Abstract
BackgroundMathematical approaches have been for decades used to probe the structure of nucleotide sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the genetic structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968.MethodsThe mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in nucleotide sequences.ResultsThe analysis indicates that the nucleotide sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each nucleotide sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality.ConclusionsThe complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.
Highlights
Mathematical approaches have been for decades used to probe the structure of nucleotide sequences
The significant peak periodicities for SARS-CoV-2 are as follows1: 1Note here that before we applied slow feature analysis (SFA) to actual nucleotide sequences, and in order to test the efficiency of SFA when the time series is a string of integers, we considered artificial sequences of known periodicities
The analysis indicates that the nucleotide sequences exhibit an elaborate and convoluted structure akin to complex networks
Summary
Mathematical approaches have been for decades used to probe the structure of nucleotide sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the genetic structure of two related viral families: those of coronaviruses and those of influenza viruses. The influenza viruses include H1N11918, H1N1-2009, H2N2-1957, and H3N2-1968. Since the early 1970s, scientists have attempted to discover some kind of order or hidden structures in nucleotide sequences. With the advent of sequencing techniques in the late 1970s, scientists had the opportunity to probe nucleic acid sequences for such order [1,2,3]. Mathematical approaches were employed to shed light in this endeavor, leading to the full-blown
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