Machine learning models exploring characteristic single-nucleotide signatures in Yellow Fever Virus

Abstract

Yellow fever virus (YFV) is the agent of the most severe mosquito-borne disease in the tropics. Recently, Brazil suffered major YFV outbreaks with a high fatality rate affecting areas where the virus has not been reported for decades, consisting of urban areas where a large number of unvaccinated people live. We developed a machine learning framework combining three different algorithms (XGBoost, random forest and regularized logistic regression). This method was applied to 56 YFV sequences from human infections and 27 from non-human primate (NHPs) infections to investigate the presence of genetic signatures possibly related to disease severity (in human related sequences) and differences in the PCR cycle threshold (Ct) values (in NHP related sequences). Our analyses reveal four non-synonymous single nucleotide variations (SNVs) on sequences from human infections, in proteins NS3 (E614D), NS4a (I69V), NS5 (R727G, V643A) and six non-synonymous SNVs on NHP sequences, in proteins E (L385F), NS1 (A171V), NS3 (I184V) and NS5 (N11S, I374V, E641D). We performed comparative protein structural analysis on these SNVs, describing possible impacts on protein function. Despite the fact that the dataset is limited in size and that this study does not consider virus-host interactions, our work highlights the use of machine learning as a versatile and fast initial approach to genomic data exploration. ImportanceYellow fever is responsible for 29-60 thousand deaths annually in South America and Africa and is the most severe mosquito-borne disease in the tropics. Given the range of clinical outcomes and the availability of YFV genomic data, the use of machine learning analysis promises to be a powerful tool in the investigation of genetic signatures that could impact disease severity and its potential of being reintroduced in an urban transmission cycle. This can assist in the search for biomarkers of severity as well as help elucidating variations in hosts Ct value. This work aims to propose a relatively fast and inexpensive computational analysis framework, which can be used as a real-time, innitial strategy associated with genomic surveillance to identify a set of single nucleotide variants putatively related to biological and clinical characteristics being observed.