15 March 2020

Routes for COVID-19 importation in Brazil

The global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has recently been declared a pandemic by the WHO. As the number of SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country. Report on MedRxiv. Paper has been published in the Journal of Travel Medicine.

28 February 2020

First cases of coronavirus disease (COVID-19) in Brazil

We provide a brief report and phylogenetic analysis of the confirmed COVID-2 cases in Brazil. From 488 suspected cases, two have so far tested positive for COVID-19. These two cases both traveled to Northern Italy. Detailed clinical and epidemiological descriptions for suspected and confirmed patients, including for the two patients reported here, are available from the National Public Health Emergency Alert and Response Network from the Brazilian Ministry of Health. Full report available in


Souza et al. (2019) Genomic Surveillance of Yellow Fever Virus Epidemic Waves in São Paulo, Brazil, 2017 – 2018, BioRxiv

Since July 2016, southeast Brazil has experienced the largest yellow fever virus (YFV) outbreak in decades. Using our validated portable sequencing protocols, we generated 46 complete novel YFV genomes and investigate the geographical and temporal distribution of observed cases in non-human primates in Sao Paulo state. We find that most cases in Sao Paulo result from a single introduction from Minas Gerais that spread at a rate of 1 km per day, consistent with a scenario of continued spread in non-human primate communities and sylvatic vector across forested patches, with occasional spillover to unvaccinated human populations.

18 November 2019

Goes de Jesus et al. (2019) Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance  BioRXiv

This study uses portable sequencing validated protocols to rapidly generate the first virus genome data from 20 cases occurring in Araraquara and São José do Rio Preto, São Paulo state, Brazil. We find that the 2019 dengue outbreak in Brazil in this region is caused by a newly introduced DENV serotype 2 genotype III (Asian/American) that is replacing previously-circulating DENV2 lineages.

14 February 2020

Gutierrez et al. (2019) The evolutionary dynamics of Oropouche Virus (OROV) in South America, Journal of Virology

The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Our results show that differing evolutionary processes on the three segments that encompass the viral genome of OROV lead to variable evolutionary rates and divergence dates that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

31 January 2020

Sabia virus infections in yellow fever suspected cases in Sao Paulo, Brazil

We provide a brief report on two Sabia virus cases detected in Sao Paulo, Brazil, in December 2019. We used CADDE’s novel metagenomic protocol and design new PCR diagnostic primers and probes that can cover a larger diversity of SABV strains in Brazil. A preliminary report on our results can be found here.