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Onnockx S, Baldo A, Pauwels K. Oncolytic Viruses: An Inventory of Shedding Data from Clinical Trials and Elements for the Environmental Risk Assessment. Vaccines (Basel) 2023; 11:1448. [PMID: 37766125 PMCID: PMC10535390 DOI: 10.3390/vaccines11091448] [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: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Attenuated and/or genetically modified oncolytic viruses (OV) gain increasing interest as a promising approach for cancer therapy. Beside the assessment of subject safety, quality and efficacy aspects of medicinal products for human use, genetically modified viruses are also governed by EU regulatory frameworks requiring an environmental risk assessment (ERA). An important element to be assessed as part of the ERA is the incidence of exposure to OV of individuals, other than the trial subjects, and the environment. The evidence-based evaluation of shedding data is considered to be decisive in that context, as it may impact the OV capacity to be transmitted. This is particularly true for OV still able to (conditionally) replicate as opposed to replication-defective viral vectors commonly used in gene therapy or vaccination. To our knowledge, this article presents the most extensive and up-to-date review of shedding data reported with OV employed in clinics. Besides the identification of a topical need for improving the collection of shedding data, this article aims at providing an aid to the design of an appropriate shedding study, thereby relying on and further complementing principles described in existing guidelines issued by European and international institutions.
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Affiliation(s)
- Sheela Onnockx
- Sciensano, Service Biosafety and Biotechnology, Rue Juliette Wytsmanstraat 14, B-1050 Brussels, Belgium; (A.B.); (K.P.)
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2
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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294416. [PMID: 37662226 PMCID: PMC10473782 DOI: 10.1101/2023.08.22.23294416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. Results We enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive ≥21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR-positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation. Conclusions In this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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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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Soofi SB, Vadsaria K, Mannan S, Habib MA, Tabassum F, Hussain I, Muhammad S, Feroz K, Ahmed I, Islam M, Bhutta ZA. Factors Associated with Vaccine Refusal (Polio and Routine Immunization) in High-Risk Areas of Pakistan: A Matched Case-Control Study. Vaccines (Basel) 2023; 11:vaccines11050947. [PMID: 37243051 DOI: 10.3390/vaccines11050947] [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: 04/05/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Pakistan has subpar childhood immunization rates and immunization activities have faced several challenges over the past years. We evaluated the social-behavioral and cultural barriers and risk factors for refusal of polio, Routine Immunization (RI), or both in high-risk areas of poliovirus circulation. METHODS A matched case-control study was conducted from April to July 2017 in eight super high-risk Union Councils of five towns in Karachi, Pakistan. A total of 3 groups, each with 250 cases, including refusals for the Oral Polio Vaccine (OPV) in campaigns (national immunization days and supplementary immunization activities), RI, and both, were matched with 500 controls and identified using surveillance records. Sociodemographic characteristics, household information, and immunization history were assessed. Study outcomes included social-behavioral and cultural barriers and reasons for vaccine refusal. Data were analyzed in STATA using conditional logistic regression. RESULTS RI refusal was associated with illiteracy and fear of the vaccine's adverse effects, while OPV refusals were linked to the mother's decision authority and the assumption that the OPV caused infertility. Conversely, higher socioeconomic status (SES) and knowledge of and willingness to vaccinate with Inactivated Polio Vaccine (IPV) were inversely associated with RI; and lower SES, walking to the vaccination point, knowledge of IPV, and an understanding of contracting polio were inversely associated with OPV refusals, with the latter two also inversely associated with complete vaccine refusal. CONCLUSION Education, knowledge and understanding of vaccines, and socioeconomic determinants influenced OPV and RI refusals among children. Effective interventions are needed to address knowledge gaps and misconceptions among parents.
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Affiliation(s)
- Sajid Bashir Soofi
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Khadija Vadsaria
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Sara Mannan
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Muhammad Atif Habib
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Farhana Tabassum
- Institute for Global Health and Development, Aga Khan University, Karachi 74800, Pakistan
| | - Imtiaz Hussain
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Sajid Muhammad
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Khalid Feroz
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Imran Ahmed
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Muhammad Islam
- Centre for Global Child Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Zulfiqar A Bhutta
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi 74800, Pakistan
- Institute for Global Health and Development, Aga Khan University, Karachi 74800, Pakistan
- Centre for Global Child Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
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Agrati C, Bartolini B, Bordoni V, Locatelli F, Capobianchi MR, Di Caro A, Castilletti C, Ippolito G. Emerging viral infections in immunocompromised patients: A great challenge to better define the role of immune response. Front Immunol 2023; 14:1147871. [PMID: 36969202 PMCID: PMC10035572 DOI: 10.3389/fimmu.2023.1147871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
The immune response to invading pathogens is characterized by the rapid establishment of a complex network of cellular interactions and soluble signals. The correct balancing of activating and regulating pathways and tissue-homing signals determines its effectiveness and persistence over time. Emerging viral pathogens have always represented a great challenge to the immune system and an often uncontrolled/imbalanced immune response has been described (e.g. cytokine storm, immune paralysis), contributing to the severity of the disease. Several immune biomarkers and cell subsets have been identified as major players in the cascade of events leading to severe diseases, highlighting the rationale for host-directed intervention strategy. There are millions of immunocompromised pediatric and adult patients worldwide (e.g. transplant recipients, hematologic patients, subjects with primary immune-deficiencies), experiencing an impaired immune reactivity, due to diseases and/or to the medical treatments. The reduced immune reactivity could have two paradoxical non-exclusive effects: a weak protective immunity on one hand, and a reduced contribution to immune-mediated pathogenetic processes on the other hand. In these sensitive contexts, the impact of emerging infections represents a still open issue to be explored with several challenges for immunologists, virologists, physicians and epidemiologists. In this review, we will address emerging infections in immunocompromised hosts, to summarize the available data concerning the immune response profile, its influence on the clinical presentation, the possible contribution of persistent viral shedding in generating new viral variants with improved immune escape features, and the key role of vaccination.
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Affiliation(s)
- Chiara Agrati
- Oncoematologia e Officina Farmaceutica, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- *Correspondence: Chiara Agrati,
| | - Barbara Bartolini
- General Directorate for Research and Health Innovation, Italian Ministry of Health, Rome, Italy
| | - Veronica Bordoni
- Oncoematologia e Officina Farmaceutica, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Oncoematologia e Officina Farmaceutica, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Pediatrics, Catholic University of the Sacred Heart, Rome, Italy
| | - Maria Rosaria Capobianchi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
- Unicamillus, International Medical University of Rome, Rome, Italy
| | - Antonino Di Caro
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
- Unicamillus, International Medical University of Rome, Rome, Italy
| | - Concetta Castilletti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Giuseppe Ippolito
- General Directorate for Research and Health Innovation, Italian Ministry of Health, Rome, Italy
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Bermingham WH, Canning B, Wilton T, Kidd M, Klapsa D, Majumdar M, Sooriyakumar K, Martin J, Huissoon AP. Case report: Clearance of longstanding, immune-deficiency-associated, vaccine-derived polio virus infection following remdesivir therapy for chronic SARS-CoV-2 infection. Front Immunol 2023; 14:1135834. [PMID: 36936936 PMCID: PMC10022663 DOI: 10.3389/fimmu.2023.1135834] [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: 01/01/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
The global polio eradication campaign has had remarkable success in reducing wild-type poliovirus infection, largely built upon the live attenuated Sabin oral poliovirus vaccine. Whilst rare, vaccine poliovirus strains may cause infection and subsequently revert to a neurovirulent type, termed vaccine-derived poliovirus (VDPV). Persistent, vaccine derived infection may occur in an immunocompromised host (iVDPV), where it is a recognised complication following receipt of the Sabin vaccine. This has significant implications for the global polio eradication campaign and there is currently no agreed global strategy to manage such patients.Here we describe a case of a 50-year-old man with common variable immune deficiency, persistently infected with a neurovirulent vaccine-derived type 2 poliovirus following vaccination in childhood. iVDPV infection had proven resistant to multiple prior attempts at treatment with human breast milk, ribavirin and oral administration of a normal human pooled immunoglobulin product. His iVDPV infection subsequently resolved after 12 days treatment with remdesivir, an adenosine analogue prodrug that is an inhibitor of viral RNA-dependent RNA polymerase, administered as treatment for a prolonged, moderate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. iVDPV from the patient, isolated prior to treatment, was subsequently demonstrated to be sensitive to remdesivir in vitro. Based on the observations made in this case, and the mechanistic rationale for use with iVDPV, there is strong justification for further clinical studies of remdesivir treatment as a potentially curative intervention in patients with iVDPV infection.
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Affiliation(s)
- William Hywel Bermingham
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- *Correspondence: William Hywel Bermingham,
| | - Benjamin Canning
- Department of Virology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Michael Kidd
- Public Health Laboratory, UK Health Security Agency, Birmingham, United Kingdom
| | - Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Kavitha Sooriyakumar
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Aarnoud P. Huissoon
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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7
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Fan Q, Ma J, Li X, Jorba J, Yuan F, Zhu H, Hu L, Song Y, Wang D, Zhu S, Yan D, Chen H, Xu W, Zhang Y. Molecular evolution and antigenic drift of type 3 iVDPVs excreted from a patient with immunodeficiency in Ningxia, China. J Med Virol 2023; 95:e28215. [PMID: 36224711 DOI: 10.1002/jmv.28215] [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: 05/29/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 01/11/2023]
Abstract
A 2.5-year-old pediatric patient with acute flaccid paralysis was diagnosed with primary immunodeficiency (PID) in Ningxia Province, China, in 2011. Twelve consecutive stool specimens were collected from the patient over a period of 10 months (18 February 2011 to 20 November 2011), and 12 immunodeficiency vaccine-derived poliovirus (iVDPV) strains (CHN15017-1 to CHN15017-12) were subsequently isolated. Nucleotide sequencing analysis of the plaque-purified iVDPVs revealed 2%-3.5% VP1-region differences from their parental Sabin 3 strain. Full-length genome sequencing showed they were all Sabin 3/Sabin 1 recombinants, sharing a common 2C-region crossover site, and the two key determinants of attenuation (U472C in the 5' untranslated region and T2493C in the VP1 region) had reverted. Temperature-sensitive experiments demonstrated that the first two iVDPV strains partially retained the temperature-sensitive phenotype's nature, while the subsequent ten iVDPV strains distinctly lost it, possibly associated with increased neurovirulence. Nineteen amino-acid substitutions were detected between 12 iVDPVs and the parental Sabin strain, of which only one (K1419R) was found on the subsequent 10 iVDPV isolates, suggesting this site's potential as a temperature-sensitive determination site. A Bayesian Monte Carlo Markov Chain phylogenetic analysis based on the P1 coding region yielded a mean iVDPV evolutionary rate of 1.02 × 10-2 total substitutions/site/year, and the initial oral-polio-vaccine dose was presumably administered around June 2009. Our findings provide valuable information regarding the genetic structure, high-temperature growth sensitivity, and antigenic properties of iVDPVs following long-term evolution in a single PID patient, thus augmenting the currently limited knowledge regarding the dynamic changes and evolutionary pathway of iVDPV populations with PID during long-term global replication.
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Affiliation(s)
- Qin Fan
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Jiangtao Ma
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan City, Ningxia Hui Autonomous Region, Yinchuan, People's Republic of China
| | - Xiaolei Li
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jaume Jorba
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fang Yuan
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan City, Ningxia Hui Autonomous Region, Yinchuan, People's Republic of China
| | - Hui Zhu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Lan Hu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yang Song
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongyan Wang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuangli Zhu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongmei Yan
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Hui Chen
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan City, Ningxia Hui Autonomous Region, Yinchuan, People's Republic of China
| | - Wenbo Xu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yong Zhang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People's Republic of China
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8
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Vaccine-associated paralytic poliomyelitis in a child: fast transformation from Sabin-like virus to vaccine-derived poliovirus triggered an epidemiological response in two countries of the European region. Int J Infect Dis 2022; 125:35-41. [PMID: 36180034 DOI: 10.1016/j.ijid.2022.09.034] [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: 06/01/2022] [Revised: 08/16/2022] [Accepted: 09/23/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The detection of a vaccine-derived poliovirus (VDPV) requires an epidemiological assessment and response. Using repeated stool sampling from a child who is immunocompetent and was vaccinated against poliomyelitis with acute flaccid paralysis, a case of an extremely rapid evolution of Sabin-like poliovirus (PV) type 3 was traced in the child's body. METHODS The case was independently identified in two countries-Tajikistan and Russia. Stool samples for the study were also independently collected in two countries on different days from the onset of paralysis. Virological, serological, and molecular methods; full genome Sanger; and high-throughput sequencing were performed to characterize isolates. RESULTS PV isolates from samples collected on days 2, 3, and 14 contained eight, seven, and seven mutations in the VP1-coding region, respectively, and were classified as Sabin-like PV type 3. The isolates from samples collected on days 15 and 18 had 11 mutations and were classified as vaccine-derived PVs, which required an epidemiological response in the two countries. CONCLUSION The results indicate the need to continue acute flaccid paralysis surveillance, maintain high vaccination coverage, and develop and introduce new effective, genetically stable PV vaccines.
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9
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Xiao T, Leng H, Zhang Q, Chen Q, Guo H, Qi Y. Isolation and characterization of a Sabin 3/Sabin 1 recombinant vaccine-derived poliovirus from a child with severe combined immunodeficiency. Virus Res 2021; 308:198633. [PMID: 34793871 DOI: 10.1016/j.virusres.2021.198633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
An 8-month-old child diagnosed with severe combined immunodeficiency (SCID) was found to be excreting vaccine-derived poliovirus (VDPVs). Five stool samples from the child and stool samples from 24 contacts were collected during the following 7 months. Complete genome sequence by next generation sequencing (NGS) identified 0.7 to 1.4% nucleotide substitutions in the capsid P1 region of the first and the last isolates compared with Sabin 3 strain. Simplot analysis revealed that all isolates were Sabin 3/Sabin 1 recombinants, sharing a single recombination breakpoint in the 2C region. Multiple nucleotide variants were identified in the 5'UTR (T472→C and G395→A); amino acid mutations were identified in residues at VP1-6 (Thr to Ile), VP1-105 (Met to Thr), VP1-286 (Arg to Lys), VP2-155 (Lys to Glu), VP3-59 (Ser to Asn) and VP3-91 (Phe to Ser). These variants were commonly observed in other PV strains, which may contribute to attenuation and temperature sensitivity. None of the 24 tested contacts of the patient and related transmits was found to be infected with poliovirus. Our study provides a rapid and reliable method for the characterization of VDPV research in Poliovirus infection. In post-OPV era, immunodeficient people with persistent and chronic infection remain a major challenge for polio eradication in China.
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Affiliation(s)
- Tianhe Xiao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; Department of Bioengineering, University of California, San Diego, CA 92093, USA
| | - Hongying Leng
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Qian Zhang
- College of pharmacy, Nankai University, Tianjin 300353, China
| | - Qiang Chen
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Hongxiong Guo
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Yuhua Qi
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China.
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10
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Persistent COVID-19 Infection in Wiskott-Aldrich Syndrome Cleared Following Therapeutic Vaccination: a Case Report. J Clin Immunol 2021; 42:32-35. [PMID: 34714497 PMCID: PMC8554737 DOI: 10.1007/s10875-021-01158-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/13/2021] [Indexed: 10/25/2022]
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11
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Schang C, Crosbie ND, Nolan M, Poon R, Wang M, Jex A, John N, Baker L, Scales P, Schmidt J, Thorley BR, Hill K, Zamyadi A, Tseng CW, Henry R, Kolotelo P, Langeveld J, Schilperoort R, Shi B, Einsiedel S, Thomas M, Black J, Wilson S, McCarthy DT. Passive Sampling of SARS-CoV-2 for Wastewater Surveillance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10432-10441. [PMID: 34264643 PMCID: PMC8291133 DOI: 10.1021/acs.est.1c01530] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 05/17/2023]
Abstract
The shedding of pathogens by infected humans enables the use of sewage monitoring to conduct wastewater-based epidemiology (WBE). Although most WBE studies use data from large sewage treatment plants, timely data from smaller catchments are needed for targeted public health action. Traditional sampling methods, like autosamplers or grab sampling, are not conducive to quick ad hoc deployments and high-resolution monitoring at these smaller scales. This study develops and validates a cheap and easily deployable passive sampler unit, made from readily available consumables, with relevance to the COVID-19 pandemic but with broader use for WBE. We provide the first evidence that passive samplers can be used to detect SARS-CoV-2 in wastewater from populations with low prevalence of active COVID-19 infections (0.034 to 0.34 per 10,000), demonstrating their ability for early detection of infections at three different scales (lot, suburb, and city). A side by side evaluation of passive samplers (n = 245) and traditionally collected wastewater samples (n = 183) verified that the passive samplers were sensitive at detecting SARS-CoV-2 in wastewater. On all 33 days where we directly compared traditional and passive sampling techniques, at least one passive sampler was positive when the average SARS-CoV-2 concentration in the wastewater equaled or exceeded the quantification limit of 1.8 gene copies per mL (n = 7). Moreover, on 13 occasions where wastewater SARS-CoV-2 concentrations were less than 1.8 gene copies per mL, one or more passive samplers were positive. Finally, there was a statistically significant (p < 0.001) positive relationship between the concentrations of SARS-CoV-2 in wastewater and the levels found on the passive samplers, indicating that with further evaluation, these devices could yield semi-quantitative results in the future. Passive samplers have the potential for wide use in WBE with attractive feasibility attributes of cost, ease of deployment at small-scale locations, and continuous sampling of the wastewater. Further research will focus on the optimization of laboratory methods including elution and extraction and continued parallel deployment and evaluations in a variety of settings to inform optimal use in wastewater surveillance.
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Affiliation(s)
- Christelle Schang
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Nicolas D. Crosbie
- Melbourne Water Corp., 990
La Trobe St., Docklands, Victoria 3001, Australia
| | - Monica Nolan
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Rachael Poon
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Miao Wang
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Aaron Jex
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Nijoy John
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Louise Baker
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Scales
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | | | - Bruce R. Thorley
- Victorian Infectious Diseases Reference Laboratory,
Royal Melbourne Hospital at the Peter Doherty Institute for Infection and
Immunity, Melbourne, Victoria 3000, Australia
| | - Kelly Hill
- Water Research Australia,
Adelaide Office, Level 2, 250 Victoria Square, Adelaide 5000, South
Australia
| | - Arash Zamyadi
- Water Research Australia,
Melbourne Office, 990 La Trobe St., Docklands, Victoria 3001,
Australia
| | - Chi-Wen Tseng
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Rebekah Henry
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Peter Kolotelo
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Jeroen Langeveld
- Department of Water Management, TU
Delft, Delft, CN 2628, The Netherlands
- Partners4UrbanWater, Nijmegen
6532 ZV, The Netherlands
| | | | - Baiqian Shi
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Steve Einsiedel
- ALS Hydrographics, 22
Dalmore Drive, Scoresby, Victoria 3179, Australia
| | - Michael Thomas
- Barwon Water, 55-67 Ryrie
St., Geelong, Victoria 3220, Australia
| | - James Black
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Simon Wilson
- Melbourne Water Corp., 990
La Trobe St., Docklands, Victoria 3001, Australia
| | - David T. McCarthy
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
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12
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Kitamura K, Shimizu H. The Molecular Evolution of Type 2 Vaccine-Derived Polioviruses in Individuals with Primary Immunodeficiency Diseases. Viruses 2021; 13:v13071407. [PMID: 34372613 PMCID: PMC8310373 DOI: 10.3390/v13071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/17/2021] [Accepted: 07/17/2021] [Indexed: 12/28/2022] Open
Abstract
The oral poliovirus vaccine (OPV), which prevents person-to-person transmission of poliovirus by inducing robust intestinal immunity, has been a crucial tool for global polio eradication. However, polio outbreaks, mainly caused by type 2 circulating vaccine-derived poliovirus (cVDPV2), are increasing worldwide. Meanwhile, immunodeficiency-associated vaccine-derived poliovirus (iVDPV) is considered another risk factor during the final stage of global polio eradication. Patients with primary immunodeficiency diseases are associated with higher risks for long-term iVDPV infections. Although a limited number of chronic iVDPV excretors were reported, the recent identification of a chronic type 2 iVDPV (iVDPV2) excretor in the Philippines highlights the potential risk of inapparent iVDPV infection for expanding cVDPV outbreaks. Further research on the genetic characterizations and molecular evolution of iVDPV2, based on comprehensive iVDPV surveillance, will be critical for elucidating the remaining risk of iVDPV2 during the post-OPV era.
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13
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Álamo-Junquera D, Politi J, Simón P, Dieli-Crimi R, Borrell RP, Colobran R, Martínez-Gallo M, Campins M, Antón A, Esperalba J, Andrés C, Codina MG, Polverino E, Narciso MR, Molinero E, Rius C. Coordinated Response to Imported Vaccine-Derived Poliovirus Infection, Barcelona, Spain, 2019-2020. Emerg Infect Dis 2021; 27:1513-1516. [PMID: 33900188 PMCID: PMC8084499 DOI: 10.3201/eid2705.204675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2019, the Public Health Agency of Barcelona, Spain, was notified of a vaccine-derived poliovirus infection. The patient had an underlying common variable immunodeficiency and no signs of acute flaccid paralysis. We describe the ongoing coordinated response to contain the infection, which included compassionate-use treatment with pocapavir.
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14
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Shulman LM, Weil M, Somech R, Stauber T, Indenbaum V, Rahav G, Mendelson E, Sofer D. Underperformed and Underreported Testing for Persistent Oropharyngeal Poliovirus Infections in Primary Immune Deficient Patients-Risk for Reemergence of Polioviruses. J Pediatric Infect Dis Soc 2021; 10:326-333. [PMID: 32538431 DOI: 10.1093/jpids/piaa053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 05/06/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND Individuals with primary immune deficiencies (PIDs) may excrete poliovirus for extended periods and remain a major reservoir for polio after eradication. Poliovirus can spread by fecal-oral or oral-oral transmission. In middle- and high-income countries, oral-oral transmission may be more prevalent than fecal-oral transmission of polioviruses where PIDs patients survive longer. Our aim was to determine the prevalence of prolonged or persistent oropharyngeal poliovirus infections in PIDs. METHODS We performed a literature search for reports of prolonged (excreting poliovirus for ≥6 months and ≤5 years) or persistent (excreting poliovirus for >5 years) poliovirus infections in PIDs. RESULTS There were 140 PID cases with prolonged or persistent poliovirus infections. All had poliovirus-positive stools. Testing of oropharyngeal mucosa was only reported for 6 cases, 4 of which were positive. Molecular analyses demonstrated independent evolution of poliovirus in the gut and oropharyngeal mucosa in 2 cases. Seven PIDs had multiple lineages of the same poliovirus serotype in stools without information about polioviruses in oropharyngeal mucosa. CONCLUSIONS Testing for persistence of poliovirus in oropharyngeal mucosa of PID patients is rare, with virus recovered in 4 of 5 cases in whom stools were positive. Multiple lineages or serotypes in 7 additional PID cases may indicate separate foci of infection, some of which might be in oropharyngeal mucosa. We recommend screening throat swabs in addition to stools for poliovirus in PID patients. Containment protocols for reducing both oral-oral and fecal-oral transmission from PID patients must be formulated for hospitals and community settings.
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Affiliation(s)
- Lester M Shulman
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, at Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Merav Weil
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, at Sheba Medical Center, Tel Hashomer, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Tali Stauber
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Victoria Indenbaum
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, at Sheba Medical Center, Tel Hashomer, Israel
| | - Galia Rahav
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Infectious Disease Unit, Sheba Medical Center, Tel Hashomer, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, at Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, at Sheba Medical Center, Tel Hashomer, Israel
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15
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Chouikha A, Rezig D, Driss N, Abdelkhalek I, Ben Yahia A, Touzi H, Meddeb Z, Ben Farhat E, Yahyaoui M, Triki H. Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades. Viruses 2021; 13:v13030380. [PMID: 33673590 PMCID: PMC7997211 DOI: 10.3390/v13030380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 11/17/2022] Open
Abstract
This report is an overview of enterovirus (EV) detection in Tunisian polio-suspected paralytic cases (acute flaccid paralysis (AFP) cases), healthy contacts and patients with primary immunodeficiencies (PID) during an 11-year period. A total of 2735 clinical samples were analyzed for EV isolation and type identification, according to the recommended protocols of the World Health Organization. Three poliovirus (PV) serotypes and 28 different nonpolio enteroviruses (NPEVs) were detected. The NPEV detection rate was 4.3%, 2.8% and 12.4% in AFP cases, healthy contacts and PID patients, respectively. The predominant species was EV-B, and the circulation of viruses from species EV-A was noted since 2011. All PVs detected were of Sabin origin. The PV detection rate was higher in PID patients compared to AFP cases and contacts (6.8%, 1.5% and 1.3% respectively). PV2 was not detected since 2015. Using nucleotide sequencing of the entire VP1 region, 61 strains were characterized as Sabin-like. Among them, six strains of types 1 and 3 PV were identified as pre-vaccine-derived polioviruses (VDPVs). Five type 2 PV, four strains belonging to type 1 PV and two strains belonging to type 3 PV, were classified as iVDPVs. The data presented provide a comprehensive picture of EVs circulating in Tunisia over an 11-year period, reveal changes in their epidemiology as compared to previous studies and highlight the need to set up a warning system to avoid unnoticed PVs.
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Affiliation(s)
- Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
- Research Laboratory, LR20IPT02, Pasteur Institute of Tunis, Tunis 1006, Tunisia
- Correspondence: ; Tel.: +216-71-843-755; Fax: +216-71-791-833
| | - Dorra Rezig
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
- Research Laboratory, LR20IPT02, Pasteur Institute of Tunis, Tunis 1006, Tunisia
| | - Nadia Driss
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
| | - Ichrak Abdelkhalek
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
| | - Ahlem Ben Yahia
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
| | - Essia Ben Farhat
- National Program of Immunization Basic Health Care Division, Ministry of Health Tunis, Tunis 1006, Tunisia; (E.B.F.); (M.Y.)
| | - Mahrez Yahyaoui
- National Program of Immunization Basic Health Care Division, Ministry of Health Tunis, Tunis 1006, Tunisia; (E.B.F.); (M.Y.)
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1068, Tunisia; (D.R.); (N.D.); (I.A.); (A.B.Y.); (H.T.); (Z.M.); (H.T.)
- Research Laboratory, LR20IPT02, Pasteur Institute of Tunis, Tunis 1006, Tunisia
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16
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Demirdag YY, Gupta S. Update on Infections in Primary Antibody Deficiencies. Front Immunol 2021; 12:634181. [PMID: 33643318 PMCID: PMC7905085 DOI: 10.3389/fimmu.2021.634181] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 11/14/2022] Open
Abstract
Bacterial respiratory tract infections are the hallmark of primary antibody deficiencies (PADs). Because they are also among the most common infections in healthy individuals, PADs are usually overlooked in these patients. Careful evaluation of the history, including frequency, chronicity, and presence of other infections, would help suspect PADs. This review will focus on infections in relatively common PADs, discussing diagnostic challenges, and some management strategies to prevent infections.
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Affiliation(s)
- Yesim Yilmaz Demirdag
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, Irvine, CA, United States
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17
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Bahar MW, Porta C, Fox H, Macadam AJ, Fry EE, Stuart DI. Mammalian expression of virus-like particles as a proof of principle for next generation polio vaccines. NPJ Vaccines 2021; 6:5. [PMID: 33420068 PMCID: PMC7794334 DOI: 10.1038/s41541-020-00267-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Global vaccination programs using live-attenuated oral and inactivated polio vaccine (OPV and IPV) have almost eradicated poliovirus (PV) but these vaccines or their production pose significant risk in a polio-free world. Recombinant PV virus-like particles (VLPs), lacking the viral genome, represent safe next-generation vaccines, however their production requires optimisation. Here we present an efficient mammalian expression strategy producing good yields of wild-type PV VLPs for all three serotypes and a thermostabilised variant for PV3. Whilst the wild-type VLPs were predominantly in the non-native C-antigenic form, the thermostabilised PV3 VLPs adopted the native D-antigenic conformation eliciting neutralising antibody titres equivalent to the current IPV and were indistinguishable from natural empty particles by cryo-electron microscopy with a similar stabilising lipidic pocket-factor in the VP1 β-barrel. This factor may not be available in alternative expression systems, which may require synthetic pocket-binding factors. VLPs equivalent to these mammalian expressed thermostabilized particles, represent safer non-infectious vaccine candidates for the post-eradication era.
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Affiliation(s)
- Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- The Pirbright Institute, Pirbright, Surrey, GU24 0NF, UK
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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18
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Baang JH, Smith C, Mirabelli C, Valesano AL, Manthei DM, Bachman MA, Wobus CE, Adams M, Washer L, Martin ET, Lauring AS. Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient. J Infect Dis 2021; 223:23-27. [PMID: 33089317 PMCID: PMC7797758 DOI: 10.1093/infdis/jiaa666] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
We describe a case of chronic coronavirus disease 2019 (COVID-19) in a patient with lymphoma and associated B-cell immunodeficiency. Viral cultures and sequence analysis demonstrate ongoing replication of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for at least 119 days. The patient had 3 admissions related to COVID-19 over a 4-month period and was treated twice with remdesivir and convalescent plasma with resolution of symptoms. The patient's lack of seroconversion and prolonged course illustrate the importance of humoral immunity in resolving SARS-CoV-2 infection. This case highlights challenges in managing immunocompromised hosts, who may act as persistent shedders and sources of transmission.
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Affiliation(s)
- Ji Hoon Baang
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher Smith
- Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew L Valesano
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Manthei
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Adams
- Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laraine Washer
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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19
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Aradhi AAM, Hasson LM, Hameed IM. Polio Outbreak Response; Evaluation of Acute Flaccid Paralysis Surveillance in Karbala, Iraq. Int J Prev Med 2020; 11:131. [PMID: 33088459 PMCID: PMC7554433 DOI: 10.4103/ijpvm.ijpvm_128_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/29/2019] [Indexed: 12/05/2022] Open
Abstract
Background: After the last outbreak of wild polio infection in Baghdad, April 2014, the Iraqi response to the outbreak was activated through solid surveillance of Acute Flaccid Paralysis (AFP) case detection in all governorates to interrupt the circulation of poliovirus in addition to the strengthening of Expanded Program on Immunization. This response to the last outbreak has to be evaluated independently to ensure effective mopping and surveillance to stop further outbreak all over the country including the holy province Karbala. We aimed to evaluate the response to the last polio outbreak by evaluating surveillance activities of acute flaccid paralysis cases whether they meet the recommended standards. Methods: Observational evaluation study conducted through August 15–25, 2015. Checking of Acute Flaccid Paralysis surveillance (AFP) activity through detection of nonPolio acute flaccid paralysis rate and immediate reporting with adequate stool sampling, and 60 days follow-up examination four districts of the province. The reviewing checked whether the surveillance system in Karbala met the global standards required for stopping wild poliovirus circulation. The evaluation included immunization coverage rates and active National Immunization days of oral polio vaccine campaigns. Results: During the period of review, the core surveillance indicators in Karbala met the globally set standards. Percent of acute flaccid paralysis cases with specimens reached to the reference laboratory within 3 days was 100%. Nonpolio cases was 4.2 per 100000 population under 15 years of age through week 33 of the year 2015. Eleven AFP cases were reported from all districts of Karbala among Population of children under 15 years of age. The percentage of cases with adequate specimens was 100% in 2015 versus 93% in 2014. The percent of AFP Cases notified within 7 days of paralysis onset (during first 33 weeks) was 100% in 2015 versus 87% in 2014. Conclusions: As Karbala response to polio outbreak met the target global indicators and standards of polio surveillance. The circulation of the virus in this locality was interrupted and further transmission of the disease is unlikely.
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20
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Abstract
Purpose: to summarize the origin and very recent history of the use of metagenomic sequencing for the diagnosis of infectious uveitis, convey the technique as described by one of the primary institutions experimenting with the technology, and present recent successful applications of the technology as well as potential advantages and pitfalls compared to other current diagnostic tools.Methods: review of peer-reviewed literature concerning metagenomic sequencing for the diagnosis of infectious uveitis.Conclusion: compared to existing diagnostic methods, metagenomic deep sequencing is a sensitive, unbiased, and comprehensive technique with great potential for diagnosing the causative pathogens of cases of infectious uveitis. However, many issues remain to be addressed in the process of developing this technology, including but not limited to the potentially overwhelming amount of information generated, definition of diagnostic thresholds, demonstration of validity, contamination, and cost.
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Affiliation(s)
- Lianna Valdes
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Paulo Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
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21
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Kabuga AI, Nejati A, Soheili P, Yousefipoor S, Yousefi M, Mollaiee Y, Shahmahmoodi S. Cell culture demonstrates superior sensitivity over one step real time RT PCR and nested VP1 amplification for Enteroviruses. J Virol Methods 2020; 287:113994. [PMID: 33068705 DOI: 10.1016/j.jviromet.2020.113994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Abstract
This study evaluated and compared the sensitivity profile of routine cell culture, nested VP1 amplification and one step real time RT PCR for Enteroviruses. Serially diluted spiked samples of four model viruses (EV71, CVA16, CVB5 and PV1) and 32 true positive samples including Poliovirus (PV1 & PV3), Coxsackie virus (CVB5, CVB3, CVB1 & CVA4, 10, 16), Echovirus (Echo 6, 7, 11, 13, 18, 25 & 30) and Enterovirus 71 (E71), and 32 true negative stool samples were subjected to cell culture, nested RT PCR and one step real time RT PCR. The result of sensitivity test indicated superior sensitivity with one step real time RT PCR (75 %, 24/32) against cell culture (71.9 %, 23/32) and nested RT PCR (65.6 %, 21/32). The most specific test was cell culture (100 %, 32/32), followed by nested RT PCR (96.9 %, 31/32). Positive predictive values were 100 %: 23/23, 95.5 %; 21/22 and 88.9 %; 24/27, for cell culture, nested RT PCR and one step real time RT PCR, respectively, and one step real time RT PCR had the highest negative predictive value (78.4 %, 29/37). Overall result indicate relatively high analytical sensitivity with all the tests, suggesting superior performance by cell culture. Therefore, cell culture is the gold standard. However, considering intensive nature of cell cultures and prolong window for results, it is wise to consider one step real time RT PCR in routine diagnosis for its added advantages. Meanwhile, selecting a combination of tests can maximize detection, depending on the laboratory strength.
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Affiliation(s)
- Auwal Idris Kabuga
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Parastoo Soheili
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Soodeh Yousefipoor
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Yousefi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaghoob Mollaiee
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shohreh Shahmahmoodi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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22
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Jorgensen D, Pons-Salort M, Shaw AG, Grassly NC. The role of genetic sequencing and analysis in the polio eradication programme. Virus Evol 2020; 6:veaa040. [PMID: 32782825 PMCID: PMC7409915 DOI: 10.1093/ve/veaa040] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to the Global Polio Eradication Initiative has grown with the increasing incidence of vaccine-derived poliovirus (VDPV) infections in Africa specifically (470 reported cases in 2019), and globally, alongside persistent transmission of serotype 1 wild-type poliovirus in Pakistan and Afghanistan (197 reported cases in 2019). Adapting what has been learned about the virus genetics and evolution to address these threats has been a major focus of recent work. Here, we review how phylogenetic and phylogeographic methods have been used to trace the spread of wild-type polioviruses and identify the likely origins of VDPVs. We highlight the analysis methods and sequencing technology currently used and the potential for new technologies to speed up poliovirus detection and the interpretation of genetic data. At a pivotal point in the eradication campaign with the threat of anti-vaccine sentiment and donor and public fatigue, innovation is critical to maintain drive and overcome the last remaining circulating virus.
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Affiliation(s)
- David Jorgensen
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Margarita Pons-Salort
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Alexander G Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Nicholas C Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
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23
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Surveillance optimisation to detect poliovirus in the pre-eradication era: a modelling study of England and Wales. Epidemiol Infect 2020; 148:e157. [PMID: 32398193 PMCID: PMC7379320 DOI: 10.1017/s0950268820001004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Surveillance for acute flaccid paralysis (AFP) cases are essential for polio eradication. However, as most poliovirus infections are asymptomatic and some regions of the world are inaccessible, additional surveillance tools require development. Within England and Wales, we demonstrate how inclusion of environmental sampling (ENV) improves the sensitivity of detecting both wild and vaccine-derived polioviruses (VDPVs) when compared to current surveillance. Statistical modelling was used to estimate the spatial risk of wild and VDPV importation and circulation in England and Wales. We estimate the sensitivity of each surveillance mode to detect poliovirus and the probability of being free from poliovirus, defined as being below a pre-specified prevalence of infection. Poliovirus risk was higher within local authorities in Manchester, Birmingham, Bradford and London. The sensitivity of detecting wild poliovirus within a given month using AFP and enterovirus surveillance was estimated to be 0.096 (95% CI 0.055–0.134). Inclusion of ENV in the three highest risk local authorities and a site in London increased surveillance sensitivity to 0.192 (95% CI 0.191–0.193). The sensitivity of ENV strategies can be compared using the framework by varying sites and the frequency of sampling. The probability of being free from poliovirus slowly increased from the date of the last case in 1993. ENV within areas thought to have the highest risk improves detection of poliovirus, and has the potential to improve confidence in the polio-free status of England and Wales and detect VDPVs.
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24
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Comparative Molecular Biology Approaches for the Production of Poliovirus Virus-Like Particles Using Pichia pastoris. mSphere 2020; 5:5/2/e00838-19. [PMID: 32161150 PMCID: PMC7067596 DOI: 10.1128/msphere.00838-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the current poliovirus immunization program has been extremely successful in reducing the number of cases of paralytic polio worldwide, now more cases are caused by vaccine-derived polioviruses than by wild poliovirus. Switching to inactivated poliovirus vaccines will reduce this over time; however, their production requires the growth of large amounts of virus. This biosafety concern can be addressed by producing just the virus capsid. The capsid serves to protect the genetic material, which causes disease when introduced into a cell. Therefore, empty capsids (virus-like particles [VLPs]), which lack the viral RNA genome, are safe both to make and to use. We exploit yeast as a versatile model expression system to produce VLPs, and here we specifically highlight the potential of this system to supply next-generation poliovirus vaccines to secure a polio-free world for the future. For enteroviruses such as poliovirus (PV), empty capsids, which are antigenically indistinguishable from mature virions, are produced naturally during viral infection. The production of such capsids recombinantly, in heterologous systems such as yeast, have great potential as virus-like particle (VLP) vaccine candidates. Here, using PV as an exemplar, we show the production of VLPs in Pichia pastoris by coexpression of the structural precursor protein P1 and the viral protease 3CD. The level of expression of the potentially cytotoxic protease relative to that of the P1 precursor was modulated by three different approaches: expression of the P1 precursor and protease from different transcription units, separation of the P1 and protease proteins using the Thosea asigna virus (TaV) 2A translation interruption sequence, or separation of the P1 and protease-coding sequences by an internal ribosome entry site sequence from Rhopalosiphum padi virus (RhPV). We also investigate the antigenicity of VLPs containing previously characterized mutations when produced in Pichia. Finally, using transmission electron microscopy and two-dimensional classification, we show that Pichia-derived VLPs exhibited the classical icosahedral capsid structure displayed by enteroviruses. IMPORTANCE Although the current poliovirus immunization program has been extremely successful in reducing the number of cases of paralytic polio worldwide, now more cases are caused by vaccine-derived polioviruses than by wild poliovirus. Switching to inactivated poliovirus vaccines will reduce this over time; however, their production requires the growth of large amounts of virus. This biosafety concern can be addressed by producing just the virus capsid. The capsid serves to protect the genetic material, which causes disease when introduced into a cell. Therefore, empty capsids (virus-like particles [VLPs]), which lack the viral RNA genome, are safe both to make and to use. We exploit yeast as a versatile model expression system to produce VLPs, and here we specifically highlight the potential of this system to supply next-generation poliovirus vaccines to secure a polio-free world for the future.
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25
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McDonald SL, Weldon WC, Wei L, Chen Q, Shaw J, Zhao K, Jorba J, Kew OM, Pallansch MA, Burns CC, Steven Oberste M. Neutralization capacity of highly divergent type 2 vaccine-derived polioviruses from immunodeficient patients. Vaccine 2020; 38:3042-3049. [PMID: 32089462 DOI: 10.1016/j.vaccine.2020.02.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 01/18/2020] [Accepted: 02/12/2020] [Indexed: 10/25/2022]
Abstract
The use of the oral poliovirus vaccine (OPV) in developing countries has reduced the incidence of poliomyelitis by >99% since 1988 and is the primary tool for global polio eradication. Spontaneous reversions of the vaccine virus to a neurovirulent form can impede this effort. In persons with primary B-cell immunodeficiencies, exposure to OPV can result in chronic infection, mutation, and excretion of immunodeficiency-associated vaccine-derived polioviruses, (iVDPVs). These iVDPVs may have the potential for transmission in a susceptible population and cause paralysis. The extent to which sera from OPV recipients are able to neutralize iVDPVs with varying degrees of antigenic site substitutions is investigated here. We tested sera from a population immunized with a combination vaccine schedule (both OPV and inactivated polio vaccine) against a panel of iVDPVs and found that increases in amino acid substitution in the P1 capsid protein resulted in a decrease in the neutralizing capacity of the sera. This study underscores the importance of maintaining high vaccine coverage in areas of OPV use as well as active surveillance of those known to be immunocompromised.
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Affiliation(s)
- Sharla L McDonald
- IHRC, Inc. Atlanta, GA, Under Contract with Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, USA
| | - William C Weldon
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ling Wei
- IHRC, Inc. Atlanta, GA, Under Contract with Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, USA
| | - Qi Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jing Shaw
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kun Zhao
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jaume Jorba
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Olen M Kew
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark A Pallansch
- 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
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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26
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Liou AT, Liao CC, Chou SF, Chang YS, Chang CS, Shih C. Hypoxia and therapeutic treatment of EV-A71 with an immune modulator TLR7 agonist in a new immunocompetent mouse model. J Biomed Sci 2019; 26:93. [PMID: 31711481 PMCID: PMC6849267 DOI: 10.1186/s12929-019-0585-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/23/2019] [Indexed: 01/10/2023] Open
Abstract
Background Enterovirus 71 (EV71 or EV-A71) was first identified in California about half a century ago. In recent years, outbreaks of EV-A71 were prevalent worldwide, including Taiwan, Malaysia, Singapore, Japan, and China. Between 2008 and 2011, China alone reported 1894 deaths associated with EV-A71 infection. In mild cases, EV-A71 can cause herpangina and hand-foot-and-mouth disease (HFMD). However, in severe cases, it could cause neurological disorders, including meningitis and encephalitis. Cardiopulmonary failure is common among hospitalized children with EV-A71 infection. No effective FDA-approved therapeutics against EV-A71 are clinically available. Methods We report the establishment of an immunocompetent wild type strain 129 (wt-129) mouse model, which can be cross-species infected with human EV-A71 clinical isolates via an intraperitoneal route. Results One intriguing disease phenotype of this new model is the development of characteristic “White-Jade” patches in the muscle, which lost sporadically the normal pink color of uninfected muscle. Viral VP1 protein and massive leukocyte infiltration were detected in muscles with or without white-jades. We demonstrated further that hypoxia is a general phenomenon associated with white-jades in both immunocompetent and immunodeficient mouse models. Therefore, hypoxia appears to be a feature intrinsic to EV-A71 infection, irrespective of its host’s immunogenetic background. To date, no effective treatment for EV-A71 is available. Here, using this new wt-129 mouse model, we showed that timely treatment with compound R837 (a TLR7 immune modulator) via oral or intraperitoneal routes, rescued the hypoxia, limb paralysis, and death at a high therapeutic efficacy. Conclusions In this new immunocompetent mouse 129 model, we observed an unexpected white-jade phenotype and its associated hypoxia. The successful treatment with TLR7 immune modulators via an oral route, provide us a new research direction for EV-A71 basic science and translational research. It remains an open issue whether R837 or its related compounds, will be a promising drug candidate in clinical trials in EV-A71 endemic or epidemic areas in the future.
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Affiliation(s)
- An-Ting Liou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shu-Fan Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Shu Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Shin Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chiaho Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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27
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Persistent Infection and Transmission of Senecavirus A from Carrier Sows to Contact Piglets. J Virol 2019; 93:JVI.00819-19. [PMID: 31434730 DOI: 10.1128/jvi.00819-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/22/2019] [Indexed: 01/14/2023] Open
Abstract
Senecavirus A (SVA) is a picornavirus that causes acute vesicular disease (VD), that is clinically indistinguishable from foot-and-mouth disease (FMD), in pigs. Notably, SVA RNA has been detected in lymphoid tissues of infected animals several weeks following resolution of the clinical disease, suggesting that the virus may persist in select host tissues. Here, we investigated the occurrence of persistent SVA infection and the contribution of stressors (transportation, immunosuppression, or parturition) to acute disease and recrudescence from persistent SVA infection. Our results show that transportation stress leads to a slight increase in disease severity following infection. During persistence, transportation, immunosuppression, and parturition stressors did not lead to overt/recrudescent clinical disease, but intermittent viremia and virus shedding were detected up to day 60 postinfection (p.i.) in all treatment groups following stress stimulation. Notably, real-time PCR and in situ hybridization (ISH) assays confirmed that the tonsil harbors SVA RNA during the persistent phase of infection. Immunofluorescence assays (IFA) specific for double-stranded RNA (dsRNA) demonstrated the presence of double-stranded viral RNA in tonsillar cells. Most importantly, infectious SVA was isolated from the tonsil of two animals on day 60 p.i., confirming the occurrence of carrier animals following SVA infection. These findings were supported by the fact that contact piglets (11/44) born to persistently infected sows were infected by SVA, demonstrating successful transmission of the virus from carrier sows to contact piglets. Results here confirm the establishment of persistent infection by SVA and demonstrate successful transmission of the virus from persistently infected animals.IMPORTANCE Persistent viral infections have significant implications for disease control strategies. Previous studies demonstrated the persistence of SVA RNA in the tonsil of experimentally or naturally infected animals long after resolution of the clinical disease. Here, we showed that SVA establishes persistent infection in SVA-infected animals, with the tonsil serving as one of the sites of virus persistence. Importantly, persistently infected carrier animals shedding SVA in oral and nasal secretions or feces can serve as sources of infection to other susceptible animals, as evidenced by successful transmission of SVA from persistently infected sows to contact piglets. These findings unveil an important aspect of SVA infection biology, suggesting that persistently infected pigs may function as reservoirs for SVA.
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28
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Affiliation(s)
- Maria Zambon
- National infection Service, Public Health England, London, United Kingdom
| | - Javier Martin
- National Institute for Biological Standards and Controls (NIBSC), Potters Bar, United Kingdom
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29
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O’Connor DJ, Buckland J, Almond N, Boyle J, Coxon C, Gaki E, Martin J, Mattiuzzo G, Metcalfe C, Page M, Rose N, Valdazo-Gonzalez B, Zhao Y, Schneider CK. Commonly setting biological standards in rare diseases. Expert Opin Orphan Drugs 2019. [DOI: 10.1080/21678707.2019.1652598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Jenny Buckland
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Neil Almond
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Jennifer Boyle
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Carmen Coxon
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Eleni Gaki
- Medicines & Healthcare products Regulatory Agency (MHRA), London, UK
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Clive Metcalfe
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Mark Page
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Nicola Rose
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Begona Valdazo-Gonzalez
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Yuan Zhao
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Christian K. Schneider
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
- Twincore Centre for Experimental and Clinical Infection Research GmbH, Hannover, Germany
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30
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Enterovirus 71 targets the cardiopulmonary system in a robust oral infection mouse model. Sci Rep 2019; 9:11108. [PMID: 31366973 PMCID: PMC6668393 DOI: 10.1038/s41598-019-47455-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Severe infection with the re-emerging enterovirus 71 (EV71 or EV-A71) can cause cardiopulmonary failure. However, in patients' heart and lung, viral protein has not been detected. In mouse models, heart disease has not been reported. EV71-infected brainstem is generally believed to be responsible for the cardiopulmonary collapse. One major limitation in EV71 research is the lack of an efficient oral infection system using non-mouse-adapted clinical isolates. In a robust oral infection NOD/SCID mouse model, we detected EV71 protein at multiple organs, including heart and lung, in 100% of moribund mice with limb paralysis. Infiltrating leukocytes were always detected in heart and muscle, and VP1-positive M2 macrophages were abundant in the lung. Functional dissection on the pathogenesis mechanism revealed severe apoptosis, inflammatory cytokines, and abnormal electrocardiogram (EKG) in orally infected hearts. Therefore, cardiopulmonary disease could be one plausible cause of death in this mouse model. Inoculation of EV71 through an oral route resulted in viral infection in the intestine, viremia, and EV71 appeared to spread to peripheral tissues via blood circulation. Infectious virus was no longer detected in the blood on day 5 post-infection by the plaque formation assay. We demonstrated that both EV71 clinical isolate and cloned virus can target the cardiopulmonary system via a natural infection-like oral route.
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31
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Mohanty MC, Madkaikar MR, Desai M, Aluri J, Varose SY, Taur P, Sharma DK, Nalavade UP, Rane SV, Gupta M, Shabarish S, Dalvi A, Deshpande JM. Natural Clearance of Prolonged VDPV Infection in a Child With Primary Immunodeficiency Disorder. Front Immunol 2019; 10:1567. [PMID: 31396204 PMCID: PMC6663979 DOI: 10.3389/fimmu.2019.01567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The emergence of immunodeficiency-associated vaccine-derived polioviruses (iVDPV) from children with primary immunodeficiency disorders poses a threat to the eradication program. Herein, we report a patient with severe combined immunodeficiency (SCID), identified as a prolonged serotype 3 iVDPV (iVDPV3) excreter with 13 VDPV3 isolates and a maximum of 10.33% nucleotide divergence, who abruptly cleared infection after a period of 2 years. Occurrence of an episode of norovirus diarrhea associated with increased activated oligoclonal cytotoxic T cells, inverse CD4:CD8 ratio, significantly elevated pro-inflammatory cytokines, and subsequent clearance of the poliovirus suggests a possible link between inflammatory diarrheal illness and clearance of iVDPV. Our findings suggest that in the absence of B cells and sufficiently activated T/NK cells, macrophages and other T cells may produce auto-inflammatory conditions by TLR/RLR ligands expressed by previous/ongoing bacterial or viral infections to clear VDPV infection. The study highlights the need to screen all the patients with combined immunodeficiency for poliovirus excretion and intermittent follow-up of their immune parameters if found positive, in order to manage the risk of iVDPV excretion in the polio eradication endgame strategy.
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Affiliation(s)
- Madhu Chhanda Mohanty
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
| | - Manisha Ranjan Madkaikar
- ICMR-National Institute of Immunohaematology, Indian Council of Medical Research, KEM Hospital, Mumbai, India
| | - Mukesh Desai
- Bai Jer Bai Wadia Childrens Hospital, Mumbai, India
| | - Jahnavi Aluri
- ICMR-National Institute of Immunohaematology, Indian Council of Medical Research, KEM Hospital, Mumbai, India
| | - Swapnil Yashwant Varose
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
| | - Prasad Taur
- Bai Jer Bai Wadia Childrens Hospital, Mumbai, India
| | - Deepa Kailash Sharma
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
| | - Uma Prajwal Nalavade
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
| | - Sneha Vijay Rane
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
| | - Maya Gupta
- ICMR-National Institute of Immunohaematology, Indian Council of Medical Research, KEM Hospital, Mumbai, India
| | - Snehal Shabarish
- ICMR-National Institute of Immunohaematology, Indian Council of Medical Research, KEM Hospital, Mumbai, India
| | - Aparna Dalvi
- ICMR-National Institute of Immunohaematology, Indian Council of Medical Research, KEM Hospital, Mumbai, India
| | - Jagadish Mohanrao Deshpande
- ICMR-National Institute of Virology, Mumbai Unit, Formerly Enterovirus Research Centre, Indian Council of Medical Research, Mumbai, India
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32
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Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C. The evolution of a super-swarm of foot-and-mouth disease virus in cattle. PLoS One 2019; 14:e0210847. [PMID: 31022193 PMCID: PMC6483180 DOI: 10.1371/journal.pone.0210847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.
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Affiliation(s)
- Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Shannon L Johnson
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Patrick S Chain
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Devendra K Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
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Duintjer Tebbens RJ, Diop OM, Pallansch MA, Oberste MS, Thompson KM. Characterising the costs of the Global Polio Laboratory Network: a survey-based analysis. BMJ Open 2019; 9:e023290. [PMID: 30670511 PMCID: PMC6347914 DOI: 10.1136/bmjopen-2018-023290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To characterise the costs, including for environmental surveillance (ES), of the Global Polio Laboratory Network (GPLN) that provides laboratory support to the Global Polio Eradication Initiative (GPEI). DESIGN AND PARTICIPANTS We conducted a survey of the network across 92 countries of the 146 GPLN laboratories plus three non-GPLN laboratories that concentrate environmental samples to collect information about their activities, characteristics and costs during 2016. We estimate the total costs using regression of reported responses and complementing the findings with GPEI data. RESULTS We received responses from 132 (89%) of the 149 laboratories, with variable response rates for individual questions. We estimate that processing samples of patients with acute flaccid paralysis leads to total costs of approximately $28 million per year (2016 US$) based on extrapolation from reported costs of $16 million, of which 61% were supported by internal (national) funds. Fifty-nine (45%) of the 132 responding laboratories reported supporting ES and we estimate an additional $5.3 million of recurring costs for ES activities performed by the laboratories. The reported costs do not include an estimated additional $10 million of annual global and regional costs to coordinate and support the GPLN. On average, the staff supported by funding for polio in the responding laboratories spent 30% of their time on non-polio activities. We estimate total costs for laboratory support of approximately $43 million (note that this estimate does not include any field or other non-laboratory costs of polio surveillance). CONCLUSIONS Although countries contribute significantly to the GPLN financing, many laboratories currently depend on GPEI funds, and these laboratories also support the laboratory component of surveillance activities for other diseases. Sustaining critical global surveillance for polioviruses and transitioning support for other disease programmes will require continued significant funding after polio certification.
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Affiliation(s)
| | - Ousmane M Diop
- Global Polio Eradication Initiative, World Health Organization, Geneva, Switzerland
| | - Mark A Pallansch
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C. The evolution of a super-swarm of foot-and-mouth disease virus in cattle. PLoS One 2019; 14:e0210847. [PMID: 31022193 DOI: 10.1101/512178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/05/2019] [Indexed: 05/21/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.
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Affiliation(s)
- Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Shannon L Johnson
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Patrick S Chain
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Devendra K Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
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Zinger T, Gelbart M, Miller D, Pennings PS, Stern A. Inferring population genetics parameters of evolving viruses using time-series data. Virus Evol 2019; 5:vez011. [PMID: 31191979 PMCID: PMC6555871 DOI: 10.1093/ve/vez011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
With the advent of deep sequencing techniques, it is now possible to track the evolution of viruses with ever-increasing detail. Here, we present Flexible Inference from Time-Series (FITS)-a computational tool that allows inference of one of three parameters: the fitness of a specific mutation, the mutation rate or the population size from genomic time-series sequencing data. FITS was designed first and foremost for analysis of either short-term Evolve & Resequence (E&R) experiments or rapidly recombining populations of viruses. We thoroughly explore the performance of FITS on simulated data and highlight its ability to infer the fitness/mutation rate/population size. We further show that FITS can infer meaningful information even when the input parameters are inexact. In particular, FITS is able to successfully categorize a mutation as advantageous or deleterious. We next apply FITS to empirical data from an E&R experiment on poliovirus where parameters were determined experimentally and demonstrate high accuracy in inference.
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Affiliation(s)
- Tal Zinger
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Maoz Gelbart
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Danielle Miller
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Pleuni S Pennings
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, USA
| | - Adi Stern
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
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36
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Oberste MS. Progress of polio eradication and containment requirements after eradication. Transfusion 2018; 58 Suppl 3:3078-3083. [DOI: 10.1111/trf.15018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/05/2018] [Indexed: 11/29/2022]
Affiliation(s)
- M. Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention Atlanta Georgia
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Altamirano J, Purington N, Behl R, Sarnquist C, Holubar M, García-García L, Ferreyra-Reyes L, Montero-Campos R, Cruz-Hervert LP, Boyle S, Modlin J, van Hoorebeke C, Leary S, Huang C, Sommer M, Ferreira-Guerrero E, Delgado-Sanchez G, Canizales-Quintero S, Díaz Ortega JL, Desai M, Maldonado YA. Characterization of Household and Community Shedding and Transmission of Oral Polio Vaccine in Mexican Communities With Varying Vaccination Coverage. Clin Infect Dis 2018; 67:S4-S17. [PMID: 30376097 PMCID: PMC6206120 DOI: 10.1093/cid/ciy650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background The World Health Assembly 2012 Polio Eradication and Endgame Strategic Plan calls for the eventual cessation of all oral polio vaccines (OPVs), to be replaced with inactivated polio vaccine (IPV); however, IPV induces less robust mucosal immunity than OPV. This study characterized household and community OPV shedding and transmission after OPV vaccination within primarily IPV-vaccinated communities. Methods Households in 3 IPV-vaccinated Mexican communities were randomized to receive 3 levels of OPV vaccination coverage (70%, 30%, or 10%). Ten stool samples were collected from all household members over 71 days. Analysis compared vaccinated subjects, household contacts of vaccinated subjects, and subjects in unvaccinated households. Logistic and Cox regression models were fitted to characterize transmission of OPV by coverage and household vaccination status. Results Among 148 vaccinated children, 380 household contacts, and 1124 unvaccinated community contacts, 78%, 18%, and 7%, respectively, shed OPV. Community and household contacts showed no differences in transmission (odds ratio [OR], 0.67; 95% confidence interval [CI], .37-1.20), in shedding trajectory (OR, 0.61; 95% CI, .35-1.07), or in time to shedding (hazard ratio, 0.68; 95% CI, .39-1.19). Transmission began as quickly as 1 day after vaccination and persisted as long as 71 days after vaccination. Transmission within unvaccinated households differed significantly across vaccination coverage communities, with the 70% community experiencing the most transmissions (15%), and the 10% community experiencing the least (4%). These trends persisted over time and in the time to first shedding analyses. Conclusions Transmission did not differ between household contacts of vaccinees and unvaccinated households. Understanding poliovirus transmission dynamics is important for postcertification control.
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Affiliation(s)
| | | | - Rasika Behl
- Stanford University School of Medicine, California
| | | | | | | | | | | | - Luis Pablo Cruz-Hervert
- Instituto Nacional de Salud Pùblica, Cuernavaca, Mexico
- Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Shanda Boyle
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - John Modlin
- Bill & Melinda Gates Foundation, Seattle, Washington
| | | | - Sean Leary
- Stanford University School of Medicine, California
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Newcastle Disease Virus-Based Vectored Vaccine against Poliomyelitis. J Virol 2018; 92:JVI.00976-18. [PMID: 29925653 DOI: 10.1128/jvi.00976-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022] Open
Abstract
The poliovirus eradication initiative has spawned global immunization infrastructure and dramatically decreased the prevalence of the disease, yet the original virus eradication goal has not been met. The suboptimal properties of the existing vaccines are among the major reasons why the program has repeatedly missed eradication deadlines. Oral live poliovirus vaccine (OPV), while affordable and effective, occasionally causes the disease in the primary recipients, and the attenuated viruses rapidly regain virulence and can cause poliomyelitis outbreaks. Inactivated poliovirus vaccine (IPV) is safe but expensive and does not induce the mucosal immunity necessary to interrupt virus transmission. While the need for a better vaccine is widely recognized, current efforts are focused largely on improvements to the OPV or IPV, which are still beset by the fundamental drawbacks of the original products. Here we demonstrate a different design of an antipoliovirus vaccine based on in situ production of virus-like particles (VLPs). The poliovirus capsid protein precursor, together with a protease required for its processing, are expressed from a Newcastle disease virus (NDV) vector, a negative-strand RNA virus with mucosal tropism. In this system, poliovirus VLPs are produced in the cells of vaccine recipients and are presented to their immune systems in the context of active replication of NDV, which serves as a natural adjuvant. Intranasal administration of the vectored vaccine to guinea pigs induced strong neutralizing systemic and mucosal antibody responses. Thus, the vectored poliovirus vaccine combines the affordability and efficiency of a live vaccine with absolute safety, since no full-length poliovirus genome is present at any stage of the vaccine life cycle.IMPORTANCE A new, safe, and effective vaccine against poliovirus is urgently needed not only to complete the eradication of the virus but also to be used in the future to prevent possible virus reemergence in a postpolio world. Currently, new formulations of the oral vaccine, as well as improvements to the inactivated vaccine, are being explored. In this study, we designed a viral vector with mucosal tropism that expresses poliovirus capsid proteins. Thus, poliovirus VLPs are produced in vivo, in the cells of a vaccine recipient, and are presented to the immune system in the context of vector virus replication, stimulating the development of systemic and mucosal immune responses. Such an approach allows the development of an affordable and safe vaccine that does not rely on the full-length poliovirus genome at any stage.
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Duintjer Tebbens RJ, Thompson KM. Polio endgame risks and the possibility of restarting the use of oral poliovirus vaccine. Expert Rev Vaccines 2018; 17:739-751. [PMID: 30056767 PMCID: PMC6168953 DOI: 10.1080/14760584.2018.1506333] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/26/2018] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Ending all cases of poliomyelitis requires successful cessation of all oral poliovirus vaccine (OPV), but the Global Polio Eradication Initiative (GPEI) partners should consider the possibility of an OPV restart. AREAS COVERED We review the risks of continued live poliovirus transmission after OPV cessation and characterize events that led to OPV restart in a global model that focused on identifying optimal strategies for OPV cessation and the polio endgame. Numerous different types of events that occurred since the globally coordinated cessation of serotype 2-containing OPV in 2016 highlight the possibility of continued outbreaks after homotypic OPV cessation. Modeling suggests a high risk of uncontrolled outbreaks once more than around 5,000 homotypic polio cases occur after cessation of an OPV serotype, at which point restarting OPV would become necessary to protect most populations. Current efforts to sunset the GPEI and transition its responsibilities to national governments poses risks that may limit the ability to implement management strategies needed to minimize the probability of an OPV restart. EXPERT COMMENTARY OPV restart remains a real possibility, but risk management choices made by the GPEI partners and national governments can reduce the risks of this low-probability but high-consequence event.
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40
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Lukashev AN, Vakulenko YA, Turbabina NA, Deviatkin AA, Drexler JF. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Rev Med Virol 2018; 28:e2002. [PMID: 30069956 DOI: 10.1002/rmv.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/05/2022]
Abstract
Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia
| | - Yulia A Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Virology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia A Turbabina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
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41
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Costa-Carvalho BT, Sullivan KE, Fontes PM, Aimé-Nobre F, Gonzales IGS, Lima ES, Granato C, de Moraes-Pinto MI. Low Rates of Poliovirus Antibodies in Primary Immunodeficiency Patients on Regular Intravenous Immunoglobulin Treatment. J Clin Immunol 2018; 38:628-634. [PMID: 30006913 DOI: 10.1007/s10875-018-0531-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/03/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Poliovirus has been nearly eliminated as part of a world-wide effort to immunize and contain circulating wild-type polio. Nevertheless, poliovirus has been detected in water supplies and represents a threat to patients with humoral immunodeficiencies where infection can be fatal. To define the risk, we analyzed antibodies to poliovirus 1, 2, and 3 in serum samples collected over a year from patients with primary immunodeficiency diseases (PID) on regular intravenous immunoglobulin (IVIG) replacement. METHODS Twenty-one patients on regular IVIG replacement therapy were evaluated: Twelve patients with common variable immune deficiency (CVID), six with X-linked agammaglobulinemia (XLA), and three with hyper IgM syndrome (HIGM). Over 1 year, four blood samples were collected from each of these patients immediately before immunoglobulin infusion. One sample of IVIG administered to each patient in the month before blood collection was also evaluated. Poliovirus antibodies were quantified by seroneutralization assay. RESULTS All IVIG samples had detectable antibodies to the three poliovirus serotypes. Despite that, only 52.4, 61.9, and 19.0% of patients showed protective antibody titers for poliovirus 1, 2, and 3, respectively. Only two patients (9.5%) had protective antibodies for the three poliovirus serotypes on all samples. Most patients were therefore susceptible to all three poliovirus serotypes. CONCLUSIONS This study demonstrates the need for ongoing vigilance regarding exposure of patients with PID to poliovirus in the community.
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Affiliation(s)
- Beatriz T Costa-Carvalho
- Division of Allergy Clinical Immunology and Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Kathleen E Sullivan
- Division of Allergy Immunology, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Patrícia M Fontes
- Division of Allergy Clinical Immunology and Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Aimé-Nobre
- Division of Allergy Clinical Immunology and Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Isabela G S Gonzales
- Division of Allergy Clinical Immunology and Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Elaine S Lima
- Division of Infectious Diseases, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Celso Granato
- Division of Infectious Diseases, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel de Moraes-Pinto
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil.
- Research Laboratory, Division of Pediatric Infectious Diseases, Federal University of Sao Paulo, Rua Pedro de Toledo, 781/9°andar, São Paulo, SP, 04039-032, Brazil.
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Kew O, Pallansch M. Breaking the Last Chains of Poliovirus Transmission: Progress and Challenges in Global Polio Eradication. Annu Rev Virol 2018; 5:427-451. [PMID: 30001183 DOI: 10.1146/annurev-virology-101416-041749] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Since the launch of the Global Polio Eradication Initiative (GPEI), paralytic cases associated with wild poliovirus (WPV) have fallen from ∼350,000 in 1988 to 22 in 2017. WPV type 2 (WPV2) was last detected in 1999, WPV3 in 2012, and WPV1 appeared to be localized to Pakistan and Afghanistan in 2017. Through continuous refinement, the GPEI has overcome operational and biological challenges far more complex and daunting than originally envisioned. Operational challenges had led to sustained WPV endemicity in core reservoirs and widespread dissemination to polio-free countries. The biological challenges derive from intrinsic limitations to the oral poliovirus vaccine: ( a) reduced immunogenicity in high-risk settings and ( b) genetic instability, leading to repeated outbreaks of circulating vaccine-derived polioviruses and prolonged infections in individuals with primary immunodeficiencies. As polio eradication enters its multifaceted endgame, the GPEI, with its technical, operational, and social innovations, stands as the preeminent model for control of vaccine-preventable diseases worldwide.
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Affiliation(s)
- Olen Kew
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA; ,
| | - Mark Pallansch
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA; ,
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Shaghaghi M, Irannejad M, Abolhassani H, Shahmahmoodi S, Hamidieh AA, Soleyman-Jahi S, Yazdani R, Azizi G, Aghamohammadi A. Clearing Vaccine-Derived Poliovirus Infection Following Hematopoietic Stem Cell Transplantation: a Case Report and Review of Literature. J Clin Immunol 2018; 38:610-616. [PMID: 29948575 DOI: 10.1007/s10875-018-0521-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/04/2018] [Indexed: 02/07/2023]
Abstract
The use of oral poliovirus vaccine in a worldwide scale has led to a 99.9% decrease in annual incidence of wild-type poliomyelitis and the eradication of serotype 2 poliovirus. However, the emergence of vaccine-derived polioviruses (VDPVs) is endangering the eradication program. Patients with combined immunodeficiencies are at increased risk of both vaccine-associated poliomyelitis and prolonged asymptomatic infection with immunodeficiency-associated VDPVs (iVDPVs). Herein, we present a severe combined immunodeficiency patient with prolonged and asymptomatic iVDPV infection. He continued to shed poliovirus during immunoglobulin replacement therapy and cleared the infection following successful hematopoietic stem cell transplantation (HSCT). To explain the efficiency of HSCT in clearing the infection, we reviewed the literature for all reports of HSCT in iVDPV-excreting patients and discussed novel ideas about the role of different immune mechanisms, including cell-mediated interactions, in mounting immune responses against poliovirus infections. This study could provide further insights into the immune mechanisms contributing to the clearance of enteroviral infections.
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Affiliation(s)
- Mohammadreza Shaghaghi
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunology in Infections, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mona Irannejad
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Shohreh Shahmahmoodi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ali Hamidieh
- Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Soleyman-Jahi
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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Tebbens RJD, Thompson KM. Using integrated modeling to support the global eradication of vaccine-preventable diseases. SYSTEM DYNAMICS REVIEW 2018; 34:78-120. [PMID: 34552305 PMCID: PMC8455164 DOI: 10.1002/sdr.1589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 02/11/2018] [Indexed: 05/17/2023]
Abstract
The long-term management of global disease eradication initiatives involves numerous inherently dynamic processes, health and economic trade-offs, significant uncertainty and variability, rare events with big consequences, complex and inter-related decisions, and a requirement for cooperation among a large number of stakeholders. Over the course of more than 16 years of collaborative modeling efforts to support the Global Polio Eradication Initiative, we developed increasingly complex integrated system dynamics models that combined numerous analytical approaches, including differential equation-based modeling, risk and decision analysis, discrete-event and individual-based simulation, probabilistic uncertainty and sensitivity analysis, health economics, and optimization. We discuss the central role of systems thinking and system dynamics in the overall effort and the value of integrating different modeling approaches to appropriately address the trade-offs involved in some of the policy questions. We discuss practical challenges of integrating different analytical tools and we provide our perspective on the future of integrated modeling.
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Dynamics of Evolution of Poliovirus Neutralizing Antigenic Sites and Other Capsid Functional Domains during a Large and Prolonged Outbreak. J Virol 2018; 92:JVI.01949-17. [PMID: 29444940 DOI: 10.1128/jvi.01949-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/06/2018] [Indexed: 12/19/2022] Open
Abstract
We followed the dynamics of capsid amino acid replacement among 403 Nigerian outbreak isolates of type 2 circulating vaccine-derived poliovirus (cVDPV2) from 2005 through 2011. Four different functional domains were analyzed: (i) neutralizing antigenic (NAg) sites, (ii) residues binding the poliovirus receptor (PVR), (iii) VP1 residues 1 to 32, and (iv) the capsid structural core. Amino acid replacements mapped to 37 of 43 positions across all 4 NAg sites; the most variable and polymorphic residues were in NAg sites 2 and 3b. The most divergent of the 120 NAg variants had no more than 5 replacements in all NAg sites and were still neutralized at titers similar to those of Sabin 2. PVR-binding residues were less variable (25 different variants; 0 to 2 replacements per isolate; 30/44 invariant positions), with the most variable residues also forming parts of NAg sites 2 and 3a. Residues 1 to 32 of VP1 were highly variable (133 different variants; 0 to 6 replacements per isolate; 5/32 invariant positions), with residues 1 to 18 predicted to form a well-conserved amphipathic helix. Replacement events were dated by mapping them onto the branches of time-scaled phylogenies. Rates of amino acid replacement varied widely across positions and followed no simple substitution model. Replacements in the structural core were the most conservative and were fixed at an overall rate ∼20-fold lower than the rates for the NAg sites and VP1 1 to 32 and ∼5-fold lower than the rate for the PVR-binding sites. Only VP1 143-Ile, a non-NAg site surface residue and known attenuation site, appeared to be under strong negative selection.IMPORTANCE The high rate of poliovirus evolution is offset by strong selection against amino acid replacement at most positions of the capsid. Consequently, poliovirus vaccines developed from strains isolated decades ago have been used worldwide to bring wild polioviruses almost to extinction. The apparent antigenic stability of poliovirus obscures a dynamic of continuous change within the neutralizing antigenic (NAg) sites. During 7 years of a large outbreak in Nigeria, the circulating type 2 vaccine-derived polioviruses generated 120 different NAg site variants via multiple independent pathways. Nonetheless, overall antigenic evolution was constrained, as no isolate had fixed more than 5 amino acid differences from the Sabin 2 NAg sites, and the most divergent isolates were efficiently neutralized by human immune sera. Evolution elsewhere in the capsid was also constrained. Amino acids binding the poliovirus receptor were strongly conserved, and extensive variation in the VP1 amino terminus still conserved a predicted amphipathic helix.
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Harvala H, Broberg E, Benschop K, Berginc N, Ladhani S, Susi P, Christiansen C, McKenna J, Allen D, Makiello P, McAllister G, Carmen M, Zakikhany K, Dyrdak R, Nielsen X, Madsen T, Paul J, Moore C, von Eije K, Piralla A, Carlier M, Vanoverschelde L, Poelman R, Anton A, López-Labrador FX, Pellegrinelli L, Keeren K, Maier M, Cassidy H, Derdas S, Savolainen-Kopra C, Diedrich S, Nordbø S, Buesa J, Bailly JL, Baldanti F, MacAdam A, Mirand A, Dudman S, Schuffenecker I, Kadambari S, Neyts J, Griffiths MJ, Richter J, Margaretto C, Govind S, Morley U, Adams O, Krokstad S, Dean J, Pons-Salort M, Prochazka B, Cabrerizo M, Majumdar M, Nebbia G, Wiewel M, Cottrell S, Coyle P, Martin J, Moore C, Midgley S, Horby P, Wolthers K, Simmonds P, Niesters H, Fischer TK. Recommendations for enterovirus diagnostics and characterisation within and beyond Europe. J Clin Virol 2018; 101:11-17. [DOI: 10.1016/j.jcv.2018.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 12/18/2022]
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Laassri M, Zagorodnyaya T, Hassin-Baer S, Handsher R, Sofer D, Weil M, Karagiannis K, Simonyan V, Chumakov K, Shulman L. Evolution of echovirus 11 in a chronically infected immunodeficient patient. PLoS Pathog 2018; 14:e1006943. [PMID: 29554133 PMCID: PMC5875893 DOI: 10.1371/journal.ppat.1006943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/29/2018] [Accepted: 02/16/2018] [Indexed: 01/20/2023] Open
Abstract
Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of 1990s. Genomic regions coding for individual viral proteins did not appear to be under strong selective pressure except for protease 3C that was remarkably conserved. This may suggest its important role in maintaining persistent infection. We describe evolution of Echovirus 11 genome in chronically infected immunodeficient patient over a period of several years and compare it with the evolution of circulating echoviruses from which it originated. Ratio of silent to missense mutations in protein coding regions suggests that chronic virus was under lower selective pressure than circulating viruses, except for a region coding for viral protease that may participate in neutralizing host cell anti-viral defense mechanisms. This suggests that adaptation to persistence in immunodeficient host may require maintaining functional viral counter-defense mechanisms.
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Affiliation(s)
- Majid Laassri
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Tatiana Zagorodnyaya
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Sharon Hassin-Baer
- Movement Disorders Institute and Department of Neurology, Sheba Medical Center, Tel Hashomer; and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Handsher
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Merav Weil
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Konstantinos Karagiannis
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Vahan Simonyan
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Konstantin Chumakov
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
- * E-mail:
| | - Lester Shulman
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
- Dept. of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Shaghaghi M, Soleyman-Jahi S, Abolhassani H, Yazdani R, Azizi G, Rezaei N, Barbouche MR, McKinlay MA, Aghamohammadi A. New insights into physiopathology of immunodeficiency-associated vaccine-derived poliovirus infection; systematic review of over 5 decades of data. Vaccine 2018; 36:1711-1719. [PMID: 29478755 DOI: 10.1016/j.vaccine.2018.02.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/26/2018] [Accepted: 02/15/2018] [Indexed: 12/25/2022]
Abstract
Widespread administration of oral poliovirus vaccine (OPV) has decreased global incidence of poliomyelitis by ≈99.9%. However, the emergence of vaccine-derived polioviruses (VDPVs) is threatening polio-eradication program. Primary immunodeficiency (PID) patients are at higher risks of vaccine-associated paralytic poliomyelitis (VAPP) and prolonged excretion of immunodeficiency-associated VDPV (iVDPV). We searched Embase, Medline, Science direct, Scopus, Web of Science, and CDC and WHO databases by 30 September 2016, for all reports of iVDPV cases. Patient-level data were extracted form eligible studies. Data on immunization coverage and income-level of countries were extracted from WHO/UNICEF and the WORLD BANK databases, respectively. We assessed bivariate associations between immunological, clinical, and virological parameters, and exploited multivariable modeling to identify independent determinants of poliovirus evolution and patients' outcomes. Study protocol was registered with PROSPERO (CRD42016052931). 4329 duplicate-removed titles were screened. A total of 107 iVDPV cases were identified from 68 eligible articles. The majority of cases were from higher income countries with high polio-immunization coverage. 74 (69.81%) patients developed VAPP. Combined immunodeficiency patients showed lower rates of VAPP (p < .001) and infection clearance (p = .02), compared to humoral immunodeficiency patients. The rate of poliovirus genomic evolution was higher at early stages of replication, decreasing over time until reaching a steady state. Independent of replication duration, higher extent (p = .04) and rates (p = .03) of genome divergence contributed to a less likelihood of virus clearance. PID type (p < .001), VAPP occurrence (p = .008), and income-level of country (p = .04) independently influenced patients' survival. With the use of OPV, new iVDPVs will emerge independent of the rate of immunization coverage. Inherent features of PIDs contribute to the clinical course of iVDPV infection and virus evolution. This finding could shed further light on poliomyelitis pathogenesis and iVDPV evolution pattern. It also has implications for public health, the polio eradication effort and the development of effective antiviral interventions.
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Affiliation(s)
- Mohammadreza Shaghaghi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Network of Immunology in Infections, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Saeed Soleyman-Jahi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Network of Immunology in Infections, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohamed-Ridha Barbouche
- Department of Immunology, Institut Pasteur de Tunis and University Tunis El-Manar, Tunis, Tunisia
| | - Mark A McKinlay
- Center for Vaccine Equity, Task Force for Global Health, Atlanta, GA, United States
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran.
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Bahl S, Bhatnagar P, Sutter RW, Roesel S, Zaffran M. Global Polio Eradication - Way Ahead. Indian J Pediatr 2018; 85:124-131. [PMID: 29302865 PMCID: PMC5775388 DOI: 10.1007/s12098-017-2586-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/09/2017] [Indexed: 01/22/2023]
Abstract
In 1988, the World Health Assembly resolved to eradicate poliomyelitis by the year 2000. Although substantial progress was achieved by 2000, global polio eradication proved elusive. In India, the goal was accomplished in 2011, and the entire South-East Asia Region was certified as polio-free in 2014. The year 2016 marks the lowest wild poliovirus type 1 case count ever, the lowest number of polio-endemic countries (Afghanistan, Nigeria and Pakistan), the maintenance of wild poliovirus type 2 eradication, and the continued absence of wild poliovirus type 3 detection since 2012. The year also marks the Global Polio Eradication Initiative (GPEI) moving into the post-cessation of Sabin type 2, after the effort of globally synchronized withdrawal of Sabin type 2 poliovirus in April 2016. Sustained efforts will be needed to ensure polio eradication is accomplished, to overcome the access and security issues, and continue to improve the quality and reach of field operations. After that, surveillance (the "eyes and ears") will move further to the center stage. Sensitive surveillance will monitor the withdrawal of all Sabin polioviruses, and with facility containment, constitute the cornerstones for eventual global certification of wild poliovirus eradication. An emergency response capacity is essential to institute timely control measures should polio still re-emerge. Simultaneously, the public health community needs to determine whether and how to apply the polio-funded infrastructure to other priorities (after the GPEI funding has stopped). Eradication is the primary goal, but securing eradication will require continued efforts, dedicated resources, and a firm commitment by the global public health community.
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Affiliation(s)
- Sunil Bahl
- World Health Organization - Regional Office for South-East Asia, New Delhi, India.
| | - Pankaj Bhatnagar
- National Polio Surveillance Project, World Health Organization, New Delhi, India
| | | | - Sigrun Roesel
- World Health Organization - Regional Office for South-East Asia, New Delhi, India
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Diagnostic Assay Development for Poliovirus Eradication. J Clin Microbiol 2018; 56:JCM.01624-17. [PMID: 29212703 DOI: 10.1128/jcm.01624-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/01/2017] [Indexed: 02/07/2023] Open
Abstract
With poliovirus eradication nearing, few pockets of active wild poliovirus (WPV) transmission remain in the world. Intratypic differentiation (ITD) plays a crucial part in laboratory surveillance as the molecular detection method that can identify and distinguish wild and vaccine-like polioviruses isolated from acute flaccid paralysis cases or environmental sources. The need to detect new variants of WPV serotype 1 (WPV1) and the containment of all serotype 2 polioviruses (PV2) in 2015 required changes to the previous version of the method. The ITD version 5.0 is a set of six real-time reverse transcription-PCR (rRT-PCR) assays that serve as accurate diagnostic tools to easily detect and differentiate PV serotypes and genotypes. We describe the creation and properties of quantitation standards, including 16 control RNA transcripts and nine plaque-isolated viruses. All ITD rRT-PCR assays were validated using these standards, and the limits of detection were determined for each assay. We designed and pilot tested two new assays targeting recently circulating WPV1 genotypes and all PV2 viruses. The WPV1 assay had 99.1% specificity and 100% sensitivity, and the PV2 assay had 97.7% specificity and 92% sensitivity. Before proceeding to the next step in the global poliovirus eradication program, we needed to gain a better understanding of the performance of the ITD 5.0 suite of molecular assays and their limits of detection and specificities. The findings and conclusions in this evaluation serve as building blocks for future development work.
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