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Development of a Standardized Sanger-Based Method for Partial Sequencing and Genotyping of Dengue Viruses
- Source :
- Journal of Clinical Microbiology. 57
- Publication Year :
- 2019
- Publisher :
- American Society for Microbiology, 2019.
-
Abstract
- The global expansion of dengue viruses (DENV-1 to DENV-4) has contributed to the divergence, transmission, and establishment of genetic lineages of epidemiological concern; however, tracking the phylogenetic relationships of these virus is not always possible due to the inability of standardized sequencing procedures in resource-limited public health laboratories. Consequently, public genomic data banks contain inadequate representation of geographical regions and historical periods. In order to improve detection of the DENV-1 to DENV-4 lineages, we report the development of a serotype-specific Sanger-based method standardized to sequence DENV-1 to DENV-4 directly from clinical samples using universal primers that detect most DENV genotypes. The resulting envelope protein coding sequences are analyzed for genotyping with phylogenetic methods. We evaluated the performance of this method by detecting, amplifying, and sequencing 54 contemporary DENV isolates, including 29 clinical samples, representing a variety of genotypes of epidemiological importance and global presence. All specimens were sequenced successfully and phylogenetic reconstructions resulted in the expected genotype classification. To further improve genomic surveillance in regions where dengue is endemic, this method was transferred to 16 public health laboratories in 13 Latin American countries, to date. Our objective is to provide an accessible method that facilitates the integration of genomics with dengue surveillance.
- Subjects :
- 0301 basic medicine
Microbiology (medical)
Genotype
Genotyping Techniques
viruses
030106 microbiology
Genomics
Genome, Viral
Computational biology
Biology
Dengue virus
Serogroup
medicine.disease_cause
Genome
DNA sequencing
Dengue fever
Dengue
03 medical and health sciences
Viral Envelope Proteins
Virology
medicine
Humans
Genotyping
Phylogeny
Molecular epidemiology
Phylogenetic tree
virus diseases
Sequence Analysis, DNA
Dengue Virus
medicine.disease
030104 developmental biology
RNA, Viral
Subjects
Details
- ISSN :
- 1098660X and 00951137
- Volume :
- 57
- Database :
- OpenAIRE
- Journal :
- Journal of Clinical Microbiology
- Accession number :
- edsair.doi.dedup.....011e6eb5ac752955f0c8b513b6a199c1
- Full Text :
- https://doi.org/10.1128/jcm.01957-18