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. 2016 Oct 12;5(10):e107.
doi: 10.1038/emi.2016.106.

Evolution of codon usage in Zika virus genomes is host and vector specific

Azeem Mehmood Butt  1 , Izza Nasrullah  1 , Raheel Qamar  1 , Yigang Tong  2
Affiliations

Evolution of codon usage in Zika virus genomes is host and vector specific

Azeem Mehmood Butt et al. Emerg Microbes Infect. .

Abstract

The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak. An interplay between codon adaptation and deoptimization may have allowed the virus to adapt to multiple host and vectors and is reported for the first time in ZIKV genomes. Combining our codon analysis with geographical data on Aedes populations in the Americas suggested that ZIKV has evolved host- and vector-specific codon usage patterns to maintain successful replication and transmission chains within multiple hosts and vectors.

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Figures

Figure 1
Figure 1
Genotype-specific comparative analysis of ENC values of ZIKV coding sequences.
Figure 2
Figure 2
Correspondence analysis (CA). Genotype-specific CA plots were constructed for whole genome and individual ZIKV coding sequences. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A. The ZIKV strain isolated from Ae. aegypti is represented as a black color diamond.
Figure 2
Figure 2
Correspondence analysis (CA). Genotype-specific CA plots were constructed for whole genome and individual ZIKV coding sequences. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A. The ZIKV strain isolated from Ae. aegypti is represented as a black color diamond.
Figure 3
Figure 3
ENC–GC3 plots. The curve indicates the expected codon usage if GC compositional constraints alone account for the codon usage bias. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.
Figure 3
Figure 3
ENC–GC3 plots. The curve indicates the expected codon usage if GC compositional constraints alone account for the codon usage bias. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.
Figure 4
Figure 4
CAI analysis of the ZIKV coding sequences in relation to its host and vectors. East African, EA; west African, WA.
Figure 5
Figure 5
RCDI analysis of the ZIKV coding sequences in relation to its host and vectors. East African, EA; west African, WA.
Figure 6
Figure 6
SiD analysis of ZIKV strains in relation to its host and vectors. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.
Figure 6
Figure 6
SiD analysis of ZIKV strains in relation to its host and vectors. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.
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References

    1. Faye O, Freire CC, Iamarino A, et al. Molecular evolution of Zika virus during its emergence in the 20(th) century. PLoS Negl Trop Dis 2014; 8: e2636. - PMC - PubMed
    1. Kuno G, Chang GJ. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch Virol 2007; 152: 687–696. - PubMed
    1. Campos GS, Bandeira AC, Sardi SI. Zika virus outbreak, Bahia, Brazil. Emerg Infect Dis 2015; 21: 1885–1886. - PMC - PubMed
    1. Duffy MR, Chen TH, Hancock WT, et al. Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med 2009; 360: 2536–2543. - PubMed
    1. Cao-Lormeau VM, Musso D. Emerging arboviruses in the Pacific. Lancet 2014; 384: 1571–1572. - PubMed

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