Abstract
BackgroundThe Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus.ResultsNucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV.ConclusionsTo our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0456-4) contains supplementary material, which is available to authorized users.
Highlights
The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever
No evidence of recombination was found among MARV genomes
Coding sequences of all 63 of the initially selected MARV genomes were included in codon usage analysis as discussed in following sections
Summary
The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. MARV belongs to family Filoviridae, which includes the highly pathogenic Ebola virus (EBOV). Egyptian fruit bats (Rousettus aegyptiacus) in endemic areas in Africa; R. aegyptiacus are considered as its natural host. This is most likely the reason that MARV outbreaks have been mostly associated with individuals such as mine workers or tourists in the regions that these bats inhabit [2]. Similar to its highly pathogenic cousin EBOV that is the cause of a recent ongoing outbreak, MARV causes fatal viral hemorrhagic fever in humans and non-human primates with a fatality rate of up to 90 %. There is a need for a detailed understanding of replication and evolution of this virus [3,4,5]
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