Generation and comparative genomics of synthetic dengue viruses

Phylogenomic analysis unravels evolution of yellow fever virus within hosts

The yellow fever virus (YFV) recently reemerged in the large outbreaks in Africa and Brazil, and the first imported patients into Asia have recalled the concerns of YFV evolution. Here we show phylogenomics of YFV with serial clinical samples of the 2016 YFV infections. Phylogenetics exhibited that the 2016 strains were close to Angola 1971 strains and only three amino acid changes presented new to other lineages. Deep sequencing of viral genomes discovered 101 intrahost single nucleotide variations (iSNVs) and 234 single nucleotide polymorphisms (SNPs). Analysis of iSNV distribution and mutated allele frequency revealed that the coding regions were under purifying selection. Comparison of the evolutionary rates estimated by iSNV and SNP showed that the intrahost rate was ~2.25 times higher than the epidemic rate, and both rates were higher than the long-term YFV substitution rate, as expected. In addition, the result also hinted that short viremia duration of YFV might further hinder the evolution of YFV.

The first importation of infections into China in 2016 and the following outbreaks in Africa and Brazil of yellow fever virus (YFV) have raised again the concerns of the potential viral spread into new territories. In this study, we aimed to know the evolution dynamics of YFV by using intrahost phylogenomics and to assess the risk of virus epidemics. Through deep sequencing of consecutive samples from 12 patients, we identified hundreds of genomic variations (iSNVs and SNPs), and noticed the nearly linear accumulation of variations within individuals. The estimated evolutionary rate within host is much higher than the epidemic evolutionary rate. In comparison with Dengue virus (DENV) and Zika virus (ZIKV), which share similar host vectors (Aedes spp.), life cycles, mutation rates and replication strategies to YFV, the lower epidemic evolutionary rate of YFV might have been hindered by the shorter viremia duration, which decreased the accumulated variations to get into the transmission cycle.