ArticlePLoS neglected tropical diseases2019
Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples.
Article in PLoS neglected tropical diseases, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 27 citations in OpenAlex.
- Tick-borne viruses: discovery, clinical aspects, influencing factors and control.Nature reviews. Microbiology · 2026Review
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- OLTA: Optimizing bait seLection for TArgeted sequencing.Bioinformatics (Oxford, England) · 2025Article
- Dengue: A review of laboratory diagnostics in the vaccine age.Journal of medical microbiology · 2024Review
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Detecting the impacts of humidity, rainfall, temperature, and season on chikungunya, dengue and Zika viruses in Aedes albopictus mosquitoes from selected sites in Cebu city, Philippines.Virology journal · 2024Article
- Genomic sequencing and neutralizing serological profiles during acute dengue infection: A 2017 cohort study in Nepal.PLOS global public health · 2024Article
- Advancing pathogen genomics in resource-limited settings.Cell genomics · 2023Review
- Genotypic Characterization ofTransboundary and emerging diseases · 2023Article
- Article
- Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.Virology journal · 2020Article
- Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches.The Journal of general virology · 2019Article
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Authors and funding
16 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The frequency of epidemics caused by Dengue viruses 1-4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009-2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% ± 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses.
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