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

Ulrich Melcher,Hongju Wang,Siqing Liu,Wenqiang Wei,Bo Zhang

doi:10.1371/journal.pone.0166260

Ulrich Melcher, Hongju Wang + Show 3 more

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https://doi.org/10.1371/journal.pone.0166260

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Abstract

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.

Highlights

Zika virus (ZIKV) is classified as a mosquito-borne arbovirus of the family Flaviviridae, genus Flavivirus [1]
The results show that 46 strains of ZIKV can be divided into two genera (I, II) and the strains isolated from the same geographic regions cluster together (Fig 1)
The GC3s content is a useful indicator of the extent of the base composition bias, representing the frequency of the nucleotides G+C at the synonymous third codon position, excluding Met, Trp, and the termination codons

Summary

Introduction

Zika virus (ZIKV) is classified as a mosquito-borne arbovirus of the family Flaviviridae, genus Flavivirus [1]. This virus was first isolated from a blood sample of a Rhesus monkey in Uganda in 1947 and, before its outbreak in Oceania in 2007, it was confined to Africa and Southeast Asia [1]. ZIKV has expanded from South America to more than 28 countries and has aroused the attention of the World Health Organization (WHO) as well as that of many governments [2, 3]. Clinical presentation of ZIKV fever is non-specific; the most common symptoms are rash, fever, arthralgia, myalgia, asthenia, and conjunctivitis.

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