Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil

Abstract

Outbreaks caused by Dengue, Zika and Chikungunya viruses can spread rapidly in immunologically naïve populations. By analysing 92 newly generated viral genome sequences from blood donors and recipients, we assess the dynamics of dengue virus serotype 4 during the 2012 outbreak in Rio de Janeiro. Phylogenetic analysis indicates that the outbreak was caused by genotype II, although two isolates of genotype I were also detected for the first time in Rio de Janeiro. Evolutionary analysis and modelling estimates are congruent, indicating a reproduction number above 1 between January and June, and at least two thirds of infections being unnoticed. Modelling analysis suggests that viral transmission started in early January, which is consistent with multiple introductions, most likely from the northern states of Brazil, and with an increase in within-country air travel to Rio de Janeiro. The combination of genetic and epidemiological data from blood donor banks may be useful to anticipate epidemic spread of arboviruses.

Fundamental principles of epidemic spread highlight the immediate need for large-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic

“…Model output on cumulative death counts ( ) is fitted to the reported time series of deaths Λ (see Data) using a Bayesian MCMC approach previously implemented in other modelling studies [7][8][9][10] . Model variables are summarized in probability of dying with severe disease θ Gaussian distribution G(M=0.14, SD=0.007) [1,2,11,17] proportion of population at risk of severe disease ρ Gamma distribution G1(S=5, R=5/0.01), G2(S=5, R=5/0.001) --population size N UK 66.87M, Italy 60M ---…”

MVSE: An R‐package that estimates a climate‐driven mosquito‐borne viral suitability index

“…Recife is located in the state of Pernambuco in the north-east of Brazil with a tropical savanna climate, while São Paulo is located in the south with a humid subtropical climate (Köppen climate classification (Peel, Finlayson, & McMahon, 2007 DENV and CHIKV (de Araújo et al, 2016;Magalhaes et al, 2017;Sabino et al, 2016). In contrast, São Paulo is yet to experience a sustained ZIKV epidemic, DENV incidence is known to be low for the national average (Teixeira, Siqueira, Ferreira, Bricks, & Joint, 2013) and transmission of mosquito-borne viruses is unstable, with phylogenetic studies showing that epidemics are seeded by new lineages almost every year (Faria et al, 2017a(Faria et al, ,2017b. In the notified dengue data that we obtained for 2007-2012 (See Data accessibility3), the total incidence per 100k individuals in Recife was approximately 11fold higher than it was in São Paulo (2184.3 notifications vs. 195.2).…”

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

“…Phylogenetic analyses can reveal a better picture of arboviral outbreak, as have been occurred in Brazil in CHIKV outbreak. Phylogenetic reconstruction suggests several separate introductions of the Asian genotype (ECSA) strain, in contrast to a unique introduction of the ECSA genotype followed by virus dissemination inside the country also in DENV outbreaks . In CHIKV Italian outbreak in September 2017, phylodynamic analysis showed that the virus was in loco at least 3 months before the outbreak and, in particular, it probably originated in Pakistan and not India as the classical epidemiology supposed …”

“…171,172 The comparison of HIV-1 intrahost genealogies from patients sampled under different conditions could help in understanding the viral reservoir dynamics, the most important knowledge for the HIV- Phylogenetic reconstruction suggests several separate introductions of the Asian genotype (ECSA) strain, in contrast to a unique introduction of the ECSA genotype followed by virus dissemination inside the country 174,175 also in DENV outbreaks. 176 In CHIKV Italian outbreak in September 2017, phylodynamic analysis showed that the virus was in loco at least 3 months before the outbreak and, in particular, it probably originated in Pakistan and not India as the classical epidemiology supposed. 177 As well as in ZIKV outbreaks, phylogenetic inference showed how the outbreak in Brazil was closely related to the French Polynesia isolates that circulated in November 2013 35,178 and that all viruses The application of Bayesian statistical inference framework, can allow the reconstruction of the geographic history of the still ongoing and never reported before epidemic on the basis of the first isolates sampled at known times.…”