Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific

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.

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

“…When evaluated in terms of their ENc value, the 44 viral genomes all lacked a strong codon bias. This result is consistent with the codon usage in most RNA viruses, such as the Citrus tristeza virus [35], Enterovirus [36], Hendra virus [37], and Nipah virus [38], in that they all lacked a strong codon bias. A possible explanation for the weak codon bias is that it is advantageous for efficient replication, re-adaption, and survival in host cells [39,40].…”

“…In the present study, we found that natural selection dominated mutational pressure in shaping codon usage. This finding agrees with the results of other studies on the Citrus tristeza virus [35], Hendra virus [37] and Influenza C virus [44], in that natural selection plays a more important role in shaping the codon usage, but it disagrees with the results of other studies on the Ebola virus [39] and Enterovirus [36] in that mutational pressure is more important in shaping the codon usage.…”

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

“…The patterns of CUB of SARS-CoV-2 showed almost absolute antagonism to that of Homo sapiens, as both of them were biased to A/U-and G/C-ending codons, respectively (Supplementary file 5). Such phenomenon was reported in many other viruses such as henipavirus, poliovirus, and hepatitis A virus (Kumar et al, 2018;Mueller et al, 2006;Sanchez et al, 2003). Codon usage is known to influence translation efficiency (and/or translation accuracy) and protein folding, as the rapid production of proteins due to higher translation rate may lead to incorrect folding and aggregation of viral protein products.…”

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species‐specific interaction of prawn‐infecting nodavirus

“…The calculated ENC values of all nodaviruses were more than 45, suggesting that almost equal usage bias of all the synonymous codon and overall codon usage bias were found to be slightly lower across all strains (RoyChoudhury & Mukherjee, ). Low codon usage bias was also been reported in most of the RNA viruses such as pestiviruses, astroviruses and henipaviruses (Chen et al, ; Gao et al, ; van Hemert et al, ; Kumar et al, ). It was postulated that the host might not recognize the virus genes as competitor for their synthesis machinery due to the low codon usage bias (Zhong, Xu, Wu, & Xu, ), thus promises a higher heterologous transcription and translation of the virus genes in the host (Gustafsson, Govindarajan, & Minshull, ).…”

“…The subsequent codon usage bias analyses of the nodavirus in this study were narrowed down to focus on beta‐ and gammanodavirus due to its significant impact on the cultured aquatic animal. The RSCU comparison of nodavirus and their hosts clearly showed the heterogeneous composition of mono‐ and dinucleotide among all strains, but reflected poorly on its host species especially gammanodavirus (Giallonardo, Schlub, Shi, & Holmes, ; Kumar et al, ). However, both viral genome and host mRNA are anticipated to share some common features due to constraint induced by host factors and their coexistence in the same cytoplasmic cellular environment (Kapoor et al, ).…”