BackgroundSince its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country.Methodology/Principal findingsWe report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima.Conclusions/SignificanceThis study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region.

No abstract

Serum samples from 150 NS1-negative (Platelia ELISA) patients presumptively diagnosed with dengue were analyzed by the TaqMan probed real-time reverse transcription PCR (TaqMan qRT-PCR) method. The qRT-PCR positive samples were tested for serotype by semi-nested RT-PCR and a qualitative immunochromatographic assay for IgG and IgM. Molecular detection methods showed 33 (22%) positive samples out of 150 NS1-antigen negative samples. Of these, 72% were collected up to day 2 after the onset of symptoms, when diagnostic sensitivity of NS1-antigen test assays is significantly enhanced. Most of the cases were not characterized as secondary infection. Twenty-eight samples were successfully serotyped, 75% of which for DENV-4, 14% for DENV-2, 7% for DENV-3 and 4% for DENV-1. These findings reaffirm the hyperendemic situation of the state of Roraima and suggest a lower sensitivity of the NS1 test, mainly when DENV-4 is the predominant serotype. Health care providers should therefore be aware of samples tested negative by NS1 antigen assays, especially when clinical symptoms and other laboratory data results show evidence of dengue infection.

Measles is a human infectious disease of global concern that is caused by the measles virus. In this study, we report the complete genome sequencing of one measles virus isolate, genotype D8, that was obtained directly from a urine sample in Boa Vista city, the capital of Roraima state in Brazil. Phylogenetic reconstruction grouped the genome described in this study with that of samples from Australia, South Korea, and Italy. To our knowledge, this is the first complete genome sequence of a wild-type measles virus reported from Latin America. Therefore, the present data strengthen the current knowledge on the molecular epidemiology of measles worldwide.

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...