Genomic and epidemiological monitoring of yellow fever virus transmission potential

Abstract

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.

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

“…For these particular examples, human infections are mainly spill over events from the zoonotic cycle (e.g. for YFV see [Faria et al., ]). Thus, while the single‐host formulation should be minded, a potential use of the index P is to parameterize suitability to the reservoir–host and reservoir–mosquito species, and interpret P as a proxy for risk of spill over to human populations.…”

“…In Africa, YFV outbreaks in Angola and other countries have recently (2016–2017) developed into a global vaccination crisis (Kraemer et al., ; Wu, Peak, Leung, & Lipsitch, ). More recently (2017–2018), YFV has also emerged from its sylvatic cycle in Brazil (Faria et al., ). Not only is the absolute scale of these outbreaks unprecedented, but the emergence of severe pathologies such as ZIKV‐related neonatal microcephaly, CHIKV‐induced Guillain–Barré syndrome and a very high YFV mortality rate have had substantial negative public health and socio‐economic impacts (Cao‐Lormeau et al., ; 16; Johansson, Mier‐y Teran‐Romero, Reefhuis, Gilboa, & Hills, ; Oehler et al., ; de Oliveira et al., ).…”

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

“…In general, target enrichment of NGS libraries is required to obtain sufficient viral genome coverage for phylogenetic and molecular clock analyses 6 . The enrichment of libraries using multiplex PCR of tiled amplicons (tiling multiplex PCR) and/or capture probe enrichment has been successfully used for the genomic surveillance of EBOV 18,19 , ZIKV [20][21][22] and yellow fever virus (YFV) outbreaks 23 . Tiling multiplex PCR usually targets only a single circulating viral strain at a time; this requires that infection from that strain be established a priori (generally by previous virus-specific PCR testing) and it is thus less practical for viruses that exhibit high sequence divergence and/or recombination (for example HIV) 24 , are present as co-infections 25 or comprise multiple genotypes (for example, hepatitis C virus (HCV), dengue (DENV)).…”

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

“…The phylogenetic analyses allowed to understand the epidemiology history and how the viruses spread in the infected countries and inside the country with the possibility to plan prevention strategies…”