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Opmeer L, Gazzoli I, Ballmann M, Willemsen M, Voshol GP, Grudniewska-Lawton M, Havenga M, Yallop C, Hamidi A, Gillissen G, Bakker WAM. High throughput AS LNA qPCR method for the detection of a specific mutation in poliovirus vaccine strains. Vaccine 2024; 42:2475-2484. [PMID: 38503660 PMCID: PMC11007389 DOI: 10.1016/j.vaccine.2024.01.103] [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: 09/13/2023] [Revised: 11/21/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
Sabin Inactivated Poliovirus Vaccine (sIPV) has become one of the preferred vaccination options for the last step in the Poliovirus eradication program. Sequencing of poliovirus samples is needed during the manufacturing of poliovirus vaccines to assure the safety and immunogenicity of these vaccines. Next-generation sequencing analysis is the current costly and time-consuming gold standard for monitoring the manufacturing processes. We developed a low-cost and quick, highly sensitive, and allele-specific locked nucleic acid-probe-based reverse transcription quantitative PCR alternative that can accurately detect mutations in poliovirus vaccine samples during process development, scaling up, and release. Using the frequently in vitro occurring and viral replication-impacting VP1-E295K mutation as a showcase, we show that this technology can accurately detect E295K mutations in poliovirus 2 samples to similar levels as NGS. The qPCR technology was developed employing a synthetic dsDNA fragment-based standard curve containing mixes of E295K-WT (wildtype) and Mut (mutant) synthetic dsDNA fragments ranging from 1 × 107 copies/µL to 1 × 102 copies/µL to achieve a linear correlation with R2 > 0.999, and PCR efficiencies of 95-105 %. Individual standard concentration levels achieved accuracies of ≥92 % (average 96 %) and precisions of ≤17 % (average 3.3 %) RSD. Specificity of locked nucleic acid (LNA)-probes was confirmed in the presence and absence of co-mutations in the probe-binding region. Application of the developed assay to Sabin Poliovirus type 2 production run samples, illustrated a linear relationship with an R2 of 0.994, and an average accuracy of 97.2 % of the variant (allele)-specific AS LNA qPCR result, compared to NGS. The assay showed good sensitivity for poliovirus samples, containing E295K mutation levels between 0 % and 95 % (quantification range). In conclusion, the developed AS LNA qPCR presents a valuable low-cost, and fast tool, suitable for the process development and quality control of polio vaccines.
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Affiliation(s)
- Lizet Opmeer
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Isabella Gazzoli
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Mónika Ballmann
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Marieke Willemsen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gerben P Voshol
- GenomeScan B.V., Plesmanlaan 1d, 2333 BZ Leiden, The Netherlands
| | | | - Menzo Havenga
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Christopher Yallop
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Ahd Hamidi
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gert Gillissen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Wilfried A M Bakker
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands.
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2
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Walter KS, Altamirano J, Huang C, Carrington YJ, Zhou F, Andrews JR, Maldonado Y. Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns. NPJ Vaccines 2023; 8:137. [PMID: 37749086 PMCID: PMC10520055 DOI: 10.1038/s41541-023-00740-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023] Open
Abstract
There is an increasing burden of circulating vaccine-derived polioviruses (cVDPVs) due to the continued use of oral poliovirus vaccine (OPV). However, the informativeness of routine OPV VP1 sequencing for the early identification of viruses carrying virulence-associated reversion mutations has not been directly evaluated in a controlled setting. We prospectively collected 15,331 stool samples to track OPV shedding from children receiving OPV and their contacts for ten weeks following an immunization campaign in Veracruz State, Mexico and sequenced VP1 genes from 358 samples. We found that OPV was genetically unstable and evolves at an approximately clocklike rate that varies across serotypes and by vaccination status. Overall, 61% (11/18) of OPV-1, 71% (34/48) OPV-2, and 96% (54/56) OPV-3 samples with available data had evidence of a reversion at the key 5' UTR attenuating position and 28% (13/47) of OPV-1, 12% (14/117) OPV-2, and 91% (157/173) OPV-3 of Sabin-like viruses had ≥1 known reversion mutations in the VP1 gene. Our results are consistent with previous work documenting rapid reversion to virulence of OPV and underscores the need for intensive surveillance following OPV use.
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Affiliation(s)
- Katharine S Walter
- Division of Epidemiology, University of Utah, Salt Lake City, UT, 84105, USA.
| | - Jonathan Altamirano
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - ChunHong Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuan J Carrington
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Frank Zhou
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yvonne Maldonado
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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3
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Wong W, Gauld J, Famulare M. From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh. Virus Evol 2023; 9:vead044. [PMID: 37692896 PMCID: PMC10491863 DOI: 10.1093/ve/vead044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
The oral poliovirus vaccines (OPVs) are one of the most effective disease eradication tools in public health. However, the OPV strains are genetically unstable and can cause outbreaks of circulating, vaccine-derived Type 2 poliovirus (cVDPV2) that are clinically indistinguishable from wild poliovirus (WPV) outbreaks. Here, we developed a Sabin 2 reversion model that simulates the reversion of Sabin 2 to reacquire a WPV-like phenotype based on the clinical differences in shedding duration and infectiousness between individuals vaccinated with Sabin 2 and those infected with WPV. Genetic reversion is informed by a canonical reversion pathway defined by three gatekeeper mutations (A481G, U2909C, and U398C) and the accumulation of deleterious nonsynonymous mutations. Our model captures essential aspects of both phenotypic and molecular evolution and simulates transmission using a multiscale transmission model that consolidates the relationships among immunity, susceptibility, and transmission risk. Despite rapid Sabin 2 attenuation reversal, we show that the emergence of a revertant virus does not guarantee a cVDPV2 outbreak. When simulating outbreaks in Matlab, Bangladesh, we found that cVDPV2 outbreaks are most likely in areas with low population-level immunity and poor sanitation. In Matlab, our model predicted that declining immunity against Type 2 poliovirus following the cessation of routine OPV vaccination was not enough to promote cVDPV2 emergence. However, cVDPV2 emergencedepended on the average viral exposure dose per contact, which was modeled as a combination of the viral concentration per fecal gram and the average fecal-oral dose per contact. These results suggest that cVDPV2 emergence risk can be mitigated by reducing the amount of infectious fecal material individuals are exposed to. Thus, a combined strategy of assessing and improving sanitation levels in conjunction with high-coverage vaccination campaigns could limit the future cVDPV2 emergence.
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Affiliation(s)
- Wesley Wong
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, SPH 1, Boston, MA 02115, USA
| | - Jillian Gauld
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, 500 5th Ave N, Seattle, WA 98109, USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, 500 5th Ave N, Seattle, WA 98109, USA
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4
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Yeh MT, Smith M, Carlyle S, Konopka-Anstadt JL, Burns CC, Konz J, Andino R, Macadam A. Genetic stabilization of attenuated oral vaccines against poliovirus types 1 and 3. Nature 2023; 619:135-142. [PMID: 37316671 PMCID: PMC10322712 DOI: 10.1038/s41586-023-06212-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
Vaccination with Sabin, a live attenuated oral polio vaccine (OPV), results in robust intestinal and humoral immunity and has been key to controlling poliomyelitis. As with any RNA virus, OPV evolves rapidly to lose attenuating determinants critical to the reacquisition of virulence1-3 resulting in vaccine-derived, virulent poliovirus variants. Circulation of these variants within underimmunized populations leads to further evolution of circulating, vaccine-derived poliovirus with higher transmission capacity, representing a significant risk of polio re-emergence. A new type 2 OPV (nOPV2), with promising clinical data on genetic stability and immunogenicity, recently received authorization from the World Health Organization for use in response to circulating, vaccine-derived poliovirus outbreaks. Here we report the development of two additional live attenuated vaccine candidates against type 1 and 3 polioviruses. The candidates were generated by replacing the capsid coding region of nOPV2 with that from Sabin 1 or 3. These chimeric viruses show growth phenotypes similar to nOPV2 and immunogenicity comparable to their parental Sabin strains, but are more attenuated. Our experiments in mice and deep sequencing analysis confirmed that the candidates remain attenuated and preserve all the documented nOPV2 characteristics concerning genetic stability following accelerated virus evolution. Importantly, these vaccine candidates are highly immunogenic in mice as monovalent and multivalent formulations and may contribute to poliovirus eradication.
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Affiliation(s)
- Ming Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew Smith
- National Institute for Biological Standards and Control, South Mimms, UK
| | - Sarah Carlyle
- National Institute for Biological Standards and Control, South Mimms, UK
| | - Jennifer L Konopka-Anstadt
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
| | - Andrew Macadam
- National Institute for Biological Standards and Control, South Mimms, UK.
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5
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Nyenswah TG, Schue JL. Halting vaccine-derived poliovirus circulation: the novel type 2 oral vaccine might not be enough. Lancet Glob Health 2023; 11:e811-e812. [PMID: 37202011 DOI: 10.1016/s2214-109x(23)00161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/15/2023] [Indexed: 05/20/2023]
Affiliation(s)
- Tolbert G Nyenswah
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, MD, USA.
| | - Jessica L Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, MD, USA
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6
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Bandyopadhyay AS, Zipursky S. A novel tool to eradicate an ancient scourge: the novel oral polio vaccine type 2 story. THE LANCET. INFECTIOUS DISEASES 2023; 23:e67-e71. [PMID: 36162417 DOI: 10.1016/s1473-3099(22)00582-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 02/01/2023]
Abstract
The recent detection of vaccine-derived poliovirus (VDPV) in London (UK) and a case of paralytic polio in New York (USA) have highlighted how the scourge of poliomyelitis has not been totally overcome and remains an international problem, not confined to Afghanistan and Pakistan (where wild-type 1 poliovirus remains endemic) or as outbreaks of circulating VDPV in countries in Africa. To address the risk of circulating VDPVs, a global collaborative effort over the past decade has enabled the development of novel oral polio vaccine type 2 (nOPV2) that is as immunogenic as the current Sabin strain and so equally effective, while being less likely to revert to neurovirulence than Sabin oral polio vaccines. The successful development of nOPV2-the first such vaccine against type 2 poliovirus and the first vaccine ever authorised by the WHO Prequalification team through its Emergency Use Listing procedure-has led to the deployment of approximately 450 million doses of nOPV2 for outbreak control in 21 countries. It also paved the way for the subsequent Emergency Use Listing approval of COVID-19 vaccines in the global pandemic. Monitoring the use of nOPV2 has confirmed it is more genetically stable and less likely to result in VDPV than the Sabin strain, suggesting that the target of the global eradication of poliomyelitis might be a little more attainable than previously believed.
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Affiliation(s)
| | - Simona Zipursky
- Polio Eradication, World Health Organisation, Geneva, Switzerland
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7
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Wahid R, Mercer LD, De Leon T, DeAntonio R, Sáez-Llorens X, Macadam A, Chumakov K, Strating J, Koel B, Konopka-Anstadt JL, Oberste MS, Burns CC, Andino R, Tritama E, Bandyopadhyay AS, Aguirre G, Rüttimann R, Gast C, Konz JO. Genetic and phenotypic stability of poliovirus shed from infants who received novel type 2 or Sabin type 2 oral poliovirus vaccines in Panama: an analysis of two clinical trials. THE LANCET. MICROBE 2022; 3:e912-e921. [PMID: 36332645 PMCID: PMC9712124 DOI: 10.1016/s2666-5247(22)00254-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 07/29/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sabin strains used in oral poliovirus vaccines (OPV) can revert to virulence and, in rare instances, cause disease or generate vaccine-derived strains leading to outbreaks in areas of low immunisation coverage. A novel OPV2 (nOPV2) was designed to stabilise the viral genome against reversion and reduce recombination events that might lead to virulent strains. In this study, we evaluated the genetic and phenotypic stability of shed poliovirus following administration of one dose of monovalent OPV2 (mOPV2) or nOPV2 to infants aged 18-22 weeks. METHODS In two similarly designed clinical trials (NCT02521974 and NCT03554798) conducted in Panama, infants aged 18-22-weeks, after immunisation with three doses of bivalent OPV (types 1 and 3) and one dose of inactivated poliovirus vaccine, were administered one or two doses of mOPV2 or nOPV2. In this analysis of two clinical trials, faecally shed polioviruses following one dose of mOPV2 or nOPV2 were isolated from stools meeting predetermined criteria related to sample timing and viral presence and quantity and assessed for nucleotide polymorphisms using next-generation sequencing. A transgenic mouse neurovirulence test was adapted to assess the effect of the possible phenotypic reversion of shed mOPV2 and nOPV2 with a logistic regression model. FINDINGS Of the 91 eligible samples, 86 were able to be sequenced, with 72 evaluated in the transgenic mouse assay. Sabin-2 poliovirus reverts rapidly at nucleotide 481, the primary attenuation site in domain V of the 5' untranslated region of the genome. There was no evidence of neurovirulence-increasing polymorphisms in domain V of shed nOPV2. Reversion of shed Sabin-2 virus corresponded with unadjusted paralysis rates of 47·6% at the 4 log10 50% cell culture infectious dose (CCID50) and 76·7% at the 5 log10 CCID50 inoculum levels, with rates of 2·8% for 4 log10 CCID50 and 11·8% for 5 log10 CCID50 observed for shed nOPV2 samples. The estimated adjusted odds ratio at 4·5 log10 of 0·007 (95% CI 0·002-0·023; p<0·0001) indicates significantly reduced odds of mouse paralysis from virus obtained from nOPV2 recipients compared with mOPV2 recipients. INTERPRETATION The data indicate increased genetic stability of domain V of nOPV2 relative to mOPV2, with significantly lower neurovirulence of shed nOPV2 virus compared with shed mOPV2. While this vaccine is currently being deployed under an emergency use listing, the data on the genetic stability of nOPV2 will support further regulatory and policy decision-making regarding use of nOPV2 in outbreak responses. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Laina D Mercer
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Tirza De Leon
- Hospital Materno Infantil José Domingo De Obaldía, David, Panama,CEVAXIN, Centro de Vacunación e Investigación, Panama City, Panama
| | | | - Xavier Sáez-Llorens
- CEVAXIN, Centro de Vacunación e Investigación, Panama City, Panama,Department of Infectious Diseases, Hospital del Niño Dr José Renán Esquivel and Sistema Nacional de Investigación at Secretaria Nacional de Ciencia y Tecnologia, Panama City, Panama
| | - Andrew Macadam
- Division of Virology, National Institute for Biological Standards and Control, South Mimms, UK
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA,Global Virus Network Center of Excellence, Baltimore, MD, USA
| | | | - Björn Koel
- Viroclinics Xplore, Viroclinics Biosciences, Rotterdam, Netherlands
| | | | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Erman Tritama
- Research and Development Division, PT Bio Farma, Bandung, West Java, Indonesia
| | | | - Gabriela Aguirre
- Fighting Infectious Diseases in Emerging Countries, Miami, FL, USA
| | | | - Chris Gast
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - John O Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA,Correspondence to: Dr John O Konz, Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
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8
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Quarleri J. Poliomyelitis is a current challenge: long-term sequelae and circulating vaccine-derived poliovirus. GeroScience 2022; 45:707-717. [PMID: 36260265 PMCID: PMC9886775 DOI: 10.1007/s11357-022-00672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/12/2022] [Indexed: 02/03/2023] Open
Abstract
For more than 20 years, the World Health Organization Western Pacific Region (WPR) has been polio-free. However, two current challenges are still polio-related. First, around half of poliomyelitis elderly survivors suffer late poliomyelitis sequelae with a substantial impact on daily activities and quality of life, experiencing varying degrees of residual weakness as they age. The post-polio syndrome as well as accelerated aging may be involved. Second, after the worldwide Sabin oral poliovirus (OPV) vaccination, the recent reappearance of strains of vaccine-derived poliovirus (VDPV) circulating in the environment is worrisome and able to persistent person-to-person transmission. Such VDPV strains exhibit atypical genetic characteristics and reversed neurovirulence that can cause paralysis similarly to wild poliovirus, posing a significant obstacle to the elimination of polio. Immunization is essential for preventing paralysis in those who are exposed to the poliovirus. Stress the necessity of maintaining high vaccination rates because declining immunity increases the likelihood of reemergence. If mankind wants to eradicate polio in the near future, measures to raise immunization rates and living conditions in poorer nations are needed, along with strict observation. New oral polio vaccine candidates offer a promissory tool for this goal.
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Affiliation(s)
- Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina. .,Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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9
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Martin J, Burns CC, Jorba J, Shulman LM, Macadam A, Klapsa D, Majumdar M, Bullows J, Frolov A, Mate R, Bujaki E, Castro CJ, Bullard K, Konz J, Hawes K, Gauld J, Blake IM, Mercer LD, Kurji F, Voorman A, Diop OM, Oberste MS, Modlin J, Macklin G, Eisenhawer M, Bandyopadhyay AS, Zipursky S. Genetic Characterization of Novel Oral Polio Vaccine Type 2 Viruses During Initial Use Phase Under Emergency Use Listing - Worldwide, March-October 2021. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2022; 71:786-790. [PMID: 35709073 DOI: 10.15585/mmwr.mm7124a2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The emergence and international spread of neurovirulent circulating vaccine-derived polioviruses (cVDPVs) across multiple countries in Africa and Asia in recent years pose a major challenge to the goal of eradicating all forms of polioviruses. Approximately 90% of all cVDPV outbreaks are caused by the type 2 strain of the Sabin vaccine, an oral live, attenuated vaccine; cVDPV outbreaks typically occur in areas of persistently low immunization coverage (1). A novel type 2 oral poliovirus vaccine (nOPV2), produced by genetic modification of the type 2 Sabin vaccine virus genome (2), was developed and evaluated through phase I and phase II clinical trials during 2017-2019. nOPV2 was demonstrated to be safe and well-tolerated, have noninferior immunogenicity, and have superior genetic stability compared with Sabin monovalent type 2 (as measured by preservation of the primary attenuation site [domain V in the 5' noncoding region] and significantly lower neurovirulence of fecally shed vaccine virus in transgenic mice) (3-5). These findings indicate that nOPV2 could be an important tool in reducing the risk for generating vaccine-derived polioviruses (VDPVs) and the risk for vaccine-associated paralytic poliomyelitis cases. Based on the favorable preclinical and clinical data, and the public health emergency of international concern generated by ongoing endemic wild poliovirus transmission and cVDPV type 2 outbreaks, the World Health Organization authorized nOPV2 for use under the Emergency Use Listing (EUL) pathway in November 2020, allowing for its first use for outbreak response in March 2021 (6). As required by the EUL process, among other EUL obligations, an extensive plan was developed and deployed for obtaining and monitoring nOPV2 isolates detected during acute flaccid paralysis (AFP) surveillance, environmental surveillance, adverse events after immunization surveillance, and targeted surveillance for adverse events of special interest (i.e., prespecified events that have the potential to be causally associated with the vaccine product), during outbreak response, as well as through planned field studies. Under this monitoring framework, data generated from whole-genome sequencing of nOPV2 isolates, alongside other virologic data for isolates from AFP and environmental surveillance systems, are reviewed by the genetic characterization subgroup of an nOPV working group of the Global Polio Eradication Initiative. Global nOPV2 genomic surveillance during March-October 2021 confirmed genetic stability of the primary attenuating site. Sequence data generated through this unprecedented global effort confirm the genetic stability of nOPV2 relative to Sabin 2 and suggest that nOPV2 will be an important tool in the eradication of poliomyelitis. nOPV2 surveillance should continue for the duration of the EUL.
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10
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Evaluating stability of attenuated Sabin and two novel type 2 oral poliovirus vaccines in children. NPJ Vaccines 2022; 7:19. [PMID: 35149714 PMCID: PMC8837630 DOI: 10.1038/s41541-022-00437-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
Novel oral poliovirus vaccine type 2 (nOPV2) is being developed to reduce the rare occurrence of disease and outbreaks associated with the genetic instability of the Sabin vaccine strains. Children aged 1 to 5 years were enrolled in two related clinical studies to assess safety, immunogenicity, shedding rates and properties of the shed virus following vaccination with nOPV2 (two candidates) versus traditional Sabin OPV type 2 (mOPV2). The anticipated pattern of reversion and increased virulence was observed for shed Sabin-2 virus, as assessed using a mouse model of poliovirus neurovirulence. In contrast, there were significantly reduced odds of mouse paralysis for shed virus for both nOPV2 candidates when compared to shed Sabin-2 virus. Next-generation sequencing of shed viral genomes was consistent with and further supportive of the observed neurovirulence associated with shed Sabin-2 virus, as well as the reduced reversion to virulence of shed candidate viruses. While shed Sabin-2 showed anticipated A481G reversion in the primary attenuation site in domain V in the 5’ untranslated region to be associated with increased mouse paralysis, the stabilized domain V in the candidate viruses did not show polymorphisms consistent with reversion to neurovirulence. The available data from a key target age group for outbreak response confirm the superior genetic and phenotypic stability of shed nOPV2 strains compared to shed Sabin-2 and suggest that nOPV2 should be associated with less paralytic disease and potentially a lower risk of seeding new outbreaks.
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11
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Pintó RM, Burns CC, Moratorio G. Editorial: Codon Usage and Dinucleotide Composition of Virus Genomes: From the Virus-Host Interaction to the Development of Vaccines. Front Microbiol 2021; 12:791750. [PMID: 34917065 PMCID: PMC8671033 DOI: 10.3389/fmicb.2021.791750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Barcelona, Spain
| | - Cara C Burns
- Division of Viral Disease, Molecular Epidemiology and Surveillance, Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Gonzalo Moratorio
- Molecular Virology Laboratory, Experimental Evolution Laboratory, Nuclear Research Centre, School of Sciences, University of la República, Institute Pasteur, Montevideo, Uruguay
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12
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Konz JO, Schofield T, Carlyle S, Wahid R, Ansari A, Strating JRPM, Yeh MT, Manukyan H, Smits SL, Tritama E, Rahmah L, Ugiyadi D, Andino R, Laassri M, Chumakov K, Macadam A. Evaluation and validation of next-generation sequencing to support lot release for a novel type 2 oral poliovirus vaccine. Vaccine X 2021; 8:100102. [PMID: 34195600 PMCID: PMC8233139 DOI: 10.1016/j.jvacx.2021.100102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 02/02/2023] Open
Abstract
Genetic variants were evaluated to assess which were important to ensure nOPV2 quality. The cDNA preparation and NGS method was validated through evaluating mixtures of Sabin-2 and nOPV2. Pre-specified validation criteria for linearity and precision were met at all positions. The method was assessed to be fit-for-purpose for vaccine lot release. Understanding the co-location of genetic variants was important to interpret NGS results.
A novel, genetically-stabilized type 2 oral polio vaccine (nOPV2), developed to assist in the global polio eradication program, was recently the first-ever vaccine granted Emergency Use Listing by the WHO. Lot release tests for this vaccine included—for the first time to our knowledge—the assessment of genetic heterogeneity using next-generation sequencing (NGS). NGS ensures that the genetically-modified regions of the vaccine virus genome remain as designed and that levels of polymorphisms which may impact safety or efficacy are controlled during routine production. The variants present in nOPV2 lots were first assessed for temperature sensitivity and neurovirulence using molecular clones to inform which polymorphisms warranted formal evaluation during lot release. The novel use of NGS as a lot release test required formal validation of the method. Analysis of an nOPV2 lot spiked with the parental Sabin-2 strain enabled performance characteristics of the method to be assessed simultaneously at over 40 positions in the genome. These characteristics included repeatability and intermediate precision of polymorphism measurement, linearity of both spike-induced and nOPV2 lot-specific polymorphisms, and the limit-of-detection of spike-induced polymorphisms. The performance characteristics of the method met pre-defined criteria for 34 spike-induced polymorphic sites and 8 polymorphisms associated with the nOPV2 preparation; these sites collectively spanned most of the viral genome. Finally, the co-location of variants of interest on genomes was evaluated, with implications for the interpretation of NGS discussed.
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Affiliation(s)
- John O Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, United States
| | - Tim Schofield
- CMC Sciences, LLC, Germantown, MD 20876, United States
| | - Sarah Carlyle
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, United Kingdom
| | - Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, United States
| | - Azeem Ansari
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, United States
| | | | - Ming Te Yeh
- University of California San Francisco, San Francisco, United States
| | - Hasmik Manukyan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Saskia L Smits
- Viroclinics Biosciences B.V., Rotterdam, the Netherlands
| | | | | | | | - Raul Andino
- University of California San Francisco, San Francisco, United States
| | - Majid Laassri
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Andrew Macadam
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, United Kingdom
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