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Ul-Rahman A, Shabbir MZ, Rasheed M, Shafi N, AbdulRazaq K, Ramzan H, Mehmood R, Khan JA. Comparative genomics and evolutionary analysis of dengue virus strains circulating in Pakistan. Virus Genes 2024; 60:603-620. [PMID: 39198368 DOI: 10.1007/s11262-024-02100-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/09/2024] [Indexed: 09/01/2024]
Abstract
Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogenetic analysis demonstrated the circulation of all four dengue virus serotypes (DENV-1, - 2, - 3, and - 4) with prevalent genotypes III and V within DENV-1, cosmopolitan genotype within DENV-2, genotype III within DENV-3, and genotype I within DENV-4 during 2006-2014. Based on the complete envelope region, genome-wide residue signature and genetic diversity indicate that there is a high level of genetic diversity among DENV-1 strains, while DENV-3 strains exhibit the least genetic diversity. Comparative analysis of all four DENV serotypes revealed that certain codons in DENV-2 and -4 were subject to strong purifying selection, while a few codon sites in the envelope region showed evidence of positive selection. These findings provided valuable insights into the comparative genomics and evolutionary pattern of DENV strains reported from Pakistan. Whether those characteristics conferred a fitness advantage to DENV-1 genotypes within a specific geography and time interval warrants further investigations. The findings of the current study will contribute to tracking disease dynamics, understanding virus transmission and evolution, and formulating effective disease control strategies.
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Affiliation(s)
- Aziz Ul-Rahman
- Faculty of Veterinary and Animal Sciences, MNS-University of Agriculture, Multan, Pakistan.
| | | | - Majeeda Rasheed
- Department of Life Sciences, Khawaja Fareed University of Engineering and Information Technology (KFUEIT), Rahim Yar Khan, 64200, Pakistan
| | - Nusrat Shafi
- Ch. Pervaiz Elahi Institute of Cardiology, Government of Pakistan, Multan, Pakistan
| | - Kalsoom AbdulRazaq
- Faculty of Veterinary and Animal Sciences, MNS-University of Agriculture, Multan, Pakistan
| | - Hamna Ramzan
- Faculty of Veterinary and Animal Sciences, MNS-University of Agriculture, Multan, Pakistan
| | - Rauf Mehmood
- Quality Control Department, Assir Cooperative Company, Muhayil Assir, 61913, Kingdom of Saudi Arabia
| | - Junaid Ali Khan
- Faculty of Veterinary and Animal Sciences, MNS-University of Agriculture, Multan, Pakistan
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2
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Heydarifard Z, Heydarifard F, Mousavi FS, Zandi M. Dengue fever: a decade of burden in Iran. Front Public Health 2024; 12:1484594. [PMID: 39507666 PMCID: PMC11537875 DOI: 10.3389/fpubh.2024.1484594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 10/09/2024] [Indexed: 11/08/2024] Open
Abstract
Since the first reported traveler case of Dengue in Tehran in 2008, the virus has gradually spread across Iran, driven by factors including international travel, climate change, and Aedes mosquito vectors. The disease has manifested in various forms, ranging from mild fever to severe dengue, with notable cases identified in Sistan and Baluchistan Province. Despite the increasing prevalence, Iran faces significant challenges in surveillance, diagnosis, and vector control. This perspective comprehensively analyzes dengue virus epidemiology in Iran, emphasizing the need for enhanced public health strategies, including genomic surveillance, targeted interventions, and health education. The findings highlight the critical importance of addressing these challenges to mitigate the potential for large-scale dengue epidemics and protect public health.
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Affiliation(s)
- Zahra Heydarifard
- Department of Virology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Fatemeh Heydarifard
- Department of Veterinary, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran
| | - Fatemeh Sadat Mousavi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Milad Zandi
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
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3
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Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [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: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
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Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
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4
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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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Hu S, Wu C, Wu X, Ma X, Shu C, Chen Q, Zheng A, Yang H, Lu J, Du P, Gao GF, Wang Q. Classification of five SARS-CoV-2 serotypes based on RBD antigenicities. Sci Bull (Beijing) 2023; 68:3003-3012. [PMID: 37919162 DOI: 10.1016/j.scib.2023.09.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/24/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a significant number of variants, particularly with the emergence of Omicron with many sub-variants. These variants have exhibited increased immune escape, leading to reduced efficacy of existing vaccines and therapeutic antibodies. Given the diminished cross-neutralization observed among these variants, it is plausible that SARS-CoV-2 has developed multiple serotypes. As the major antigenic site, the receptor-binding domain (RBD) of viral spike (S) protein was chosen for serotyping. We selected 23 representative variants, including pre-Omicron variants and Omicron sub-variants, and classified them into five serotypes based on systematic evaluation of the antigenicities of their RBDs. Each serotype includes several genetically distinct variants. Serotype-I encompasses all pre-Omicron variants (with two subtypes), while the remaining four serotypes are all comprised of Omicron sub-variants at different stages of evolution. We propose that these serotypes can serve as a foundation for rapid classification of newly emerging SARS-CoV-2 variants, and guide the development of future broad-spectrum vaccines and neutralizing antibodies against the coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Shixiong Hu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunli Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xinkai Wu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuehui Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Chen
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiting Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Lu
- School of Life Sciences, Peking University, Beijing 100871, China.
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qihui Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Yunnan University, Kunming 650091, China; Faculty of Health Sciences, University of Macau, Macau 999078, China.
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Ciuoderis KA, Usuga J, Moreno I, Perez-Restrepo LS, Flórez DY, Cardona A, Cloherty GA, Berg MG, Hernandez-Ortiz JP, Osorio JE. Characterization of Dengue Virus Serotype 2 Cosmopolitan Genotype Circulating in Colombia. Am J Trop Med Hyg 2023; 109:1298-1302. [PMID: 37972339 PMCID: PMC10793056 DOI: 10.4269/ajtmh.23-0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023] Open
Abstract
Dengue virus (DENV) is the etiological agent of dengue fever (DF), which is among the most prevalent vector-borne diseases in the tropics. In 2022, the Colombian health surveillance system reported more than 69,000 cases of DF. As part of a hospital-based fever surveillance study, acute-phase sera were collected from 4,545 patients with suspected dengue between 2020 and 2023 in three municipalities of Colombia. Combined reverse transcription-polymerase chain reaction and antigen rapid testing confirmed that 376 patients (8.3%) had DF. The virus was isolated in cell culture from 166 of these patients (44.1%), and genome sequencing was performed successfully on 122 (73.5%). Three DENV serotypes (1, 2, and 3) were identified. Phylogenetic analyses of the DENV-2 sequences revealed that 42 of 50 of the isolates (84%) belonged to the DENV-2 cosmopolitan genotype lineage, clustering with sequences from Asia, Peru, and Brazil. We report the detection, isolation, and whole-genome sequencing (11 Kb) of the DENV-2 cosmopolitan genotype and its recent introduction to Colombia.
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Affiliation(s)
- Karl A. Ciuoderis
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jaime Usuga
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Isabel Moreno
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | | | - Diana Y. Flórez
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Andres Cardona
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Gavin A. Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois
| | - Michael G. Berg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois
| | - Juan P. Hernandez-Ortiz
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
- Department of Materials and Nanotechnology, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jorge E. Osorio
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin
- Global Health Institute, University of Wisconsin, Madison, Wisconsin
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7
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Anantharaj A, Agrawal T, Shashi PK, Tripathi A, Kumar P, Khan I, Pareek M, Singh B, Pattabiraman C, Kumar S, Pandey R, Chandele A, Lodha R, Whitehead SS, Medigeshi GR. Neutralizing antibodies from prior exposure to dengue virus negatively correlate with viremia on re-infection. COMMUNICATIONS MEDICINE 2023; 3:148. [PMID: 37857747 PMCID: PMC10587183 DOI: 10.1038/s43856-023-00378-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND India is hyperendemic to dengue and over 50% of adults are seropositive. There is limited information on the association between neutralizing antibody profiles from prior exposure and viral RNA levels during subsequent infection. METHODS Samples collected from patients with febrile illness was used to assess seropositivity by indirect ELISA. Dengue virus (DENV) RNA copy numbers were estimated by quantitative RT-PCR and serotype of the infecting DENV was determined by nested PCR. Focus reduction neutralizing antibody titer (FRNT) assay was established using Indian isolates to measure the levels of neutralizing antibodies and also to assess the cross-reactivity to related flaviviruses namely Zika virus (ZIKV), Japanese encephalitis virus (JEV) and West Nile virus (WNV). RESULTS In this cross-sectional study, we show that dengue seropositivity increased from 52% in the 0-15 years group to 89% in >45 years group. Antibody levels negatively correlate with dengue RNAemia on the day of sample collection and higher RNAemia is observed in primary dengue as compared to secondary dengue. The geometric mean FRNT50 titers for DENV-2 is significantly higher as compared to the other three DENV serotypes. We observe cross-reactivity with ZIKV and significantly lower or no neutralizing antibodies against JEV and WNV. The FRNT50 values for international isolates of DENV-1, DENV-3 and DENV-4 is significantly lower as compared to Indian isolates. CONCLUSIONS Majority of the adult population in India have neutralizing antibodies to all the four DENV serotypes which correlates with reduced RNAemia during subsequent infection suggesting that antibodies can be considered as a good correlate of protection.
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Affiliation(s)
- Anbalagan Anantharaj
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Tanvi Agrawal
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Pooja Kumari Shashi
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Alok Tripathi
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Parveen Kumar
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Imran Khan
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Madhu Pareek
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Balwant Singh
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | | | - Saurabh Kumar
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Stephen S Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guruprasad R Medigeshi
- Bioassay laboratory and Clinical and Cellular Virology lab, Translational Health Science and Technology Institute, Faridabad, Haryana, India.
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Thongsripong P, Edgerton SV, Bos S, Saborío S, Kuan G, Balmaseda A, Harris E, Bennett SN. Phylodynamics of dengue virus 2 in Nicaragua leading up to the 2019 epidemic reveals a role for lineage turnover. BMC Ecol Evol 2023; 23:58. [PMID: 37770825 PMCID: PMC10537812 DOI: 10.1186/s12862-023-02156-4] [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: 09/07/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Dengue is a mosquito-borne viral disease posing a significant threat to public health. Dengue virus (DENV) evolution is often characterized by lineage turnover, which, along with ecological and immunological factors, has been linked to changes in dengue phenotype affecting epidemic dynamics. Utilizing epidemiologic and virologic data from long-term population-based studies (the Nicaraguan Pediatric Dengue Cohort Study and Nicaraguan Dengue Hospital-based Study), we describe a lineage turnover of DENV serotype 2 (DENV-2) prior to a large dengue epidemic in 2019. Prior to this epidemic, Nicaragua had experienced relatively low levels of DENV transmission from 2014 to 2019, a period dominated by chikungunya in 2014/15 and Zika in 2016. RESULTS Our phylogenetic analyses confirmed that all Nicaraguan DENV-2 isolates from 2018 to 2019 formed their own clade within the Nicaraguan lineage of the Asian/American genotype. The emergence of the new DENV-2 lineage reflects a replacement of the formerly dominant clade presiding from 2005 to 2009, a lineage turnover marked by several shared derived amino acid substitutions throughout the genome. To elucidate evolutionary drivers of lineage turnover, we performed selection pressure analysis and reconstructed the demographic history of DENV-2. We found evidence of adaptive evolution by natural selection at the codon level as well as in branch formation. CONCLUSIONS The timing of its emergence, along with a statistical signal of adaptive evolution and distinctive amino acid substitutions, the latest in the NS5 gene, suggest that this lineage may have increased fitness relative to the prior dominant DENV-2 strains. This may have contributed to the intensity of the 2019 DENV-2 epidemic, in addition to previously identified immunological factors associated with pre-existing Zika virus immunity.
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Affiliation(s)
- Panpim Thongsripong
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Sean V Edgerton
- Interdisciplinary Studies Graduate Program, The University of British Columbia, Vancouver, BC, Canada
| | - Sandra Bos
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Saira Saborío
- Centro Nacional de Diagnóstico y Referencia, Laboraorio Nacional de Virología, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Centro Nacional de Diagnóstico y Referencia, Laboraorio Nacional de Virología, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Shannon N Bennett
- Department of Microbiology, California Academy of Sciences, San Francisco, CA, USA.
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Changing Ecotypes of Dengue Virus 2 Serotype in Nigeria and the Emergence of Cosmopolitan and Asian I Lineages, 1966–2019. Vaccines (Basel) 2023; 11:vaccines11030547. [PMID: 36992135 DOI: 10.3390/vaccines11030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
Dengue virus (DENV) is a leading mosquito-borne virus with a wide geographical spread and a major public health concern. DENV serotype 1 (DENV-1) and serotype 2 (DENV-2) were first reported in Africa in 1964 in Ibadan, Nigeria. Although the burden of dengue is unknown in many African countries, DENV-2 is responsible for major epidemics. In this study, we investigated the activities of DENV-2 to determine the circulating strains and to appraise the changing dynamics in the epidemiology of the virus in Nigeria. Nineteen DENV-2 sequences from 1966–2019 in Nigeria were retrieved from the GenBank of the National Center of Biotechnology Information (NCBI). A DENV genotyping tool was used to identify the specific genotypes. The evolutionary history procedure was performed on 54 DENV-2 sequences using MEGA 7. There is a deviation from Sylvatic DENV-2 to other genotypes in Nigeria. In 2019, the Asian I genotype of DENV-2 was predominant in southern Edo State, located in the tropical rainforest region, with the first report of the DENV-2 Cosmopolitan strain. We confirmed the circulation of other non-assigned genotypes of DENV-2 in Nigeria. Collectively, this shows that DENV-2 dynamics have changed from Sylvatic transmission reported in the 1960s with the identification of the Cosmopolitan strain and Asian lineages. Sustained surveillance, including vectorial studies, is required to fully establish the trend and determine the role of these vectors.
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Zerfu B, Kassa T, Legesse M. Epidemiology, biology, pathogenesis, clinical manifestations, and diagnosis of dengue virus infection, and its trend in Ethiopia: a comprehensive literature review. Trop Med Health 2023; 51:11. [PMID: 36829222 PMCID: PMC9950709 DOI: 10.1186/s41182-023-00504-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Dengue fever is a dengue virus infection, emerging rapidly and posing public health threat worldwide, primarily in tropical and subtropical countries. Nearly half of the world's population is now at risk of contracting the dengue virus, including new countries with no previous history-like Ethiopia. However, little is known about the epidemiology and impact of the disease in different countries. This is especially true in countries, where cases have recently begun to be reported. This review aims to summarize epidemiology, biology, pathogenesis, clinical manifestations, and diagnosis of dengue virus infection and its trend in Ethiopia. It may help countries, where dengue fever is not yet on the public health list-like Ethiopia to alert healthcare workers to consider the disease for diagnosis and treatment. The review retrieved and incorporated 139 published and organizational reports showing approximately 390 million new infections. About 100 million of these infections develop the clinical features of dengue, and thousands of people die annually from severe dengue fever in 129 countries. It is caused by being bitten by a dengue virus-infected female mosquito, primarily Aedes aegypti and, lesser, Ae. albopictus. Dengue virus is a member of the Flavivirus genus of the Flaviviridae family and has four independent but antigen-related single-stranded positive-sense RNA virus serotypes. The infection is usually asymptomatic but causes illnesses ranging from mild febrile illness to fatal dengue hemorrhagic fever or shock syndrome. Diagnosis can be by detecting the virus genome using nucleic acids amplification tests or testing NS1 antigen and/or anti-dengue antibodies from serum, plasma, circulating blood cells, or other tissues. Dengue cases and outbreaks have increased in recent decades, with a significant public health impact. Ethiopia has had nearly annual outbreaks since 2013, devastating an already fragmented health system and economy. Standardization of medication, population-level screening for early diagnosis and prompt treatment, and minimization of mosquito bites reduce overall infection and mortality rates.
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Affiliation(s)
- Biruk Zerfu
- Department of Medical Laboratory Science, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia. .,Aklilu Lema Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Tesfu Kassa
- grid.7123.70000 0001 1250 5688Aklilu Lema Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- grid.7123.70000 0001 1250 5688Aklilu Lema Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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[Phosphoproteomic analysis of human umbilical venous endothelial cells with DENV-2 infection]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:29-38. [PMID: 36856207 DOI: 10.12122/j.issn.1673-4254.2023.01.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To analyze the differentially phosphorylated proteins in DENV-2-infected human umbilical venous endothelial cells (HUVECs) and explore the possible pathogenic mechanism of DENV-2 infection. METHODS The total proteins were extracted from DENV-2-infected HUVECs and blank control HUVEC using SDT lysis method. The phosphorylated proteins were qualitatively and quantitatively analyzed using tandem mass spectrometry (TMT). The identified differentially phosphorylated proteins were analyzed by bioinformatics analyses such as subcellular localization analysis, GO enrichment analysis, KEGG pathway analysis and protein-protein interaction (PPI) analysis. Western blotting was used to detect the expressions of phosphorylated Jun, map2k2 and AKT1 proteins in DENV-2-infected HUVECs. RESULTS A total of 2918 modified peptides on 1385 different proteins were detected, and among them 1346 were significantly upregulated (FC > 1.2, P < 0.05) and 1572 were significantly downregulated (FC < 0.83, P < 0.05). A total of 49 phosphorylated conserved motifs were obtained by amino acid conservative motif analysis. The most abundant differentially phosphorylated peptides in protein domain analysis included RNA recognition motif, protein kinase domain and PH domain. Subcellular localization analysis showed that the differentially modified peptides were mainly localized in the nucleus and cytoplasm. GO enrichment and KEGG pathway analysis showed that the differential peptides were mainly enriched in the regulation of stimulation response, biosynthesis of small molecules containing nuclear bases, and migration of phagosomes and leukocytes across the endothelium. PPI and KEGG joint analysis showed that the up-regulated and down-regulated differentially phosphorylated proteins were enriched in 15 pathways. In DENV-2-infected HUVECs, Western blotting detected differential expressions of phosphorylated proteins related with the autophagy pathway, namely JUN, MAP2K2 and AKT1, and among them p-JUN was significantly down-regulated and p-AKT1 and p-MAP2K2 were significantly upregulated (P < 0.01). CONCLUSION DENV-2 infected HUVECs show numerous differentially expressed proteins. The downregulation of p-JUN and upregulation of p-MAP2K2 and p-AKT1 suggest their potential roles in regulating autophagy, which is probably involved in the mechanism of DENV-2 infection.
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12
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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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13
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Li L, Guo X, Zhang X, Zhao L, Li L, Wang Y, Xie T, Yin Q, Jing Q, Hu T, Li Z, Wu R, Zhao W, Xin SX, Shi B, Liu J, Xia S, Peng Z, Yang Z, Zhang F, Chen XG, Zhou X. A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics. Infect Dis Poverty 2022; 11:107. [PMID: 36224651 PMCID: PMC9556283 DOI: 10.1186/s40249-022-01024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative surveillance. METHODS Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and phylodynamics. RESULTS The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2-6%, 0.8-2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The increasing cross-transmission trends were also demonstrated. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross-regional, and cross-continental diffusions of dengue, which can potentially trigger large epidemics. CONCLUSIONS The framework and its utilization in quantitatively assessing DENV-1 epidemics has laid a foundation and re-unveiled the urgency for establishing a stratified coordinated surveillance platform for blocking global spreading of dengue. This framework is also expected to bridge classical DENV-1 genotyping with genomic epidemiology and risk modeling. We will promote it to the public and update it periodically.
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Affiliation(s)
- Liqiang Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiang Guo
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqing Zhang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Lingzhai Zhao
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Li Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yuji Wang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Tian Xie
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qingqing Yin
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qinlong Jing
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Tian Hu
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Ziyao Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Rangke Wu
- School of Foreign Studies, Southern Medical University, Guangzhou, 510515, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Sherman Xuegang Xin
- Laboratory of Biophysics, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Benyun Shi
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, 211816, China
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Shang Xia
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, Shanghai, People's Republic of China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhiqiang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Zhicong Yang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Fuchun Zhang
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
| | - Xiao-Guang Chen
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Xiaohong Zhou
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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Prajapati A, Tandon A, Nain V. Towards the diagnosis of dengue virus and its serotypes using designed CRISPR/Cas13 gRNAs. Bioinformation 2022; 18:661-668. [PMID: 37323556 PMCID: PMC10266368 DOI: 10.6026/97320630018661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 09/20/2023] Open
Abstract
Dengue Virus (DENV) is a mosquito-borne virus that is prevalent in the world's tropical and subtropical regions. Therefore, early detection and surveillance can help in the management of this disease. Current diagnostic methods rely primarily on ELISA, PCR, and RT-PCR, among others, which can only be performed in specialized laboratories and require sophisticated instruments and technical expertise. CRISPR-based technologies on the other hand have field-deployable viral diagnostics capabilities that could be used in the development of point-of-care molecular diagnostics. The first step in the field of CRISPR-based virus diagnosis is to design and screen gRNAs for high efficiency and specificity. In the present study, we employed a bioinformatics approach to design and screen DENV CRISPR/Cas13 gRNAs for conserved and serotype-specific variable genomic regions in the DENV genome. We identified one gRNA sequence specific for each of the lncRNA and NS5 regions and identified one gRNA against each of DENV1, DENV2, DENV3, and DENV4 to distinguish the four DENV serotypes. These CRISPR/Cas13 gRNA sequences will be useful in diagnosing the dengue virus and its serotypes for in vitro validation and diagnostics.
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Affiliation(s)
- Archana Prajapati
- School of Biotechnology, Gautam Buddha University, Greater Noida-201312, Uttar Pradesh, India
| | - Ashmita Tandon
- School of Biotechnology, Gautam Buddha University, Greater Noida-201312, Uttar Pradesh, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida-201312, Uttar Pradesh, India
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15
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Jaglan A, Satija S, Singh D, Phartyal R, Verma M. Intra-genomic heterogeneity in CpG dinucleotide composition in dengue virus. Acta Trop 2022; 232:106501. [PMID: 35513073 DOI: 10.1016/j.actatropica.2022.106501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Dengue virus is a life-threatening virus and cases of dengue infection have been increasing steadily in the past decades causing millions of deaths every year. So far, there is no vaccine that works effectively on all serotypes. Recently, CpG-recoded vaccines have proved to be effective against few viruses. METHODS In this study, evaluation and interpretation of more than 4547 Dengue virus genome sequences were included for analyzing novel CpG dinucleotides rich regions which are shared amid all serotypes. Genomic regions of DENV were synonymously CpG recoded using in silico methods and analyzed for adaptation in both human and Aedes spp. hosts based on CAI scores. RESULTS The analysis mirrored that serotypes 1, 3, and 4 shared CpG islands present in common regions. DENV-2 CpG islands showed no similarity with any of the CpG islands present in other serotypes. While DENV-3 sequences were found to possess the maximum number of conserved CpG islands stretches; DENV-2 was found to possess the lowest number. We found that all serotypes (with an exception of serotype 2) have CpG island in their 3' UTR. In silico CpG recoding of DENV genomic regions resulted in ∼ 3 fold increase of CpG dinucleotide frequency and comparative analysis based on CAI scores showed decreased adaptive fitness of CpG recoded DENV inside human host. CONCLUSION These CG-dinucleotide-enriched RNA sequences can be targeted by ZAP (zinc-finger antiviral protein) which can differentiate between host mRNA and viral mRNA. Our in silico findings can further be exploited for CpG-recoding of DENV genomes which can evoke cellular and humoral immune responses by recruiting ZAP-induced RNA degradation machinery and hence providing a promising approach for vaccine development.
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16
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El-Kady AM, Osman HA, Alemam MF, Marghani D, Shanawaz MA, Wakid MH, Al-Megrin WAI, Elshabrawy HA, Abdella OH, Allemailem KS, Almatroudi A, El-Amir MI. Circulation of Dengue Virus Serotype 2 in Humans and Mosquitoes During an Outbreak in El Quseir City, Egypt. Infect Drug Resist 2022; 15:2713-2721. [PMID: 35668858 PMCID: PMC9165652 DOI: 10.2147/idr.s360675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction In recent decades, the rate of infection with dengue virus (DENV) has risen significantly, now affecting nearly 400 million individuals annually. Dengue fever among humans is caused via specific mosquito vectors bites. Sporadic cases have been reported in Egypt. The goal of this study was to identify the serotype of the DENV outbreak in both human and mosquito vector along the coast of the Red Sea, Upper Egypt, in 2017. Identification of the serotype of the virus may help identify its source and assist in applying epidemiological and control measures. Materials and Methods The current study was carried out in El Quseir City, Red Sea Governorate, Upper Egypt, on 144 patients complaining of symptoms indicative of dengue fever at the time of the 2017 Egypt outbreak. Human blood samples and the mosquito reservoirs were identified as having dengue virus infection serologically and molecularly. Results Overall, 97 (67.4%) patients were positive for dengue virus IgM antibodies. Molecular examination of the human samples and pools of mosquitoes revealed that DENV-2 virus was the serotype responsible for the outbreak. Only one pool of female mosquitoes containing Aedes aegypti was infected with dengue fever virus (DENV-2). Conclusion This was the first serotyping of the DENV responsible for dengue virus outbreak in Egypt in 2017. Determining the serotype of dengue virus can help to avoid and monitor outbreaks. The serotype identified in this study was DENV-2, while DENV-1 was the serotype found in the previous outbreak in 2015 in the province of Assiut. This study thus raises concerns that a new dengue serotype could have been introduced into Egypt. It is necessary for a comprehensive risk assessment to be carried out in the country, including an entomological survey, to assess the presence and potential geographical expansion of mosquito vectors there.
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Affiliation(s)
- Asmaa M El-Kady
- Department of Medical Parasitology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Heba A Osman
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Mohamed Farouk Alemam
- Department of Clinical Pathology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Dina Marghani
- Clinical Laboratory Science Department, Faculty of Applied Medical Science, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Mohammed A Shanawaz
- Department of Public Health, Applied Medical Sciences College, Albaha University, Albaha, Saudi Arabia
| | - Majed H Wakid
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia, Jeddah, 21589, Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wafa Abdullah I Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Hatem A Elshabrawy
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX, 77304, USA
| | - Osama H Abdella
- Department of Medical Parasitology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Mostafa I El-Amir
- Department of Medical Microbiology and Immunology, Faculty of Medicine, South Valley University, Qena, Egypt
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17
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Zhu X, Chen W, Ma C, Wang X, Sun J, Nie J, Shi J, Hu Y. Whole genome analysis identifies intra-serotype recombinants and positive selection sites of dengue virus in mainland China from 2015 to 2020. Virus Res 2022; 311:198705. [PMID: 35121087 DOI: 10.1016/j.virusres.2022.198705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Immune selection pressure can drive the virus to mutate, so as to achieve immune escape and epidemic of the virus. Thus, surveillance of recombinants and positively selected mutants of the dengue virus (DENV) are vital for preventing and controlling the dengue fever outbreak. However, little is known about recombinants and positively selected mutants of circulating DENV strains in mainland China. In this study, those variants with recombination and adaptive evolutionary sites of circulating DENV strains were identified during 2015-2020. Phylogenetic analysis showed that the DENV-2 was the dominant epidemic serotype, and the dengue epidemic in China was closely related to the imported virus from Southeast Asian countries. Recombination analysis based on 291 complete genomes of naturally circulating DENV identified 10 new intra-serotype recombinant variants. Two or three recombination regions in a single dengue isolate were also observed. The breakpoints of recombinants were distributed in different regions of the genome. In particular, two recombinant strains (strain DENV-4/China/YN/15DGR394 (2015) and XLLM10666) with extremely large exchange fragments were detected. This large-scale gene fragment exchange (eight genomic regions) of strain DENV-4/China/YN/15DGR394 (2015) with substitutions at both the 5' and 3' ends of the genome, had never been described before. Moreover, selection pressure analyses revealed seven positive selection sites located in regions encoding the NS1, NS3 and NS5 proteins. Overall, this study is the first to report ten specific intra-serotype recombinants and seven positive selection sites of Chinese epidemic strains of DENV, which highlight their significance for DENV surveillance and effective control.
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Affiliation(s)
- Xiaoli Zhu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; Kunming Medical University, Kunming, Yunnan, China; Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wanxin Chen
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Chunli Ma
- Kunming Medical University, Kunming, Yunnan, China
| | - Xin Wang
- Kunming Medical University, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jianyun Nie
- Kunming Medical University, Kunming, Yunnan, China; Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
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Genotype-Dependent Immunogenicity of Dengue Virus Type 2 Asian I and Asian/American Genotypes in Common Marmoset ( Callithrix jacchus): Discrepancy in Neutralizing and Infection-Enhancing Antibody Levels between Genotypes. Microorganisms 2021; 9:microorganisms9112196. [PMID: 34835327 PMCID: PMC8618970 DOI: 10.3390/microorganisms9112196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Owing to genotype-specific neutralizing antibodies, analyzing differences in the immunogenic variation among dengue virus (DENV) genotypes is central to effective vaccine development. Herein, we characterized the viral kinetics and antibody response induced by DENV type 2 Asian I (AI) and Asian/American (AA) genotypes using marmosets (Callithrix jacchus) as models. Two groups of marmosets were inoculated with AI and AA genotypes, and serial plasma samples were collected. Viremia levels were determined using quantitative reverse transcription-PCR, plaque assays, and antigen enzyme-linked immunosorbent assay (ELISA). Anti-DENV immunoglobulin M and G antibodies, neutralizing antibody titer, and antibody-dependent enhancement (ADE) activity were determined using ELISA, plaque reduction neutralization test, and ADE assay, respectively. The AI genotype induced viremia for a longer duration, but the AA genotype induced higher levels of viremia. After four months, the neutralizing antibody titer induced by the AA genotype remained high, but that induced by the AI genotype waned. ADE activity toward Cosmopolitan genotypes was detected in marmosets inoculated with the AI genotype. These findings indicate discrepancies between heterologous genotypes that influence neutralizing antibodies and viremia in marmosets, a critical issue in vaccine development.
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19
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Khan H, Khan A. Genome-wide population structure inferences of human coxsackievirus-A; insights the genotypes diversity and evolution. INFECTION GENETICS AND EVOLUTION 2021; 95:105068. [PMID: 34492386 DOI: 10.1016/j.meegid.2021.105068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Coxsackievirus-A (CV-A) is a causative agent of Hand Foot Mouth Disease (HFMD) worldwide. It belongs to the Human Enterovirus genus of the family Picornaviridae. The genomics data availability of CV-A samples, isolated from human host across different continental regions, provide an excellent opportunity to study its genetic composition, diversity, and evolutionary events. The complete genome sequences of 424 CV-A isolates were analyzed through a model-based population genetic approach implemented in the STRUCTURE program. Twelve genetically distinct sub-populations were identified for CV-A isolates with a marked Fst distinction of 0.76991 (P-value = 0.00000). Besides, genetically admixed strains were characterized in the G-Id, G-IIIb clusters constituted by the CV-A12 and CV-A6 enterovirus serotypes. The serotypes depicted inter/intra-genotype recombination and episodic positive selection signatures in the structural and non-structural protein-coding regions. The observed genetic composition of CV-A samples was also deduced by the phylogenetic tree analyses, where a uniform genetic structure was inferred for most of the CV-A genotypes. However, the CV-A6 serotype samples genetically stratified into three sub-populations that may lead to the emergence of new lineages in future. These informations may implicate in planning the effective strategies to combat the coxsackievirus-A-mediated infection.
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Affiliation(s)
- Hizbullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan.
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Poltep K, Phadungsombat J, Nakayama EE, Kosoltanapiwat N, Hanboonkunupakarn B, Wiriyarat W, Shioda T, Leaungwutiwong P. Genetic Diversity of Dengue Virus in Clinical Specimens from Bangkok, Thailand, during 2018-2020: Co-Circulation of All Four Serotypes with Multiple Genotypes and/or Clades. Trop Med Infect Dis 2021; 6:tropicalmed6030162. [PMID: 34564546 PMCID: PMC8482112 DOI: 10.3390/tropicalmed6030162] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Dengue is an arboviral disease highly endemic in Bangkok, Thailand. To characterize the current genetic diversity of dengue virus (DENV), we recruited patients with suspected DENV infection at the Hospital for Tropical Diseases, Bangkok, during 2018-2020. We determined complete nucleotide sequences of the DENV envelope region for 111 of 276 participant serum samples. All four DENV serotypes were detected, with the highest proportion being DENV-1. Although all DENV-1 sequences were genotype I, our DENV-1 sequences were divided into four distinct clades with different distributions in Asian countries. Two genotypes of DENV-2 were identified, Asian I and Cosmopolitan, which were further divided into two and three distinct clades, respectively. In DENV-3, in addition to the previously dominant genotype III, a cluster of 6 genotype I viruses only rarely reported in Thailand was also observed. All of the DENV-4 viruses belonged to genotype I, but they were separated into three distinct clades. These results indicated that all four serotypes of DENV with multiple genotypes and/or clades co-circulate in Bangkok. Continuous investigation of DENV is warranted to further determine the relationship between DENV within Thailand and neighboring countries in Southeast Asia and Asia.
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Affiliation(s)
- Kanaporn Poltep
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
| | - Borimas Hanboonkunupakarn
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Witthawat Wiriyarat
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
- Correspondence: (T.S.); (P.L.)
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
- Correspondence: (T.S.); (P.L.)
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21
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Dieng I, Ndione MHD, Fall C, Diagne MM, Diop M, Gaye A, Barry MA, Diop B, Ndiaye M, Bousso A, Fall G, Loucoubar C, Faye O, Sall AA, Faye O. Multifoci and multiserotypes circulation of dengue virus in Senegal between 2017 and 2018. BMC Infect Dis 2021; 21:867. [PMID: 34429064 PMCID: PMC8383925 DOI: 10.1186/s12879-021-06580-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022] Open
Abstract
Background Dengue fever is a mosquito born disease associated with self-limited to life threatening illness. First detected in Senegal in the nineteenth century, and despite its growing incidence this last decade, significant knowledge gaps exist in our knowledge of genetic diversity of circulating strains. This study highlights the circulating serotypes and genotypes between January 2017 and December 2018 and their spatial and temporal distribution throughout all regions of Senegal. Methods We used 56 dengue virus (DENV) strains for the analysis collected from 11 sampling areas: 39 from all regions of Senegal, and 17 isolates from Thiès, a particular area of the country. Two real time RT-qPCR systems were used to confirm dengue infection and corresponding serotypes. For molecular characterization, CprM gene was sequenced and submitted to phylogenetic analysis for serotypes and genotypes assignment. Results Three dengue virus serotypes (DENV-1–3) were detected by all used methods. DENV-3 was detected in 50% (28/56) of the isolates, followed by DENV-1 and DENV-2, each representing 25% (14/56) of the isolates. DENV-3 belongs to genotype III, DENV-1 to genotype V and DENV-2 to Cosmopolitan genotype. Serotype 3 was detected in 7 sampling locations and a co-circulation of different serotypes was observed in Thiès, Fatick and Richard-toll. Conclusions These results emphasize the need of continuous DENV surveillance in Senegal to detect DENV cases, to define circulating serotypes/genotypes and to prevent the spread and the occurrence of severe cases. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06580-z.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal.
| | - Marie Henriette Dior Ndione
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Cheikh Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Moussa Moïse Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Unit, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Unit, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Unit, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Boly Diop
- Prevention Department, Ministry of Health, Dakar, Senegal
| | - Mamadou Ndiaye
- Prevention Department, Ministry of Health, Dakar, Senegal
| | | | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Unit, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, 220, Dakar, Senegal
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22
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Tissera HA, Jayamanne BDW, Raut R, Janaki SMD, Tozan Y, Samaraweera PC, Liyanage P, Ghouse A, Rodrigo C, de Silva AM, Fernando SD. Severe Dengue Epidemic, Sri Lanka, 2017. Emerg Infect Dis 2021; 26:682-691. [PMID: 32186490 PMCID: PMC7101108 DOI: 10.3201/eid2604.190435] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2017, a dengue epidemic of unexpected magnitude occurred in Sri Lanka. A total of 186,101 suspected cases and 440 dengue-related deaths occurred. We conducted a comprehensive analysis of this epidemic by comparing national surveillance data for 2017 with data from the preceding 5 years. In all Sri Lanka districts, dengue incidence in 2017 increased significantly over incidence during the previous 5 years. Older schoolchildren and young adults were more clinically symptomatic than those at extremes of age. Limited virologic surveillance showed the dominant circulating variant was dengue virus type 2 cosmopolitan genotype in the most affected district. One quarter of total annual cases were reported 5 weeks after the southwest monsoon started. Changes in vector abundance were not predictive of the increased incidence. Direct government expenditures on dengue control activities in 2017 were US $12.7 million. The lessons learned from this outbreak are useful for other tropical nations facing increasing dengue incidence.
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23
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Carrillo-Hernandez MY, Ruiz-Saenz J, Jaimes-Villamizar L, Robledo-Restrepo SM, Martinez-Gutierrez M. Phylogenetic and evolutionary analysis of dengue virus serotypes circulating at the Colombian-Venezuelan border during 2015-2016 and 2018-2019. PLoS One 2021; 16:e0252379. [PMID: 34048474 PMCID: PMC8162668 DOI: 10.1371/journal.pone.0252379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023] Open
Abstract
Dengue is an endemic disease in Colombia. Norte de Santander is a region on the border of Colombia and Venezuela and has reported the co-circulation and simultaneous co-infection of different serotypes of the dengue virus (DENV). This study aimed to conduct a phylogenetic analysis on the origin and genetic diversity of DENV strains circulating in this bordering region. Serum samples were collected from patients who were clinically diagnosed with febrile syndrome associated with dengue during two periods. These samples were tested for DENV and serotyping was performed using reverse transcriptase-polymerase chain reaction. Subsequently, positive samples were amplified and the envelope protein gene of DENV was sequenced. Phylogenetic and phylogeographic analyses were performed using the sequences obtained. Basic local alignment search tool analysis confirmed that six and eight sequences belonged to DENV-1 and DENV-2, respectively. The phylogenetic analysis of DENV-1 showed that the sequences belonged to genotype V and clade I; they formed two groups: in the first group, two sequences showed a close phylogenetic relationship with strains from Ecuador and Panama, whereas the other four sequences were grouped with strains from Venezuela and Colombia. In the case of DENV-2, the analysis revealed that the sequences belonged to the Asian–American genotype and clade III. Furthermore, they formed two groups; in the first group, three sequences were grouped with strains from Colombia and Venezuela, whereas the other five were grouped with strains from Venezuela, Colombia and Honduras. This phylogenetic analysis suggests that the geographical proximity between Colombia and Venezuela is favourable for the export and import of different strains among serotypes or clades of the same DENV serotype, which could favour the spread of new outbreaks caused by new strains or genetic variants of this arbovirus. Therefore, this information highlights the importance of monitoring the transmission of DENV at border regions.
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Affiliation(s)
- Marlen Yelitza Carrillo-Hernandez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | | | - Sara Maria Robledo-Restrepo
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, Colombia
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
- * E-mail:
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24
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Abstract
Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Angela C O'Donnell
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
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25
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Complete genome characterization of the 2018 dengue outbreak in Hunan, an inland province in central South China. Virus Res 2021; 297:198358. [PMID: 33667623 DOI: 10.1016/j.virusres.2021.198358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/26/2020] [Accepted: 02/25/2021] [Indexed: 11/22/2022]
Abstract
In 2018, a small-scale dengue epidemic broke out in Hunan Province, an inland province in central South China, with 172 people infected. To verify the causative agent, complete genome information was obtained by PCR and sequencing based on the viral RNAs extracted from patient serum samples. Mutation and evolutionary analysis were performed by MEGA7.0 software. The online softwares "Predict protein" and "Mfold" were used to predict the secondary structure of proteins and untranslated regions, respectively. Phylogenetic analysis showed that all five isolates in this study were DENV type 2, which is most closely related to the Zhejiang strain (2017-MH110588). Compared with the DENV-2 standard strain, 773 nucleotide mutations occurred in the isolated strain, of which 666 were nonsense mutations. Of the 80 mutated amino acids, 22 occurred in the structural protein region (2 in C region, 8 in PrM/M region, 12 in E region), and 58 in the non-structural (NS) protein region (9 in NS1 region, 10 in NS2 region, 12 in NS3 region, 7 in NS4 region, 20 in NS5 region). The prM/M region had the highest AA mutation rate, while NS4B was conservative. Three amino acid mutations (E: N390thS, and NS5: S676thN, K800thT) may important for the replication and virulence of the DENV. Secondary structure prediction observed 28 changes in polynucleotide binding regions and 110 changes in protein binding sites of coding sequence. 2 and 4 base substitutions resulted in 2 and 6 significant changes in the RNA secondary structure of 5' UTR and 3' UTR, respectively. Two significant positive selection sites were observed in NS5. To our knowledge, this research is the first complete genome analysis of the epidemic strain of the 2018 dengue outbreak in Hunan and will benefit further research for virus traceability and vaccine development.
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26
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Qi M, Yang M, Xu L, Ma C, Huang P, Sun J, Shi J, Hu Y. Complete genome analysis identifies recombinant events and positive selection sites of hepatitis C virus from mainland China during 2010-2019. Virus Res 2021; 296:198354. [PMID: 33639223 DOI: 10.1016/j.virusres.2021.198354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 11/18/2022]
Abstract
Identification of new recombinant HCV strains and positive selection sites are crucially important for the formulation of virus intervention measures. However, little is known about the recombinant variant information and positive selection sites of circulating HCV strains in mainland China. In this study, we systematically identified recombinant variants and positive selection sites of HCV in mainland China during the 2010-2019. Phylogenetic analysis results indicated that HCV-6 was one of the dominant genotypes in mainland China during 2010-2019, whereas genotypes 7 and 8 were not detected. Recombinant analysis based on 102 full-length genome sequences of Chinese epidemic strains of HCV identified four intra-genotypic recombinants (strains WYHCV286, GB28, GZ2983, and HCV156) and one inter-genotypic recombinant (strain HH075). Specifically, two breakpoints in the 5' UTR of two recombinants, the strains HH075 and WYHCV286, are rather unusual and has not been described before. Further, selection pressure analyses revealed five positive selective sites, which were located in the core, E2, and NS5B protein. Notably, positive selective sites in NS5B and core protein may be partially responsible for the drug resistance and immune evasion. To the best of our knowledge, this study firstly reported five specific intertypic and intratypic recombinants of Chinese epidemic strains of HCV, which highlight their significance for anti-HCV treatment and vaccine development.
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Affiliation(s)
- Mengdi Qi
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Mengmei Yang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Liangzi Xu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Chunli Ma
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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27
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Fang Y, Tambo E, Xue JB, Zhang Y, Zhou XN, Khater EIM. Detection of DENV-2 and Insect-Specific Flaviviruses in Mosquitoes Collected From Jeddah, Saudi Arabia. Front Cell Infect Microbiol 2021; 11:626368. [PMID: 33718273 PMCID: PMC7947193 DOI: 10.3389/fcimb.2021.626368] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Mosquito-borne diseases are rapidly spreading due to increasing international travel and trade. Routine mosquito surveillance and screening for mosquito-borne pathogens can be early indicators for local disease transmission and outbreaks. However, arbovirus detection in mosquito vectors has rarely been reported in Saudi Arabia. Methods A total of 769,541 Aedes and Culex mosquitoes were collected by Black Hole traps during routine mosquito surveillance in the first half of 2016. Culex. quinquefasciatus and Ae. aegypti were the most prevalent species observed. Twenty-five and 24 randomly selected pools of Ae. aegypti and Cx. quinquefasciatus, respectively, were screened for arboviruses by RT-PCR. Results Dengue 2 (DENV-2) and four strains of insect-specific flaviviruses, including one of cell-fusing agent virus (CFAV) and three of Phlebotomus-associated flavivirus (PAFV) were detected in pools of Ae. aegypti. We also detected 10 strains of Culex flavivirus (CxFV) in pools of Cx. quinquefasciatus. Phylogenetic analysis using whole genome sequences placed the DENV strain into the cosmopolitan 1 sub-DENV-2 genotype, and the CxFVs into the African/Caribbean/Latin American genotype. These analyses also showed that the DENV-2 strain detected in the present study was closely related to strains detected in China in 2014 and in Japan in 2018, which suggests frequent movement of DENV-2 strains among these countries. Furthermore, the phylogenetic analysis suggested at least five introductions of DENV-2 into Saudi Arabia from 2014 through 2018, most probably from India. Conclusions To our knowledge, this study reports the first detection of four arboviruses DENV, CFAV, PAFV, and CxFV in mosquitoes in Saudi Arabia, which shows that they are co-circulating in Jeddah. Our findings show a need for widespread mosquito-based arbovirus surveillance programs in Saudi Arabia, which will improve our understanding of the transmission dynamics of the mosquito-borne arboviruses within the country and help early predict and mitigate the risk of human infections and outbreaks.
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Affiliation(s)
- Yuan Fang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Ernest Tambo
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah, Saudi Arabia
| | - Jing-Bo Xue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Emad I M Khater
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah, Saudi Arabia.,Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
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28
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Kong W, Mao J, Yang Y, Yuan J, Chen J, Luo Y, Lai T, Zuo L. Mechanisms of mTOR and Autophagy in Human Endothelial Cell Infected with Dengue Virus-2. Viral Immunol 2021; 33:61-70. [PMID: 31978319 DOI: 10.1089/vim.2019.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mechanistic mammalian target of rapamycin (mTOR) plays a crucial role in response to many major cellular processes, including cellular metabolism, proliferation, and autophagy. Both mTOR and autophagy are suggested to be involved in the viral infection. However, little is known about the role of mTOR and autophagy in human endothelial cell infected with dengue virus-2 (DENV-2), this study is to investigate the role of mTOR and autophagy in human umbilical vein endothelial cells (HUVECs) infected with DENV-2 and related regulatory mechanisms. HUVECs were cultured in epithelial cell medium. A series of experiments involving immunohistochemistry, TCID50 method, real-time PCR, western blot, and laser confocal were performed in this study. The cell line was identified as HUVEC by the expression of cell factor VIII. The expression level of DENV-2 mRNA increased and showed an upward trend. Compared with the control group, the fluorescence of autophagy-labeled protein LC3B and lysosome-labeled protein lysosome-associated membrane protein 1 (LAMP1) in the cytoplasm of HUVEC induced by rapamycin was observed, and intensity was significantly enhanced under confocal laser scanning microscope, after fluorescence synthesis, the fluorescence of autophagy-labeled protein LC3B and lysosome-labeled protein LAMP1 overlaps were reduced. The intensity of fluorescence of autophagy-labeled protein LC3B and lysosome-labeled protein LAMP1 increased in 1 × 104 TCID50 DENV-2 infection group, after fluorescence synthesis, fluorescence of autophagy-labeled protein LC3B, lysosome-labeled protein LAMP1, and DEN2 NS1 overlapped. Compared with the control group, the phosphorylation level of mTOR, Atg13, and p-ULK1 in DENV-2-infected group or Rapa treatment group decreased significantly (p < 0.05), and the level of LC3-II increased significantly (p < 0.05). These results suggest that DENV-2 induces autophagy in HUVECs through mTOR signaling molecule.
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Affiliation(s)
- Weiying Kong
- Department of Immunology, Guizhou Medical University, Guiyang, China
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jiaxuan Mao
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Yang Yang
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Jing Yuan
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Junhao Chen
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Yu Luo
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Tao Lai
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Li Zuo
- Department of Immunology, Guizhou Medical University, Guiyang, China
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29
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Laureti M, Paradkar PN, Fazakerley JK, Rodriguez-Andres J. Superinfection Exclusion in Mosquitoes and Its Potential as an Arbovirus Control Strategy. Viruses 2020; 12:v12111259. [PMID: 33167513 PMCID: PMC7694488 DOI: 10.3390/v12111259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/19/2022] Open
Abstract
The continuing emergence of arbovirus disease outbreaks around the world, despite the use of vector control strategies, warrants the development of new strategies to reduce arbovirus transmission. Superinfection exclusion, a phenomenon whereby a primary virus infection prevents the replication of a second closely related virus, has potential to control arbovirus disease emergence and outbreaks. This phenomenon has been observed for many years in plants, insects and mammalian cells. In this review, we discuss the significance of identifying novel vector control strategies, summarize studies exploring arbovirus superinfection exclusion and consider the potential for this phenomenon to be the basis for novel arbovirus control strategies.
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Affiliation(s)
- Mathilde Laureti
- Peter Doherty Institute for Infection and Immunity and Faculty of Veterinary and Agricultural Sciences, University of Melbourne, VIC 3000 Melbourne, Australia;
- CSIRO Health & Biosecurity, Australian Centre for Diseases Preparedness, VIC 3220 Geelong, Australia;
- Correspondence: (M.L.); (J.R.-A.)
| | - Prasad N. Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Diseases Preparedness, VIC 3220 Geelong, Australia;
| | - John K. Fazakerley
- Peter Doherty Institute for Infection and Immunity and Faculty of Veterinary and Agricultural Sciences, University of Melbourne, VIC 3000 Melbourne, Australia;
| | - Julio Rodriguez-Andres
- Peter Doherty Institute for Infection and Immunity and Faculty of Veterinary and Agricultural Sciences, University of Melbourne, VIC 3000 Melbourne, Australia;
- Correspondence: (M.L.); (J.R.-A.)
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Antigenic Variation of the Dengue Virus 2 Genotypes Impacts the Neutralization Activity of Human Antibodies in Vaccinees. Cell Rep 2020; 33:108226. [PMID: 33027653 PMCID: PMC7583086 DOI: 10.1016/j.celrep.2020.108226] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/04/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022] Open
Abstract
Dengue virus (DENV) infects an estimated 390 million people each year worldwide. As tetravalent DENV vaccines have variable efficacy against DENV serotype 2 (DENV2), we evaluated the role of genetic diversity within the pre-membrane (prM) and envelope (E) proteins of DENV2 on vaccine performance. We generated a recombinant DENV2 genotype variant panel with contemporary prM and E isolates that are representative of global genetic diversity. The DENV2 genotype variants differ in growth kinetics, morphology, and virion stability. Importantly, the DENV2 genotypic variants are differentially neutralized by monoclonal antibodies, polyclonal serum neutralizing antibodies from DENV2-infected human subjects, and vaccine-elicited antibody responses from the TV003 NIH DENV2 monovalent and DENV tetravalent vaccines. We conclude that DENV2 prM and E genetic diversity significantly modulates antibody neutralization activity. These findings have important implications for dengue vaccines, which are being developed under the assumption that intraserotype variation has minimal impact on neutralizing antibodies. Martinez et al. demonstrate that dengue virus serotype 2 (DENV2) genetic variation modulates neutralizing antibody activity from infection and vaccination. This observation underlines that genotypic variation impacts dengue virus 2 evasion from humoral immunity, suggesting that intraserotype genotypic variation should be considered in designing dengue vaccines.
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31
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Kaur N, Rahim SSSA, Jaimin JJ, Dony JJF, Khoon KT, Ahmed K. The east coast districts are the possible epicenter of severe dengue in Sabah. J Physiol Anthropol 2020; 39:19. [PMID: 32795350 PMCID: PMC7427916 DOI: 10.1186/s40101-020-00230-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/02/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Malaysia recorded the highest number of dengue cases between 2014 and 2017. There are 13 states and three federal territories in Malaysia, and each area varies in their prevalence of dengue. Sabah is one of the states situated in Borneo, Malaysia. Although dengue has been increasing for the last several years, no study was being done to understand the burden and serotype distribution of the dengue virus (DENV) in Sabah. Therefore, the present study was carried out to understand the epidemiology of the dengue infection and the factors responsible for severe dengue in Sabah. METHODS Data on dengue infection were extracted from the dengue database of the state of Sabah from 2013 through 2018. DENV NS-1-positive serum samples from multiple sites throughout Sabah were sent to the state public health laboratory, Kota Kinabalu Public Health Laboratory, for serotype determination. The analysis of factors associated with severe dengue was determined from the data of 2018 only. RESULTS In 2013, there were 724 dengue cases; however, from 2014, dengue cases increased exponentially and resulted in 3423 cases in 2018. Increasing dengue cases also led to increased dengue mortality. The number of dengue deaths in 2013 was only five which then gradually increased, and in 2018, 29 patients died. This is an increase of 580% from 2013 to 2018. Deaths were considerably more in the districts of the east coast of Sabah compared with districts in the west coast. During the study period, all DENV serotypes could be identified as serotypes circulating in Sabah. In 2018, the predominant serotype was DENV-3. The monthly peak of dengue infection varied in different years. In the logistic regression analysis, it was identified that children were 6.5 times, patients infected with mixed serotype of DENV were 13 times, and cases from the districts of the east coast were 5.2 times more likely to develop severe dengue. CONCLUSIONS An increasing trend of dengue infection has been observed in Sabah. The burden of dengue, severe dengue, and mortality was noted especially in the districts of the east coast of Sabah. Severe dengue was most likely developed in children, cases from the east coast, and patients infected with mixed serotype of DENV.
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Affiliation(s)
- Narinderjeet Kaur
- Department of Community and Family Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Syed Sharizman Syed Abdul Rahim
- Department of Community and Family Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Joel Judson Jaimin
- Public Health Lab, Kota Kinabalu Public Health Laboratory, Sabah State Health Department, 88300, Kota Kinabalu, Sabah, Malaysia
| | - Jiloris Julian Frederick Dony
- Public Health Lab, Kota Kinabalu Public Health Laboratory, Sabah State Health Department, 88300, Kota Kinabalu, Sabah, Malaysia
| | - Koay Teng Khoon
- Vector borne Unit, Sabah State Health Department, 88590, Kota Kinabalu, Sabah, Malaysia
| | - Kamruddin Ahmed
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
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Hwang EH, Kim G, Oh H, An YJ, Kim J, Kim JH, Hwang ES, Park JH, Hong J, Koo BS. Molecular and evolutionary analysis of dengue virus serotype 2 isolates from Korean travelers in 2015. Arch Virol 2020; 165:1739-1748. [PMID: 32409874 PMCID: PMC7351809 DOI: 10.1007/s00705-020-04653-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/10/2020] [Indexed: 12/17/2022]
Abstract
In Korea, dengue infection has been frequently reported in travelers to tropical and subtropical countries. Global warming increases the probability of autochthonous dengue outbreaks in Korea. In this report, the molecular and evolutionary properties of four dengue virus (DENV) type 2 isolates from Korean overseas travelers were examined. Three of these isolates were classified as Cosmopolitan genotypes and further divided into sublineages 1 (43,253, 43,254) and 2 (43,248), while the other isolate (KBPV-VR29) was related to American genotypes. The variable amino acid motifs related to virulence and replication were identified in the structural and non-structural proteins. A negative selection mechanism was clearly verified in all of the DENV proteins. Potential recombination events were identified in the NS5 protein of the XSBN10 strain. The substitution rate (5.32 × 10-4 substitutions per site) and the time of the most recent common ancestor (TMRCA) for each evolutionary group were determined by the Bayesian skyline coalescent method. This study shows that DENV type 2 strains with distinct phylogenetic, evolutionary, and virulence characteristics have been introduced into Korea by overseas travelers and have the potential to trigger autochthonous dengue outbreaks.
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Affiliation(s)
- Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - You Jung An
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Jiyeon Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Jung Heon Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Eung-Soo Hwang
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Jong-Hwan Park
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - JungJoo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
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Langat SK, Eyase FL, Berry IM, Nyunja A, Bulimo W, Owaka S, Ofula V, Limbaso S, Lutomiah J, Jarman R, Distelhorst J, Sang RC. Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages. Virus Evol 2020; 6:veaa026. [PMID: 32523778 PMCID: PMC7266482 DOI: 10.1093/ve/veaa026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dengue fever (DF) is an arboviral disease caused by dengue virus serotypes 1-4 (DENV 1-4). Globally, DF incidence and disease burden have increased in the recent past. Initially implicated in a 1982 outbreak, DENV-2 recently reemerged in Kenya causing outbreaks between 2011 and 2014 and more recently 2017–8. The origin and the evolutionary patterns that may explain the epidemiological expansion and increasing impact of DENV-2 in Kenya remain poorly understood. Using whole-genome sequencing, samples collected during the 2011–4 and 2017–8 dengue outbreaks were analyzed. Additional DENV-2 genomes were downloaded and pooled together with the fourteen genomes generated in this study. Bioinformatic methods were used to analyze phylogenetic relationships and evolutionary patterns of DENV-2 causing outbreaks in Kenya. The findings from this study have shown the first evidence of circulation of two different Cosmopolitan genotype lineages of DENV-2; Cosmopolitan-I (C-I) and Cosmopolitan-II (C-II), in Kenya. Our results put the origin location of C-I lineage in India in 2011, and C-II lineage in Burkina Faso between 1979 and 2013. C-I lineage was the most isolated during recent outbreaks, thus showing the contribution of this newly emerged strain to the increased DENV epidemics in the region. Our findings, backed by evidence of recent local epidemics that have been associated with C-I in Kenya and C-II in Burkina Faso, add to the growing evidence of expanding circulation and the impact of multiple strains of DENV in the region as well as globally. Thus, continued surveillance efforts on DENV activity and its evolutionary trends in the region, would contribute toward effective control and the current vaccine development efforts.
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Affiliation(s)
- Solomon K Langat
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Fredrick Lunyagi Eyase
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya.,Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology
| | | | - Albert Nyunja
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Wallace Bulimo
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya.,Department of Biochemistry, University of Nairobi
| | - Samuel Owaka
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Victor Ofula
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Samson Limbaso
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya.,Center for Virus Research, Kenya Medical Research Institute
| | - Joel Lutomiah
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya.,Center for Virus Research, Kenya Medical Research Institute
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research
| | - John Distelhorst
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Rosemary C Sang
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya.,Center for Virus Research, Kenya Medical Research Institute
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Darcy AW, Kanda S, Dalipanda T, Joshua C, Shimono T, Lamaningao P, Mishima N, Nishiyama T. Multiple arboviral infections during a DENV-2 outbreak in Solomon Islands. Trop Med Health 2020; 48:33. [PMID: 32435149 PMCID: PMC7225641 DOI: 10.1186/s41182-020-00217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022] Open
Abstract
Background Solomon Islands, a country made up of tropical islands, has suffered cyclic dengue fever (DF) outbreaks in the past three decades. An outbreak of dengue-like illness (DLI) that occurred in April 2016 prompted this study, which aimed to determine the population’s immunity status and identify the arboviruses circulating in the country. Methods A household survey, involving 188 participants in two urban areas (Honiara and Gizo), and a parallel hospital-based clinical survey were conducted in April 2016. The latter was repeated in December after a surge in DLI cases. Arbovirus IgG ELISA were performed on the household blood samples to determine the prevalence of arboviruses in the community, while qPCR testing of the clinical samples was used to identify the circulating arboviruses. Dengue virus (DENV)-positive samples were further characterized by amplifying and sequencing the envelope gene. Results The overall prevalence rates of DENV, Zika virus, and chikungunya virus were 83.4%, 7.6%, and 0.9%, respectively. The qPCR positivity rates of the clinical samples collected in April 2016 were as follows: DENV 39.6%, Zika virus 16.7%, and chikungunya virus 6.3%, which increased to 74%, 48%, and 20% respectively in December 2016. The displacement of the circulating serotype-3, genotype-1, with DENV serotype 2, genotype cosmopolitan was responsible for the outbreak in 2016. Conclusions A DENV outbreak in Solomon Islands was caused by the introduction of a single serotype. The high prevalence of DENV provided transient cross-protection, which prevented the introduction of a new serotype from the hyperendemic region for at least 3 years. The severe outcomes seen in the recent outbreak probably resulted from changes in the causative viruses and the effects of population immunity and changes in the outbreak pattern. Solomon Islands needs to step up surveillance to include molecular tools, increase regional communication, and perform timely interventions.
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Kubiszeski JR, Vieira CJDSP, Thies SF, Silva DJFD, Barreto ES, Mondini A, Bronzoni RVDM. Detection of the Asian II genotype of dengue virus serotype 2 in humans and mosquitoes in Brazil. Rev Soc Bras Med Trop 2020; 53:e20190439. [PMID: 32321091 PMCID: PMC7182292 DOI: 10.1590/0037-8682-0439-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION DENV-2 is the cause of most dengue epidemics worldwide and is associated with severe cases. METHODS We investigated arboviruses in 164 serum samples collected from patients presenting with clinical symptoms of dengue fever and 152 mosquito pools. RESULTS We detected the Asian II genotype of DENV-2 in humans and mosquitoes. Our results confirmed the circulation of the Asian II genotype in Brazil, in addition to the prevalent Asian/American genotype. CONCLUSIONS The detection of Asian II genotype of DENV-2 in mosquito pools collected in a forest park may be related to a spillback event of human dengue virus.
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Affiliation(s)
| | | | | | | | - Eriana Serpa Barreto
- Universidade Federal de Mato Grosso, Instituto de Ciências da Saúde, Sinop, MT, Brasil
| | - Adriano Mondini
- Universidade de São Paulo, Departamento de Ciências Farmacêuticas, Araraquara, SP, Brasil
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Carreño MF, Jiménez-Silva CL, Rey-Caro LA, Conde-Ocazionez SA, Flechas-Alarcón MC, Velandia SA, Ocazionez RE. Dengue in Santander State, Colombia: fluctuations in the prevalence of virus serotypes are linked to dengue incidence and genetic diversity of the circulating viruses. Trop Med Int Health 2019; 24:1400-1410. [PMID: 31596525 DOI: 10.1111/tmi.13311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To investigate the link between fluctuations in the prevalence of dengue virus (DENV) serotypes and the number of dengue cases in the metropolitan area of Bucaramanga, Santander State, Colombia, in the 2007-2010 and 2014-2017 periods. METHOD Viruses were isolated from febrile patient samples by direct application to C6/36-HT cells and typed using monoclonal antibodies. We performed autocorrelation and cross-correlation analyses to determine whether fluctuations in the prevalence of DENV serotypes and dengue cases were correlated. Full envelope (E) gene sequences were employed to examine the genetic diversity of serotypes circulating by using a phylogenetic approach. RESULTS All four dengue virus serotypes were detected. DENV-1 was the dominant serotype in both periods followed by DENV-3 or DENV-2 depending on the period; DENV-4 was the least prevalent virus in both periods. Cross-correlation analyses suggest a temporal relation between the fluctuations in the prevalence of DENV serotypes, which were almost simultaneous (lag = 0) or related to recent past fluctuations (lag > 1.0) in the number of dengue cases. Data suggest that a sustained predominance of DENV-1, an increase of the DENV-4 prevalence, and a switch from DENV-3 to DENV-2 could be linked to an outbreak. Circulating viruses were grouped into Genotype V, Asia/American III and II for DENV-1, -2, -3 and -4, respectively; intragenotypic diversity was detected. CONCLUSIONS The present work highlights the need of comprehensive studies on dynamics of DENV in Colombia to understand transmission of dengue and evaluate the effectiveness of a vaccination programme.
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Affiliation(s)
- María Fernanda Carreño
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Cinthy Lorena Jiménez-Silva
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Luz Aida Rey-Caro
- Centro de Investigaciones Epidemiológicas, Escuela de Medicina, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Sergio Andrés Conde-Ocazionez
- Laboratorio de Neurociencias, Facultad de Ciencias de la Salud, Escuela de Medicina, Universidad de Santander, Bucaramanga, Colombia
| | - María Camila Flechas-Alarcón
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Sindi Alejandra Velandia
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Raquel Elvira Ocazionez
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales, Universidad Industrial de Santander, Bucaramanga, Colombia
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Pascalis H, Turpin J, Roche M, Krejbich P, Gadea G, Nten CA, Desprès P, Mavingui P. The epidemic of Dengue virus type-2 Cosmopolitan genotype on Reunion Island relates to its active circulation in the Southwestern Indian Ocean neighboring islands. Heliyon 2019; 5:e01455. [PMID: 31008393 PMCID: PMC6458493 DOI: 10.1016/j.heliyon.2019.e01455] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 11/20/2022] Open
Abstract
Reunion Island is currently experiencing an epidemic caused by Dengue virus type-2 (DENV-2) resulting in over 6,763 cases from austral summer 2017 to winter 2018. Phylogenetic analyses on two non-imported cases of dengue infection from Reunion Island highlight a regional circulation of DENV-2 Cosmopolitan lineage 1 virus on both Reunion Island and the Seychelles.
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Affiliation(s)
- Hervé Pascalis
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Jonathan Turpin
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Marjolaine Roche
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Pascale Krejbich
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Gilles Gadea
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Célestine Atyame Nten
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Philippe Desprès
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, UMR PIMIT "Processus Infectieux en Milieu Insulaire Tropical", INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Clotilde, La Réunion, France
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Meagher RJ, Priye A, Light YK, Huang C, Wang E. Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA. Analyst 2019; 143:1924-1933. [PMID: 29620773 DOI: 10.1039/c7an01897e] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMP or RT-LAMP assays. In this study, we examine the impact of primer dimers and hairpins on previously published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter that can be correlated to the probability of non-specific amplification associated with LAMP primers.
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Affiliation(s)
- Robert J Meagher
- Sandia National Laboratories, Biotechnology and Bioengineering Department, PO Box 969, Livermore, CA 94550, USA.
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Ahamed SF, Rosario V, Britto C, Dias M, Nayak K, Chandele A, Kaja MK, Shet A. Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India. Int J Infect Dis 2019; 84S:S34-S43. [PMID: 30639622 DOI: 10.1016/j.ijid.2019.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012-13/2014-15 outbreaks in southern India. METHODS Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. RESULTS In 2012-13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014-15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012-13 and 2014-15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012-13, ceding to GI predominance (80.8%) in 2014-15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. CONCLUSIONS New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.
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Affiliation(s)
- Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, 560064, Karnataka, India.
| | - Vivek Rosario
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Carl Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; Department of Microbiology, St. John's Medical College Hospital, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Murali-Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, 415 N Washington St, Baltimore 21231, USA.
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Kar M, Nisheetha A, Kumar A, Jagtap S, Shinde J, Singla M, M S, Pandit A, Chandele A, Kabra SK, Krishna S, Roy R, Lodha R, Pattabiraman C, Medigeshi GR. Isolation and molecular characterization of dengue virus clinical isolates from pediatric patients in New Delhi. Int J Infect Dis 2018; 84S:S25-S33. [PMID: 30528666 DOI: 10.1016/j.ijid.2018.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE To characterize the in vitro replication fitness, viral diversity, and phylogeny of dengue viruses (DENV) isolated from Indian patients. METHODS DENV was isolated from whole blood collected from patients by passaging in cell culture. Passage 3 viruses were used for growth kinetics in C6/36 mosquito cells. Parallel efforts also focused on the isolation of DENV RNA from plasma samples of the same patients, which were processed for next-generation sequencing. RESULTS It was possible to isolate 64 clinical isolates of DENV, mostly DENV-2. Twenty-five of these were further used for growth curve analysis in vitro, which showed a wide range of replication kinetics. The highest viral titers were associated with isolates from patients with dengue with warning signs and severe dengue cases. Full genome sequences of 21 DENV isolates were obtained. Genome analysis mapped the circulating DENV-2 strains to the Cosmopolitan genotype. CONCLUSIONS The replication kinetics of isolates from patients with mild or severe infection did not differ significantly, but the viral titers varied by two orders of magnitude between the isolates, suggesting differences in replication fitness among the circulating DENV-2.
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Affiliation(s)
- Meenakshi Kar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amul Nisheetha
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anuj Kumar
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Jitendra Shinde
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Saranya M
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, ICGEB Campus, New Delhi, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India; Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India; Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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41
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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42
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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: 48] [Impact Index Per Article: 8.0] [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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43
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Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus. Viruses 2018; 10:v10040193. [PMID: 29652824 PMCID: PMC5923487 DOI: 10.3390/v10040193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/12/2018] [Accepted: 03/30/2018] [Indexed: 01/26/2023] Open
Abstract
Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health.
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Lourenço J, Tennant W, Faria NR, Walker A, Gupta S, Recker M. Challenges in dengue research: A computational perspective. Evol Appl 2018; 11:516-533. [PMID: 29636803 PMCID: PMC5891037 DOI: 10.1111/eva.12554] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/08/2017] [Indexed: 01/12/2023] Open
Abstract
The dengue virus is now the most widespread arbovirus affecting human populations, causing significant economic and social impact in South America and South-East Asia. Increasing urbanization and globalization, coupled with insufficient resources for control, misguided policies or lack of political will, and expansion of its mosquito vectors are some of the reasons why interventions have so far failed to curb this major public health problem. Computational approaches have elucidated on dengue's population dynamics with the aim to provide not only a better understanding of the evolution and epidemiology of the virus but also robust intervention strategies. It is clear, however, that these have been insufficient to address key aspects of dengue's biology, many of which will play a crucial role for the success of future control programmes, including vaccination. Within a multiscale perspective on this biological system, with the aim of linking evolutionary, ecological and epidemiological thinking, as well as to expand on classic modelling assumptions, we here propose, discuss and exemplify a few major computational avenues-real-time computational analysis of genetic data, phylodynamic modelling frameworks, within-host model frameworks and GPU-accelerated computing. We argue that these emerging approaches should offer valuable research opportunities over the coming years, as previously applied and demonstrated in the context of other pathogens.
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Affiliation(s)
| | - Warren Tennant
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
| | | | | | | | - Mario Recker
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
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Azami NAM, Moi ML, Ami Y, Suzaki Y, Lim CK, Taniguchi S, Saijo M, Takasaki T, Kurane I. Genotype-specific and cross-reactive neutralizing antibodies induced by dengue virus infection: detection of antibodies with different levels of neutralizing activities against homologous and heterologous genotypes of dengue virus type 2 in common marmosets (Callithrix jacchus). Virol J 2018; 15:51. [PMID: 29587780 PMCID: PMC5870686 DOI: 10.1186/s12985-018-0967-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/19/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A vaccine against all four dengue virus (DENV) serotypes includes the formulation of one genotype of each serotype. Although genetic similarities among genotypes within a serotype are higher as compared to those among serotypes, differences in the immunogenicity of the included genotypes would be a critical issue in maximizing successful dengue vaccine development. Thus, we determined the neutralizing antibody responses against three genotypes of dengue virus serotype 2 (DENV-2), namely Cosmopolitan, Asian I, and Asian/American, after primary and secondary inoculation with DENV-2 in a dengue animal model, the common marmoset (Callithrix jacchus). METHODS A total of fifty-four plasma samples were obtained from thirty-four marmosets that were inoculated with clinically-isolated DENV strains or DENV candidate vaccines, were used in this study. Plasma samples were obtained from marmosets after primary inoculation with DENV-2 infection, secondary inoculation with homologous or heterologous genotypes, and tertiary inoculation with heterologous DENV. Neutralizing antibody titers against DENV-2 (Cosmopolitan, Asian I, and Asian/American genotypes) and DENV-1 were determined using a conventional plaque reduction neutralization assay. RESULTS In marmosets that were inoculated with the Cosmopolitan genotype in primary infection, neutralizing antibody neutralized 3 genotypes, and the titers to Asian I genotype were significantly higher than those to homologous Cosmopolitan genotype. After secondary DENV-2 infection with heterologous genotype (Asian I in primary and Asian/American in secondary), neutralizing antibody titers to Asian/American genotype was significantly higher than those against Cosmopolitan and Asian I genotypes. Following tertiary infection with DENV-1 following DENV-2 Asian I and Cosmopolitan genotypes, neutralizing antibody titers to Asian/American were also significantly higher than those against Cosmopolitan and Asian I genotypes. CONCLUSION The present study demonstrated that different levels of neutralizing antibodies were induced against variable DENV-2 genotypes after primary, secondary and tertiary infections, and that neutralizing antibody titers to some heterologous genotypes were higher than those to homologous genotypes within a serotype. The results indicate that heterogeneity and homogeneity of infecting genotypes influence the levels and cross-reactivity of neutralizing antibodies induced in following infections. The results also suggest that certain genotypes may possess advantage in terms of breakthrough infections against vaccination.
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Affiliation(s)
- Nor Azila Muhammad Azami
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Meng Ling Moi
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yasushi Ami
- Division of Experimental Animal Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuriko Suzaki
- Division of Experimental Animal Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chang-Kweng Lim
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Taniguchi
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Ichiro Kurane
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan
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Waman VP, Kale MM, Kulkarni-Kale U. Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. INFECTION GENETICS AND EVOLUTION 2017; 49:234-240. [PMID: 28126562 DOI: 10.1016/j.meegid.2017.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/14/2017] [Accepted: 01/21/2017] [Indexed: 11/29/2022]
Abstract
Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity. DENV-3 population is observed to be stratified into five major subpopulations. Genotype I and II formed independent subpopulations while genotype III is subdivided into three subpopulations (GIII-a, GIII-b and GIII-c) and is therefore heterogeneous. Genotypes I, II and GIII-a subpopulations comprise of Asian strains whereas GIII-c comprises of American strains. GIII-b subpopulation includes mainly of American strains along with a few strains from Sri Lanka. Genetic admixture is predominantly observed in Sri Lankan strains of genotype III and all strains of genotype V. Inter-genotype recombination was observed to occur in non-structural region of several Asian strains whereas extent of recombination was limited in American strains. Significant positive selection was found to be operational on all genes and observed to be the main driving force of genetic diversity. Positive selection was strongly operational on the branches leading to Asian genotypes and helped to delineate the genetic differences between Asian and American lineages. Thus, inter-genotype recombination, migration and adaptive evolution are the major determinants of evolution of DENV-3.
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Affiliation(s)
- Vaishali P Waman
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Mohan M Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India.
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