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Carrazco-Montalvo A, Gutiérrez-Pallo D, Arévalo V, Ponce P, Rodríguez-Polit C, Alarcón D, Echeverría-Garcés G, Coloma J, Nipaz V, Cevallos V. Whole Genome Sequencing of DENV-2 isolated from Aedes aegypti mosquitoes in Esmeraldas, Ecuador. Genomic epidemiology of genotype III Southern Asian-American in the country. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579255. [PMID: 38370752 PMCID: PMC10871324 DOI: 10.1101/2024.02.06.579255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Ecuador is a tropical country reporting Dengue virus (DENV) outbreaks with areas of hyperendemic viral transmission. Entomo-virological surveillance and monitoring effort conducted in the Northwestern border province of Esmeraldas in April 2022, five pools of female Aedes aegypti mosquitoes from a rural community tested positive for DENV serotype 2 by RT-qPCR. One pool was sequenced by Illumina MiSeq, and it corresponded to genotype III Southern Asian-American. Comparison with other genomes revealed genetic similarity to a human DENV genome sequenced in 2021, also from Esmeraldas. Potential introduction events to the country could have originated from Colombia, considering the vicinity of the collection sites to the neighboring country and high human movement. The inclusion of genomic information complements entomo-virological surveillance, providing valuable insights into genetic variants. This contribution enhances our understanding of Dengue virus (DENV) epidemiology in rural areas and guides evidence-based decisions for surveillance and interventions.
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Affiliation(s)
- Andrés Carrazco-Montalvo
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática (GENSBIO), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Diana Gutiérrez-Pallo
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática (GENSBIO), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Valentina Arévalo
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Patricio Ponce
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Cristina Rodríguez-Polit
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática (GENSBIO), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Damaris Alarcón
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática (GENSBIO), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática (GENSBIO), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Victoria Nipaz
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Varsovia Cevallos
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública (INSPI), Quito, Ecuador
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2
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Morais VDS, Reis Santana LM, Bezerra JF, Cruz FE, Rocha de Souza T, Tahmasebi R, Alves Raposo RA, Marcatti R, Garcia Barbosa EM, Hefford PM, Buccheri R, Cerdeira Sabino E, Charlys da Costa A. Detection of coinfection with Primate Erythroparvovirus 1 and arboviruses (DENV, CHIKV and ZIKV) in individuals with acute febrile illness in the state of Rio Grande do Norte in 2016. PLoS Negl Trop Dis 2023; 17:e0011701. [PMID: 37917659 PMCID: PMC10645361 DOI: 10.1371/journal.pntd.0011701] [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: 11/18/2022] [Revised: 11/14/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Arthropod-borne viruses, known as arboviruses, pose substantial risks to global public health. Dengue (DENV), Chikungunya (CHIKV) and Zika (ZIKV) viruses stand out as significant concerns in Brazil and worldwide. Their overlapping clinical manifestations make accurate diagnosis a challenge, underscoring the need for reliable laboratory support. This study employs a comprehensive molecular diagnostic approach to track viral infections in individuals with acute febrile illness, a period marked by widespread outbreaks of DENV, CHIKV and ZIKV. METHODS Between January and August 2016, we received a total of 713 serum samples obtained from individuals with acute febrile illness, previously tested for DENV, CHIKV or ZIKV, with initial negative results, from LACEN-NATAL. Of the total 713 samples, 667 were from females (354 of them pregnant) and 46 from males. Molecular diagnosis was conducted using the Multiplex RT-qPCR technique for simultaneous detection of DENV, CHIKV and ZIKV. Additionally, we performed differential diagnosis by RT-qPCR for other viruses of the Flavivirus, Alphavirus Enterovirus genera and qPCR for Primate Erythroparvovirus 1 (B19V) species, in accordance with Ministry of Health guidelines. RESULTS Among the 713 cases, 78.2% tested positive for viral infections, including 48% with CHIKV viremia, 0.6% with DENV and 0.1% with ZIKV. Arboviral coinfections totaled 2.4%, including DENV-CHIKV (1.7%) and CHIKV-ZIKV (0.7%). Moreover, 8% exhibited B19V viremia. Simultaneous infections were identified in 17.5%, encompassing B19V-CHIKV (17.1%), B19V-DENV (0.1%), and B19V-ZIKV (0.3%) Triple infections were observed in 1.3% of cases with B19V-DENV-CHIKV (1%) and B19V-CHIKV-ZIKV (0.3%). CONCLUSION Molecular testing demonstrated high efficacy in diagnosing prevalent arboviruses and detecting multiple coinfections. This approach helps to elucidate etiologies for symptomatic cases, especially during arbovirus outbreaks, and aids comprehensive surveillance. Our findings underscore the importance of monitoring co-circulating pathogens, such as B19V, with implications for clinical management, particularly in pregnant individuals. This study enhances our understanding of arbovirus epidemiology and reinforces the critical role of molecular diagnosis in disease surveillance and control.
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Affiliation(s)
| | - Lídia Maria Reis Santana
- Sao Paulo Health Department/Epidemiological Surveillance Center “Prof. Alexandre Vranjac”, Sao Paulo, Brazil
- Federal University of São Paulo, Sao Paulo, Brazil
| | | | | | | | - Roozbeh Tahmasebi
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
| | | | - Roberta Marcatti
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
| | | | | | - Renata Buccheri
- Vitalant Research Institute, Department of Epidemiology, San Francisco, California, United States of America
| | - Ester Cerdeira Sabino
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
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3
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Talmi-Frank D, Byas AD, Murrieta R, Weger-Lucarelli J, Rückert C, Gallichotte EN, Yoshimoto JA, Allen C, Bosco-Lauth AM, Graham B, Felix TA, Brault AC, Ebel GD. Intracellular Diversity of WNV within Circulating Avian Peripheral Blood Mononuclear Cells Reveals Host-Dependent Patterns of Polyinfection. Pathogens 2023; 12:767. [PMID: 37375457 DOI: 10.3390/pathogens12060767] [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: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Arthropod-borne virus (arbovirus) populations exist as mutant swarms that are maintained between arthropods and vertebrates. West Nile virus (WNV) population dynamics are host-dependent. In American crows, purifying selection is weak and population diversity is high compared to American robins, which have 100- to 1000-fold lower viremia. WNV passed in robins leads to fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows for higher genetic diversity within individual avian peripheral blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a molecularly barcoded WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes in each. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to the maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation.
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Affiliation(s)
- Dalit Talmi-Frank
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alex D Byas
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Reyes Murrieta
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - James Weger-Lucarelli
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology & Natural Resources, University of Nevada, Reno, NV 89557, USA
| | - Emily N Gallichotte
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Janna A Yoshimoto
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Chris Allen
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Angela M Bosco-Lauth
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Barbara Graham
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Todd A Felix
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Lakewood, CO 80228, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Gregory D Ebel
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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4
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Carvalho DO, Costa-da-Silva AL, Petersen V, de Souza MS, Ioshino RS, Marques ICS, Franz AWE, Olson KE, James AA, Capurro ML. Transgene-induced cell death following dengue-2 virus infection in Aedes aegypti. Sci Rep 2023; 13:5958. [PMID: 37045866 PMCID: PMC10097671 DOI: 10.1038/s41598-023-32895-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Dengue viruses (DENVs) are mosquito-borne flaviviruses causing millions of human infections each year and pose a challenge for public health systems worldwide. Aedes aegypti is the principal vector species transmitting DENVs to humans. Controlling Ae. aegypti is difficult due to the abundance of breeding sites and increasing insecticide resistance in the vector populations. Developing new vector control strategies is critical for decreasing the disease burden. One potential approach is genetically replacing Ae. aegypti populations with vector populations highly resistant to DENV transmission. Here, we focus on an alternative strategy for generating dengue 2 virus (DENV-2) resistance in genetically-modified Ae. aegypti in which the mosquitoes express an inactive form of Michelob_x (Mx), an antagonist of the Inhibitor of Apoptosis (IAP), to induce apoptosis in those cells in which actively replicating DENV-2 is present. The inactive form of Mx was flanked by the RRRRSAG cleavage motif, which was recognized by the NS2B/NS3 protease of the infecting DENV-2 thereby releasing and activating Mx which then induced apoptosis. Our transgenic strain exhibited a significantly higher mortality rate than the non-transgenic control when infected with DENV-2. We also transfected a DNA construct containing inactive Mx fused to eGFP into C6/36 mosquito cells and indirectly observed Mx activation on days 3 and 6 post-DENV-2 infections. There were clear signs that the viral NS2B/NS3 protease cleaved the transgene, thereby releasing Mx protein into the cytoplasm, as was confirmed by the detection of eGFP expression in infected cells. The present study represents proof of the concept that virus infection can be used to induce apoptosis in infected mosquito cells.
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Affiliation(s)
- Danilo O Carvalho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Andre L Costa-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivian Petersen
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil
| | - Micael Santana de Souza
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaella S Ioshino
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel C S Marques
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Ken E Olson
- Center for Vector-Borne Infectious Diseases (CVID), Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523-1685, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Margareth L Capurro
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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5
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Frank DT, Byas AD, Murrieta R, Weger-Lucarelli J, Rückert C, Gallichotte E, Yoshimoto JA, Allen C, Bosco-Lauth AM, Graham B, Felix TA, Brault A, Ebel GD. Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525959. [PMID: 36747638 PMCID: PMC9900929 DOI: 10.1101/2023.01.27.525959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Error-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure. Author Summary WNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.
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Affiliation(s)
- Dalit Talmi Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alex D. Byas
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Reyes Murrieta
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - James Weger-Lucarelli
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology & Natural Resources, University of Nevada, Reno, Nevada, USA
| | - Emily Gallichotte
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Janna A. Yoshimoto
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Chris Allen
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Angela M. Bosco-Lauth
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Barbara Graham
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Todd A. Felix
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Golden, CO, USA
| | - Aaron Brault
- Division of Vector-borne Diseases, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention Fort Collins, Colorado, USA
| | - Gregory D. Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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6
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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7
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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8
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Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
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Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
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9
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Di Paola N, Mesquita FS, Oliveira DBLD, Villabona-Arenas CJ, Zaki Pour S, de Sousa-Capra C, Lopes GP, Santana RAF, Pinho JRR, Balarini K, Pereira da Fonseca CRT, Zanotto PMDA. An Outbreak of Human Parvovirus B19 Hidden by Dengue Fever. Clin Infect Dis 2020; 68:810-817. [PMID: 30304533 DOI: 10.1093/cid/ciy630] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/01/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Seasonal outbreaks of dengue often result in hundreds of dengue-suspected cases where a clinical diagnosis cannot be confirmed. Usually, during large outbreaks of dengue and other pathogens that can cause acute febrile illnesses, the search for secondary pathogens with similar disease outcomes is rare. METHODS Using total RNA sequencing and targeted diagnostic assays, we discovered an outbreak of parvovirus B19 in dengue-suspected patients that occurred from November 2013 to February 2014. RESULTS Of the 182 cases investigated, 63% were viremic for the B19 virus. Moreover, we found that >43% of infected patients had no serological evidence of prior infection. Parvovirus B19 is a typical childhood infection, yet we observed that 82% of the infected patients were adults. Additionally, we perceived that infected adults had significantly higher presentations of myalgia than in children. We also obtained viral protein (VP) 1/VP2 gene nucleotide sequences from 43 patients. CONCLUSIONS Our results support the utility of next-generation sequencing for symptomatic patients with unknown etiologies during seasonal outbreaks of dengue and other arborviruses. Our findings could improve the vigilance of hospitals and laboratories by raising awareness of co-circulating pathogens such as parvovirus B19 that may be hidden in plain sight.
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Affiliation(s)
- Nicholas Di Paola
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Flávio S Mesquita
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | | | - Christian Julián Villabona-Arenas
- Recherches translationelles sur le virus de l'immunodéficience et les maladies infectieuses, Institut de Recherche pour le Développement, University of Montpellier, Institut national de la santé et de la recherche médicale, France
| | - Shahab Zaki Pour
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | | | | | | | - João Renato Rebello Pinho
- Hospital Israelita Albert Einstein, Brazil.,Laboratório de Medicina Laboratorial/Laboratório de Gastroenterologia Clínica e Experimental Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Karime Balarini
- Itapema Laboratório de Análises Clínicas, Guarujá, São Paulo, Brazil
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10
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Oliveira FAA, Buri MV, Rodriguez BL, Costa-da-Silva AL, Araújo HRC, Capurro ML, Lu S, Tanaka AS. The first characterization of a cystatin and a cathepsin L-like peptidase from Aedes aegypti and their possible role in DENV infection by the modulation of apoptosis. Int J Biol Macromol 2020; 146:141-149. [PMID: 31857170 DOI: 10.1016/j.ijbiomac.2019.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/29/2022]
Abstract
Recently, a salivary gland transcriptome study demonstrated that the transcripts of a putative cystatin gene (SeqID AAEL013287; Aacystatins) from Aedes aegypti were increased in DENV2-infected mosquitoes and that silencing of the Aacystatin gene resulted in an increase in DENV titres. In this work, Aacystatin was biochemically characterized; the purified recombinant inhibitor was able to inhibit typical cysteine proteases with a Ki in the nM range. Pulldown assays using Aag2 cell extracts identified a cathepsin L-like peptidase (AaCatL) as a possible target of Aacystatin. Purified recombinant AaCatL had an optimal pH of 5.0 and displayed a preference for Leu, Val and Phe residues at P2, which is common for other cathepsin L-like peptidases. Transcription analysis of Aacystatin and AaCatL in the salivary glands and midgut of DENV2-infected mosquitoes revealed a negative correlation between DENV2 titres and levels of the inhibitor and peptidase, suggesting their involvement in DENV2-mosquito interactions. Considering that apoptosis may play an important role during viral infections, the possible involvement of Aacystatin in staurosporine-induced apoptosis in Aag2 cells was investigated; the results showed higher expression of the inhibitor in treated cells; moreover, pre incubation with rAacystatin was able to increase Aag2 cell viability.
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Affiliation(s)
- Felipe A A Oliveira
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Brazil
| | - Marcus V Buri
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Brazil
| | - Boris L Rodriguez
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Brazil
| | - André L Costa-da-Silva
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), Brazil
| | - Helena R C Araújo
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), Brazil
| | - Margareth L Capurro
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), Brazil
| | - Stephen Lu
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Brazil.
| | - Aparecida S Tanaka
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Brazil.
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11
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Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population. Sci Rep 2019; 9:13047. [PMID: 31506595 PMCID: PMC6736937 DOI: 10.1038/s41598-019-49660-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
In an attempt to control the mosquito-borne diseases yellow fever, dengue, chikungunya, and Zika fevers, a strain of transgenically modified Aedes aegypti mosquitoes containing a dominant lethal gene has been developed by a commercial company, Oxitec Ltd. If lethality is complete, releasing this strain should only reduce population size and not affect the genetics of the target populations. Approximately 450 thousand males of this strain were released each week for 27 months in Jacobina, Bahia, Brazil. We genotyped the release strain and the target Jacobina population before releases began for >21,000 single nucleotide polymorphisms (SNPs). Genetic sampling from the target population six, 12, and 27-30 months after releases commenced provides clear evidence that portions of the transgenic strain genome have been incorporated into the target population. Evidently, rare viable hybrid offspring between the release strain and the Jacobina population are sufficiently robust to be able to reproduce in nature. The release strain was developed using a strain originally from Cuba, then outcrossed to a Mexican population. Thus, Jacobina Ae. aegypti are now a mix of three populations. It is unclear how this may affect disease transmission or affect other efforts to control these dangerous vectors. These results highlight the importance of having in place a genetic monitoring program during such releases to detect un-anticipated outcomes.
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12
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Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts. mSphere 2019; 4:4/3/e00291-19. [PMID: 31243074 PMCID: PMC6595145 DOI: 10.1128/msphere.00291-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies. RNA viruses are infamous for their high rates of mutation, which produce swarms of genetic variants within individual hosts. To date, analyses of intrahost genetic diversity have focused on the primary genome sequence. However, virus phenotypes are shaped not only by primary sequence but also by the secondary structures into which this sequence folds. Such structures enable viral replication, translation, and binding of small RNAs, yet within-host variation at the structural level has not been adequately explored. We characterized the structural diversity of the 5′ untranslated region (UTR) of populations of West Nile virus (WNV) that had been subject to five serial passages in triplicate in each of three bird species. Viral genomes were sampled from host serum samples at each passage (n = 45 populations) and subjected to next-generation sequencing. For populations derived from passages 1, 3, and 5 (n = 9 populations), we predicted the impact of each mutation occurring at a frequency of ≥1% on the secondary structure of the 5′ UTR. As expected, mutations in double-stranded (DS) regions of the 5′ UTR stem structures caused structural changes of significantly greater magnitude than did mutations in single-stranded (SS) regions. Despite the greater impact of mutations in DS regions, mutations in DS and SS regions occurred at similar frequencies, with no evidence of enhanced selection against mutation in DS regions. In contrast, mutations in two regions that mediate genome cyclization and thereby regulate replication and translation, the 5′ cyclization sequence and the UAR flanking stem (UFS), were suppressed in all three hosts. IMPORTANCE The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies.
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13
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Shaji Mathew J, Menon VP, Menon VP, Mallick S, Sivasankara Pillai Thankamony Amma B, Balakrishnan D, Gopalakrishnan U, Narayana Menon R, Athira PP, Jagan OA, Surendran S. Dengue virus transmission from live donor liver graft. Am J Transplant 2019; 19:1838-1846. [PMID: 30672135 DOI: 10.1111/ajt.15270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/25/2023]
Abstract
Arboviral transmission through transplanted organs is rare. We report a highly probable case of dengue viral transmission during live donor liver transplantation. Fever with severe thrombocytopenia was observed in the donor and recipient within 6 and 9 days after transplantation, respectively. Dengue diagnosis was confirmed by testing blood and explant tissue from the donor and recipient using dengue-specific NAT (nucleic acid testing) and serology. Serology indicated the donor had secondary dengue infection that ran a mild course. However, the dengue illness in the recipient was severe and deteriorated rapidly, eventually proving fatal. The recipient's explant liver tissue tested negative for viral RNA indicative of a pretransplant naïve status. The prM-Envelope gene sequence analysis of the donor and recipient viral RNA identified a similar serotype (DENV1) with almost 100% sequence identity in the envelope region. Molecular phylogenetic analysis of donor and recipient viral envelope sequences with regional and local dengue strains further confirmed their molecular similarity, suggesting a probable donor-to-recipient transmission via organ transplantation. Screening of living donors for dengue virus may be considered in endemic regions.
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Affiliation(s)
- Johns Shaji Mathew
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Vidya P Menon
- Department of Clinical Infectious Diseases, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Veena P Menon
- Department of Virology, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Shweta Mallick
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | | | - Dinesh Balakrishnan
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Unnikrishnan Gopalakrishnan
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Ramachandran Narayana Menon
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Padmanabhan P Athira
- Department of Virology, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Ozhiparambil A Jagan
- Department of Virology, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
| | - Sudhindran Surendran
- Department of Solid Organ Transplant, Amrita Institute of Medical Sciences & Research Centre, Amrita University, Kochi, India
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14
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Salvo MA, Aliota MT, Moncla LH, Velez ID, Trujillo AI, Friedrich TC, Osorio JE. Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia. PLoS One 2019; 14:e0212947. [PMID: 30845200 PMCID: PMC6405123 DOI: 10.1371/journal.pone.0212947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/12/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue virus (DENV) is a flavivirus responsible for the most common and burdensome arthropod-borne viral disease of humans[1]. DENV evolution has been extensively studied on broad geographic and time scales, using sequences from a single gene[2,3]. It is believed that DENV evolution in humans is dominated primarily by purifying selection due to the constraint of maintaining fitness in both humans and mosquitoes[4,5]. Few studies have explored DENV evolutionary dynamics using whole genome sequences, nor have they explored changes in viral diversity that occur during intra-epidemic periods. We used deep sequencing of the viral coding region to characterize DENV-1 evolution in a Colombian population sampled during two high-prevalence dengue seasons in which serotype dominance shifted. Our data demonstrate patterns of strain extinction and replacement within DENV-1 as its prevalence waned and DENV-3 became established. A comparison of whole-genome versus single-gene-based phylogenetic analyses highlights an important difference in evolutionary patterns. We report a trend of higher nonsynonymous to synonymous diversity ratios among non-structural (NS) genes, and statistically significantly higher values among these ratios in the NS1 gene after DENV-1 strain replacement. These results suggest that positive selection could be driving DENV evolution within individual communities. Signals of positive selection coming from distinct samples may be drowned out when combining multiple regions with differing patterns of endemic transmission as commonly done by large-scale geo-temporal assessments. Here, we frame our findings within a small, local transmission history which aids significance. Moreover, these data suggest that the NS1 gene, rather than the E gene, may be a target of positive selection, although not mutually exclusive, and potentially useful sentinel of adaptive changes at the population level.
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Affiliation(s)
- Mauricio A. Salvo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ivan D. Velez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Andrea I. Trujillo
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jorge E. Osorio
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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15
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Huang SW, Hung SJ, Wang JR. Application of deep sequencing methods for inferring viral population diversity. J Virol Methods 2019; 266:95-102. [PMID: 30690049 DOI: 10.1016/j.jviromet.2019.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/11/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022]
Abstract
The first deep sequencing method was announced in 2005. Due to an increasing number of sequencing data and a reduction in the costs of each sequencing dataset, this innovative technique was soon applied to genetic investigations of viral genome diversity in various viruses, particularly RNA viruses. These deep sequencing findings documented viral epidemiology and evolution and provided high-resolution data on the genetic changes in viral populations. Here, we review deep sequencing platforms that have been applied in viral quasispecies studies. Further, we discuss recent deep sequencing studies on viral inter- and intrahost evolution, drug resistance, and humoral immune selection, especially in emerging and re-emerging viruses. Deep sequencing methods are becoming the standard for providing comprehensive results of viral population diversity, and their applications are discussed.
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Affiliation(s)
- Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Su-Jhen Hung
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
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16
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Keasey SL, Smith JL, Fernandez S, Durbin AP, Zhao BM, Ulrich RG. Impact of Dengue Virus Serotype 2 Strain Diversity on Serological Immune Responses to Dengue. ACS Infect Dis 2018; 4:1705-1717. [PMID: 30347144 DOI: 10.1021/acsinfecdis.8b00185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1-4) that are loosely categorized by sequence commonalities and antibody recognition profiles. The highly variable envelope protein (E) that is prominently displayed on the surface of DENV is an essential component of vaccines currently under development, yet the impact of using single strains to represent each serotype in tetravalent vaccines has not been adequately studied. We synthesized chimeric E by replacing highly variable residues from a dengue virus serotype 2 vaccine strain (PUO-218) with those from 16 DENV2 lineages spanning 60 years of antigen evolution. Examining sera from human and rhesus macaques challenged with single strains of DENV2, antibody-E interactions were markedly inhibited or enhanced by residues mainly focused within a 480 Å2 footprint displayed on the E backbone. The striking impact of E diversity on polyclonal immune responses suggests that frequent antigen updates may be necessary for vaccines to counter shifts in circulating strains.
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Affiliation(s)
- Sarah L. Keasey
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Jessica L. Smith
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Anna P. Durbin
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, 624 North Broadway, Room 251, Baltimore, Maryland 21205, United States
| | - Bryan M. Zhao
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Robert G. Ulrich
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
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17
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Ko HY, Li YT, Chao DY, Chang YC, Li ZRT, Wang M, Kao CL, Wen TH, Shu PY, Chang GJJ, King CC. Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan. PLoS Negl Trop Dis 2018; 12:e0006827. [PMID: 30286095 PMCID: PMC6191158 DOI: 10.1371/journal.pntd.0006827] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/16/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022] Open
Abstract
Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts. However, very few studies have been performed to investigate the viral genetic changes within (intra-host) and between (inter-host) humans in a spatio-temporal scale. Viruses of different serotypes from various countries imported to Taiwan cause annual outbreaks. During 2001-2003, two consecutive outbreaks were caused by dengue virus serotype 2 (DENV-2) and resulted in a larger-scale epidemic with more severe dengue cases in the following year. Phylogenetic analyses showed that the viruses from both events were similar and related to the 2001 DENV-2 isolate from the Philippines. We comprehensively analyzed viral sequences from representative dengue patients and identified three consensus genetic variants, group Ia, Ib and II, with different spatio-temporal population dynamics. The phylodynamic analysis suggested group Ib variants, characterized by lower genetic diversity, transmission rate, and intra-host variant numbers, might play the role of maintenance variants. The residential locations among the patients infected by group Ib variants were in the outer rim of case clusters throughout the 2001-2003 period whereas group Ia and II variants were located in the centers of case clusters, suggesting that group Ib viruses might serve as "sheltered overwintering" variants in an undefined ecological niche. Further deep sequencing of the viral envelope (E) gene directly from individual patient serum samples confirmed the emergence of variants belonging to three quasi-species (group Ia, Ib, and II) and the ancestral role of the viral variants in the latter phase of the 2001 outbreak contributed to the later, larger-scale epidemic beginning in 2002. These findings enhanced our understanding of increasing epidemic severity over time in the same epidemic area. It also highlights the importance of combining phylodynamic and deep sequencing analysis as surveillance tools for detecting dynamic changes in viral variants, particularly searching for and monitoring any specific viral subpopulation. Such subpopulations might have selection advantages in both fitness and transmissibility leading to increased epidemic severity.
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Affiliation(s)
- Hui-Ying Ko
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yao-Tsun Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Day-Yu Chao
- School of Veterinary Medicine, Institute of Microbiology and Public Health, National Chung-Hsing University, Taichung, Taiwan, Republic of China
- * E-mail: (DYC); (GJC); (CCK)
| | - Yun-Cheng Chang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Zheng-Rong T. Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Melody Wang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chuan-Liang Kao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Tzai-Hung Wen
- Department of Geography, College of Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Pei-Yun Shu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taiwan, Republic of China
| | - Gwong-Jen J. Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- * E-mail: (DYC); (GJC); (CCK)
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
- * E-mail: (DYC); (GJC); (CCK)
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18
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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19
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Tramontini Gomes de Sousa Cardozo F, Baimukanova G, Lanteri MC, Keating SM, Moraes Ferreira F, Heitman J, Pannuti CS, Pati S, Romano CM, Cerdeira Sabino E. Serum from dengue virus-infected patients with and without plasma leakage differentially affects endothelial cells barrier function in vitro. PLoS One 2017; 12:e0178820. [PMID: 28586397 PMCID: PMC5460851 DOI: 10.1371/journal.pone.0178820] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/21/2017] [Indexed: 11/18/2022] Open
Abstract
Background Although most of cases of dengue infections are asymptomatic or mild symptomatic some individuals present warning signs progressing to severe dengue in which plasma leakage is a hallmark. Methodology/Principal findings The present study used Electric Cell-substrate Impedance Sensing (ECIS®) which allows for electrical monitoring of cellular barrier function measuring changes in Transendothelial Electric Resistance (TEER) to investigate the parameters associated with dengue induced leakage. Three groups of individuals were tested: dengue-positives with plasma leakage (leakage), dengue-positives without plasma leakage (no leakage), and dengue-negatives (control). Data show that TEER values of human umbilical vein endothelial cells (HUVECs) was significantly lower after incubation with serum from subjects of the leakage group in comparison to the no leakage or control groups. The serum levels of CXCL1, EGF, eotaxin, IFN-γ, sCD40L, and platelets were significantly decreased in the leakage group, while IL-10, IL-6, and IP-10 levels were significantly increased. We also found a strong correlation between TEER values and augmented levels of IP-10, GM-CSF, IL-1α, and IL-8, as well as decreased levels of CXCL1 and platelets. Conclusions/Significance The present work shows that the magnitude of the immune response contributes to the adverse plasma leakage outcomes in patients and that serum components are important mediators of changes in endothelial homeostasis during dengue infections. In particular, the increased levels of IP-10 and the decreased levels of CXCL1 and platelets seem to play a significant role in the disruption of vascular endothelium associated with leakage outcomes after DENV infection. These findings may have important implications for both diagnostic and therapeutic approaches to predict and mitigate vascular permeabilization in those experiencing the most severe clinical disease outcomes after dengue infection.
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Affiliation(s)
| | - Gyulnar Baimukanova
- Blood Systems Research Institute, BSRI, San Francisco, California, United States
| | - Marion Christine Lanteri
- Blood Systems Research Institute, BSRI, San Francisco, California, United States
- Department of Laboratory Medicine, University of California, San Francisco, California, United States
| | - Sheila Marie Keating
- Blood Systems Research Institute, BSRI, San Francisco, California, United States
- Department of Laboratory Medicine, University of California, San Francisco, California, United States
| | - Frederico Moraes Ferreira
- University of São Paulo School of Medicine, Division of Immunology - Heart Institute, São Paulo, São Paulo, Brazil
- University of Santo Amaro, São Paulo, São Paulo, Brazil
| | - John Heitman
- Blood Systems Research Institute, BSRI, San Francisco, California, United States
| | - Cláudio Sérgio Pannuti
- Department of Infectious and Parasitic Diseases, Institute of Tropical Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Shibani Pati
- Blood Systems Research Institute, BSRI, San Francisco, California, United States
| | - Camila Malta Romano
- Department of Infectious and Parasitic Diseases, Institute of Tropical Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Department of Infectious and Parasitic Diseases, Institute of Tropical Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
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20
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Evolutionary dynamics of dengue virus populations within the mosquito vector. Curr Opin Virol 2016; 21:47-53. [DOI: 10.1016/j.coviro.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 07/23/2016] [Accepted: 07/27/2016] [Indexed: 02/05/2023]
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21
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Cruz CD, Torre A, Troncos G, Lambrechts L, Leguia M. Targeted full-genome amplification and sequencing of dengue virus types 1-4 from South America. J Virol Methods 2016; 235:158-167. [PMID: 27334982 DOI: 10.1016/j.jviromet.2016.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 12/20/2022]
Abstract
We report optimized workflows for full-genome sequencing of dengue viruses (DENVs) 1-4. Based on alignments of publicly available complete genomes we modified and expanded existing primers sets to amplify DENV genotypes that were previously difficult or impossible to sequence. We also report improvements to streamline laboratory handling, including a dual amplification strategy for easy and difficult to sequence "high-copy" and "low-copy" templates, respectively, and normalization of PCR cycling conditions across serotypes. High-copy templates can be sequenced following amplification of as few as 5 overlapping segments covering the complete viral genome, whereas low-copy templates can be sequenced following amplification of no more than 10 overlapping segments of smaller size. These changes have been validated using a balanced set of wild-type DENV genomes (11 of DENV1, 14 of DENV2, 13 of DENV3 and 7 of DENV4) derived from human serum samples collected throughout South America over the past 15 years. The changes described enable generation of complete DENV genomes from wild-type samples without the need for viral enrichment via passaging through laboratory cell lines. This should facilitate quick and cost-effective generation of DENV full-genome sequences of the type needed for accurate epidemiological surveillance and thorough evolutionary studies of wild-type DENVs.
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Affiliation(s)
- Cristopher D Cruz
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Av. Venezuela c36s/n, Bellavista, Callao 2, Peru.
| | - Armando Torre
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Av. Venezuela c36s/n, Bellavista, Callao 2, Peru.
| | - Gilda Troncos
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Av. Venezuela c36s/n, Bellavista, Callao 2, Peru.
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France.
| | - Mariana Leguia
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Av. Venezuela c36s/n, Bellavista, Callao 2, Peru.
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22
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Increasing Clinical Severity during a Dengue Virus Type 3 Cuban Epidemic: Deep Sequencing of Evolving Viral Populations. J Virol 2016; 90:4320-4333. [PMID: 26889031 PMCID: PMC4836355 DOI: 10.1128/jvi.02647-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/05/2016] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED During the dengue virus type 3 (DENV-3) epidemic that occurred in Havana in 2001 to 2002, severe disease was associated with the infection sequence DENV-1 followed by DENV-3 (DENV-1/DENV-3), while the sequence DENV-2/DENV-3 was associated with mild/asymptomatic infections. To determine the role of the virus in the increasing severity demonstrated during the epidemic, serum samples collected at different time points were studied. A total of 22 full-length sequences were obtained using a deep-sequencing approach. Bayesian phylogenetic analysis of consensus sequences revealed that two DENV-3 lineages were circulating in Havana at that time, both grouped within genotype III. The predominant lineage is closely related to Peruvian and Ecuadorian strains, while the minor lineage is related to Venezuelan strains. According to consensus sequences, relatively few nonsynonymous mutations were observed; only one was fixed during the epidemic at position 4380 in the NS2B gene. Intrahost genetic analysis indicated that a significant minor population was selected and became predominant toward the end of the epidemic. In conclusion, greater variability was detected during the epidemic's progression in terms of significant minority variants, particularly in the nonstructural genes. An increasing trend of genetic diversity toward the end of the epidemic was observed only for synonymous variant allele rates, with higher variability in secondary cases. Remarkably, significant intrahost genetic variation was demonstrated within the same patient during the course of secondary infection with DENV-1/DENV-3, including changes in the structural proteins premembrane (PrM) and envelope (E). Therefore, the dynamic of evolving viral populations in the context of heterotypic antibodies could be related to the increasing clinical severity observed during the epidemic. IMPORTANCE Based on the evidence that DENV fitness is context dependent, our research has focused on the study of viral factors associated with intraepidemic increasing severity in a unique epidemiological setting. Here, we investigated the intrahost genetic diversity in acute human samples collected at different time points during the DENV-3 epidemic that occurred in Cuba in 2001 to 2002 using a deep-sequencing approach. We concluded that greater variability in significant minor populations occurred as the epidemic progressed, particularly in the nonstructural genes, with higher variability observed in secondary infection cases. Remarkably, for the first time significant intrahost genetic variation was demonstrated within the same patient during the course of secondary infection with DENV-1/DENV-3, including changes in structural proteins. These findings indicate that high-resolution approaches are needed to unravel molecular mechanisms involved in dengue pathogenesis.
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23
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Hapuarachchi HC, Koo C, Kek R, Xu H, Lai YL, Liu L, Kok SY, Shi Y, Chuen RLT, Lee KS, Maurer-Stroh S, Ng LC. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission. Sci Rep 2016; 6:22592. [PMID: 26940650 PMCID: PMC4778070 DOI: 10.1038/srep22592] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
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Affiliation(s)
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Relus Kek
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Helen Xu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Lilac Liu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Suet Yheng Kok
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yuan Shi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Raphael Lee Tze Chuen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore 599489
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551.,National Public Health Laboratory (NPHL), Ministry of Health (MOH), 3 Biopolis Drive, #05-14 to 16, Synapse, Singapore 138623
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
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24
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Sim S, Hibberd ML. Genomic approaches for understanding dengue: insights from the virus, vector, and host. Genome Biol 2016; 17:38. [PMID: 26931545 PMCID: PMC4774013 DOI: 10.1186/s13059-016-0907-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The incidence and geographic range of dengue have increased dramatically in recent decades. Climate change, rapid urbanization and increased global travel have facilitated the spread of both efficient mosquito vectors and the four dengue virus serotypes between population centers. At the same time, significant advances in genomics approaches have provided insights into host–pathogen interactions, immunogenetics, and viral evolution in both humans and mosquitoes. Here, we review these advances and the innovative treatment and control strategies that they are inspiring.
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Affiliation(s)
- Shuzhen Sim
- Infectious Diseases, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, Singapore, 138672, Singapore. .,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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25
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Grubaugh ND, Massey A, Shives KD, Stenglein MD, Ebel GD, Beckham JD. West Nile Virus Population Structure, Injury, and Interferon-Stimulated Gene Expression in the Brain From a Fatal Case of Encephalitis. Open Forum Infect Dis 2015; 3:ofv182. [PMID: 26730392 PMCID: PMC4697916 DOI: 10.1093/ofid/ofv182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 11/24/2022] Open
Abstract
Background. West Nile virus (WNV) infection in humans can result in severe, acute encephalitis typically involving subcortical gray matter brain regions. West Nile virus replication within specific human brain regions from a human case of acute encephalitis has not been studied. Methods. We describe a fatal case of WNV encephalitis in which we obtained tissue from specific brain regions at autopsy to evaluate viral-host interactions using next-generation sequencing and immunohistochemistry analysis. Results. We found that WNV populations in the injured subcortical brain regions exhibited increased amino acid variation and increased expression of specific interferon genes compared with cortical tissues despite similar viral burden. Conclusions. These observational, patient-based data suggest that neuronal injury and the strength of viral selection pressure may be associated with the level of the innate immune responses. Further studies in human and animal models evaluating the role of innate immune responses on injury patterns and viral selection pressure are needed.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Microbiology Immunology and Pathology , College of Veterinary Medicine and Biomedical Sciences, Colorado State University , Fort Collins
| | - Aaron Massey
- Departments of Medicine and Neurology, Division of Infectious Diseases , University of Colorado School of Medicine
| | - Katherine D Shives
- Department of Immunology and Microbiology , University of Colorado Anschutz Medical Campus , Aurora
| | - Mark D Stenglein
- Department of Microbiology Immunology and Pathology , College of Veterinary Medicine and Biomedical Sciences, Colorado State University , Fort Collins
| | - Gregory D Ebel
- Department of Microbiology Immunology and Pathology , College of Veterinary Medicine and Biomedical Sciences, Colorado State University , Fort Collins
| | - J David Beckham
- Departments of Medicine and Neurology, Division of Infectious Diseases, University of Colorado School of Medicine; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora
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26
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Choudhury MA, Lott WB, Banu S, Cheng AY, Teo YY, Ong RTH, Aaskov J. Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing. PLoS One 2015; 10:e0142473. [PMID: 26566128 PMCID: PMC4643897 DOI: 10.1371/journal.pone.0142473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/22/2015] [Indexed: 12/23/2022] Open
Abstract
Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009–0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.
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Affiliation(s)
- Md Abu Choudhury
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- * E-mail:
| | - William B Lott
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- School of Chemistry, Physics, and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Shahera Banu
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Anthony Youzhi Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - John Aaskov
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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27
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Amorim JH, dos Santos Alves RP, Bizerra R, Araújo Pereira S, Ramos Pereira L, Nascimento Fabris DL, Santos RA, Romano CM, de Souza Ferreira LC. Antibodies are not required to a protective immune response against dengue virus elicited in a mouse encephalitis model. Virology 2015; 487:41-9. [PMID: 26496698 DOI: 10.1016/j.virol.2015.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Generating neutralizing antibodies have been considered a prerequisite to control dengue virus (DENV) infection. However, T lymphocytes have also been shown to be important in a protective immune state. In order to investigate the contribution of both humoral and cellular immune responses in DENV immunity, we used an experimental model in which a non-lethal DENV2 strain (ACS46) is used to intracranially prime Balb/C mice which develop protective immunity against a lethal DENV2 strain (JHA1). Primed mice generated envelope-specific antibodies and CD8(+) T cell responses targeting mainly non-structural proteins. Immune sera from protected mice did not confer passive protection to naïve mice challenged with the JHA1 strain. In contrast, depletion of CD4(+) and CD8(+) T lymphocytes significantly reduced survival of ACS46-primed mice challenged with the JHA1 strain. Collectively, results presented in this study show that a cellular immune response targeting non-structural proteins are a promising way in vaccine development against dengue.
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Affiliation(s)
- Jaime Henrique Amorim
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Universidade de São Paulo, Brasil.
| | | | - Raíza Bizerra
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Universidade de São Paulo, Brasil
| | - Sara Araújo Pereira
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Universidade de São Paulo, Brasil
| | - Lennon Ramos Pereira
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Universidade de São Paulo, Brasil
| | | | - Robert Andreata Santos
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Universidade de São Paulo, Brasil
| | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias (LIMHC), Universidade de São Paulo, Brasil
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28
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Complete Genome Sequence of an Atypical Dengue Virus Serotype 2 Lineage Isolated in Brazil. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00779-15. [PMID: 26184939 PMCID: PMC4505127 DOI: 10.1128/genomea.00779-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here, we report the complete polyprotein sequence of a dengue virus 2 strain isolated in Brazil. This virus belongs to the American genotype and has the ability to cause neurovirulence in immunocompetent adult mice. The data presented here may help understand the genetic determinants responsible for neurovirulence.
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29
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Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M. Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. BMC Bioinformatics 2015; 16:202. [PMID: 26123018 PMCID: PMC4486422 DOI: 10.1186/s12859-015-0607-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/29/2015] [Indexed: 11/16/2022] Open
Abstract
Background Infection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity measurements, which reflect replication ability and the virus response to various conditions, to test whether diversity of virulent FIV in lymphoid tissues is altered in the presence of PLV. Our data consisted of the 3′ half of the FIV genome from three tissues of animals infected with FIV alone, or with FIV and PLV, sequenced by 454 technology. Results Since rare variants dominate virus populations, we had to carefully distinguish sequence variation from errors due to experimental protocols and sequencing. We considered an exponential-normal convolution model used for background correction of microarray data, and modified it to formulate an error correction approach for minor allele frequencies derived from high-throughput sequencing. Similar to accounting for over-dispersion in counts, this accounts for error-inflated variability in frequencies – and quite effectively reproduces empirically observed distributions. After obtaining error-corrected minor allele frequencies, we applied ANalysis Of VAriance (ANOVA) based on a linear mixed model and found that conserved sites and transition frequencies in FIV genes differ among tissues of dual and single infected cats. Furthermore, analysis of minor allele frequencies at individual FIV genome sites revealed 242 sites significantly affected by infection status (dual vs. single) or infection status by tissue interaction. All together, our results demonstrated a decrease in FIV diversity in bone marrow in the presence of PLV. Importantly, these effects were weakened or undetectable when error correction was performed with other approaches (thresholding of minor allele frequencies; probabilistic clustering of reads). We also queried the data for cytidine deaminase activity on the viral genome, which causes an asymmetric increase in G to A substitutions, but found no evidence for this host defense strategy. Conclusions Our error correction approach for minor allele frequencies (more sensitive and computationally efficient than other algorithms) and our statistical treatment of variation (ANOVA) were critical for effective use of high-throughput sequencing data in understanding viral diversity. We found that co-infection with PLV shifts FIV diversity from bone marrow to lymph node and spleen. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0607-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Liu
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Howard Ross
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand.
| | - Raunaq Malhotra
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Daniel Elleder
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA. .,Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 14000, Czech Republic.
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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30
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Bruno L, Cortese M, Rappuoli R, Merola M. Lessons from Reverse Vaccinology for viral vaccine design. Curr Opin Virol 2015; 11:89-97. [PMID: 25829256 DOI: 10.1016/j.coviro.2015.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/02/2015] [Accepted: 03/03/2015] [Indexed: 12/17/2022]
Abstract
Although almost 15 years have passed since the birthdate of Reverse Vaccinology (RV), there are very limited applications of this approach to viral vaccines discovery. Undeniably, RV presents a series of advantages as it can virtually identify all potential antigens coded by a genome, irrespective of their abundance, phase of expression and immunogenicity. Additionally, it can be applied to all pathogens, including those that cannot be grown in vitro. In this review we summarize the few examples of RV application to viruses, in particular the Herpesviridae, and report the advantage and limitations of this approach. Next we focus on the novel approaches and additional technologies to vaccine development including structure based approach (Structural Vaccinology [SV]), synthetic biology and some examples of their application in the development of viral vaccines.
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Affiliation(s)
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Germany
| | | | - Marcello Merola
- Novartis Vaccines, Siena, Italy; Department of Biology, University of Naples 'Federico II', Naples, Italy
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Gustavsen JA, Winget DM, Tian X, Suttle CA. High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities. Front Microbiol 2014; 5:703. [PMID: 25566218 PMCID: PMC4266044 DOI: 10.3389/fmicb.2014.00703] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/26/2014] [Indexed: 01/26/2023] Open
Abstract
Viruses in the order Picornavirales infect eukaryotes, and are widely distributed in coastal waters. Amplicon deep-sequencing of the RNA dependent RNA polymerase (RdRp) revealed diverse and highly uneven communities of picorna-like viruses in the coastal waters of British Columbia (BC), Canada. Almost 300 000 pyrosequence reads revealed 145 operational taxonomic units (OTUs) based on 95% sequence similarity at the amino-acid level. Each sample had between 24 and 71 OTUs and there was little overlap among samples. Phylogenetic analysis revealed that some clades of OTUs were only found at one site; whereas, other clades included OTUs from all sites. Since most of these OTUs are likely from viruses that infect eukaryotic phytoplankton, and viral isolates infecting phytoplankton are strain-specific; each OTU probably arose from the lysis of a specific phytoplankton taxon. Moreover, the patchiness in OTU distribution, and the high turnover of viruses in the mixed layer, implies continuous infection and lysis by RNA viruses of a diverse array of eukaryotic phytoplankton taxa. Hence, these viruses are likely important elements structuring the phytoplankton community, and play a significant role in nutrient cycling and energy transfer.
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Affiliation(s)
- Julia A Gustavsen
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Danielle M Winget
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Xi Tian
- Bioinformatics Graduate Program, Faculty of Science, University of British Columbia Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada ; Departments of Botany, and Microbiology & Immunology, University of British Columbia Vancouver, BC, Canada ; Canadian Institute for Advanced Research Toronto, ON, Canada
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Reif KE, Palmer GH, Crowder DW, Ueti MW, Noh SM. Restriction of Francisella novicida genetic diversity during infection of the vector midgut. PLoS Pathog 2014; 10:e1004499. [PMID: 25392914 PMCID: PMC4231110 DOI: 10.1371/journal.ppat.1004499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/02/2014] [Indexed: 11/26/2022] Open
Abstract
The genetic diversity of pathogens, and interactions between genotypes, can strongly influence pathogen phenotypes such as transmissibility and virulence. For vector-borne pathogens, both mammalian hosts and arthropod vectors may limit pathogen genotypic diversity (number of unique genotypes circulating in an area) by preventing infection or transmission of particular genotypes. Mammalian hosts often act as “ecological filters” for pathogen diversity, where novel variants are frequently eliminated because of stochastic events or fitness costs. However, whether vectors can serve a similar role in limiting pathogen diversity is less clear. Here we show using Francisella novicida and a natural tick vector of Francisella spp. (Dermacentor andersoni), that the tick vector acted as a stronger ecological filter for pathogen diversity compared to the mammalian host. When both mice and ticks were exposed to mixtures of F. novicida genotypes, significantly fewer genotypes co-colonized ticks compared to mice. In both ticks and mice, increased genotypic diversity negatively affected the recovery of available genotypes. Competition among genotypes contributed to the reduction of diversity during infection of the tick midgut, as genotypes not recovered from tick midguts during mixed genotype infections were recovered from tick midguts during individual genotype infection. Mediated by stochastic and selective forces, pathogen genotype diversity was markedly reduced in the tick. We incorporated our experimental results into a model to demonstrate how vector population dynamics, especially vector-to-host ratio, strongly affected pathogen genotypic diversity in a population over time. Understanding pathogen genotypic population dynamics will aid in identification of the variables that most strongly affect pathogen transmission and disease ecology. Co-infection, the presence of multiple genotypes of the same pathogen species within an infected individual, is common. Genotype diversity, defined as the number of unique genotypes, and the interaction between genotypes, can strongly influence virulence and pathogen transmission. Understanding how genotypic diversity affects transmission of pathogens that naturally cycle among disparate hosts, such as vector-borne pathogens, is especially important as the capacity of the host and vector to sustain genotypic diversity may differ. To address this, we exposed Dermacentor andersoni ticks, via infected mice, to variably diverse populations of Francisella novicida genotypes. Interestingly, we found that ticks served as greater ecological filters for genotypic diversity compared to mice. This loss in genotypic diversity was due to both stochastic and selective forces. Based on these data and a model, we determined that high numbers of ticks in an environment support high genotypic diversity, while genotypic diversity will be lost rapidly in environments with low tick numbers. Together, these results provide evidence that vector population dynamics, vector-to-host ratios, and competition among pathogen genotypes play critical roles in the maintenance of pathogen genotypic diversity.
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Affiliation(s)
- Kathryn E. Reif
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
- * E-mail:
| | - Guy H. Palmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
| | - David W. Crowder
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
| | - Massaro W. Ueti
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
| | - Susan M. Noh
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
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Nitsche C, Holloway S, Schirmeister T, Klein CD. Biochemistry and medicinal chemistry of the dengue virus protease. Chem Rev 2014; 114:11348-81. [PMID: 25268322 DOI: 10.1021/cr500233q] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Steven Holloway
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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Satoto TBT, Umniyati SR, Astuti FD, Wijayanti N, Gavotte L, Devaux C, Frutos R. Assessment of vertical dengue virus transmission in Aedes aegypti and serotype prevalence in Bantul, Indonesia. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014. [DOI: 10.1016/s2222-1808(14)60677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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van de Weg CAM, Pannuti CS, van den Ham HJ, de Araújo ESA, Boas LSV, Felix AC, Carvalho KI, Levi JE, Romano CM, Centrone CC, Rodrigues CLDL, Luna E, van Gorp ECM, Osterhaus ADME, Kallas EG, Martina BEE. Serum angiopoietin-2 and soluble VEGF receptor 2 are surrogate markers for plasma leakage in patients with acute dengue virus infection. J Clin Virol 2014; 60:328-35. [PMID: 24928471 DOI: 10.1016/j.jcv.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 12/07/2022]
Abstract
BACKGROUND Endothelial cell dysfunction is believed to play an important role in the pathogenesis of plasma leakage in patients with acute dengue virus (DENV) infection. Several factors, produced by activated endothelial cells, have been associated with plasma leakage or severe disease in patients with infectious diseases. OBJECTIVES The aim of this study was to investigate which of these markers could serve as a surrogate marker for the occurrence of plasma leakage in patients with acute DENV infection. STUDY DESIGN A case-control study was performed in patients with acute DENV infection in Santos, Brazil. Plasma leakage was detected with X-ray and/or ultrasound examination at admission. Serum levels of soluble endoglin, endothelin-1, angiopoietin-2, VEGF, soluble VEGFR-2, MMP-2, MMP-9, TIMP-1 and TIMP-2 were determined using commercially available ELISAs. RESULTS Increased levels of angiopoietin-2, endothelin-1 and MMP-2 and decreased levels of soluble VEGFR-2 were significantly associated with the occurrence of plasma leakage. An unsupervised cluster analysis confirmed that angiopoietin-2 and soluble VEGFR-2 were strongly associated with clinical apparent vascular leakage. CONCLUSION Angiopoietin-2 and soluble VEGFR-2 can serve as surrogate markers for the occurrence of plasma leakage in patients with acute DENV infection.
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Affiliation(s)
- Cornelia A M van de Weg
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Cláudio S Pannuti
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Henk-Jan van den Ham
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Evaldo S A de Araújo
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil; Department of Infectious Diseases, Hospital Ana Costa, Rua Pedro Américo 60, Campo Grande 11075-400, Santos, Brazil
| | - Lucy S V Boas
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Alvina C Felix
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Karina I Carvalho
- Hospital Albert Einstein, Av. Albert Einstein 627, CEP 05652-000 São Paulo, Brazil
| | - José E Levi
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Camila M Romano
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Cristiane C Centrone
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Celia L de Lima Rodrigues
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Expedito Luna
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Eric C M van Gorp
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Esper G Kallas
- Disciplina de Imunologia Clínica e Alergia (LIM-60), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 155, CEP 05403-000 São Paulo, Brazil
| | - Byron E E Martina
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
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Yamashita A, Sasaki T, Kurosu T, Yasunaga T, Ikuta K. Origin and distribution of divergent dengue virus: novel database construction and phylogenetic analyses. Future Virol 2013. [DOI: 10.2217/fvl.13.99] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dengue virus (DENV), a mosquito-borne agent that exists as four serotypes (DENV-1–4), induces dengue illness. DENV has a positive-sense, ssRNA genome of approximately 11 kb that encodes a capsid protein, a premembrane protein and an envelope glycoprotein, in addition to seven nonstructural proteins. These individual genes show sequence variations that can be analyzed phylogenetically to yield several genotypes within each serotype. Here, the sequences of individual DENV genes were collected and used to construct a novel DENV database. This database was then used to characterize the evolution of individual genotypes in several countries. Interestingly, the database provided evidence for recombination between two or three different genotypes to yield new genotypes. This novel database will be available on the internet and is expected to be highly useful for dengue genetic studies, including phylogenetic analyses.
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Affiliation(s)
- Akifumi Yamashita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tadahiro Sasaki
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takeshi Kurosu
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Teruo Yasunaga
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuyoshi Ikuta
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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