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Black A, Moncla LH, Laiton-Donato K, Potter B, Pardo L, Rico A, Tovar C, Rojas DP, Longini IM, Halloran ME, Peláez-Carvajal D, Ramírez JD, Mercado-Reyes M, Bedford T. Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC Infect Dis 2019; 19:963. [PMID: 31718580 PMCID: PMC6852897 DOI: 10.1186/s12879-019-4566-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia. METHODS We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia. RESULTS We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela. CONCLUSIONS Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.
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Affiliation(s)
- Allison Black
- Department of Epidemiology, University of Washington, Seattle, Washington, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Katherine Laiton-Donato
- Laboratorio de Virología, Subdirección de Laboratorio Nacional de Referencia, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Barney Potter
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Lissethe Pardo
- Laboratorio de Virología, Subdirección de Laboratorio Nacional de Referencia, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Angelica Rico
- Laboratorio de Virología, Subdirección de Laboratorio Nacional de Referencia, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Catalina Tovar
- Grupo de Enfermedades Tropicales y Resistencia Bacteriana, Facultad de Ciencias de la Salud, Universidad del Sinú, Montería, Córdoba, Colombia
| | - Diana P Rojas
- Department of Biostatistics, University of Florida, Gainesville, Florida, United States
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, Florida, United States
| | - M Elizabeth Halloran
- Department of Epidemiology, University of Washington, Seattle, Washington, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States.,Department of Biostatistics, University of Washington, Seattle, Washington, United States
| | - Dioselina Peláez-Carvajal
- Laboratorio de Virología, Subdirección de Laboratorio Nacional de Referencia, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Juan D Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología,Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Marcela Mercado-Reyes
- Laboratorio de Virología, Subdirección de Laboratorio Nacional de Referencia, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, Washington, United States. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States.
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2
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Turpin J, Frumence E, Desprès P, Viranaicken W, Krejbich-Trotot P. The ZIKA Virus Delays Cell Death Through the Anti-Apoptotic Bcl-2 Family Proteins. Cells 2019; 8:cells8111338. [PMID: 31671831 PMCID: PMC6912272 DOI: 10.3390/cells8111338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022] Open
Abstract
Zika virus (ZIKV) is an emerging human mosquito-transmitted pathogen of global concern, known to be associated with complications such as congenital defects and neurological disorders in adults. ZIKV infection is associated with induction of cell death. However, previous studies suggest that the virally induced apoptosis occurs at a slower rate compared to the course of viral production. In this present study, we investigated the capacity of ZIKV to delay host cell apoptosis. We provide evidence that ZIKV has the ability to interfere with apoptosis whether it is intrinsically or extrinsically induced. In cells expressing viral replicon-type constructions, we show that this control is achieved through replication. Finally, our work highlights an important role for anti-apoptotic Bcl-2 family protein in the ability of ZIKV to control apoptotic pathways, avoiding premature cell death and thereby promoting virus replication in the host-cell.
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Affiliation(s)
- Jonathan Turpin
- PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, 97490 Sainte-Clotilde, Ile de La Réunion, France.
| | - Etienne Frumence
- PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, 97490 Sainte-Clotilde, Ile de La Réunion, France.
| | - Philippe Desprès
- PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, 97490 Sainte-Clotilde, Ile de La Réunion, France.
| | - Wildriss Viranaicken
- PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, 97490 Sainte-Clotilde, Ile de La Réunion, France.
| | - Pascale Krejbich-Trotot
- PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, 97490 Sainte-Clotilde, Ile de La Réunion, France.
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3
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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4
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The Polyphenol-Rich Extract from Psiloxylon mauritianum, an Endemic Medicinal Plant from Reunion Island, Inhibits the Early Stages of Dengue and Zika Virus Infection. Int J Mol Sci 2019; 20:ijms20081860. [PMID: 30991717 PMCID: PMC6515236 DOI: 10.3390/ijms20081860] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
The recent emergence and re-emergence of viral infections transmitted by vectors, such as the Zika virus (ZIKV) and Dengue virus (DENV), is a cause for international concern. These highly pathogenic arboviruses represent a serious health burden in tropical and subtropical areas of the world. Despite the high morbidity and mortality associated with these viral infections, antiviral therapies are missing. Medicinal plants have been widely used to treat various infectious diseases since millenaries. Several compounds extracted from plants exhibit potent effects against viruses in vitro, calling for further investigations regarding their efficacy as antiviral drugs. Here, we demonstrate that an extract from Psiloxylon mauritianum, an endemic medicinal plant from Reunion Island, inhibits the infection of ZIKV in vitro without exhibiting cytotoxic effects. The extract was active against different ZIKV African and Asian strains, including an epidemic one. Time-of-drug-addition assays revealed that the P. mauritianum extract interfered with the attachment of the viral particles to the host cells. Importantly, the P. mauritianum extract was also able to prevent the infection of human cells by four dengue virus serotypes. Due to its potency and ability to target ZIKV and DENV particles, P. mauritianum may be of value for identifying and characterizing antiviral compounds to fight medically-important flaviviruses.
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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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6
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The Flavonoid Isoquercitrin Precludes Initiation of Zika Virus Infection in Human Cells. Int J Mol Sci 2018; 19:ijms19041093. [PMID: 29621184 PMCID: PMC5979602 DOI: 10.3390/ijms19041093] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/16/2022] Open
Abstract
The medical importance of Zika virus (ZIKV) was fully highlighted during the recent epidemics in South Pacific islands and Americas due to ZIKV association with severe damage to fetal brain development and neurological complications in adult patients. A worldwide research effort has been undertaken to identify effective compounds to prevent or treat ZIKV infection. Fruits and vegetables may be sources of compounds with medicinal properties. Flavonoids are one class of plant compounds that emerge as promising antiviral molecules against ZIKV. In the present study, we demonstrated that flavonoid isoquercitrin exerts antiviral activity against African historical and Asian epidemic strains of ZIKV in human hepatoma, epithelial, and neuroblastoma cell lines. Time-of-drug addition assays showed that isoquercitrin acts on ZIKV entry by preventing the internalisation of virus particles into the host cell. Our data also suggest that the glycosylated moiety of isoquercitrin might play a role in the antiviral effect of the flavonoid against ZIKV. Our results highlight the importance of isoquercitrin as a promising natural antiviral compound to prevent ZIKV infection.
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7
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Bos S, Viranaicken W, Turpin J, El-Kalamouni C, Roche M, Krejbich-Trotot P, Desprès P, Gadea G. The structural proteins of epidemic and historical strains of Zika virus differ in their ability to initiate viral infection in human host cells. Virology 2018; 516:265-273. [PMID: 29395111 DOI: 10.1016/j.virol.2017.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Abstract
Mosquito-borne Zika virus (ZIKV) recently emerged in South Pacific islands and Americas where large epidemics were documented. In the present study, we investigated the contribution of the structural proteins C, prM and E in the permissiveness of human host cells to epidemic strains of ZIKV. To this end, we evaluated the capacity of the epidemic strain BeH819015 to infect epithelial A549 and neuronal SH-SY5Y cells in comparison to the African historical MR766 strain. For that purpose, we generated a molecular clone of BeH819015 and a chimeric clone of MR766 which contains the BeH819015 structural protein region. We showed that ZIKV containing BeH819015 structural proteins was much less efficient in cell-attachment leading to a reduced susceptibility of A549 and SH-SY5Y cells to viral infection. Our data illustrate a previously underrated role for C, prM, and E in ZIKV epidemic strain ability to initiate viral infection in human host cells.
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Affiliation(s)
- Sandra Bos
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Wildriss Viranaicken
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Jonathan Turpin
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Chaker El-Kalamouni
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Marjolaine Roche
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Pascale Krejbich-Trotot
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Philippe Desprès
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.
| | - Gilles Gadea
- Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.
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8
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Baez CF, Barel VA, de Souza AMT, Rodrigues CR, Varella RB, Cirauqui N. Analysis of worldwide sequence mutations in Zika virus proteins E, NS1, NS3 and NS5 from a structural point of view. MOLECULAR BIOSYSTEMS 2017; 13:122-131. [PMID: 27805221 DOI: 10.1039/c6mb00645k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Zika virus (ZIKV) is an emergent arbovirus that has attracted attention in the last year as a possible causative agent of congenital malformation; it shows a remarkably increased microcephaly risk during otherwise healthy pregnancies. We present here an analysis of all ZIKV sequences available in Genbank up to April 2016, studying the mutations in the whole polyprotein and their possible structural implications for the proteins E, NS1, NS3 and NS5. This study suggests that microcephaly is not a consequence of any particular amino acid substitution but, conceivably, is a feature of ZIKV itself. Moreover, the structural analysis of ZIKV proteins, together with the mutational landscape of ZIKV and a structure-sequence comparison with other flaviviruses, allows the suggestion of regions that could be exploited as anti-ZIKV targets, including some allosteric sites found in the NS3 and NS5 proteins of DENV.
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Affiliation(s)
- C F Baez
- Preventive Medicine Department, Rio de Janeiro Federal University Hospital, Brazil
| | - V A Barel
- ModMolQSAR Laboratory, Faculty of Pharmaceutical Sciences, Rio de Janeiro Federal University, Brazil.
| | - A M T de Souza
- ModMolQSAR Laboratory, Faculty of Pharmaceutical Sciences, Rio de Janeiro Federal University, Brazil.
| | - C R Rodrigues
- ModMolQSAR Laboratory, Faculty of Pharmaceutical Sciences, Rio de Janeiro Federal University, Brazil.
| | - R B Varella
- Microbiology and Parasitology Department, Biomedical Institute, Fluminense Federal University, Brazil
| | - N Cirauqui
- ModMolQSAR Laboratory, Faculty of Pharmaceutical Sciences, Rio de Janeiro Federal University, Brazil.
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9
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Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE. Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses. PLoS One 2017; 12:e0178199. [PMID: 28562637 PMCID: PMC5451039 DOI: 10.1371/journal.pone.0178199] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 05/09/2017] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) is a member of the Flavivirus genus of positive-sense single-stranded RNA viruses, which includes Dengue, West Nile, Yellow Fever, and other mosquito-borne arboviruses. Infection by ZIKV can be difficult to distinguish from infection by other mosquito-borne Flaviviruses due to high sequence similarity, serum antibody cross-reactivity, and virus co-circulation in endemic areas. Indeed, existing serological methods are not able to consistently differentiate ZIKV from other Flaviviruses, which makes it extremely difficult to accurately calculate the incidence rate of Zika-associated Guillain-Barre in adults, microcephaly in newborns, or asymptomatic infections within a geographical area. In order to identify Zika-specific peptide regions that could be used as serology reagents, we have applied comparative genomics and protein structure analyses to identify amino acid residues that distinguish each of 10 Flavivirus species and subtypes from each other by calculating the specificity, sensitivity, and surface exposure of each residue in relevant target proteins. For ZIKV we identified 104 and 116 15-mer peptides in the E glycoprotein and NS1 non-structural protein, respectively, that contain multiple diagnostic sites and are located in surface-exposed regions in the tertiary protein structure. These sensitive, specific, and surface-exposed peptide regions should serve as useful reagents for seroprevalence studies to better distinguish between prior infections with any of these mosquito-borne Flaviviruses. The development of better detection methods and diagnostic tools will enable clinicians and public health workers to more accurately estimate the true incidence rate of asymptomatic infections, neurological syndromes, and birth defects associated with ZIKV infection.
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Affiliation(s)
- Alexandra J. Lee
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Roshni Bhattacharya
- J. Craig Venter Institute, La Jolla, California, United States of America
- Biological and Medical Informatics, San Diego State University, San Diego, California, United States of America
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, California, United States of America
- Department of Pathology, University of California, San Diego, California, United States of America
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Brett E. Pickett
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail:
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10
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Liang D, Leung RKK, Lee SS, Kam KM. Insights into intercontinental spread of Zika virus. PLoS One 2017; 12:e0176710. [PMID: 28448611 PMCID: PMC5407806 DOI: 10.1371/journal.pone.0176710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 04/16/2017] [Indexed: 12/02/2022] Open
Abstract
The epidemic of Zika virus (ZIKV) infection in South America has led to World Health Organization's declaration of a Public Health Emergency of International Concern. To further inform effective public health policy, an understanding of ZIKV's transmission mechanisms is crucial. To characterize the intercontinental transmission of ZIKV, we compiled and analyzed more than 250 gene sequences together with their sequence-related geographic and temporal information, sampled across 27 countries spanning from 1947 to 2016. After filtering and selecting appropriate sequences, extensive phylogenetic analyses were performed. Although phylogeographic reconstruction supported the transmission route of the virus in Africa, South-eastern Asia, Oceania and Latin America, we discovered that the Eastern Africa origin of ZIKV was disputable. On a molecular level, purifying selection was found to be largely responsible for the evolution of non-structural protein 5 and envelope protein E. Our dataset and ancestral sequences reconstruction analysis captured previously unidentified amino acid changes during evolution. Finally, based on the estimation of the time to the most recent common ancestors for the non-structural protein 5 gene, we hypothesized potential specific historic events that occurred in the 1940s and might have facilitated the spread of Zika virus from Africa to South-eastern Asia. Our findings provide new insights into the transmission characteristics of ZIKV, while further genetic and serologic studies are warranted to support the design of tailored prevention strategies.
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Affiliation(s)
- Dachao Liang
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Ross Ka Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Shui Shan Lee
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Man Kam
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
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Cella E, Ceccarelli G, Vita S, Lai A, Presti AL, Blasi A, Palco ML, Guarino MPL, Zehender G, Angeletti S, Ciccozzi M. First epidemiological and phylogenetic analysis of Hepatitis B virus infection in migrants from Mali. J Med Virol 2016; 89:639-646. [PMID: 27576107 DOI: 10.1002/jmv.24671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2016] [Indexed: 12/17/2022]
Abstract
The armed conflict in Mali caused a migration crisis since 2012. Most Malian refugees were in Italy. In Sub-Saharan Africa, the seroprevalence of anti-HBV antibodies is particularly high. Genotype E is the most prevalent throughout a crescent covering area from Angola to Senegal, including Mali. We report 16 HBV positive individual from 136 Malian asylum seekers in order to investigate the genetic diversity of HBV in this population. Sequencing and phylogenetic analysis has been used. The HBV genotype E isolates from Mali did not cluster together but were intermixed, with the other African sequences. Only three supported clade were evidenced and closely related to sequences from Burkina Faso. The estimated evolutionary rate was 9.29 × 104 . The root of the tree dated back to February 2008 in (95% HPD: 2006-2011). From this ancestor six main statistically supported clusters (pp > 0.80) were identified. The most recent Clade dated back to May 2015. The BSP showed that the effective number of infections softly increased from 2011 to the 2015. Phylogenetic analysis helped in understanding how two on sixteen individuals, have been infected in Italy, and give an important improvement in prevention campaigns and monitoring of the viral infection in migrants. J. Med. Virol. 89:639-646, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Eleonora Cella
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Giancarlo Ceccarelli
- Public Health and Infectious Diseases, Sapienza University, Rome, Italy.,Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Serena Vita
- Public Health and Infectious Diseases, Sapienza University, Rome, Italy.,Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Alessandra Lo Presti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Aletheia Blasi
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
| | - Maurizio Lo Palco
- Sanitary Bureau of Asylum Seekers Center of Castelnuovo di Porto, Rome, Italy.,Auxilium Società Cooperativa Sociale, Senise (PZ), Italy
| | | | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
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Lo Presti A, Cella E, Angeletti S, Ciccozzi M. Molecular epidemiology, evolution and phylogeny of Chikungunya virus: An updating review. INFECTION GENETICS AND EVOLUTION 2016; 41:270-278. [PMID: 27085290 DOI: 10.1016/j.meegid.2016.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus belonging to the Togaviridae family, causing a febrile illness associated with severe arthralgia and rash. In this review, we summarized a series of articles published from 2013 to 2016 concerning CHIKV epidemiology, phylogeny, vaccine and therapies, to give an update of our most recent article written in 2014 (Lo Presti et al.,2014). CHIKV infection was first reported in 1952 from Makonde plateaus and since this time caused many outbreaks worldwide, involving the Indian Ocean region, African countries, American continent and Italy. CHIKV infection is still underestimated and it is normally associated with clinical symptoms overlapping with dengue virus, recurring epidemics and mutations within the viral genome. These characteristics promote the geographical spread and the inability to control vector-mediated transmission of the virus. For these reasons, the majority of studies were aimed to describe outbreaks and to enhance knowledge on CHIKV biology, pathogenesis, infection treatment, and prevention. In this review, 16 studies on CHIKV phylogenetic and phylodinamics were considered, during the years 2013-2016. Phylogenetic and phylodinamic analysis are useful tools to investigate how the genealogy of a pathogen population is influenced by pathogen's demographic history, host immunological milieu and environmental/ecological factors. Phylogenetic tools were revealed important to reconstruct the geographic spread of CHIKV during the epidemics wave and to have information on the circulating strains of the virus, that are important for the prediction and control of the epidemics, as well as for vaccines and antiviral drugs development. In conclusion, this updating review can give a critical appraisal of the epidemiology, therapeutic and phylogenesis of CHIKV, reinforcing the need to monitor the geographic spread of virus and vectors.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy.
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