A-Z Index × Submit A-Z Index × Submit A-Z Index Search Dropdown × Submit Facebook Twitter LinkedIn Syndicate Emerging Infectious Disease journal ISSN: 1080-6059 Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
We report the detection and genomic characterization of chikungunya virus, an arbovirus, during a 2025 outbreak in Bolivia. We identified the circulating chikungunya virus lineage and the transmission dynamics by using genomic surveillance and phylogenetic analyses. Our findings highlight the utility of sustained genomic surveillance for monitoring emerging arboviruses.
Chikungunya virus (CHIKV) is a positive-sense RNA virus, belonging to the genus Alphavirus (family Togaviridae), primarily transmitted by Aedes aegypti and A. albopictus mosquitoes. CHIKV is comprised of 3 major lineages: West African, Asian, and East/Central/South African (ECSA). The Asian lineage was introduced into the Americas in 2013, and the ECSA lineage was introduced in 2014. Those introductions gave rise to the Asian-American and ECSA-American sublineages ( 1 ). Chikungunya infection is typically characterized by acute febrile illness with polyarthralgia, although severe manifestations, including neurologic complications, can occur ( 1 ). Globally, CHIKV has expanded greatly, with an estimated 16.9 million cases annually and >5.6 billion persons living in at-risk areas ( 1 ). The Asian-American lineage was first detected in Bolivia in 2015, followed by outbreaks in 2016 and 2017 ( 2 ). In 2025, a major CHIKV outbreak took place in Bolivia after several years without any reported cases. That outbreak included 4,696 confirmed cases, and most cases (90.8%) were in Santa Cruz ( 3 ). This resurgence highlights the vulnerability of previously affected regions to new CHIKV outbreaks and underscores the need for sustained surveillance.
Figure 1 . Geographic distribution of sequenced chikungunya virus genomes in a study of chikungunya virus in Bolivia, 2025. Colors indicate the numeric range of genomes per department.
This work is part of the routine arbovirus genomic surveillance implemented in Bolivia. Samples used in this study were obtained anonymously from material exceeding routine arbovirus diagnostics within Bolivia’s public health laboratory network. To investigate the origin and transmission dynamics of the 2025 outbreak, we implemented genomic surveillance of CHIKV in Bolivia. We selected 78 quantitative reverse transcription PCR–positive samples (cycle threshold [Ct] < 30), collected from February–June 2025 from 4 departments (Chuquisaca, Cochabamba, Santa Cruz, and Tarija) for our analysis on the basis of Ct value and available metadata ( Figure 1 ).
We used a multiplex PCR approach to amplify CHIKV RNA ( 4 ), and we sequenced CHIKV by using Illumina (Illumina, https://www.illumina.com ) and Oxford Nanopore (Oxford Nanopore, https://nanoporetech.com ) platforms. We generated consensus genomes by using combined de novo and reference-based approaches ( 5 ). We conducted a phylogenetic analysis by using genomes from the 78 selected samples together with the 972 publicly available ECSA sequences from the National Center for Biotechnology Information database, which included complete sequences, sampling date, and geographic origin. We performed multiple sequence alignment by using MAFFT ( 6 ), and we inferred maximum-likelihood p…