DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus

• Published in: BMC genomics Vol. 25; no. 1; p. 433
• Main Authors: Vogels, Chantal B F, Hill, Verity, Breban, Mallery I, Chaguza, Chrispin, Paul, Lauren M, Sodeinde, Afeez, Taylor-Salmon, Emma, Ott, Isabel M, Petrone, Mary E, Dijk, Dennis, Jonges, Marcel, Welkers, Matthijs R A, Locksmith, Timothy, Dong, Yibo, Tarigopula, Namratha, Tekin, Omer, Schmedes, Sarah, Bunch, Sylvia, Cano, Natalia, Jaber, Rayah, Panzera, Charles, Stryker, Ian, Vergara, Julieta, Zimler, Rebecca, Kopp, Edgar, Heberlein, Lea, Herzog, Kaylee S, Fauver, Joseph R, Morrison, Andrea M, Michael, Scott F, Grubaugh, Nathan D
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 01.05.2024; BioMed Central; BMC
• Subjects: Amplicon sequencing; Biological diversity; COVID-19; Dengue - diagnosis; Dengue - virology; Dengue fever; Dengue virus; Dengue Virus - classification; Dengue Virus - genetics; Dengue Virus - isolation & purification; Dengue viruses; Design; DNA sequencing; Gene sequencing; Genetic aspects; Genetic diversity; Genetic variation; Genome, Viral; Genomes; Genomic surveillance; Genomics; Genotype; Genotypes; High-Throughput Nucleotide Sequencing - methods; Human diseases; Humans; Next-generation sequencing; Nucleotide sequencing; Public health; RNA; RNA, Viral - genetics; Sequencing; Serogroup; Serotypes; Surveillance; Testing; Vector-borne diseases; Viruses; Whole genome sequencing; Whole Genome Sequencing - methods; Genomic surveillance; Next-generation sequencing; Dengue virus; Whole-genome sequencing; Amplicon sequencing
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10350-x

The 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 of all four dengue virus serotypes. We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.