48 49 50 51 52 Corresponding authors: luiz.alcantara@ioc.fiocruz.br and nuno.faria@zoo.ox.ac.uk 3 53 Abstract 54 Background 55 Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has 56 affected 51 countries in the Americas. The CHIKV epidemic in the Americas was 57 caused by the CHIKV-Asian genotype. In August 2014, local transmission of the 58 CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a 59 distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was 60 detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The 61 genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region 62 remains poorly understood despite its importance to better understand the 63 epidemiological spread and public health impact of CHIKV in the country. 64 65 Methodology/Principal Findings 66 We report a large CHIKV outbreak (5,928 notified cases between August 2014 and 67 August 2018) in Boa vista municipality, capital city of Roraima's state, located in the 68 Brazilian Amazon region. In just 48 hours, we generated 20 novel CHIKV-ECSA 69 genomes from the Brazilian Amazon region using MinION portable genome 70 sequencing. Phylogenetic analyses revealed that despite an early introduction of the 71 Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista 72 was caused by an ECSA-lineage most likely introduced from northeastern Brazil. 73 Epidemiological analyses suggest a basic reproductive number of R 0 of 1.66, which 74 translates in an estimated 39 (95% CI: 36 to 45) % of Roraima's population infected 75 with CHIKV-ECSA. Finally, we find a strong association between Google search 76 activity and the local laboratory-confirmed CHIKV cases in Roraima. 77 78 Conclusions/Significance 79 This study highlights the potential of combining traditional surveillance with portable 80 genome sequencing technologies and digital epidemiology to inform public health 81 surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in 82 Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement 83 of the Asian genotype by the ECSA genotype in the Amazon region. 84 85 4 86 Author Summary 87 Until the end of 2017, Brazil notified the highest number of infections caused by 88 chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV 89 outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable 90 genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that 91 ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. 92 Epidemiological analyses suggest a basic reproductive number of R 0 of 1.66, which 93 suggests that approximately 39% of Roraima's population was infected with CHIKV-94 ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data 95 highlights the rapid spread of a less understood and poorly characterized CHIKV-96 ECSA genotype in Brazil. Investigations on p...