Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak

• DOI: 10.1186/s12864-024-10879-x
• Publication Date: 2024-10-24T13:02:53Z
• Authors: Rajindra Napit; Annie Elong Ngono; Kathie A. Mihindu...; Aunji Pradhan; Binod Khadka; Smita Shrestha; Lindsay Droit; Anne Paredes; Lata Karki; Rabindra Khatiwada; Mamata Tamang; Bimal Sharma Chalise; Manisha Rawal; Bimalesh Kumar Jha; David Wang; Scott A. Handley; Sujan Shresta; Krishna Das Manan...
• Keywords: Male; Adult; Whole Genome Sequencing; Research; Capacity building; Dengue outbreak; Genome, Viral; QH426-470; Dengue Virus; Serogroup; Dengue virus; Disease Outbreaks; Dengue; Nepal; Whole genome sequencing; Genomic surveillance; Genetics; Humans; Female; TP248.13-248.65; Phylogeny; Biotechnology

Abstract Background The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly disease, and are spreading globally from tropical subtropical areas to more temperate ones. Nepal provides a microcosm this global phenomenon, having met these grim benchmarks. To better understand DENV transmission dynamics spread into new areas, we chose study in and, so doing, build the onsite infrastructure needed manage future, larger studies. Methods results During 2022 season, enrolled 384 patients presenting at hospital Kathmandu with dengue-like symptoms; 79% participants had active or recent infection (NS1 antigen IgM). identify circulating serotypes, screened serum 50 NS1 + by RT-PCR identified DENV1, 2, 3 – DENV1 codominant. We also performed whole-genome sequencing DENV, for first time Nepal, using our on-site capacity. Sequencing analysis demonstrated genomes clustered sequences reported India 2019, DENV2 genome sequence China 2018. Conclusion These findings highlight DENV’s geographic expansion neighboring countries, as likely origin cases demonstrate feasibility building capacity rapid genomic surveillance DENV. ongoing efforts promise protect populations beyond informing development deployment drugs vaccines real time.