Abstract
Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation in different hosts is lacking. A study of codon usage patterns in henipaviruses may provide some fruitful insight into their evolutionary processes of synonymous codon usage and host-adapted evolution. Here, we performed a systematic evolutionary and codon usage bias analysis of henipaviruses. We found a low codon usage bias in the coding sequences of henipaviruses and that natural selection, mutation pressure, and nucleotide compositions shapes the codon usage patterns of henipaviruses, with natural selection being more important than the others. Also, henipaviruses showed the highest level of adaptation to bats of the genus Pteropus in the codon adaptation index (CAI), relative to the codon de-optimization index (RCDI), and similarity index (SiD) analyses. Furthermore, a comparison to recently identified henipa-like viruses indicated a high tRNA adaptation index of henipaviruses for human beings, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in human beings, particularly when paired with frequent exposure to direct/indirect bat excretions.
Highlights
Henipaviruses, especially Hendra virus (HeV) and Nipah virus (NiV), are reckoned to be among the deadliest viruses for which bat has been implicated as a natural reservoir host.These viruses are prototypical members of the genus Henipavirus and family Paramyxoviridae [1]
To counteract the pitfalls associated with a small data set, we employed various state-of-the-art methods to explore the key factors responsible for the codon usage bias in henipaviruses and their evolution and adaptation to different hosts
The phylogenetic analysis suggested that HeV and NiV had differential evolutionary patterns
Summary
Henipaviruses, especially Hendra virus (HeV) and Nipah virus (NiV), are reckoned to be among the deadliest viruses for which bat has been implicated as a natural reservoir host.These viruses are prototypical members of the genus Henipavirus and family Paramyxoviridae (subfamily–Paramyxovirinae) [1]. Certain unique features of HeV and NiV distinguish them from the other members of the Paramyxoviridae family, which include bigger genome size (18,234 and 18,246 nt, respectively, while rest member’s genome size varies from 15–16 kbps), broad host range (bat, pig, horse, human, and dog), high virulence and zoonotic potential [3,4]. Their genome is composed of single-stranded, non-segmented, and negative-sense. The V and W proteins are expressed by insertion of a single or two non-templated G residues, respectively, at the editing site within the P gene, while the C protein is expressed from an alternative open reading frame (ORF) [4]
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