2023
DOI: 10.1101/2023.10.13.23296997
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DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus

Chantal B.F. Vogels,
Verity Hill,
Mallery I. Breban
et al.

Abstract: BackgroundThe increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing o… Show more

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Cited by 4 publications
(4 citation statements)
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“…This benchmark dataset, designed primarily for SARS-CoV-2, presents a flexible model suitable for various pathogens. The increasing use of multiplexed amplicon sequencing in pathogen surveillance, including Dengue [36], Mpox [37], and Plasmodium falciparum drug resistance and analysis of vaccine targets [38], underscores its importance. Our findings reveal a complex interplay of variables in the sequencing process, highlighting the need for meticulous quality assurance.…”
Section: Resultsmentioning
confidence: 99%
“…This benchmark dataset, designed primarily for SARS-CoV-2, presents a flexible model suitable for various pathogens. The increasing use of multiplexed amplicon sequencing in pathogen surveillance, including Dengue [36], Mpox [37], and Plasmodium falciparum drug resistance and analysis of vaccine targets [38], underscores its importance. Our findings reveal a complex interplay of variables in the sequencing process, highlighting the need for meticulous quality assurance.…”
Section: Resultsmentioning
confidence: 99%
“…Further, much of the existing research uses genotypes to characterize circulating variants (e.g. (S. C. , ensure adequate genomic diversity for sequencing panels (Santiago et al 2013;Vogels et al 2024), identify new introductions leading to outbreaks (Ma et al 2021), explore differences in viral fitness, and disease association (Cologna, Armstrong, and Rico-Hesse 2005). However, there has been a huge increase in publicly available sequence data, both in terms of number and regions from which samples are being sequenced, since these genotype classification systems were established.…”
Section: Resultsmentioning
confidence: 99%
“…Clinical specimens from Vietnam were sampled mostly from Southern Vietnam between 2010 and 2023. They were sequenced at the Yale School of Public Health using the recently developed amplicon sequencing DengueSeq protocol (Vogels et al 2024). Libraries were prepared using the Illumina COVIDSeq test (RUO version) with the pan-serotype primer pools, and sequenced on the Illumina NovaSeq 6000 or X Plus (paired-end 150) at the Yale Center for Genome Analysis.…”
Section: Case Studiesmentioning
confidence: 99%
“…The resulting DNA amplicons were purified using AMPure XP beads (Beckman Coulter, Brea, USA). Library preparation of the purified amplicons was conducted using the COVIDseq Kit (Illumina, San Diego, USA) which was originally designed for SARS-CoV-2 genomic research but has been adapted for other viruses (11, 12, 13). The subsequent sequencing process was carried out utilizing the Illumina MiSeq platform (Illumina, San Diego, USA), adhering closely to the manufacturer’s recommended protocols.…”
Section: Methodsmentioning
confidence: 99%