1
|
Doté J, Joffret ML, Beta BN, Ait-Ahmed M, Banga-Mingo V, Knowles NJ, Jouvenet N, MBaïkoua MN, Gouandjika-Vasilache I, Bessaud M. Characterization of enteroviruses circulating among farm animals and children in Central African Republic. Emerg Microbes Infect 2024; 13:2368212. [PMID: 38864685 PMCID: PMC11212570 DOI: 10.1080/22221751.2024.2368212] [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: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
To characterize enteroviruses (EVs) circulating in farm animals in Central African Republic (CAR), we screened 192 stools of animals under 12 months belonging to family farms located in or near Bangui. To assess whether EV exchanges exist between these animals and humans, we also screened 195 stools of children who lived in contact with farm animals, as well as control stools of 358 children with no contact with farm animals. EVs were typed based on their capsid sequences.In children, all EVs belonged to species A, B and C, with EV-Cs accounting for 60%. Some EV-Cs shared recent common ancestors with lineages of vaccine-derived poliovirus that emerged in the country in 2019-2020. In animals, we identified EV-Gs that belonged to 10 different types, including a previously unknown one that we named EV-G28, while no EV-E or EV-F were observed. The CAR EV-Gs were genetically closely related to specimens sampled in other continents and some of them harboured the torovirus-derived insertion already reported in some EV-Gs. The worldwide circulation of EV-Gs is likely due the massive international trade of live animals. Besides, two human EV-Cs (coxsackievirus A17 and coxsackievirus A24) were detected in pigs, suggesting that these viruses could cross the species barrier. Our work provides original data on the epidemiology and ecology of EVs circulating among herd animals in Africa.
Collapse
Affiliation(s)
- Joël Doté
- Institut Pasteur de Bangui, Laboratoire des virus entériques/rougeole, Bangui, Central African Republic
| | - Marie-Line Joffret
- Institut Pasteur, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
- Laboratoire associé au Centre national de référence entérovirus/paréchovirus, Paris, France
| | - Bertille Ndombari Beta
- Institut Pasteur de Bangui, Laboratoire des virus entériques/rougeole, Bangui, Central African Republic
| | - Mohand Ait-Ahmed
- Institut Pasteur, Université de Paris Cité, Pôle de coordination de la Recherche clinique, Paris, France
| | - Virginie Banga-Mingo
- Institut Pasteur de Bangui, Laboratoire des virus entériques/rougeole, Bangui, Central African Republic
| | | | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
| | | | | | - Maël Bessaud
- Institut Pasteur, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
- Laboratoire associé au Centre national de référence entérovirus/paréchovirus, Paris, France
| |
Collapse
|
2
|
Bardossy ES, Volpe S, Suzuki Y, Merwaiss F, Faraj S, Montes M, Saleh MC, Alvarez DE, Filomatori CV. Molecular basis of RNA recombination in the 3'UTR of chikungunya virus genome. Nucleic Acids Res 2024; 52:9727-9744. [PMID: 39051569 PMCID: PMC11381336 DOI: 10.1093/nar/gkae650] [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: 09/20/2023] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Chikungunya virus (CHIKV) is a rapidly spreading re-emergent virus transmitted from mosquitoes to humans. The emergence of epidemic variants has been associated with changes in the viral genome, such as the duplication of repeated sequences in the 3' untranslated region (UTR). Indeed, blocks of repeated sequences seemingly favor RNA recombination, providing the virus with a unique ability to continuously change the 3'UTR architecture during host switching. In this work, we provide experimental data on the molecular mechanism of RNA recombination and describe specific sequence and structural elements in the viral 3'UTR that favor template switching of the viral RNA-dependent RNA polymerase on the 3'UTR. Furthermore, we found that a 3'UTR deletion mutant that exhibits markedly delayed replication in mosquito cells and impaired transmission in vivo, recombines in reference laboratory strains of mosquitoes. Altogether, our data provide novel experimental evidence indicating that RNA recombination can act as a nucleic acid repair mechanism to add repeated sequences that are associated to high viral fitness in mosquito during chikungunya virus replication.
Collapse
Affiliation(s)
- Eugenia S Bardossy
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Sebastiano Volpe
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Yasutsugu Suzuki
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Fernando Merwaiss
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain
| | - Santiago Faraj
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Mónica Montes
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Diego E Alvarez
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
| | - Claudia V Filomatori
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| |
Collapse
|
3
|
Fernandez-Garcia MD, Faye M, Diez-Fuertes F, Moreno-Docón A, Chirlaque-López MD, Faye O, Cabrerizo M. Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021. Front Cell Infect Microbiol 2023; 13:1168355. [PMID: 37201115 PMCID: PMC10185892 DOI: 10.3389/fcimb.2023.1168355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction In 2021, a type 2 vaccine-derived poliovirus (VDPV2) was isolated from the stool of a patient with acute flaccid paralysis (AFP) admitted to Spain from Senegal. A virological investigation was conducted to characterize and trace the origin of VDPV2. Methods We used an unbiased metagenomic approach for the whole-genome sequencing of VDPV2 from the stool (pre-treated with chloroform) and from the poliovirus-positive supernatant. Phylogenetic analyses and molecular epidemiological analyses relying on the Bayesian Markov Chain Monte Carlo methodology were used to determine the geographical origin and estimate the date of the initiating dose of the oral poliovirus vaccine for the imported VDPV2. Results We obtained a high percentage of viral reads per total reads mapped to the poliovirus genome (69.5% for pre-treated stool and 75.8% for isolate) with a great depth of sequencing coverage (5,931 and 11,581, respectively) and complete genome coverage (100%). The two key attenuating mutations in the Sabin 2 strain had reverted (A481G in the 5'UTR and Ile143Thr in VP1). In addition, the genome had a recombinant structure between type-2 poliovirus and an unidentified non-polio enterovirus-C (NPEV-C) strain with a crossover point in the protease-2A genomic region. VP1 phylogenetic analysis revealed that this strain is closely related to VDPV2 strains circulating in Senegal in 2021. According to Bayesian phylogenetics, the most recent common ancestor of the imported VDPV2 could date back 2.6 years (95% HPD: 1.7-3.7) in Senegal. We suggest that all VDPV2s circulating in 2020-21 in Senegal, Guinea, Gambia, and Mauritania have an ancestral origin in Senegal estimated around 2015. All 50 stool samples from healthy case contacts collected in Spain (n = 25) and Senegal (n = 25) and four wastewater samples collected in Spain were poliovirus negative. Discussion By using a whole-genome sequencing protocol with unbiased metagenomics from the clinical sample and viral isolate with high sequence coverage, efficiency, and throughput, we confirmed the classification of VDPV as a circulating type. The close genomic linkage with strains from Senegal was consistent with their classification as imported. Given the scarce number of complete genome sequences for NPEV-C in public databases, this protocol could help expand poliovirus and NPEV-C sequencing capacity worldwide.
Collapse
Affiliation(s)
- Maria Dolores Fernandez-Garcia
- Enterovirus and Viral Gastroenteritis Unit/National Polio Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Consortium of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Maria Dolores Fernandez-Garcia,
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Francisco Diez-Fuertes
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid, Spain
- Consortium of Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Moreno-Docón
- Microbiology Department, Hospital U. Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, Murcia University, Murcia, Spain
| | - Maria Dolores Chirlaque-López
- Consortium of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, Murcia University, Murcia, Spain
- Department of Epidemiology, Murcia Regional Health Council, Murcia, Spain
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Maria Cabrerizo
- Enterovirus and Viral Gastroenteritis Unit/National Polio Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Consortium of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
4
|
Razafindratsimandresy R, Joffret ML, Raharinantoanina J, Polston P, Andriamamonjy NS, Razanajatovo IM, Diop OM, Delpeyroux F, Héraud JM, Bessaud M. Strengthened surveillance revealed a rapid disappearance of the poliovirus serotype 2 vaccine strain in Madagascar after its removal from the oral polio vaccine. J Med Virol 2022; 94:5877-5884. [PMID: 35977919 DOI: 10.1002/jmv.28071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/03/2022] [Accepted: 08/16/2022] [Indexed: 01/06/2023]
Abstract
To assess circulation of the Sabin 2 poliovirus vaccine strain in Madagascar after its withdrawal from the oral polio vaccine in April 2016, a reinforced poliovirus surveillance was implemented in three regions of Madagascar from January 2016 to December 2017. Environmental samples and stool specimens from healthy children were screened using the Global Polio Laboratory Network algorithm to detect the presence of polioviruses. Detected polioviruses were molecularly typed and their genomes fully sequenced. Polioviruses were detected during all but 4 months of the study period. All isolates were related to the vaccine strains and no wild poliovirus was detected. The majority of isolates belong to the serotype 3. The last detection of Sabin 2 occurred in July 2016, 3 months after its withdrawal. No vaccine-derived poliovirus of any serotype was observed during the study. Only few poliovirus isolates contained sequences from non-polio origin. The genetic characterization of all the poliovirus isolates did not identify isolates that were highly divergent compared to the vaccine strains. This observation is in favor of a good vaccine coverage that efficiently prevented long-lasting transmission chains between unvaccinated persons. This study underlines that high commitment in the fight against polioviruses can succeed in stopping their circulation even in countries where poor sanitation remains a hurdle.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ousmane M Diop
- Polio Eradication, Director General's Office, World Health Organization, Geneva, Switzerland
| | | | | | | |
Collapse
|
5
|
Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
Collapse
Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
6
|
Famulare M, Wong W, Haque R, Platts-Mills JA, Saha P, Aziz AB, Ahmed T, Islam MO, Uddin MJ, Bandyopadhyay AS, Yunus M, Zaman K, Taniuchi M. Multiscale model for forecasting Sabin 2 vaccine virus household and community transmission. PLoS Comput Biol 2021; 17:e1009690. [PMID: 34932560 PMCID: PMC8726461 DOI: 10.1371/journal.pcbi.1009690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/04/2022] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
Since the global withdrawal of Sabin 2 oral poliovirus vaccine (OPV) from routine immunization, the Global Polio Eradication Initiative (GPEI) has reported multiple circulating vaccine-derived poliovirus type 2 (cVDPV2) outbreaks. Here, we generated an agent-based, mechanistic model designed to assess OPV-related vaccine virus transmission risk in populations with heterogeneous immunity, demography, and social mixing patterns. To showcase the utility of our model, we present a simulation of mOPV2-related Sabin 2 transmission in rural Matlab, Bangladesh based on stool samples collected from infants and their household contacts during an mOPV2 clinical trial. Sabin 2 transmission following the mOPV2 clinical trial was replicated by specifying multiple, heterogeneous contact rates based on household and community membership. Once calibrated, the model generated Matlab-specific insights regarding poliovirus transmission following an accidental point importation or mass vaccination event. We also show that assuming homogeneous contact rates (mass action), as is common of poliovirus forecast models, does not accurately represent the clinical trial and risks overestimating forecasted poliovirus outbreak probability. Our study identifies household and community structure as an important source of transmission heterogeneity when assessing OPV-related transmission risk and provides a calibratable framework for expanding these analyses to other populations. Trial Registration: ClinicalTrials.gov This trial is registered with clinicaltrials.gov, NCT02477046.
Collapse
Affiliation(s)
- Michael Famulare
- Institute for Disease Modeling, Global Good, Intellectual Ventures, Bellevue, Washington, United States of America
| | - Wesley Wong
- Institute for Disease Modeling, Global Good, Intellectual Ventures, Bellevue, Washington, United States of America
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - James A. Platts-Mills
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Parimalendu Saha
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Asma B. Aziz
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Tahmina Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md Ohedul Islam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md Jashim Uddin
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Mohammed Yunus
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Khalequ Zaman
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mami Taniuchi
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Engineering Systems and Environment, University of Virginia, Charlottesville, Virginia, United States of America
| |
Collapse
|