Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018.

Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA's basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.

Chikungunya fever: How accurate is the clinical-epidemiological diagnosis compared to the gold standard of molecular and serological laboratory diagnosis?

OBJECTIVE: To evaluate the accuracy of the current World Health Organization' (WHO) Chikungunya fever (CHIKF) clinical-epidemiological case definition against the gold standard of laboratory diagnosis. METHODS: This was a prospective study of patients seeking medical care at an Emergency Department in the metropolitan area of Rio de Janeiro, Brazil, from January to June 2018. Clinical features were recorded. Screening for CHIKF was performed using the RT-qPCR and ELISA-IgM antibody assay. Clinical features of CHIKF RT-qPCR/IgM positive cases were compared with those with other febrile illnesses. RESULTS: 27,900 ED visits were recorded, of which 172 (0.61 %) patients were screened for arboviral illness. The prevalence of laboratory-confirmed CHIKF (Lab-CHIKF) was 110/172 [64 %]. Chikungunya virus RNA was detected in 92/172 (53.5 %) patients, while in 18/80 (10.5 %), only IgM was positive. Compared to CHIKV-negative subjects, patients with CHIKF presented much earlier after the onset of symptoms (2 [1-4] vs. 3.5 [2.5-5], p = 0.007), and more frequently reported arthritis (61.8 % vs. 33.9 %, p < 0.0001), arthralgia (96.4 % vs. 79 %, p < 0.0001), and conjunctivitis (35.5 % vs. 16.1 %, p = 0.007). After adjustments for other clinical predictors, arthritis/arthralgia [aOR: 6 (95 % CI 1.8-19.7)] and the presence of conjunctivitis [aOR: 2.85 (95 % CI 1.30-6.24] were positively associated with lab-CHIKF. The sensitivity, specificity, positive predictive value, and negative predictive value of the WHO CHIKF clinical case definition was 96.3 %, 20.9 %, 68.3 % and 76.4 %, respectively, and accuracy was 0.69 [AUC: 0.69 (95 % CI 0.61-0.75)]. CONCLUSION: The WHO case definition needs to be improved for better accuracy, especially in areas in epidemics in areas with co-circulation of arboviruses.