An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia

• Published in: PLoS neglected tropical diseases 2020-12, Vol.14 (12), p.e0008934-e0008934
• Main Authors: Stubbs, Samuel C B, Johar, Edison, Yudhaputri, Frilasita A, Yohan, Benediktus, Santoso, Marsha S, Hayati, Rahma F, Denis, Dionisius, Blacklaws, Barbara A, Powers, Ann M, Sasmono, R Tedjo, Myint, Khin Saw Aye, Frost, Simon D W
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Annual reports; Biology and life sciences; Chikungunya fever; Chikungunya Fever - epidemiology; Chikungunya Fever - virology; Chikungunya virus; Chikungunya virus - genetics; Chikungunya virus - immunology; Child; Child, Preschool; Computer and Information Sciences; Dengue; Dengue fever; Disease Outbreaks; Distribution; DNA; Epidemics; Epidemiology; Female; Genomes; Genotype & phenotype; Human diseases; Humans; Indonesia - epidemiology; Infant; Male; Management; Medical research; Medicine and Health Sciences; Medicine, Experimental; Middle Aged; Mosquitoes; Nucleic acids; Nucleotide sequence; Outbreaks; PCR; People and Places; Phylogenetics; Phylogeny; Polymerase chain reaction; Prevalence studies (Epidemiology); Research and Analysis Methods; Ribonucleic acid; RNA; RNA, Viral - genetics; Seroepidemiologic Studies; Serology; Tropical diseases; Vector-borne diseases; Viruses; Young Adult
• ISSN: 1935-2735; 1935-2727; 1935-2735
• DOI: 10.1371/journal.pntd.0008934

Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited. Four hundred and seventy nine acutely febrile patients presenting between September 2017-2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4-3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands. Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia.