Fig 1.
A. Map showing municipalities of Roraima state, including Boa Vista, bordering countries (Venezuela and French Guiana) and bordering Brazilian federal states (Amazonas and Pará). B. Map of Brazilian states, showing the states from which CHIKV sequence data in this study was analysed (Bahia, Alagoas, Pernambuco, Paraíba, Amazonas and Roraima). C. Barplot showing the annual number of notified CHIKV cases in selected states of Brazil (data obtained from the Brazilian Ministry of Health). Map was made with Natural Earth. Free vector and raster map data at naturalearthdata.com.
Table 1.
Epidemiological data for virus isolates from Roraima (RR) and Amazonas (AM).
CT = cycle threshold, d = days from onset of symptoms to sample collection. Corresponding sequencing statistics are available in S1 Table. Isolates were collected around 2.3 (range: 0–5) days after onset of symptoms. Acc. Number = GenBank accession number.
Fig 2.
Sequencing statistics, temporal signal and evolutionary rates of the CHIKV-ECSA lineage.
A. Genome coverage plotted against RT-qPCR CT-values for the newly generated sequence data. B. Genetic divergence regressed against dates of sample collection for dataset 2 (CHIKV-ECSA-Br lineage). C. Evolutionary rate estimates for the CHIKV-ECSA-Br lineage obtained by this study (circle number 1) compared to published evolutionary rates obtained for other lineages. Circles numbered 2 to 8 represent point estimates reported in [1, 9, 80]. Horizontal bars represent 95% highest posterior density credible intervals for evolutionary rates.
Fig 3.
Genetic analysis of the CHIKV-ECSA genotype.
A. Maximum likelihood phylogeny depicting the monophyletic clade containing all the Brazilian ECSA isolates (ECSA-Br lineage). B. Time-calibrated phylogeny of all available CHIKV-ECSA whole genome sequences from Brazil, including 18 novel genomes from Roraima and Amazonas states. Colours correspond to state of sample collection. Violin plots show 95% Bayesian credible intervals for associated node heights [39].
Fig 4.
Digital surveillance of chikungunya in the Brazilian Brazil.
Notified (orange) and confirmed (purple) cases in the central public health laboratories in Roraima state (a) and the Amazonas state (c) from January 2016 to January 2018. Dashed grey lines in (a) and (c) represent Google Trends activity for the term “chikungunya” in Roraima and Amazonas, respectively. Panels b and d show the correlation between Google Trends activity and cases notified in Roraima and Amazonas, respectively. Strength of the association was measured using the Spearman’s rank correlation coefficient (in panel b: p-value < 0.001; panel d: p-value = 5.183e-09).