A detailed comparative analysis of codon usage bias in Zika virus

Cristina, Juan; Fajardo, Álvaro; Sóñora, Martín; Moratorio, Gonzalo; Musto, Héctor

doi:10.1016/j.virusres.2016.06.022

Cited by 38 publications

(29 citation statements)

References 37 publications

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“…Our result is consistent with a previous study that showed that recent Asian lineage spread is linked to the codon usage adaptation of the NS1 protein to human housekeeping genes [50]. During the preparation of this manuscript, two papers were published employing some ZIKV strains to analyze the codon usage [51, 52]. They concluded that mutation pressure is an important determinant of the codon usage bias of ZIKV mainly based on the result of a GC3s-ENc analysis [51].…”

Section: Resultssupporting

confidence: 90%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.

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Section: Resultssupporting

confidence: 90%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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“…Specifically, the fast transition rates of A → G (i.e., as introduced by ADAR) and C → U convert CA → CG and CA → UA, respectively (Graur, ). However, for viruses, both CG and UA can be deleterious as the former is recognized by the host innate immune system as a pathogen tag (Dorn & Kippenberger, ; Kawai & Akira, ), whereas the latter constitutes a potential source of spurious UA‐rich regulatory elements and premature stop codons (Cristina et al., ; Karlin & Burge, ). Thus, despite being a strong ADAR target, purifying selection opposes the fixation of CA → CG ADAR edits, which thereby leads to CA conservation, enrichment, and preference for NCA codons.…”

Section: Discussionmentioning

confidence: 99%

RNA editing by the host ADAR system affects the molecular evolution of the Zika virus

Piontkivska

Frederick

Miyamoto

et al. 2017

Ecology and Evolution

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Zika virus (ZIKV) is a mosquito‐transmitted flavivirus, linked to microcephaly and fetal death in humans. Here, we investigate whether host‐mediated RNA editing of adenosines (ADAR) plays a role in the molecular evolution of ZIKV. Using complete coding sequences for the ZIKV polyprotein, we show that potential ADAR substitutions are underrepresented at the ADAR‐resistant GA dinucleotides of both the positive and negative strands, that these changes are spatially and temporally clustered (as expected of ADAR editing) for three branches of the viral phylogeny, and that ADAR mutagenesis can be linked to its codon usage. Furthermore, resistant GA dinucleotides are enriched on the positive (but not negative) strand, indicating that the former is under stronger purifying selection than the latter. ADAR editing also affects the evolution of the rhabdovirus sigma. Our study now documents that host ADAR editing is a mutation and evolutionary force of positive‐ as well as negative‐strand RNA viruses.

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“…A successful infection requires that viruses possess the ability to enter the host cell, and efficiently produce new viruses. The degenerate genetic code unequally uses synonymous codons, which code for the same amino acid (Cristina et al 2016;Kanaya et al 2001;Shackelton et al 2006;Tsai et al 2007). The redundancy of the genetic code provides the opportunity to shape the efficiency and accuracy of protein production, while maintaining the same amino acid sequence (Chaney and Clark 2015;Plotkin and Kudla 2011;Stoletzki and Eyre-Walker 2007).…”

Section: Introductionmentioning

confidence: 99%

“…Because the virus relies on the host's cellular machinery for its replication, codon usage bias was suggested to play a role in the adaptation of a virus to its host. Codon usage bias is common in viruses (Butt et al 2014;Castells et al 2017;Cristina et al 2016;He et al 2017;Li et al 2017;Moratorio et al 2013;Singh et al 2016;Su et al 2017;Xu et al 2017;Zang et al 2017;Zhao et al 2016). Efficient replication seemingly requires that a virus and host have similar codon usage patterns to share a tRNA pool.…”

Section: Introductionmentioning

confidence: 99%

The adaptation of codon usage of +ssRNA viruses to their hosts

Tian

Shen

Murphy

et al. 2018

Infection, Genetics and Evolution

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Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).

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A detailed comparative analysis of codon usage bias in Zika virus

Cited by 38 publications

References 37 publications

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

RNA editing by the host ADAR system affects the molecular evolution of the Zika virus

The adaptation of codon usage of +ssRNA viruses to their hosts

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