for specificity, linearity, accuracy, precision, LOQ, and range; rcDNA size distribution was assessed by qPCR of five overlapping β-actin amplicons from 59 bp to 620 bp.
Limitations
- Stated in the paper: the qPCR method cannot detect residual DNA shorter than the amplicon size; the smallest alpha-satellite amplicon assessed was 90 bp, though smaller fragments were not expected to pose significant safety risk.
- Stated in the paper: size evaluation is impossible for products with very low rcDNA, e.g. less than 1 pg/mL in Drug Substance, and BPL fragment-size effects could not be determined for the RMAO-free rabies vaccine because rcDNA levels were very low.
- Evident from the text: all authors are employees of Sanofi Pasteur and the study was funded by Sanofi Pasteur, so the comparative conclusions favoring the in-house qPCR assay may be subject to conflict-of-interest concerns; the competitor comparison was limited to five rabies vaccines.
Model-written summary. Check it against the paper before relying on it.
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Cites
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Claims the paper makes
2 of 17 cited sources checked · 1 supported · 0 flagged · accuracy not yet measured
- Findingnone given
Some products contain very low levels of rcDNA (e.g., less than 1 pg/mL in the Drug Substance).
“Some products contain very low levels of rcDNA (e.g. less than 1 pg/mL in the Drug Substance); in these cases, it is impossible to evaluate the size of the DNA fragments with the current best performing assays such as qPCR.”
Quote in the paperSubstantial claim - Findingown data
It was not possible to determine any effect of BPL on RMAO-free rabies vaccine rcDNA fragment content due to the very low level of rcDNA.
“It was not possible to determine any effect on RMAO-free rabies vaccine rcDNA fragments content due to the very low level of rcDNA.”
Quote in the paperNot a substantial claim - Findingown data
For IPV, the lower limit of the linearity domain was about 400-fold lower for Vero alpha-satellite qPCR than for the Threshold assay.
“The upper limit of the linearity domain were validated at a similar level between the two assays, but the lower end was much lower for qPCR (about 400-fold lower) than the Threshold ® assay.”
Quote in the paperSubstantial claim - Findingown data
For the Threshold assay at the LOQ of 230 pg/mL, the 95% CI of intermediate precision for two independent runs with one measurement is x/÷1.31.
“The 95% CI of intermediate precision at the LOQ of 230 pg/mL for two independent runs with one measurement was equal to x/÷ 1.31.”
Quote in the paperNot a substantial claim - Findingown data
The quantity of rcDNA determined may be influenced by the analytical method used.
“These results confirm that the quantity of rcDNA determined may be influenced by the analytical method used; in three of the five vaccines from competitors, qPCR appears to measure higher rcDNA content than the”
Quote in the paperSubstantial claim
- Findingown data
The qPCR assay demonstrated greater sensitivity and specificity versus the hybridization and Threshold ® methods.
“The qPCR assay demonstrated greater sensitivity and specificity versus the hybridization and Threshold ® methods.”
Quote in the paperSubstantial claim - Findingown data
For DS RMAO-free rabies vaccine, Vero alpha-satellite qPCR recovery was 77-90%.
“The recovery is 77-90%”
Quote in the paperSubstantial claim - Findingown data
For DS Dengue vaccine, Vero alpha-satellite qPCR linearity range was 0.50-652 pg/mL.
“0.50-652 pg/ mL”
Quote in the paperNot a substantial claim - Findingown data
For DS IPV, Vero alpha-satellite qPCR LOQ was 0.58 pg/mL.
“• 0.58 pg/mL”
Quote in the paperNot a substantial claim - Findingown data
The 95% CI of intermediate precision at the LOQ of 0.50 pg/mL for one run with one measurement was equal to x/÷ 1.99 for the dengue vaccine.
“The 95% CI of intermediate precision at the LOQ of 0.50 pg/mL for one run with one measurement was equal to x/÷ 1.99.”
Quote in the paperNot a substantial claim - Findingown data
For the Threshold assay, the 95% CI of repeatability for two runs with one measurement is x/÷1.21.
“The method was precise with 95% CI of repeatability and intermediate precision for two runs with one measurement equal to x/÷ 1.21 and x/÷ 1.20, respectively.”
Quote in the paperNot a substantial claim - Findingown data
The quantity of rcDNA measured is influenced by the analytical method used.
“We demonstrate that the quantity of rcDNA measured is influenced by the analytical method used.”
Quote in the paperSubstantial claim - Findingown data
One rabies vaccine from competitors had rcDNA fragments of 407 and 620 bp.
“When size distribution was compared, one vaccine from the competitors was reported to have rcDNA fragments of 407 and 620 bp.”
Quote in the paperNot a substantial claim - Findingown data
For DS RMAO-free rabies vaccine, Vero alpha-satellite qPCR specificity was verified using BLASTn showing 100% identity with Vero alpha sequence DNA only.
“Specificity of the set of primers and probe was verified using BLASTn showing 100% identity with Vero alpha sequence DNA only.”
Quote in the paperSubstantial claim - Findingown data
For the RMAO-free rabies vaccine, no significant batch effect was observed for BPL inactivation effect on rcDNA content.
“Again, no significant batch effect was observed.”
Quote in the paperNot a substantial claim - Findingown data
For the RMAO-free rabies vaccine, inactivation with BPL resulted in an average reduction in rcDNA content of 46%.
“Similarly, for Sanofi Pasteur's Vero cell RMAO-free rabies vaccine, inactivation with BPL resulted in an average reduction in rcDNA content of 46% (Table 7).”
Quote in the paperNot a substantial claim - Findingreasoning
The Vero alpha-satellite qPCR method cannot detect residual DNA of a length less than the amplicon size.
“The only relative limitation of our qPCR method is that residual DNA of a length less than the amplicon size cannot be detected; nonetheless, the smallest amplicon size assessed for the alphasatellite sequence was 90 bp and smaller fragments are not expected to pose a significant safety risk.”
Quote in the paperNot a substantial claim - Findingown data
Inactivation of VERORAB with BPL resulted in an average 30% reduction in rcDNA content.
“Inactivation of Sanofi Pasteur's Vero cell rabies vaccine (VERORAB ® ) with BPL resulted in an average 30% reduction in rcDNA content (Table 5).”
Quote in the paperNot a substantial claim - Findingown data
The rcDNA content measured is dependent on the analytical methods used.
“The rcDNA content measured is dependent on the analytical methods used, as clearly demonstrated by the direct comparison of the hybridization assay, the Threshold ® assay and qPCR during a benchmarking assessment comparing Sanofi Pasteur's rabies vaccine (VERORAB ® ) with rabies vaccines from five competitors.”
Quote in the paperSubstantial claim - Findingown data
In some competitor rabies vaccines where the Threshold assay reported higher rcDNA than qPCR, complementary analyses demonstrated the presence of mycoplasma DNA that contributed to total DNA content measured with the Threshold assay.
“Where the rcDNA content reported with the Threshold ® assay was found to be higher than with qPCR in rabies vaccines from competitors, in this particular case, complementary analyses demonstrated the presence of mycoplasma DNA in the vaccines that contributed to total DNA content measured with the Threshold ® assay (data not shown).”
Quote in the paperNot a substantial claim - Findingnone given
The paper developed a qPCR assay specifically adapted for products with low amounts of fragmented rcDNA.
“In summary, we have developed a qPCR assay specifically adapted for products with low amounts of fragmented rcDNA.”
Quote in the paperSubstantial claim - Findingreasoning
The qPCR system uses a DNA standard purified from the Vero cell line.
“This system uses a DNA standard purified from the Vero cell line, and is therefore representative of the actual residual DNA from these cell substrates.”
Quote in the paperSubstantial claim - Findingown data
There was poor correlation between the hybridization, Threshold, and qPCR methods in the benchmarking assessment.
“In all cases there was poor correlation between methods (hybridization, Threshold ® and qPCR).”
Quote in the paperSubstantial claim - Findingown data
The qPCR method was precise with 95% CI of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.30 and x/÷ 1.57, respectively, for the Inactivated Poliovirus Vaccine.
“The method was precise with 95% CI of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.30 and x/÷ 1.57, respectively.”
Quote in the paperSubstantial claim - Findingown data
For the Threshold assay, the 95% CI of intermediate precision for two runs with one measurement is x/÷1.20.
“The method was precise with 95% CI of repeatability and intermediate precision for two runs with one measurement equal to x/÷ 1.21 and x/÷ 1.20, respectively.”
Quote in the paperNot a substantial claim - Findingown data
For DS Dengue vaccine, Vero alpha-satellite qPCR recovery was 83-104%.
“The recovery is 83-104%”
Quote in the paperNot a substantial claim - Findingown data
For DS Dengue vaccine, Vero alpha-satellite qPCR LOQ was 0.50 pg/mL.
“• 0.50 pg/mL”
Quote in the paperNot a substantial claim - Findingown data
For DS RMAO-free rabies vaccine, Vero alpha-satellite qPCR linearity range was 0.40-1084 pg/mL.
“R 2 = 09965 0.40-1084 pg/ mL”
Quote in the paperNot a substantial claim - Findingown data
For DS RMAO-free rabies vaccine, the Vero alpha-satellite qPCR assay result was <1 pg/mL for PER.C6, CHO and CEF cells, demonstrating satisfactory specificity.
“The assay result is < 1 pg/mL for the PER.C6, CHO and CEF cells demonstrated a satisfactory specificity of the detection system”
Quote in the paperSubstantial claim - Findingown data
For a given vaccine, rcDNA was reported to be higher with qPCR than with the Threshold assay.
“Moreover, the rcDNA for a given vaccine was reported to be higher with qPCR than reported with the Threshold ® assay.”
Quote in the paperSubstantial claim - Findingown data
The Threshold assay is specific for the assessment of IPV.
“The Threshold ® assay was considered specific and linear over the range 230-1840 pg/mL for the assessment of IPV, and accurate over the same range, with an average recovery of 95% (Table 3).”
Quote in the paperSubstantial claim - Findingown data
The LOQ of the Threshold assay is 230 pg/mL.
“The LOQ was defined at 230 pg/mL as the lower level at which the method was precise and accurate.”
Quote in the paperNot a substantial claim - Findingown data
BPL inactivation of VERORAB and the RMAO-free rabies vaccine resulted in a marked reduction in rcDNA content and DNA fragments above 240 bp.
“We found that inactivation of Sanofi Pasteur's Vero cell rabies vaccines (VERORAB ® and the rabies vaccine produced in a RMAO-free process) with BPL resulted in a marked reduction in rcDNA content and DNA fragments above 240 bp, suggesting that functional genes are unlikely to be present after BPL treatment.”
Quote in the paperSubstantial claim - Findingown data
The hybridization assay underestimates rcDNA content compared to the qPCR method.
“The results obtained using hybridization underestimate the rcDNA content compared to the qPCR method.”
Quote in the paperSubstantial claim - Findingown data
For DS IPV, Vero alpha-satellite qPCR recovery was 94-128%.
“The recovery is 94-128%”
Quote in the paperNot a substantial claim - Findingown data
In three of five rabies vaccines from competitors, qPCR measured higher rcDNA content than the Threshold assay.
“These results confirm that the quantity of rcDNA determined may be influenced by the analytical method used; in three of the five vaccines from competitors, qPCR appears to measure higher rcDNA content than the”
Quote in the paperSubstantial claim - Findingown data
For DS IPV, Vero alpha-satellite qPCR linearity range was 0.60-1743 pg/mL.
“0.60-1743 pg/ mL”
Quote in the paperNot a substantial claim - Findingown data
For IPV, the upper limit of the linearity domain was validated at a similar level between the Threshold assay and Vero alpha-satellite qPCR.
“The upper limit of the linearity domain were validated at a similar level between the two assays, but the lower end was much lower for qPCR (about 400-fold lower) than the Threshold ® assay.”
Quote in the paperNot a substantial claim - Findingown data
In harvests H2 and H3, BPL inactivation reduced the rcDNA content of fragments 108 bp or greater by more than 50%.
“BPL inactivation resulted in marked reduction in rcDNA content of fragments 240 bp or larger; of note, the rcDNA content of fragments 108 bp or greater in harvests H2 and H3 were reduced by more than 50% (Table 6).”
Quote in the paperNot a substantial claim - Findingown data
The 95% CI of intermediate precision at the LOQ of 0.60 pg/mL for one run with one measurement was equal to x/÷ 1.41 for the Inactivated Poliovirus Vaccine.
“The 95% CI of intermediate precision at the LOQ of 0.60 pg/mL for one run with one measurement was equal to x/÷ 1.41.”
Quote in the paperNot a substantial claim - Findingown data
BPL inactivation resulted in marked reduction in rcDNA content of fragments 240 bp or larger.
“BPL inactivation resulted in marked reduction in rcDNA content of fragments 240 bp or larger; of note, the rcDNA content of fragments 108 bp or greater in harvests H2 and H3 were reduced by more than 50% (Table 6).”
Quote in the paperNot a substantial claim - Findingown data
For DS RMAO-free rabies vaccine, Vero alpha-satellite qPCR LOQ was 0.40 pg/mL.
“• 0.40 pg/mL”
Quote in the paperNot a substantial claim - Findingown data
The qPCR method was precise with 95% confidence intervals (CI) of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.28 and x/÷ 1.46, respectively, for the rabies vaccine produced in a RMAO-free process.
“The method was precise with 95% confidence intervals (CI) of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.28 and x/÷ 1.46, respectively.”
Quote in the paperNot a substantial claim - Findingown data
The 95% CI of intermediate precision at the LOQ of 0.40 pg/mL for one run with one measurement was equal to x/÷ 1.58 for the rabies vaccine produced in a RMAO-free process.
“The 95% CI of intermediate precision at the LOQ of 0.40 pg/mL for one run with one measurement was equal to x/÷ 1.58.”
Quote in the paperNot a substantial claim - Findingown data
The Threshold assay is accurate over the range 230-1840 pg/mL for the assessment of IPV, with an average recovery of 95%.
“The Threshold ® assay was considered specific and linear over the range 230-1840 pg/mL for the assessment of IPV, and accurate over the same range, with an average recovery of 95% (Table 3).”
Quote in the paperSubstantial claim - Findingnone given
The qPCR method was specifically adapted to low DNA content in highly purified vaccines.
“The qPCR method was specifically adapted to low DNA content in highly purified vaccines, and should be preferred over the hybridization or the Threshold ® assays for the quantitation of rcDNA in vaccines produced in Vero cells.”
Quote in the paperSubstantial claim - Findingown data
The Threshold assay is linear over the range 230-1840 pg/mL for the assessment of IPV.
“The Threshold ® assay was considered specific and linear over the range 230-1840 pg/mL for the assessment of IPV, and accurate over the same range, with an average recovery of 95% (Table 3).”
Quote in the paperSubstantial claim - Findingown data
The smallest amplicon size assessed for the alphasatellite sequence was 90 bp.
“The only relative limitation of our qPCR method is that residual DNA of a length less than the amplicon size cannot be detected; nonetheless, the smallest amplicon size assessed for the alphasatellite sequence was 90 bp and smaller fragments are not expected to pose a significant safety risk.”
Quote in the paperSubstantial claim - Interpretationown data
Functional genes are unlikely to be present after BPL treatment.
“We found that inactivation of Sanofi Pasteur's Vero cell rabies vaccines (VERORAB ® and the rabies vaccine produced in a RMAO-free process) with BPL resulted in a marked reduction in rcDNA content and DNA fragments above 240 bp, suggesting that functional genes are unlikely to be present after BPL treatment.”
Quote in the paperSubstantial claim - Interpretationreasoning
The qPCR method provides greater opportunity to measure rcDNA in highly purified vaccines in many cases to ≤10 pg per dose.
“Consequently, the qPCR method provides greater opportunity to measure rcDNA in highly purified vaccines in many cases to ≤10 pg per dose.”
Quote in the paperSubstantial claim - Premisecitation
The Threshold ® assay is negatively impacted by short DNA fragments (20 to 80 bp) through competitive inhibition preventing the formation of complete reaction complexes.
“The Threshold ® assay is also negatively impacted by short DNA fragments (20 to 80 bp) through competitive inhibition preventing the formation of complete reaction complexes (King and Panfili, 1991).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites King and Panfili, 1991 source
- Study design and conductcitation
The accuracy, precision, repeatability, intermediate precision, specificity, quantitation limit, linearity and range of the methods for quantitative detection of rcDNA were validated according to the International Conference on Harmonisation (ICH) tripartite guidelines Q2(R1).
“The accuracy, precision, repeatability, intermediate precision, specificity, quantitation limit, linearity and range of the methods for quantitative detection of rcDNA were validated according to the International Conference on Harmonisation (ICH) tripartite guidelines Q2(R1) (ICH, 2005).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites ICH, 2005
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
The specification for IPV is ≤100 pg/dose.
“Therefore, the former is not sufficiently sensitive for detection of rcDNA in highly purified vaccines or biologicals produced in Vero cells such as IPV for which the specification is ≤100 pg/dose (European Pharmacopoeia, Monograph 0214, 2019a).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites European Pharmacopoeia, Monograph 0214, 2019a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
A collaborative study across 15 laboratories revealed that the hybridization assay was associated with a high degree of variability in determining rcDNA content.
“However, a collaborative study across 15 laboratories revealed that the hybridization assay was associated with a high degree of variability in determining rcDNA content (Robertson and Heath, 1992).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Robertson and Heath, 1992 source
- Interpretationreasoning
If the number of target sequences per genome is not the same in the DNA standard as in the rcDNA from the product, the relative quantitation will be biased.
“If the number of target sequences per genome is not the same in the DNA standard as in the rcDNA from the product, the relative quantitation will be biased.”
Quote in the paperSubstantial claim- Rests on an assumption: The number of repeats of universal target genes may vary from one species to another.
- Interpretationreasoning
The Vero alpha-satellite qPCR method is superior to the Threshold and hybridization assays for quantitation of rcDNA in Vero cell vaccines.
“It is a robust method shown to be superior to previously used methods (Threshold ® and hybridization assays).”
Quote in the paperSubstantial claim - Interpretationnone given
When rcDNA is less than 1 pg/mL in the Drug Substance, it is impossible to evaluate the size of DNA fragments with current best performing assays such as qPCR.
“Some products contain very low levels of rcDNA (e.g. less than 1 pg/mL in the Drug Substance); in these cases, it is impossible to evaluate the size of the DNA fragments with the current best performing assays such as qPCR.”
Quote in the paperNot a substantial claim - Study design and conductreasoning
The Vero DNA standard was free of proteins, nucleases, RNA and other components or inhibitors.
“After extraction, DNA was free of proteins, nucleases, RNA and other components or inhibitors.”
Quote in the paperNot a substantial claim - Interpretationreasoning
The Vero alpha-satellite qPCR assay is applicable for use on a wide range of vaccines produced on Vero cells, including live vaccines and formaldehyde- or BPL-inactivated vaccines.
“as such it would be applicable for use on a wide range of vaccines produced on Vero cells including live vaccines and formaldehyde or BPL-inactivated vaccines.”
Quote in the paperSubstantial claim - Interpretationreasoning
The universal qPCR described by Andre et al. is not sufficiently sensitive for detection of rcDNA in highly purified vaccines or biologicals produced in Vero cells such as IPV.
“Therefore, the former is not sufficiently sensitive for detection of rcDNA in highly purified vaccines or biologicals produced in Vero cells such as IPV for which the specification is ≤100 pg/dose (European Pharmacopoeia, Monograph 0214, 2019a).”
Quote in the paperSubstantial claim - Interpretationown data
Vero alpha-satellite sequence qPCR is a specific and sensitive method for the assessment of the quantity of Vero rcDNA in highly purified vaccines.
“Vero alpha-satellite sequence qPCR is a specific and sensitive method for the assessment of the quantity of Vero rcDNA in the highly purified vaccines.”
Quote in the paperSubstantial claim - Interpretationown data
The rcDNA amounts in these three vaccines are far below the limit of detection of the universal qPCR method described by Andre et al.
“The three vaccines involved in the analytical validation studies (rabies vaccine produced in a RMAO-free process, dengue vaccine and IPV), contained only small amounts of rcDNA (approximately 40 pg/ mL, < 0.50 pg/mL and < 0.60 pg/mL, respectively), which is far below the limit of detection of the universal qPCR method described by Andre et al (Andre et al., 2016).”
Quote in the paperSubstantial claim - Interpretationreasoning
The qPCR method allows rcDNA to be quantified and characterized in samples from different bioprocessing stages of purification/inactivation that would otherwise be undetectable by other methods.
“The improved sensitivity achieved with qPCR allows rcDNA to be quantified and characterized in samples from different bioprocessing stages of purification/inactivation that would otherwise be undetectable by other methods.”
Quote in the paperSubstantial claim - Premisecitation
Hybridization methods have a previously documented lack of robustness.
“Based on these limitations and previously documented lack of robustness of hybridization methods (Robertson and Heath, 1992), the waiving of this method from compendial monographs should be considered.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Robertson and Heath, 1992 source
- Classified as probably not a substantial claim. 15
- May combine two claims. 20
- The quote only partly states this claim. 1
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe main risks associated with rcDNA in viral vaccines are infectivity and oncogenicity.
“The main risks associated with rcDNA in viral vaccines are infectivity and oncogenicity; rcDNA might be capable of transmitting viral infections if retroviral proviruses, integrated copies of DNA viruses, or extra chromosomal genomes are present (FDA, 2010;Sheng-Fowler et al., 2009), or may pose a potential risk for oncogenesis if viral or cell substrate (derived from tumors or which are tumorigen”
Quote in the paperNot a substantial claim1 of 3 sources checkedClassified as probably not a substantial claim.
PremisecitationResidual host cell DNA (rcDNA) from continuous cell lines used for manufacturing biological medicinal products has been considered a safety risk.
“Residual host cell DNA (rcDNA) from continuous cell lines used for manufacturing of biological medicinal products has been considered as safety risk.”
Quote in the paperSubstantial claim1 of 3 sources checked- cites FDA, 2010
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Sheng-Fowler et al., 2009 source
- cites Sheng-Fowler et al., 2010 source
The Introduction (page not available in our copy) says residual DNA from cells used to produce viral vaccines has been considered a potential safety risk, particularly when the cells are tumorigenic or derived from tumors. It does not extend that assessment to biological medicinal products generally or specifically identify continuous cell lines as the source of the risk. (LLM, conf=0.85)
Experimental — accuracy not yet measured
May combine two claims.
Findingown dataThe qPCR method was accurate over the range 0.50-652 pg/mL for the dengue vaccine, with a recovery of 83-104%.
“The method was found to be specific and linear over the range 0.50-652 pg/mL, and accurate over the same range, with a recovery of 83-104%.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn four of five rabies vaccines from competitors, qPCR measured higher rcDNA than the hybridization assay; for the fifth, results were comparable.
“In four of the five vaccines from competitors, qPCR measured higher rcDNA than hybridization assay, for the fifth vaccine from competitors the results were comparable.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe qPCR method was specific and linear over the range 0.60-1743 pg/mL for the Inactivated Poliovirus Vaccine.
“The method was found to be specific and linear over the range 0.60-1743 pg/mL, and accurate over the same range, with a recovery of 94-128%.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe Sanofi Pasteur rabies vaccine had fragmented rcDNA ranging 59-240 bp, with 81% of rcDNA less than 108 bp.
“The Sanofi Pasteur rabies vaccine was found to have fragmented rcDNA ranging 59-240 bp, with 81% of rcDNA less than 108 bp.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe LOQ was defined at 0.50 pg/mL for the dengue vaccine.
“The LOQ was defined at 0.50 pg/mL as the lower level at which the method was precise and accurate.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe qPCR method was specific and linear over the range 0.40-1084 pg/mL for the rabies vaccine produced in a RMAO-free process.
“The method was shown to be specific and linear over the range 0.40-1084 pg/mL, and accurate over the same range, with a recovery of 77-90%.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataVero cell DNA-specific qPCR assay was shown to be robust with a large dynamic range and no matrix interference on a range of products.
“Vero cell DNA-specific qPCR assay was shown to be robust with a large dynamic range and no matrix interference on a range of products.”
Quote in the paperSubstantial claimMay combine two claims.
FindingreasoningThe proposed qPCR targeting Vero alpha-satellite sequences is a specific and sensitive validated method for Vero DNA across several viral vaccines, with a low LOQ.
“Our proposed qPCR, targeting Vero alpha-satellite sequences, shows that it is possible to have a specific and sensitive validated method for Vero DNA across several viral vaccines, with a low LOQ.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe qPCR method was accurate over the range 0.60-1743 pg/mL for the Inactivated Poliovirus Vaccine, with a recovery of 94-128%.
“The method was found to be specific and linear over the range 0.60-1743 pg/mL, and accurate over the same range, with a recovery of 94-128%.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe qPCR method was specific and linear over the range 0.50-652 pg/mL for the dengue vaccine.
“The method was found to be specific and linear over the range 0.50-652 pg/mL, and accurate over the same range, with a recovery of 83-104%.”
Quote in the paperSubstantial claimThe quote only partly states this claim.
Findingown dataThe qPCR method was precise with 95% CI of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.42 and x/÷ 1.60, respectively, for the dengue vaccine.
“The method was precise with 95% CI of repeatability and intermediate precision for one run with one measurement equal to x/÷ 1.42 and x/÷ 1.60, respectively.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe effect of BPL inactivation on rcDNA content in VERORAB did not differ significantly by individual harvest or by batch.
“Though some variability was observed among the individual harvests, there was no significant effect according to individual harvests or by batch.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe LOQ was defined at 0.60 pg/mL for the Inactivated Poliovirus Vaccine.
“The LOQ was defined at 0.60 pg/mL as the lower level at which the method was precise and accurate.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe three vaccines involved in analytical validation studies contained only small amounts of rcDNA: approximately 40 pg/mL for RMAO-free rabies vaccine, <0.50 pg/mL for dengue vaccine, and <0.60 pg/mL for IPV.
“The three vaccines involved in the analytical validation studies (rabies vaccine produced in a RMAO-free process, dengue vaccine and IPV), contained only small amounts of rcDNA (approximately 40 pg/ mL, < 0.50 pg/mL and < 0.60 pg/mL, respectively), which is far below the limit of detection of the universal qPCR method described by Andre et al (Andre et al., 2016).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe limit of quantitation (LOQ) was defined at 0.40 pg/mL for the rabies vaccine produced in a RMAO-free process.
“The limit of quantitation (LOQ) was defined at 0.40 pg/mL as the lower level at which the method was precise and accurate.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe qPCR method was accurate over the range 0.40-1084 pg/mL for the rabies vaccine produced in a RMAO-free process, with a recovery of 77-90%.
“The method was shown to be specific and linear over the range 0.40-1084 pg/mL, and accurate over the same range, with a recovery of 77-90%.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationBPL alters the structure and capability of rcDNA to be used as a template by various polymerases.
“In addition, BPL alters the structure (Kubinski and Szybalski, 1975;Perrin and Morgeaux, 1995) and capability of rcDNA to be used as a template by various polymerases, further reducing the potential associated risk.”
Quote in the paperSubstantial claim0 of 2 sources checkedClassified as probably not a substantial claim. May combine two claims.
Premisenone givenTest results provide a ratio of each amplicon relative to the shortest; this ratio is proportional to the fraction of residual Vero DNA greater than 59 bp that is also greater than the size of the target amplicon.
“Test results provide a ratio of each amplicon relative to the shortest.This ratio is proportional to the fraction of residual Vero DNA greater than 59 bp (the value of total residual DNA) that is also greater than the size of the target amplicon.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductown dataFor each series of extractions, there was a negative extraction control and a positive extraction control.
“For each series of extractions, there was a negative extraction control (500 μL of nuclease-free water) and a positive extraction control (500 μL of a vaccine with a known amount of Vero rcDNA for the qPCR assay; 500 μL of ZC spiked with 50 pg High Calibrator DNA for the Threshold ® assay; 500 μL of a solution of Vero cell DNA at 200 pg/mL for the hybridization assay).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe IC was quantitated in parallel to Vero DNA by qPCR using a homologous standard range to determine the recovery of the spike, individually for each sample.
“The IC was then quantitated in parallel to Vero DNA by qPCR using a homologous standard range to determine the recovery of the spike, individually for each sample.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe membrane hybridization and Threshold ® assays have traditionally been used for the quantitation of host rcDNA in biopharmaceuticals.
“The membrane hybridization and Threshold ® assays have traditionally been used for the quantitation of host rcDNA in biopharmaceuticals.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Chinese Pharmacopoeia, Chapter 3407, 2015
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites USP, General information chapter < 1130 >, 2018
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisereasoningPCR-based technologies are generally considered the most practical and robust method for routine rcDNA quantitation because they are species/sequence specific, sensitive, quick to undertake and amenable to high-throughput formats.
“Polymerase chain reaction (PCR)-based technologies have gained in popularity for the detection and quantitation of rcDNA in recent years, and are generally considered the most practical and robust method for routine rcDNA quantitation as they are species/sequence specific, sensitive, quick to undertake and amenable to high-throughput formats.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationnone givenqPCR can be used for DNA sizing for complementary characterization of the product where applicable.
“In parallel, qPCR can be used for DNA sizing for complementary characterization of the product where applicable.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenFor the Threshold ® assay, all samples and negative controls (ZC) are assayed with and without a 50 pg DNA spiking.
“For the Threshold ® assay, all samples and negative controls (ZC) are assayed with and without a 50 pg DNA spiking.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisereasoningTargeting genes that are highly conserved among mammalian species to detect mammalian rcDNA, such as the multicopy ribosomal 18S RNA gene or Alu sequences, may be susceptible to the presence of human DNA in the environment or contamination during experimental procedure and would be difficult to control.
“For example, targeting genes that are highly conserved among mammalian species to detect mammalian rcDNA, such as the multicopy ribosomal 18S RNA gene or Alu sequences, may be susceptible to the presence of human DNA in the environment or contamination during experimental procedure and would be difficult to control.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataThe Vero alpha-satellite qPCR assay is robust in terms of performance, sensitivity, specificity, and precision, with a large dynamic range and no matrix interference.
“The analytical validation of our Vero alpha-satellite qPCR assay performed on three different vaccines shows that the method is robust in terms of performance, sensitivity, specificity, and precision, with a large dynamic range and no matrix interference; as such it would be applicable for use on a wide range of vaccines produced on Vero cells including live vaccines and formaldehyde or BPL-inact”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationThe choice of the targeted genome region has an impact on the assay results; selecting target DNA sequences that are found in multiple copies in the host genome would increase the likelihood of detection and accurate quantitation of rcDNA.
“The choice of the targeted genome region has an impact on the assay results; selecting target DNA sequences that are found in multiple copies in the host genome would increase the likelihood of detection and accurate quantitation of rcDNA (Wang et al., 2012).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wang et al., 2012 source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationDNA extraction using the DNA Extractor ® Kit is recognized as an appropriate method for rcDNA recovery.
“Recognized as an appropriate method for rcDNA recovery (USP, General information chapter < 1130 > , 2018), residual Vero cell DNA was extracted from 500 μL of sample using the DNA Extractor ® Kit (Wako Chemicals GmbH, Neuss, Germany) according to the manufacturer's instructions.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites USP, General information chapter < 1130 >, 2018
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Classified as probably not a substantial claim.
Study design and conductnone givenAll samples were assayed with a spike of 5 × 10 4 copies of the IC before DNA extraction.
“All samples were assayed with a spike of 5 × 10 4 copies of the IC before DNA extraction.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S4 (based).
InterpretationreasoningThe DNA standard purified from the Vero cell line is representative of the actual residual DNA from Vero cell substrates.
“This system uses a DNA standard purified from the Vero cell line, and is therefore representative of the actual residual DNA from these cell substrates.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningThe susceptibility of conserved mammalian gene targets to human DNA contamination would limit the method sensitivity, making it inappropriate for highly purified products with the most stringent specifications.
“This would limit the method sensitivity, making it inappropriate for highly purified products with the most stringent specifications.”
Quote in the paperSubstantial claim
The paper relies on this without support.
There is no universally appropriate method for the quantitation of rcDNA of animal origin.
“Although rcDNA assay can be undertaken at various stages throughout the manufacturing processes using appropriate methods, there is no universally appropriate method for the quantitation of rcDNA of animal origin.”
The paper relies on this without support.
The Threshold ® assay is limited in the detection of fragments shorter than 800 bp and may be inhibited by high DNA concentration (> 1 ng/mL) through the consumption of reagents or generation of signals too high to accurately quantitate.
“The Threshold ® assay is limited in the detection of fragments shorter than 800 bp, and may be inhibited by high DNA concentration (> 1 ng/mL) through the consumption of reagents or generation of signals too high to accurately quantitate.”
The paper relies on this without support.
The most appropriate stage to quantify impurities, including rcDNA, is the most concentrated purified stage before formulation, i.e. the drug substance.
“For highly purified vaccines containing very low levels of rcDNA, the most appropriate stage to quantify impurities, including rcDNA, is the most concentrated purified stage before formulation, i.e. the drug substance.”
The paper relies on this without support.
The number of repeats of universal target genes may vary from one species to another.
“Indeed, the number of repeats of the universal target genes may vary from one species to another.”
The paper relies on this without support.
Generic qPCR assays may be associated with a high risk of contamination, high background measurements, and reduced sensitivity.
“Generic qPCR assays may also be associated with a high risk of contamination increasing the difficulty in managing negative controls, as well as high background measurements, thus reducing the sensitivity of the assay.”
The paper relies on this without support.
Residual DNA fragments smaller than the amplicon size (e.g., <90 bp) do not pose a significant safety risk.
“smaller fragments are not expected to pose a significant safety risk.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Table 6 reports a size fraction above 100%
MinorFor harvest H3 before inactivation, the fraction at ≥108 bp is reported as 108%, although the fraction at ≥59 bp-the defined total-is 100%. The ≥108 bp fraction cannot exceed that total.
“| H3 | ≥59 | 100 | 100 | | | ≥108 | 108 | 34 |”
“Test results provide a ratio of each amplicon relative to the shortest.This ratio is proportional to the fraction of residual Vero DNA greater than 59 bp (the value of total residual DNA) that is also greater than the size of the target amplicon.”
Table 4 has more DNA at 620 bp than at 240 bp
MinorFor competitor vaccine #5, the reported fraction at 620 bp is 84%, exceeding the 56% reported at 240 bp. Under the paper's definition of these fractions, DNA at least 620 bp long must also be at least 240 bp long.
“| Rabies Vaccine for human use (Vero cell) #5 | 600,000 | 147,450 | 584,000 | 100 | 82 | 56 | MD | 84 |”
“This ratio is proportional to the fraction of residual Vero DNA greater than 59 bp (the value of total residual DNA) that is also greater than the size of the target amplicon.”
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Inactivation of DNA by β-propiolactone
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Issues associated with residual cell-substrate DNA in viral vaccines
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Cited by
Sorted by citations
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“gov/ ct2/show/NCT04608305) the residual levels of hc-DNA are substantially lower than the 10 ng per dose recommended by the WHO, the US Food and Drug Administration (FDA), and the European Pharmacopoeia based on case-by-case risk assessment [35].”
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“Reported values for rabies, dengue, and inactivated poliovirus vaccine have spike recoveries that range from 77 to 128% using a highly specific qPCR methodology (9).”
MethodChip-based digital PCR as a direct quantification method for residual DNA in mRNA drugs
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“Trace amounts of Vero cell-derived DNA are known as residual host cell DNA (rcDNA), and qPCR is considered the most practical method for rcDNA quantitation [12].”
MethodA high-sensitivity qPCR method for detecting residual Vero cell DNA in rabies vaccine production
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- Authors
- Vernay, O., Sarcey, E., Detrez, V., Abachin, E., Riou, P., Mouterde, B., Bonnevay, T., & Mallet, L.
- Affiliations
- Sanofi (France) (FR)
- Corresponding author
- Vernay, Olivier
- Venue
- Journal of Virological Methods
- Publisher
- Elsevier BV
- Published
- 2019-06
- Volume
- 268
- Pages
- 9-16
- ISSN
- 0166-0934 (ISSN-L)
- OpenAlex
- W2908092951
- Semantic Scholar
- 63070bdbe826feb67d9e0da67f27210d4e704e9c
- Cited by
- 14
- References
- 10
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 1 · 2023: 2 · 2022: 1 · 2021: 2 · 2020: 2 · 2019: 1
- FWCI
- 0.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Virological Methods (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Sanofi
- Sanofi Pasteur
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
- Physical Sciences › Chemistry › Analytical Chemistry › Analytical Methods in Pharmaceuticals
- Keywords
- viral vaccines, Vero cells, hybridization assay, beta-propiolactone inactivation, analytical method comparison, method sensitivity and specificity
- MeSH terms
- Host Microbial Interactions, Animals, Chlorocebus aethiops, DNA, Humans, Vero Cells, Viral Vaccines, Virology, DNA Contamination
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-28.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-28.
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Statistics and arithmetic are recomputed, not judged.
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