Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus.
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 pe...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0278982 |
| _version_ | 1811177203181813760 |
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| author | Álvaro Salgado Raquel C de Melo-Minardi Marta Giovanetti Adriano Veloso Francielly Morais-Rodrigues Talita Adelino Ronaldo de Jesus Stephane Tosta Vasco Azevedo José Lourenco Luiz Carlos J Alcantara |
| author_facet | Álvaro Salgado Raquel C de Melo-Minardi Marta Giovanetti Adriano Veloso Francielly Morais-Rodrigues Talita Adelino Ronaldo de Jesus Stephane Tosta Vasco Azevedo José Lourenco Luiz Carlos J Alcantara |
| author_sort | Álvaro Salgado |
| collection | DOAJ |
| description | 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) to analyze YFV genomic sequences. 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 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. |
| first_indexed | 2024-04-10T22:57:48Z |
| format | Article |
| id | doaj.art-32dbbe877581438daca310297309c136 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-10T22:57:48Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-32dbbe877581438daca310297309c1362023-01-14T05:31:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-011712e027898210.1371/journal.pone.0278982Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus.Álvaro SalgadoRaquel C de Melo-MinardiMarta GiovanettiAdriano VelosoFrancielly Morais-RodriguesTalita AdelinoRonaldo de JesusStephane TostaVasco AzevedoJosé LourencoLuiz Carlos J AlcantaraYellow 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) to analyze YFV genomic sequences. 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 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.https://doi.org/10.1371/journal.pone.0278982 |
| spellingShingle | Álvaro Salgado Raquel C de Melo-Minardi Marta Giovanetti Adriano Veloso Francielly Morais-Rodrigues Talita Adelino Ronaldo de Jesus Stephane Tosta Vasco Azevedo José Lourenco Luiz Carlos J Alcantara Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. PLoS ONE |
| title | Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. |
| title_full | Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. |
| title_fullStr | Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. |
| title_full_unstemmed | Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. |
| title_short | Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. |
| title_sort | machine learning models exploring characteristic single nucleotide signatures in yellow fever virus |
| url | https://doi.org/10.1371/journal.pone.0278982 |
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