Dengue dynamics in Bali: Serotype shifts, genotype replacement and multiple virus lineage circulation in the last 10 years.

Abstract

Background: Bali, one of the world's most popular tourist destinations, is hyper-endemic to dengue, an acute febrile illness caused by infection with dengue virus (DENV). Outbreaks of dengue occur annually with worrisome rates of morbidity and mortality. Despite this, comprehensive and continuous virus surveillance is yet to be established. We conducted DENV serotype and genotype surveillance in Bali to monitor viral transmission dynamics.

Methods: We enrolled febrile patients with dengue clinical symptoms in hospitals in Denpasar, Bali. Clinical evaluations and laboratory assessments were conducted, and blood samples were collected. DENV serotypes were determined using RT-PCR, and genotyping was performed by sequencing the envelope protein gene and the complete genomes. Subsequently, phylogenetic analyses were conducted to analyse the recent data alongside retrospective sequence data.

Results: A total of 62 and 66 dengue patients were recruited during 2018-2020 and 2022, and from these, we obtained DENV serotype data for 49 and 48 individuals, respectively. Among the DENV analysed, the most prevalent serotype in 2018-2020 was DENV-1 (30%) and shifted to DENV-3 (57.6%) in 2022. When compared to data from the last 10 years, serotype shifting was clearly observed. We sequenced the genomes of 60 isolates and observed the presence of multiple virus lineages and the replacement of Genotype IV of DENV-1 with Genotype I. The Cosmopolitan, Genotype I and Genotype II remained the predominant genotypes for DENV-2, DENV-3 and DENV-4, respectively.

Conclusion: We reveal that DENV serotype predominance in Bali has been shifting in the past 10 years. While genotype replacement occurred, continuous circulation of local endemic viruses was responsible for the annual outbreak of dengue. These findings indicate the genetic diversity and dynamic nature of DENV circulating in Bali. Routine virus surveillance is important to understand the cyclical patterns of DENV serotypes that is useful to predict the future outbreaks.