1
|
Paz-Bailey G, Adams LE, Deen J, Anderson KB, Katzelnick LC. Dengue. Lancet 2024; 403:667-682. [PMID: 38280388 DOI: 10.1016/s0140-6736(23)02576-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 01/29/2024]
Abstract
Dengue, caused by four closely related viruses, is a growing global public health concern, with outbreaks capable of overwhelming health-care systems and disrupting economies. Dengue is endemic in more than 100 countries across tropical and subtropical regions worldwide, and the expanding range of the mosquito vector, affected in part by climate change, increases risk in new areas such as Spain, Portugal, and the southern USA, while emerging evidence points to silent epidemics in Africa. Substantial advances in our understanding of the virus, immune responses, and disease progression have been made within the past decade. Novel interventions have emerged, including partially effective vaccines and innovative mosquito control strategies, although a reliable immune correlate of protection remains a challenge for the assessment of vaccines. These developments mark the beginning of a new era in dengue prevention and control, offering promise in addressing this pressing global health issue.
Collapse
Affiliation(s)
| | - Laura E Adams
- Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Jacqueline Deen
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines, Manila, Philippines
| | - Kathryn B Anderson
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Yang CR, Chang SY, Gong YN, Huang CG, Tung TH, Liu W, Chan TC, Hung KS, Shang HS, Tsai JJ, Kao CL, Wu HL, Daisy Liu LY, Lin WY, Fan YC, King CC, Ku CC. The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak. Heliyon 2023; 9:e22436. [PMID: 38107297 PMCID: PMC10724543 DOI: 10.1016/j.heliyon.2023.e22436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.
Collapse
Affiliation(s)
- Chin-Rur Yang
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
| | - Sui-Yuan Chang
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Dept. of Laboratory Medicine, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
| | - Chung-Guei Huang
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
- Dept. of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
| | - Tsung-Hua Tung
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
- Dept. of Health, Taipei City Government, Taipei, Taiwan, ROC
| | - Wei Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Ta-Chien Chan
- Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Dept. of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Jih-Jin Tsai
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
| | - Chuan-Liang Kao
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Hui-Lin Wu
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
| | - Li-Yu Daisy Liu
- Division of Biometry, Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Yi-Chin Fan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chia-Chi Ku
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
| |
Collapse
|
4
|
Rivera JA, Rengifo AC, Rosales-Munar A, Díaz-Herrera TH, Ciro JU, Parra E, Alvarez-Díaz DA, Laiton-Donato K, Caldas ML. Genotyping of dengue virus from infected tissue samples embedded in paraffin. Virol J 2023; 20:100. [PMID: 37231481 DOI: 10.1186/s12985-023-02072-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/14/2023] [Indexed: 05/27/2023] Open
Abstract
Dengue has become one of the vector-borne diseases that affect humans worldwide. In Latin American countries, Colombia is historically one of the most affected by epidemics of this flavivirus. The underreporting of signs and symptoms of probable cases of dengue, the lack of characterization of the serotypes of the infection, and the few detailed studies of postmortem necropsies of patients are among other conditions that have delayed progress in the knowledge of the pathogenesis of the disease. This study presents the results of fragment sequencing assays on paraffin-embedded tissue samples from fatal DENV cases during the 2010 epidemic in Colombia. We found that the predominant serotype was DENV-2, with the Asian/American genotype of lineages 1 and 2. This work is one of the few reports of the circulating genotypes of dengue during the 2010 epidemic in Colombia, one of the most lethal dates in the country's history.
Collapse
Grants
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
Collapse
Affiliation(s)
- Jorge Alonso Rivera
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - Aura Caterine Rengifo
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia.
| | - Alicia Rosales-Munar
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - Taylor H Díaz-Herrera
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - José Usme Ciro
- CIST-Centro de Investigaciones en Salud Para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, 47003, Colombia
| | - Edgar Parra
- Dirección de Redes en Salud Pública, Grupo de Patología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diego A Alvarez-Díaz
- Dirección de investigación en Salud Pública, Grupo de Genómica de Microorganismos Emergentes, Instituto Nacional de Salud, Bogotá, Colombia
| | - Katherine Laiton-Donato
- Dirección de investigación en Salud Pública, Grupo de Genómica de Microorganismos Emergentes, Instituto Nacional de Salud, Bogotá, Colombia
| | - María Leonor Caldas
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| |
Collapse
|
5
|
Márquez S, Lee G, Gutiérrez B, Bennett S, Coloma J, Eisenberg JNS, Trueba G. Phylogenetic Analysis of Transmission Dynamics of Dengue in Large and Small Population Centers, Northern Ecuador. Emerg Infect Dis 2023; 29:888-897. [PMID: 37080979 PMCID: PMC10124659 DOI: 10.3201/eid2905.221226] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Although dengue is typically considered an urban disease, rural communities are also at high risk. To clarify dynamics of dengue virus (DENV) transmission in settings with characteristics generally considered rural (e.g., lower population density, remoteness), we conducted a phylogenetic analysis in 6 communities in northwestern Ecuador. DENV RNA was detected by PCR in 121/488 serum samples collected from febrile case-patients during 2019-2021. Phylogenetic analysis of 27 samples from Ecuador and other countries in South America confirmed that DENV-1 circulated during May 2019-March 2020 and DENV-2 circulated during December 2020-July 2021. Combining locality and isolation dates, we found strong evidence that DENV entered Ecuador through the northern province of Esmeraldas. Phylogenetic patterns suggest that, within this province, communities with larger populations and commercial centers were more often the source of DENV but that smaller, remote communities also play a role in regional transmission dynamics.
Collapse
|
6
|
Hughes HR, Velez JO, Davis EH, Laven J, Gould CV, Panella AJ, Lambert AJ, Staples JE, Brault AC. Fatal Human Infection with Evidence of Intrahost Variation of Eastern Equine Encephalitis Virus, Alabama, USA, 2019. Emerg Infect Dis 2021; 27:1886-1892. [PMID: 34152960 PMCID: PMC8237905 DOI: 10.3201/eid2707.210315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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
Eastern equine encephalitis virus (EEEV) is an arbovirus in the family Togaviridae, genus Alphavirus, found in North America and associated with freshwater/hardwood swamps in the Atlantic, Gulf Coast, and Great Lakes regions. EEEV disease in humans is rare but causes substantial illness and death. To investigate the molecular epidemiology and microevolution of EEEV from a fatal case in Alabama, USA, in 2019, we used next-generation sequencing of serum and cerebrospinal fluid (CSF). Phylogenetic inference indicated that the infecting strain may be closely related to isolates from Florida detected during 2010-2014, suggesting potential seeding from Florida. EEEV detected in serum displayed a higher degree of variability with more single-nucleotide variants than that detected in the CSF. These data refine our knowledge of EEEV molecular epidemiologic dynamics in the Gulf Coast region and demonstrate potential quasispecies bottlenecking within the central nervous system of a human host.
Collapse
|
7
|
Wu T, Wu Z, Li YP. Dengue fever and dengue virus in the People's Republic of China. Rev Med Virol 2021; 32:e2245. [PMID: 34235802 DOI: 10.1002/rmv.2245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 01/05/2023]
Abstract
Infection with dengue virus (DENV) leads to symptoms variable from dengue fever to severe dengue, which has posed a huge socioeconomic and disease burden to the world population, particularly in tropical and subtropical regions. To date, four serotypes of DENV (DENV-1 to DENV-4) have been identified to sustain the transmission cycle in humans. In the past decades, dengue incidences have become more frequent, and four serotypes and various genotypes have been identified in PR China. Several large-scale dengue outbreaks and frequent local endemics occurred in the southern and coastal provinces, and the imported dengue cases accounted primarily for the initiation of the epidemics. No antiviral drug exists for dengue, and no vaccine has been approved to use in PR China, however strategies including public awareness, national reporting system of infectious diseases and public health emergencies, vector mosquito control, personal protection, and improved environmental sanitation have greatly reduced dengue prevalence. Some new technologies in vector mosquito control are emerging and being applied for dengue control. China's territory spans tropical, subtropical, and temperate climates, hence understanding the dengue status in China will be of beneficial for the global prevention and control of dengue. Here, we review the dengue status in PR China for the past decades and the strategies emerging for dengue control.
Collapse
Affiliation(s)
- Tiantian Wu
- Institute of Human Virology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
| |
Collapse
|
8
|
Fung CK, Li T, Pollett S, Alera MT, Yoon IK, Hang J, Macareo L, Srikiatkhachorn A, Ellison D, Rothman AL, Fernandez S, Jarman RG, Maljkovic Berry I. Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies. J Gen Virol 2021; 102:001553. [PMID: 33591246 PMCID: PMC8515859 DOI: 10.1099/jgv.0.001553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
Collapse
Affiliation(s)
| | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - In-Kyu Yoon
- Coalition for Epidemic Preparedness Innovations, Washington, DC, USA
| | - Jun Hang
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Louis Macareo
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of Rhode Island, Kingston, RI, USA
| | - Damon Ellison
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | |
Collapse
|
9
|
Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence. Nat Rev Microbiol 2021; 19:184-195. [PMID: 33432235 PMCID: PMC7798019 DOI: 10.1038/s41579-020-00482-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 01/31/2023]
Abstract
Transmission of arthropod-borne viruses (arboviruses) involves infection and replication in both arthropod vectors and vertebrate hosts. Nearly all arboviruses are RNA viruses with high mutation frequencies, which leaves them vulnerable to genetic drift and fitness losses owing to population bottlenecks during vector infection, dissemination from the midgut to the salivary glands and transmission to the vertebrate host. However, despite these bottlenecks, they seem to avoid fitness declines that can result from Muller's ratchet. In addition, founder effects that occur during the geographic introductions of human-amplified arboviruses, including chikungunya virus and Zika virus, can affect epidemic and endemic circulation, as well as virulence. In this Review, we discuss the role of genetic drift following population bottlenecks and founder effects in arboviral evolution and spread, and the emergence of human disease.
Collapse
|
10
|
Ho TS, Weng TC, Wang JD, Han HC, Cheng HC, Yang CC, Yu CH, Liu YJ, Hu CH, Huang CY, Chen MH, King CC, Oyang YJ, Liu CC. Comparing machine learning with case-control models to identify confirmed dengue cases. PLoS Negl Trop Dis 2020; 14:e0008843. [PMID: 33170848 PMCID: PMC7654779 DOI: 10.1371/journal.pntd.0008843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 10/01/2020] [Indexed: 01/10/2023] Open
Abstract
In recent decades, the global incidence of dengue has increased. Affected countries have responded with more effective surveillance strategies to detect outbreaks early, monitor the trends, and implement prevention and control measures. We have applied newly developed machine learning approaches to identify laboratory-confirmed dengue cases from 4,894 emergency department patients with dengue-like illness (DLI) who received laboratory tests. Among them, 60.11% (2942 cases) were confirmed to have dengue. Using just four input variables [age, body temperature, white blood cells counts (WBCs) and platelets], not only the state-of-the-art deep neural network (DNN) prediction models but also the conventional decision tree (DT) and logistic regression (LR) models delivered performances with receiver operating characteristic (ROC) curves areas under curves (AUCs) of the ranging from 83.75% to 85.87% [for DT, DNN and LR: 84.60% ± 0.03%, 85.87% ± 0.54%, 83.75% ± 0.17%, respectively]. Subgroup analyses found all the models were very sensitive particularly in the pre-epidemic period. Pre-peak sensitivities (<35 weeks) were 92.6%, 92.9%, and 93.1% in DT, DNN, and LR respectively. Adjusted odds ratios examined with LR for low WBCs [≤ 3.2 (x103/μL)], fever (≥38°C), low platelet counts [< 100 (x103/μL)], and elderly (≥ 65 years) were 5.17 [95% confidence interval (CI): 3.96-6.76], 3.17 [95%CI: 2.74-3.66], 3.10 [95%CI: 2.44-3.94], and 1.77 [95%CI: 1.50-2.10], respectively. Our prediction models can readily be used in resource-poor countries where viral/serologic tests are inconvenient and can also be applied for real-time syndromic surveillance to monitor trends of dengue cases and even be integrated with mosquito/environment surveillance for early warning and immediate prevention/control measures. In other words, a local community hospital/clinic with an instrument of complete blood counts (including platelets) can provide a sentinel screening during outbreaks. In conclusion, the machine learning approach can facilitate medical and public health efforts to minimize the health threat of dengue epidemics. However, laboratory confirmation remains the primary goal of surveillance and outbreak investigation.
Collapse
Affiliation(s)
- Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Ting-Chia Weng
- Department of Occupational and Environmental Medicine, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China
- Department of Family Medicine, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China
| | - Jung-Der Wang
- Department of Occupational and Environmental Medicine, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Department of Public Heath, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Hsieh-Cheng Han
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Hao-Chien Cheng
- Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering & Computer Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chun-Chieh Yang
- Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering & Computer Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chih-Hen Yu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Yen-Jung Liu
- Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering & Computer Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chien Hsiang Hu
- Department of Medical Informatics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Chun-Yu Huang
- Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering & Computer Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Ming-Hong Chen
- Department of Medical Informatics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yen-Jen Oyang
- Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering & Computer Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan, Republic of China
| |
Collapse
|
11
|
Christofferson RC, Parker DM, Overgaard HJ, Hii J, Devine G, Wilcox BA, Nam VS, Abubakar S, Boyer S, Boonnak K, Whitehead SS, Huy R, Rithea L, Sochantha T, Wellems TE, Valenzuela JG, Manning JE. Current vector research challenges in the greater Mekong subregion for dengue, Malaria, and Other Vector-Borne Diseases: A report from a multisectoral workshop March 2019. PLoS Negl Trop Dis 2020; 14:e0008302. [PMID: 32730249 PMCID: PMC7392215 DOI: 10.1371/journal.pntd.0008302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Rebecca C. Christofferson
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Daniel M. Parker
- University of California, Irvine, California, United States of America
| | | | | | - Gregor Devine
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Bruce A. Wilcox
- ASEAN Institute for Health Development, Mahidol University, Nakhon Pathom, Thailand
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Sazaly Abubakar
- Tropical Infectious Diseases Research and Education Center, Kuala Lumpur, Malaysia
| | | | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stephen S. Whitehead
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Rekol Huy
- National Center for Parasitology Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Leang Rithea
- National Center for Parasitology Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Tho Sochantha
- National Center for Parasitology Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Jesus G. Valenzuela
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Jessica E. Manning
- US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| |
Collapse
|
12
|
Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
Collapse
Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| |
Collapse
|
13
|
Syenina A, Vijaykrishna D, Gan ES, Tan HC, Choy MM, Siriphanitchakorn T, Cheng C, Vasudevan SG, Ooi EE. Positive epistasis between viral polymerase and the 3' untranslated region of its genome reveals the epidemiologic fitness of dengue virus. Proc Natl Acad Sci U S A 2020; 117:11038-11047. [PMID: 32366663 PMCID: PMC7245076 DOI: 10.1073/pnas.1919287117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. While low herd immunity levels to any one of the four antigenic types of DENV predispose populations to outbreaks, viral genetic determinants that confer greater fitness for epidemic spread is an important but poorly understood contributor of dengue outbreaks. Here we report that positive epistasis between the coding and noncoding regions of the viral genome combined to elicit an epidemiologic fitness phenotype associated with the 1994 DENV2 outbreak in Puerto Rico. We found that five amino acid substitutions in the NS5 protein reduced viral genomic RNA (gRNA) replication rate to achieve a more favorable and relatively more abundant subgenomic flavivirus RNA (sfRNA), a byproduct of host 5'-3' exoribonuclease activity. The resulting increase in sfRNA relative to gRNA levels not only inhibited type I interferon (IFN) expression in infected cells through a previously described mechanism, but also enabled sfRNA to compete with gRNA for packaging into infectious particles. We suggest that delivery of sfRNA to new susceptible cells to inhibit type I IFN induction before gRNA replication and without the need for further de novo sfRNA synthesis could form a "preemptive strike" strategy against DENV.
Collapse
Affiliation(s)
- Ayesa Syenina
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
| | - Dhanasekaran Vijaykrishna
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Esther Shuyi Gan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Milly M Choy
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Tanamas Siriphanitchakorn
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Department of Biological Sciences, National University of Singapore, 117558 Singapore
| | - Colin Cheng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore;
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
- SingHealth Duke-National University of Singapore Global Health Institute, 169857 Singapore
| |
Collapse
|
14
|
Zhou Y, Chen D, Yang L, Zou W, Duan Z, Zhang Y, Wen J. Dengue virus envelope protein domain III-elicited antibodies mediate cross-protection against Zika virus in a mouse model. Virus Res 2020; 278:197882. [DOI: 10.1016/j.virusres.2020.197882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 01/01/2020] [Accepted: 01/21/2020] [Indexed: 12/22/2022]
|
15
|
Liao F, Chen H, Xie J, Zhan S, Pan P, Lao Z, Fan Y, Lin L, Lai Y, Lin S, Wu J, Liu X, Li G. Molecular epidemiological characteristics of dengue virus carried by 34 patients in Guangzhou in 2018. PLoS One 2019; 14:e0224676. [PMID: 31725752 PMCID: PMC6855448 DOI: 10.1371/journal.pone.0224676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/19/2019] [Indexed: 11/18/2022] Open
Abstract
Dengue fever is a major worldwide public health problem that, as estimated by the WHO, causes epidemics in over 100 countries, resulting in hundreds of millions of dengue virus (DENV) infections every year. In China, dengue fever mainly occurs in coastal areas. Recurring dengue outbreaks were reported by Guangdong Province almost every year since the first epidemic in 1978. DENV infections persisted in Guangzhou in consecutive years since 2000, with the dengue epidemic reaching a historical peak in 2014. Because Guangzhou is one of the largest cities for opening up in China, understanding the epidemiological characteristics of dengue fever in the city can hopefully provide a significant basis for developing effective dengue prevention strategies. In this study, a total of 34 DENV strains, including 29 DENV-1 strains and 5 DENV-2 strains, were isolated from a blood samples drawn from patients who were diagnosed with dengue fever by hospitals in Guangzhou during 2018. To explore the epidemiological characteristics of dengue fever, the envelope (E) gene obtained from the isolates was amplified for phylogenetic analysis. The results from the phylogenetic analysis showed that DENV in Guangzhou was mainly imported from Southeast Asian countries. Additionally, propagation paths based on phylogeographical analysis suggested potential local dengue transmission in Guangzhou.
Collapse
Affiliation(s)
- Feng Liao
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huini Chen
- Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jieliang Xie
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Pan Pan
- College of Life Sciences, WuHan university, Wuhan, China
| | - Zizhao Lao
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaohua Fan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lupin Lin
- Guangzhou eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yanni Lai
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuangfeng Lin
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianguo Wu
- Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xiaohong Liu
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- * E-mail:
| |
Collapse
|