Previous phylogenetic analyses indicated that the ZIKV epidemic was caused by the introduction of a single Asian genotype lineage into the Americas around late 2013, at least one year before its detection there 4 . An estimated 100 million people in the Americas are predicted to be at risk of acquiring ZIKV once the epidemic has reached its full extent 5 . However, little is known about the genetic diversity and transmission history of the virus in different regions in Brazil 6 . Reconstructing ZIKV spread from case reports alone is challenging because symptoms (typically fever, headache, joint pain, rashes, and conjunctivitis) overlap with those caused by co-circulating arthropod-borne viruses 7 and due to a lack of nationwide ZIKV-specific surveillance in Brazil before 2016. [Figure 1 around here]To address this we undertook a collaborative investigation of ZIKV molecular epidemiology in Brazil, including results from a mobile genomics laboratory that travelled through NE Brazil during June 2016 (the ZiBRA project; http://www.zibraproject.org). Of five regions of Brazil (Fig. 1a), the Northeast region (NE Brazil) has the most notified ZIKV cases (40% of Brazilian cases) and the most confirmed microcephaly cases (76% of Brazilian cases, to 31 Dec 2016 2 ), raising questions about why the region has been so severely affected 8 . Further, NE Brazil is the most populous region of Brazil with the potential for year-round ZIKV transmission 9 . With the support of the Brazilian Ministry of Health and other institutions (Acknowledgements), the ZiBRA lab screened 1330 samples (almost exclusively serum or blood) from patients residing in 82 municipalities across five federal states in NE Brazil ( Fig. 1 On average, ZIKV viremia persists for 10 days after infection; symptoms develop ~6 days after infection and can last 1-2 weeks 10 . In line with previous observations in Colombia 11 , we found that the RT-qPCR+ samples in NE Brazil were, on average, collected only two days after onset of symptoms. The median RT-qPCR cycle threshold (Ct) value of positive samples was correspondingly high, at 36 (Extended Data Fig. 1). For NE Brazil, the time series of RT-qPCR+ cases was positively correlated with the number of weekly-notified cases (Pearson's ρ=0.62; Fig. 1b).The ability of the mosquito vector Aedes aegypti to transmit ZIKV is determined by ecological factors that affect adult survival, viral replication, and infective periods 12 .To investigate the receptivity of each Brazilian region to ZIKV transmission, we used a measure of vector climatic suitability derived from monthly temperature, relative humidity, and precipitation data 9 . Using linear regression we find that, for each Brazilian region, there is a strong association between estimated climatic suitability and weekly notified cases (Figs. 1b,1c; adjusted R 2 >0.84, P<0.001; Extended Data Table 2). Similar to previous findings obtained for dengue virus outbreaks 13,14 , notified ZIKV cases lag climatic suitability by ~4 to 6 weeks in all regions, except NE Brazil,...

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Hepatitis E virus (HEV) circulation in humans and swine has been extensively studied in South America over the last two decades. Nevertheless, only 2.1% of reported HEV strains are available as complete genome sequences. Therefore, many clinical, epidemiological, and evolutionary aspects of circulating HEV in the continent still need to be clarified. Here, we conducted a retrospective evolutionary analysis of one human case and six swine HEV strains previously reported in northeastern, southern, and southeastern Brazil. We obtained two complete and four nearly complete genomic sequences. Evolutionary analysis comparing the whole genomic and capsid gene sequences revealed high genetic variability. This included the circulation of at least one unrecognized unique South American subtype. Our results corroborate that sequencing the whole capsid gene could be used as an alternative for HEV subtype assignment in the absence of complete genomic sequences. Moreover, our results substantiate the evidence for zoonotic transmission by comparing a larger genomic fragment recovered from the sample of the autochthonous human hepatitis E case. Further studies should continuously investigate HEV genetic diversity and zoonotic transmission of HEV in South America.

Mayaro virus (MAYV) is transmitted by Haemagogus spp. mosquitoes and has been circulating in Amazon areas in the North and Central West regions of Brazil since the 1980s, with an increase in human case notifications in the last 10 years. MAYV introduction in urban areas is a public health concern once the infection can cause severe symptoms similar to other Alphaviruses. Regarding to urban transmission, studies with Aedes aegypti demonstrate the potential vector competence of the species and the detection of MAYV in urban populations of mosquitoes. Considering the two most abundant urban mosquito species in Brazil, we investigated the dynamics of MAYV transmission by Ae. aegypti and Culex quinquefasciatus in a mice model. Mosquito colonies were artificially fed with blood containing MAYV and infection (IR) and dissemination rates (DR) were evaluated. On the 7th post-infection day (dpi), IFNAR BL/6 mice were made available as a blood source to both mosquito's species. After the appearance of clinical signs of infection, a second blood feeding was performed with a new group of non-infected mosquitoes. RT-q PCR and plaque assay were carried out with animal and mosquito's tissues. We found for Ae. aegypti a IR of 97,5-100% and a DR of 100% in both 7th and 14th dpi. Regarding Cx. quinquefasciatus, the IR found was 13.1-14.81% and DR ranged from 60% to 80%. To evaluate the mosquito-mice transmission rate, 18 mice were evaluated (Test=12 and Control=6) for Ae. aegypti and 12 animals (Test=8 and Control=4) for Cx. quinquefasciatus. All mice bitten by infected Ae. aegypti showed clinical signs of infection while all mice exposed to infected Cx. quinquefasciatus mosquitoes remained healthy. Viremia found in those animals ranged from 2.5 x 108 to 5 x 109 PFU/ml. Ae. aegypti from the second blood feeding showed a 50% infection rate. Our study showed the applicability of an efficient model to complete arbovirus transmission cycle studies and suggests that the Ae. aegypti population evaluated is a competent vector for MAYV highlighting the risk of establishment of MAYV urban cycle. The mice model employed here can be used more extensively for arthropod-vector transmission studies, with laboratory and field mosquito populations, as well as with other arboviruses.