Mutant Analysis By PCR And Restriction Enzyme Cleavage Research Articles

Methods to Monitor Molecular Consistency of Oral Polio Vaccine.

Replication of viruses leads to emergence of mutations and their content in viral populations can increase by selection depending on growth conditions. Some of these mutations have deleterious effect on vaccine safety, such as neurovirulent reversions in the 5'-UTR of attenuated Sabin strains of poliovirus. Their content in vaccine batches must be tightly controlled during vaccine manufacture to ensure safety of the product. This chapter describes a quantitative molecular procedure called mutant analysis by PCR and restriction enzyme cleavage (MAPREC) that is used to monitor content of neurovirulent revertants in Oral Polio Vaccine (OPV). The method can be used for quantitative analysis of any other mutation in a viral population.

Allele-specific PCR for quantitative analysis of mutants in live viral vaccines

Monitoring consistency of genetic composition of oral polio vaccine (OPV) is a part of its quality control. It is performed by mutant analysis by PCR and restriction enzyme cleavage (MAPREC) used to quantify neurovirulent revertants in the viral genome. Here an alternative method based on quantitative PCR is proposed. Allele-specific quantitative polymerase chain reaction (asqPCR) uses a “tethered” oligonucleotide primer consisting of two specific parts connected by a polyinosine stretch. Homogeneous DNA from plasmids containing wild Leon/37 and attenuated Sabin 3 sequences with 100% 472C and 100% 472T could only be amplified using homologous primers. Real-time implementation of the allele-specific PCR resulted in sensitive detection of 472C revertants with the limit of quantitation of less than 0.05%. Monovalent vaccine batches and international viral references for MAPREC test were used to validate the method. asqPCR performed with the WHO references and monovalent batches of vaccine showed that the new method could measure accurately and reproducibly the content of revertants producing values comparable to MAPREC results. This suggests that asqPCR could be used as an alternative to MAPREC for lot release of OPV. The method could also be used for the quantitation of other mutants in populations of microorganisms.

MAPREC assay for quantitation of mutants in a recombinant flavivirus vaccine strain using near-infrared fluorescent dyes

Mutant analysis by PCR and restriction enzyme cleavage (MAPREC) is a quantitative assay of revertants in batches of live viral vaccines. The assay is highly sensitive and reliable but requires radioactive isotopes, which complicates its use in quality control laboratories. To quantify mutants in the cDNA of the West Nile (WN)/Dengue 4 chimera that was proposed as a new candidate of live vaccine against West Nile disease, alternative MAPREC protocols using non-radioactive dyes were explored. To compare the utility of different fluorescent dyes for MAPREC, the G2337→C mutation that was revealed by microarray hybridization in WN/Dengue 4 chimera virus was used as a model. DNA fragments produced by restriction endonuclease digestion were visualized in polyacrylamide gels by visible-range fluorescent dyes including ethidium bromide (EtBr) and SYBR Green I as well as by near-infrared (NIR) dye SYTO 60 and NIR dyes 700 and 800. The MAPREC assay performed with SYTO 60 and SYBR Green I was more sensitive than with EtBr but less sensitive than with NIR dyes 700 or 800. The NIR dyes 700 and 800 exhibited a wide linear range that may enable the detection of 0.05% of mutants in viral stocks. The NIR-based MAPREC assay was validated by using World Health Organization (WHO) international references for poliovirus type 3 with known contents of mutants. Values of mutant content produced by the non-radioactive assay were similar to the values determined in a previous WHO international collaborative study. The modified MAPREC assay could be used as an alternative to the radioisotope-based standard protocol for quality control of live viral vaccines.

Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines

Intrinsic genetic instability of RNA viruses may lead to the accumulation of revertants during manufacture of live viral vaccines, requiring rigorous quality control to ensure vaccine safety. Each lot of oral poliovirus vaccine (OPV) is tested for neurovirulence in animals and also for the presence of neurovirulent revertants. Mutant analysis by PCR and restriction enzyme cleavage (MAPREC) is used to measure the frequency of neurovirulent mutations at the 5' untranslated region (UTR) of the viral genome that correlate with the level of neurovirulence determined by the monkey neurovirulence test. However, MAPREC can only monitor mutations at a few genomic loci and miss mutations at other sites that could adversely affect vaccine quality. Here we propose to use massively parallel sequencing (MPS) for sensitive detection and quantification of all mutations in the entire genome of attenuated viruses. Analysis of vaccine samples and reference preparations demonstrated a perfect agreement with MAPREC results. Quantitative MPS analysis of validated reference preparations tested by MAPREC produced identical results, suggesting that the method could take advantage of the existing reference materials and be used as a replacement for the MAPREC procedure in lot release of OPV. Patterns of mutations present at a low level in vaccine preparations were characteristic of seed viruses used for their manufacture and could be used for identification of individual batches. This approach may represent the ultimate tool for monitoring genetic consistency of live viral vaccines.

Comparative pre-clinical and clinical experience with oral polio vaccine produced on MRC-5 cells or on primary monkey kidney cells

The need to avoid using primates has prompted the replacement of primary monkey kidney cells (PMKC) as a substrate for oral polio vaccine (OPV) production. Here, we report on OPV produced on MRC-5 cells using an industrial process capable of producing over 1 billion doses. All serotypes produced on MRC-5 cells proved satisfactory in the monkey and transgenic mice neurovirulence tests. All the type 3 MRC-5 lots tested by Mutant Analysis by PCR and Restriction Enzyme Cleavage (MAPREC) had a 472-C content below the acceptable limit and similar to that of PMKC derived lots. The safety/reactogenicity and immunogenicity profiles following vaccination in infants and children were similar for OPV MRC-5 and OPV PMKC vaccine lots. Excretion rates and prevalence of revertants for the three serotypes following vaccination were also similar for both vaccines. These data support the use of MRC-5 cells as an alternative to PMKC for OPV production.

Prevalence of vaccine-derived polioviruses in the environment.

A survey of poliovirus in river and sewage water was conducted from October 1993 to September 1995 in Toyama Prefecture, Japan. In this study, 25 isolates differentiated as type 2 vaccine-derived polioviruses (VDPVs) were characterized using mutant analysis by PCR and restriction-enzyme cleavage (MAPREC) to estimate the ratio of 481-G revertants correlated to neurovirulence in a virus population. Of these isolates, 23 (92%) comprised between 44 and 96% 481-G revertants by MAPREC. The other two isolates had revertant percentages close to the 0.6% of the attenuated reference strain. It was presumed that these 23 isolates would be variant with potential neurovirulence by MAPREC analysis. Of the 23 isolates, three were isolated from river water. Moreover, our results by MAPREC showed that type 2 poliovirus was phenotypically more variable than type 1 (69%) or type 3 (55%), as determined in previous studies. The prevalence of virulent-type VDPVs in river and sewage water suggested that the oral poliovaccine itself had led to wide environmental pollution in nature. To terminate the cycle of virus transmission in nature, the ecology of VDPVs should be studied further. A hygiene programme, inactivated poliovirus vaccine immunization and well-maintained herd immunity may play key roles in reducing the potential risk of infection by virulent VDPVs.

Neurovirulence of type 1 polioviruses isolated from sewage in Japan.

Sixteen type 1 poliovirus strains were isolated from a sewage disposal plant located downstream of the Oyabe River in Japan between October 1993 and September 1995. The isolates were intratypically differentiated as vaccine-derived strains. Neutralizing antigenicity analysis with monoclonal antibodies and estimation of neurovirulence by mutant analysis by PCR and restriction enzyme cleavage (MAPREC) were performed for 13 type 1 strains of these isolates. The isolates were classified into three groups. Group I (five strains) had a variant type of antigenicity and neurovirulent phenotype. Group II (four strains) had the vaccine type of antigenicity and neurovirulent phenotype. Group III (four strains) had the vaccine type of antigenicity and an attenuated phenotype. Furthermore, it was demonstrated that the virulent isolates were neutralized by human sera obtained after oral poliomyelitis vaccine (OPV) administration, and the sera of rats immunized with inactivated poliovirus vaccine. Although vaccination was effective against virulent polioviruses, virulent viruses will continue to exist in the environment as long as OPV is in use.

Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry.

RNA viruses exist as quasispecies, heterogeneous and dynamic mixtures of mutants having one or more consensus sequences. An adequate description of the genomic structure of such viral populations must include the consensus sequence(s) plus a quantitative assessment of sequence heterogeneities. For example, in quality control of live attenuated viral vaccines, the presence of even small quantities of mutants or revertants may indicate incomplete or unstable attenuation that may influence vaccine safety. Previously, we demonstrated the monitoring of oral poliovirus vaccine with the use of mutant analysis by PCR and restriction enzyme cleavage (MAPREC). In this report, we investigate genetic variation in live attenuated mumps virus vaccine by using both MAPREC and a platform (DNA MassArray) based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Mumps vaccines prepared from the Jeryl Lynn strain typically contain at least two distinct viral substrains, JL1 and JL2, which have been characterized by full length sequencing. We report the development of assays for characterizing sequence variants in these substrains and demonstrate their use in quantitative analysis of substrains and sequence variations in mixed virus cultures and mumps vaccines. The results obtained from both the MAPREC and MALDI-TOF methods showed excellent correlation. This suggests the potential utility of MALDI-TOF for routine quality control of live viral vaccines and for assessment of genetic stability and quantitative monitoring of genetic changes in other RNA viruses of clinical interest.

Analysis of the accumulation of mutants in Sabin attenuated polio vaccine viruses passaged in Vero cells

To confirm the safety of oral poliomyelitis vaccine (OPV) cultured in Vero cells, the genetic stability of cultured polio vaccine viruses was analysed by MAPREC (mutant analysis by PCR and restriction enzyme cleavage). The rates of mutant accumulation of the viruses passaged in Vero cells under a low multiplicity of infection (MOI) condition (approximately 10 −3.5 CCID 50/cell; the same as under usual OPV production conditions) were higher than those passaged in secondary cultured monkey kidney cells. However, the rates of mutant accumulation were restrained when the viruses were cultured under a high MOI condition (approximately 10 −1.5 CCID 50/cell) in Vero cells. Furthermore, neurovirulence of the passaged viruses in pollovirus susceptible transgenic mice PVR-Tg21 was shown to correlate highly with the results of MAPREC. It is expected that our results will contribute to the large scale preparation of safe and effective OPV using Vero cells.

Characterisation of vaccine-derived polioviruses isolated from sewage and river water in Japan

A nucleotide change from U to C at position 472 in the 5' non-coding region of the type 3 poliovirus is associated with increased neurovirulence. Moreover, the proportion of type 3 polioviruses containing this mutation (472-C revertants) correlates with the neurovirulence of a particular sample. We used mutant analysis by PCR and restriction-enzyme cleavage (MAPREC) to estimate the neurovirulence of environmental samples obtained from Toyama prefecture, Japan. Sewage and river water were collected between October, 1993, and September, 1995, and concentrated samples were inoculated into three different cell types. Isolated type 3 viruses were analysed to determine whether they were derived from the live oral poliovirus vaccine strain; they were then tested for neurovirulence by MAPREC. 29 type 3 strains were isolated--all of which were vaccine-derived. 16 (55%) comprised between 2% and 91% 472-C revertants by MAPREC and were expected to have high neurovirulence. The remaining strains included less than 0.25% revertants, and were regarded as attenuated viruses. Both types were isolated about 3 months after routine oral poliovirus vaccine administrations in May and October. Three strains isolated from river water were of the virulent type. Our results emphasise that there is an environmental risk of vaccine-associated paralytic poliomyelitis as long as live oral poliovirus vaccine is not replaced by inactivated polio vaccine.

Increased safety level of serotype 3 sabin oral poliomyelitis vaccine lots by improved seed virus, and tissue culture and virus infection conditions

The content of 472U to 472C revertant virus in serotype 3 oral poliomyelitis monovalent bulk vaccines can be quantified by MAPREC (Mutant Analysis by PCR and Restriction Enzyme Cleavage). Besides other wildtype reversions identified in propagated type 3 Sabin strain populations, the 472U to 472C reversion correlates most prominently with neurovirulence in the monkey neurovirulence test. Therefore, the results can be used for the discrimination of ‘good’ and ‘bad’ vaccines on the molecular level. In international collaborative studies it has been well established that vaccine lots containing revertant genomes below a critical threshold pass the in vivo monkey neurovirulence test (MNVT), while vaccine lots containing more revertants fail the MNVT. In this communication we show that the MAPREC test is a sensitive tool for quality control and the demonstration of consistency in large scale production. Furthermore, MAPREC offers a possibility to assess the effect of changed production conditions on the rate of reversion and to find conditions for consistent production with low reversion rates.

Limited genetic changes in the Sabin 1 strain of poliovirus occurring in the central nervous system of monkeys

Replication of attenuated poliovirus strains results in their partial deattenuation. Recently we identified mutations accumulating in the Sabin 1 poliovirus in cell cultures. Here we report genetic changes occurring in this virus during replication in the central nervous system (CNS) of monkeys. Viruses isolated from different parts of the CNS of rhesus monkeys (inoculated into the spinal cord) were screened for sequence heterogeneities and newly identified mutations were independently confirmed and quantified using mutant analysis by PCR and restriction enzyme cleavage (MAPREC). All consistently accumulating mutations identified in this study were located in untranslated regions: GU-->AU or GU-->GC substitution at a complementary pair formed by nucleotides 480 and 525, U-->C substitution at nucleotide 612, and GU-->AU or GU-->GC substitution of a base pair formed by the nucleotides 7427/7441 immediately preceding the poly(A) tract. All these mutations except one (7427) were previously identified in cell culture passages or stool isolates from vaccinees. Sequencing of 11 CNS isolates also identified a few random silent mutations that accumulated as neutral 'passengers', passively co-selected with genuinely selectable mutations present on the same RNA molecule. One isolate also contained the wild-type base at nucleotide 2741 (Ala88-->Thr in VP1). Our results demonstrate a remarkable genetic stability of the Sabin 1 poliovirus in the CNS of monkeys, suggesting that deattenuation is determined by a very limited number of mutations. These mutations can be assayed by MAPREC to monitor the consistency of oral poliovirus vaccine (OPV) production.

Genetic Stability and Mutant Selection in Sabin 2 Strain of Oral Poliovirus Vaccine Grown under Different Cell Culture Conditions

Mutations that consistently accumulated in the attenuated Sabin 2 strain of poliovirus during propagation in cell cultures were identified by sequence heterogeneity assay and quantified by mutant analysis by PCR and restriction enzyme cleavage (MAPREC). Eight additional sites previously identified in stool isolates were also examined by MAPREC in the virus passages. The pattern of selectable mutations and the rate of their accumulation depended on the type and confluence of the cell culture and the temperature of virus growth. Five unstable genomic sites were identified in Sabin 2 virus passaged 10 times at 34° in African green monkey kidney (AGMK) cells, with the mutations accumulating in the range 1 to 24%. Accumulation of these mutations did not appear to result in a loss of attenuated phenotype since the virus passaged under these conditions passed the monkey neurovirulence test (MNVT). The content of the 481-G revertant known to be related to neurovirulence in monkeys did not increase. Thus, our results suggest that upon growth of Sabin 2 virus in AGMK cells at 34°, the key determinant(s) of attenuation remained stable, and the mutations that occurred did not affect monkey neurovirulence. In virus passaged to times at 37° in AGMK cells, 4 unstable genomic sites were identified, in some of them accumulating up to 12% of the mutants. This virus sample severely failed the MNVT. Virus passaged in Vero cells at 34 and 37° accumulated mutants at 7 and 14 genomic sites, respectively, including 481-G in both cases, with almost complete substitution of the original nucleotides at some of the sites. We tested 44 commercial monopools of Type 2 OPV and found out that all of them contained 481-G revertants in the range 0.4-1.1%. An increase in the 481-G revertants in passaged viruses to the level of 4% and above correlated with failure of these samples by the MNVT. Since the pattern of selectable mutations differed in viruses grown in the two cell cultures used in this study, specific mutation profiles should be determined for each cell substrate used for vaccine production to assess manufacturing consistency.

Microevolution of Sabin 1 Strain in Vitro and Genetic Stability of Oral Poliovirus Vaccine

Mutants consistently accumulating in Sabin 1 poliovirus during serial passaging in vitro were identified by sequence heterogeneity assay and quantitated using mutant analysis by PCR and restriction enzyme cleavage (MAPREC). Only four unstable genomic sites were identified in virus passaged 10 times in African green monkey kidney (AGMK) cells, and eight sites in virus passaged in Vero cells. Mutations accumulated both in untranslated regions of RNA (nucleotides 480, 525 and 7441) and in coding sequences, as missense (nucleotides 1449, 4944, and 6203) or silent (nucleotides 1123 and 1141) mutations. The most prominent selectable mutations were found at complementary nucleotides 480 and 525 of the 5′-untranslated region (5′-UTR) of the Sabin strain, changing the G:U pair in F-domain to either A:U or G:C variants. These two variants have been shown previously to have an increased neurovirulence in monkeys. The G:C variant accumulated during passage in Vero cells, while A:U variant accumulated in CV-1 cells. Virus passaged in AGMK cells accumulated both variants. Higher temperature (37 instead of 34°) strongly favored selection of mutants in Vero cells, had a smaller effect on mutant accumulation in AGMK cells, and had no effect in CV-1 cells. Monopools of type 1 oral poliovirus vaccine (OPV) made by seven manufacturers were found to contain both 480-A and 525-C revertants at a combined level of 1.1-2.7%. Viral samples with increased amounts of these revertants had higher neurovirulence in monkeys. Our results suggest that quantitation of these reversions by MAPREC may be prognostic for results of the monkey neorovirulence test (MNVT) and can be used for monitoring type 1 OPV consistency.

Quantitative aspects of the mutant analysis by PCR and restriction enzyme cleavage (MAPREC).

Quantitation of virus revertants by PCR and restriction enzyme cleavage may give nonlinear results and, in some cases, produce artifacts caused by nucleotide misincorporation and heteroduplex formation, occurring during PCR. Modifications of the procedure allowed us to overcome these problems and develop a highly sensitive and reliable method of mutant quantitation. This procedure can be used to assess the quality of live vaccines and to study heterogeneity of viral and bacterial populations.