Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil.

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016-2019.

The recent reemergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the rapid dissemination of the virus in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil, we generated 18 complete and nearly complete genomes from the peak of the epidemic curve from nonhuman primates (NHPs) and human infected cases across the Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the estimated timing, source, and likely routes of yellow fever virus transmission and dispersion during one of the largest outbreaks ever registered in Brazil. We showed that during the recent epidemic, YFV was reintroduced from Minas Gerais to the Espírito Santo and Rio de Janeiro states multiple times between 2016 and 2019. The analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce the idea that continued genomic surveillance strategies can provide information on virus genetic diversity and transmission dynamics that might assist in understanding arbovirus epidemics.IMPORTANCE Arbovirus infections in Brazil, including yellow fever, dengue, zika, and chikungunya, result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by the limited availability of genomic data. In this study, we investigated the genetic diversity and spatial distribution of YFV during the current outbreak by analyzing genomic data from areas in southeastern Brazil not covered by other previous studies. To gain insights into the routes of YFV introduction and dispersion, we tracked the virus by sequencing YFV genomes sampled from nonhuman primates and infected patients from the southeastern region. Our study provides an understanding of how YFV initiates transmission in new Brazilian regions and illustrates that genomics in the field can augment traditional approaches to infectious disease surveillance and control.

Correction to: Accuracy and reliability of an NS1 rapid immunochromatographic test for DENV-1 diagnosis at point of care and in the laboratory.

An error occurred during the publication of the original article [1].

Precisão e confiabilidade de um teste imuno-cromatográfico rápido NS1 para diagnóstico DENV-1 no ponto de atendimento e no laboratório.

BACKGROUND: Rapid immunochromatographic tests (ICT) for dengue non-structural protein 1 (NS1) have shown good performance for diagnosing acute-phase dengue in serum in laboratory settings, but rarely have been assessed in whole blood and at point of care (POC). This study compare the accuracy and inter- and intra-observer reliability of the NS1 Bioeasy™ ICT in whole blood at POC versus serum in the laboratory, during a DENV-1 epidemic. METHODS: Cross-sectional study involving 144 adults spontaneously demanding care in an emergency department within 4 days of onset of acute febrile illness. Accuracy of NS1 Bioeasy™ ICT was compared in whole blood and serum, both at 15 and 30 min, blinded to the reference RT-PCR or NS1 ELISA. Non-dengue patients were also tested for Zika virus with RT-PCR. Reliability of whole blood and serum readings by the same or different observers was measured by simple kappa (95% CI). RESULTS: At 15 min, sensitivity (Sn) of NS1 Bioeasy™ ICT in whole blood/POC was 76.7% (95% CI: 68.0-84.1) and specificity (Sp) was 87.0% (95% CI: 66.4-97.2). Sn in serum/laboratory was 82% (95% CI: 74.1-88.6) and Sp 100% (95% CI: 85.8-100). Positive likelihood ratio was 5.9 (95% CI: 2.0-17.0) for whole blood/POC and 19.8 (95% CI: 2.9-135.1) for serum/laboratory. Reliability of matched readings of whole blood/POC and serum/laboratory by the same observer (k = 0.83, 95% CI: 0.74-0.93) or different observers (k = 0.81, 95% CI: 0.72-0.92) was almost perfect, with higher discordant levels in the absence of dengue. Results did not differ statistically at 5%. CONCLUSIONS: NS1 Bioeasy™ ICT in DENV-1 epidemics is a potentially confirmatory test. Invalid results at 15 min should be reread at 30 min. To optimize impact of implementing ICT in the management of false-negatives it should be incorporated into an algorithm according to setting and available specimen. TRIAL REGISTRATION: UTN U1111-1145-9451 .