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Rodríguez-Aguilar ED, Gutiérrez-Millán E, Rodríguez MH. Accurate Recapitulation of Chikungunya Virus Complete Coding Sequence Phylogeny Using Variable Genome Regions for Genomic Surveillance. Viruses 2024; 16:926. [PMID: 38932218 PMCID: PMC11209212 DOI: 10.3390/v16060926] [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: 05/03/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Chikungunya virus (CHIKV) is transmitted by mosquito bites and causes chikungunya fever (CHIKF). CHIKV has a single-stranded RNA genome and belongs to a single serotype with three genotypes. The Asian lineage has recently emerged in the Western Hemisphere, likely due to travel-associated introduction. Genetic variation accumulates in the CHIKV genome as the virus replicates, creating new lineages. Whole genome sequencing is ideal for studying virus evolution and spread but is expensive and complex. This study investigated whether specific, highly variable regions of the CHIKV genome could recapitulate the phylogeny obtained with a complete coding sequence (CDS). Our results revealed that concatenated highly variable regions accurately reconstructed CHIKV phylogeny, exhibiting statistically indistinguishable branch lengths and tree confidence compared to CDS. In addition, these regions adequately inferred the evolutionary relationships among CHIKV isolates from the American outbreak with similar results to the CDS. This finding suggests that highly variable regions can effectively capture the evolutionary relationships among CHIKV isolates, offering a simpler approach for future studies. This approach could be particularly valuable for large-scale surveillance efforts.
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Affiliation(s)
| | | | - Mario H. Rodríguez
- Center for Infectious Disease Research, National Institute of Public Health of Mexico, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (E.G.-M.)
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2
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Bukhari MH, Shad MY, Nguyen USDT, Treviño C JA, Jung W, Bajwa WU, Gallego-Hernández AL, Robinson R, Corral-Frías NS, Hamer GL, Wang P, Annan E, Ra CK, Keellings D, Haque U. A Bayesian spatiotemporal approach to modelling arboviral diseases in Mexico. Trans R Soc Trop Med Hyg 2023; 117:867-874. [PMID: 37681342 DOI: 10.1093/trstmh/trad064] [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: 12/13/2022] [Revised: 07/23/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND The objective of this study was to evaluate the spatial and temporal patterns of disease prevalence clusters of dengue (DENV), chikungunya (CHIKV) and Zika (ZIKV) virus and how socio-economic and climatic variables simultaneously influence the risk and rate of occurrence of infection in Mexico. METHODS To determine the spatiotemporal clustering and the effect of climatic and socio-economic covariates on the rate of occurrence of disease and risk in Mexico, we applied correlation methods, seasonal and trend decomposition using locally estimated scatterplot smoothing, hotspot analysis and conditional autoregressive Bayesian models. RESULTS We found cases of the disease are decreasing and a significant association between DENV, CHIKV and ZIKV cases and climatic and socio-economic variables. An increment of cases was identified in the northeastern, central west and southeastern regions of Mexico. Climatic and socio-economic covariates were significantly associated with the rate of occurrence and risk of the three arboviral disease cases. CONCLUSION The association of climatic and socio-economic factors is predominant in the northeastern, central west and southeastern regions of Mexico. DENV, CHIKV and ZIKV cases showed an increased risk in several states in these regions and need urgent attention to allocate public health resources to the most vulnerable regions in Mexico.
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Affiliation(s)
| | - Muhammad Yousaf Shad
- Department of Statistics, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Mathematics, Namal University, Talagang Road, Mianwali 42250, Pakistan
| | - Uyen-Sa D T Nguyen
- Department of Biostatistics and Epidemiology, University of North Texas Health Science Centre, Fort Worth, TX 76107, USA
| | - Jesús A Treviño C
- Department of Urban Affairs, School of Architecture, Universidad Autónoma de NUevo León ÚV. Universidad s/n, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, Mexico
| | - Woojin Jung
- School of Social Work, Rutgers University, New Brunswick, NJ, USA
| | - Waheed U Bajwa
- Department of Electrical and Computer Engineering, Department of Statistics, Rutgers University, New Brunswick, NJ 08854, USA
| | | | - Renee Robinson
- College of Pharmacy, Idaho State University, Pocatello, Idaho 83209, USA
| | | | - Gabriel L Hamer
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Penghua Wang
- Department of Immunology, School of Medicine, U Conn Health, Room L3057, Farmington CT 06030, USA
| | - Esther Annan
- Center for Health and Well-being, School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Chaelin K Ra
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - David Keellings
- Department of Geography, University of Florida, Gainesville, FL 32611, USA
| | - Ubydul Haque
- Department of Biostatistics and Epidemiology and Rutgers Global Health Institute, School of Public Health, Rutgers University, Piscataway, NJ, USA
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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Rodríguez-Aguilar ED, Martínez-Barnetche J, González-Bonilla CR, Tellez-Sosa JM, Argotte-Ramos R, Rodríguez MH. Genetic Diversity and Spatiotemporal Dynamics of Chikungunya Infections in Mexico during the Outbreak of 2014-2016. Viruses 2021; 14:v14010070. [PMID: 35062275 PMCID: PMC8779743 DOI: 10.3390/v14010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022] Open
Abstract
Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes, which causes Chikungunya fever. Three CHIKV genotypes have been identified: West African, East-Central-South African and Asian. In 2014, CHIKV was detected for the first time in Mexico, accumulating 13,569 confirmed cases in the following three years. Studies on the molecular diversification of CHIKV in Mexico focused on limited geographic regions or investigated only one structural gene of the virus. To describe the dynamics of this outbreak, we analyzed 309 serum samples from CHIKV acute clinical cases from 15 Mexican states. Partial NSP3, E1, and E2 genes were sequenced, mutations were identified, and their genetic variability was estimated. The evolutionary relationship with CHIKV sequences sampled globally were analyzed. Our sequences grouped with the Asian genotype within the Caribbean lineage, suggesting that the Asian was the only circulating genotype during the outbreak. Three non-synonymous mutations (E2 S248F and NSP3 A437T and L451F) were present in our sequences, which were also identified in sequences of the Caribbean lineage and in one Philippine sequence. Based on the phylogeographic analysis, the viral spread was reconstructed, suggesting that after the introduction through the Mexican southern border (Chiapas), CHIKV dispersed to neighboring states before reaching the center and north of the country through the Pacific Ocean states and Quintana Roo. This is the first viral phylogeographic reconstruction in Mexico characterizing the CHIKV outbreak across the country.
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Affiliation(s)
- Eduardo D. Rodríguez-Aguilar
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (J.M.-B.); (J.M.T.-S.); (R.A.-R.)
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (J.M.-B.); (J.M.T.-S.); (R.A.-R.)
| | | | - Juan M. Tellez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (J.M.-B.); (J.M.T.-S.); (R.A.-R.)
| | - Rocío Argotte-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (J.M.-B.); (J.M.T.-S.); (R.A.-R.)
| | - Mario H. Rodríguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (J.M.-B.); (J.M.T.-S.); (R.A.-R.)
- Correspondence: ; Tel.: +52-1-777-3293087 (ext. 1109)
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Chaudhary S, Jain J, Kumar R, Shrinet J, Weaver SC, Auguste AJ, Sunil S. Chikungunya virus molecular evolution in India since its re-emergence in 2005. Virus Evol 2021; 7:veab074. [PMID: 34754512 PMCID: PMC8570154 DOI: 10.1093/ve/veab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005-20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.
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Affiliation(s)
| | - Jaspreet Jain
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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6
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Torres-Longoria B, Fragoso-Fonseca DE, Núñez-León A, de la Luz Torres M, Vázquez-Pichardo M, Escobar-Escamilla N, Wong-Arámbula C, Ramírez-González JE, Méndez-Tenorio A, Castro-Mussot ME, Moreno-Altamirano MMB, Membrillo-Hernández J, López-Martínez I, Díaz-Quiñónez JA. Epidemiological surveillance of chikungunya fever in Mexico since its introduction in 2014-2016 and identification of circulating genotypes. Mol Biol Rep 2021; 48:1967-1975. [PMID: 33523371 DOI: 10.1007/s11033-021-06151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/12/2021] [Indexed: 11/28/2022]
Abstract
In 2014, the chikungunya virus (CHIKV) was detected for the first time in Mexico, the identified strain was the one corresponding to the Asian genotype which was phylogenetically grouped with the strains that circulated in the British Virgin Islands outbreak and was later classified with lineages of Caribbean strains. In three years, 13,569 cases of chikungunya were registered in Mexico. Although the transmission and spread of the virus are now considered a moderate risk, the danger that the virus reemerges is not ruled out due to the infestation of Aedes mosquitoes. In this study, we reviewed the chikungunya fever (CHIKF) cases reported between 2014 and 2016 to reanalyze the data. Seventeen cases were selected from different states where the circulation of the virus had been reported. Statistical data were analyzed and a retrospective analysis was carried out. Nucleic acid sequences were determined of these 17 samples. 2015 was the year with the highest number of cases (92.8%) and they were detected in 28 states of the country. There is a predominance of females, and the most affected age group was between 25 and 44 years. In 2016, CHIKV genotypes were not known, in this study the presence of the Asian genotype of Caribbean lineage was confirmed. The presence of the West African and ECSA genotypes was phylogenetically ruled out. The sequences obtained were deposited in GeneBank.
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Affiliation(s)
- Belem Torres-Longoria
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.,Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - David Esaú Fragoso-Fonseca
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Alma Núñez-León
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - María de la Luz Torres
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Mauricio Vázquez-Pichardo
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Noé Escobar-Escamilla
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María Eugenia Castro-Mussot
- Laboratorio de Inmunología Celular e Inmunopatogénesis, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - María M B Moreno-Altamirano
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - Irma López-Martínez
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - José Alberto Díaz-Quiñónez
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Two distinct lineages of chikungunya virus cocirculated in Aruba during the 2014-2015 epidemic. INFECTION GENETICS AND EVOLUTION 2019; 78:104129. [PMID: 31786339 DOI: 10.1016/j.meegid.2019.104129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
Abstract
Chikungunya virus (CHIKV), a positive-sense, single-stranded RNA virus in the family Togaviridae, is transmitted by Aedes mosquitoes. Of three known CHIKV genotypes, the Asian genotype was introduced into the Caribbean islands and rapidly spread throughout Central and South Americas. We previously found patients with symptoms compatible with chikungunya fever in 2014-2015 in Aruba, a Caribbean island of 180 km2. We here describe the full genome sequences of eight CHIKV strains isolated from patient sera of the Aruban outbreak. Phylogenetic analysis revealed that two closely related but distinct lineages of Asian-genotype CHIKV circulated simultaneously during the epidemic in 2014-2015. These results suggested that CHIKV was introduced into Aruba more than once in a short period, reflecting the importance of Aruba as a travel hub within the region.
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