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

The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV...

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Published in:	BMC genomics Vol. 25; no. 1; pp. 998 - 12
Main Authors:	Napit, Rajindra, Elong Ngono, Annie, Mihindukulasuriya, Kathie A, Pradhan, Aunji, Khadka, Binod, Shrestha, Smita, Droit, Lindsay, Paredes, Anne, Karki, Lata, Khatiwada, Rabindra, Tamang, Mamata, Chalise, Bimal Sharma, Rawal, Manisha, Jha, Bimalesh Kumar, Wang, David, Handley, Scott A, Shresta, Sujan, Manandhar, Krishna Das
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 24-10-2024 BioMed Central BMC
Subjects:	Adult Analysis Antigens Benchmarks Bioinformatics Blood Capacity building Climatic changes Dengue Dengue - epidemiology Dengue - virology Dengue fever Dengue outbreak Dengue virus Dengue Virus - classification Dengue Virus - genetics Dengue Virus - isolation & purification Dengue viruses Disease Outbreaks Disease transmission DNA sequencing Drug development Enrollments Epidemics Female Gene sequencing Genetic aspects Genome, Viral Genomes Genomic surveillance Genomics Genotype & phenotype Health aspects Humans Immunoglobulin M Infections Infectious diseases Male Nepal - epidemiology Nucleotide sequence Nucleotide sequencing Onsite Phylogeny Prevention Risk factors Serogroup Serotypes Surveillance Vector-borne diseases Whole genome sequencing Whole Genome Sequencing - methods Nepal United States China India United States > US Genomic surveillance Capacity building Dengue outbreak Dengue virus Whole genome sequencing
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Summary:	The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1471-2164 1471-2164
DOI:	10.1186/s12864-024-10879-x