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Kasbergen LMR, Nieuwenhuijse DF, de Bruin E, Sikkema RS, Koopmans MPG. The increasing complexity of arbovirus serology: An in-depth systematic review on cross-reactivity. PLoS Negl Trop Dis 2023; 17:e0011651. [PMID: 37738270 PMCID: PMC10550177 DOI: 10.1371/journal.pntd.0011651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 10/04/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
Diagnosis of arbovirus infection or exposure by antibody testing is becoming increasingly difficult due to global expansion of arboviruses, which induce antibodies that may (cross-)react in serological assays. We provide a systematic review of the current knowledge and knowledge gaps in differential arbovirus serology. The search included Medline, Embase and Web of Science databases and identified 911 publications which were reduced to 102 after exclusion of studies not providing data on possible cross-reactivity or studies that did not meet the inclusion criteria regarding confirmation of virus exposure of reference population sets. Using a scoring system to further assess quality of studies, we show that the majority of the selected papers (N = 102) provides insufficient detail to support conclusions on specificity of serological outcomes with regards to elucidating antibody cross-reactivity. Along with the lack of standardization of assays, metadata such as time of illness onset, vaccination, infection and travel history, age and specificity of serological methods were most frequently missing. Given the critical role of serology for diagnosis and surveillance of arbovirus infections, better standards for reporting, as well as the development of more (standardized) specific serological assays that allow discrimination between exposures to multiple different arboviruses, are a large global unmet need.
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Affiliation(s)
| | - David F. Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reina S. Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
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2
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Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB. OUP accepted manuscript. Virus Evol 2022; 8:veac029. [PMID: 35478717 PMCID: PMC9035895 DOI: 10.1093/ve/veac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.
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Affiliation(s)
| | | | | | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 rue du Dr Roux, Paris F-75015, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25-28 rue du Dr Roux, Paris F-75015, France
| | | | - Hanna Nebenzahl-Guimaraes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | | | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Herestraat 49 - box 1030, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP 264/3, 50 av. F.D. Roosevelt, Bruxelles B-1050, Belgium
| | | | | | | | | | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Ana B Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
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3
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Osman S, Preet R. Dengue, chikungunya and Zika in GeoSentinel surveillance of international travellers: a literature review from 1995 to 2020. J Travel Med 2020; 27:6007546. [PMID: 33258476 DOI: 10.1093/jtm/taaa222] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION GeoSentinel is a global surveillance network of travel medicine providers seeing ill-returned travellers. Much of our knowledge on health problems and infectious encountered by international travellers has evolved as a result of GeoSentinel surveillance, providing geographic and temporal trends in morbidity among travellers while contributing to improved pre-travel advice. We set out to synthesize epidemiological information, clinical manifestations and time trends for dengue, chikungunya and Zika in travellers as captured by GeoSentinel. METHODS We conducted a systematic literature search in PubMed on international travellers who presented with dengue, chikungunya or Zika virus infections to GeoSentinel sites around the world from 1995 until 2020. RESULTS Of 107 GeoSentinel publications, 42 articles were related to dengue, chikungunya and/or Zika. The final analyses and synthesis of and results presented here are based on the findings from 27 original articles covering the three arboviral diseases. CONCLUSIONS Dengue is the most frequent arboviral disease encountered in travellers presenting to GeoSentinel sites, with increasing trends over the past two decades. In Southeast Asia, annual proportionate morbidity increased from 50 dengue cases per 1000 ill returned travellers in non-epidemic years to an average of 159 cases per 1000 travellers during epidemic years. The highest number of travellers with chikungunya virus infections was reported during the chikungunya outbreak in the Americas and the Caribbean in the years 2013-16. Zika was first reported by GeoSentinel already in 2012, but notifications peaked in the years 2016-17 reflecting the public health emergency in the Americas at the time.
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Affiliation(s)
- S Osman
- Department of Epidemiology and Global Health, Faculty of Medicine, Umeå University, Umeå, 90185, Sweden
| | - R Preet
- Department of Epidemiology and Global Health, Faculty of Medicine, Umeå University, Umeå, 90185, Sweden
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Thomazella MV, Lima Neto QA, Duarte Junior FF, Jorge FA, de Castro Moreira D, Leal Junior AD, Presibella MM, Riediger IN, da Silva RA, de Carvalho IMVG, Bertolini DA. Insights on Zika virus envelope gene conservation in American outbreaks. Braz J Microbiol 2020; 51:1601-1605. [PMID: 32749573 PMCID: PMC7688768 DOI: 10.1007/s42770-020-00349-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/25/2020] [Indexed: 10/23/2022] Open
Abstract
Phylogenetic studies with Zika virus (ZIKV) have been conducted in Brazil. In this study, we sequenced 8 new sequences of the ZIKV envelope (E) gene from strains of cases from the Paraná and Mato Grosso do Sul states in 2016. A low phylogenetic signal was observed, with more than 40% of unresolved quartets, and the Maximum Likelihood Tree grouped all sequences in the Brazilian branches within the Asian genotype. In addition, a Shannon entropy analysis was conducted, showing a high stability in the E protein through the ZIKV polyprotein. Taken together, these results suggest a high degree of conservation in the ZIKV E gene from the recent American outbreaks.
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Affiliation(s)
- Mateus V Thomazella
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil.
| | - Quirino A Lima Neto
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Francisco F Duarte Junior
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Fernando A Jorge
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Déborah de Castro Moreira
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Amauri D Leal Junior
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Mayra M Presibella
- Laboratório Central do Estado do Paraná - LACEN-PR, Curitiba, Paraná, Brazil
| | - Irina N Riediger
- Laboratório Central do Estado do Paraná - LACEN-PR, Curitiba, Paraná, Brazil
| | - Rafael A da Silva
- Instituto Butantan, São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo - UNIFESP/EPM, São Paulo, São Paulo, Brazil
| | - Isabel Maria V G de Carvalho
- Instituto Butantan, São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo - UNIFESP/EPM, São Paulo, São Paulo, Brazil
| | - Dennis A Bertolini
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
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5
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Basak SC, Majumdar S, Nandy A, Roy P, Dutta T, Vracko M, Bhattacharjee AK. Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus. Pharmaceuticals (Basel) 2019; 12:E157. [PMID: 31623241 PMCID: PMC6958466 DOI: 10.3390/ph12040157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.
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Affiliation(s)
- Subhash C Basak
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, MN 55812, USA.
| | | | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Tathagata Dutta
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Marjan Vracko
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.
| | - Apurba K Bhattacharjee
- Biomedical Graduate Research Organization, Department of Microbiology and Immunology School of Medicine, Georgetown University, Washington, DC 20057, USA.
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Ebranati E, Veo C, Carta V, Percivalle E, Rovida F, Frati ER, Amendola A, Ciccozzi M, Tanzi E, Galli M, Baldanti F, Zehender G. Time-scaled phylogeography of complete Zika virus genomes using discrete and continuous space diffusion models. INFECTION GENETICS AND EVOLUTION 2019; 73:33-43. [PMID: 30974264 DOI: 10.1016/j.meegid.2019.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 01/09/2023]
Abstract
Zika virus (ZIKV), a vector-borne infectious agent that has recently been associated with neurological diseases and congenital microcephaly, was first reported in the Western hemisphere in early 2015. A number of authors have reconstructed its epidemiological history using advanced phylogenetic approaches, and the majority of Zika phylogeography studies have used discrete diffusion models. Continuous space diffusion models make it possible to infer the possible origin of the virus in real space by reconstructing its ancestral location on the basis of geographical coordinates deduced from the latitude and longitude of the sampling locations. We analysed all the ZIKV complete genome isolates whose sampling times and localities were available in public databases at the time the study began, using a Bayesian approach for discrete and continuous phylogeographic reconstruction. The discrete phylogeographic analysis suggested that ZIKV emerged to become endemic/epidemic in the first decade of the 1900s in the Ugandan rainforests, and then reached Western Africa and Asia between the 1930s and 1950s. After a long period of about 40 years, it spread to the Pacific islands and reached Brazil from French Polynesia. Continuous phylogeography of the American epidemic showed that the virus entered in north-eastern Brazil in late 2012 and started to spread in early 2013 from two high probability regions: one corresponding to the entire north-east Brazil and the second surrounding the city of Rio de Janeiro, in a mainly northwesterly direction to Central America, the north-western countries of south America and the Caribbean islands. Our data suggest its cryptic circulation in both French Polynesia and Brazil, thus raising questions about the mechanisms underlying its undetected persistence in the absence of a known animal reservoir, and underline the importance of continuous diffusion models in making more reliable phylogeographic reconstructions of emerging viruses.
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Affiliation(s)
- Erika Ebranati
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy; CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy
| | - Carla Veo
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy; CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy
| | - Valentina Carta
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elena Rosanna Frati
- CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy; Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Antonella Amendola
- CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy; Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | - Elisabetta Tanzi
- CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy; Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy; CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy; CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milano, Italy.
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