Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution

Background. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus.
Results. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV.
Conclusions. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.

背景. 马尔堡病毒（Marburg virus, MARV）具有负义单链RNA基因组，隶属于丝状病毒科（Filoviridae），可引发多起高致死性出血热暴发。病毒的密码子使用模式反映了一系列进化改变，这些改变使病毒能够调控自身在外部环境，尤其是宿主中的存活率与适应度。为从密码子层面解析马尔堡病毒的进化机制，本研究对马尔堡病毒基因组的同义密码子使用模式开展了全面分析。本研究采用多种密码子分析方法与统计学手段，明确了马尔堡病毒的整体密码子使用模式、密码子使用偏性，并解析了突变压力、自然选择以及其两类宿主——智人（Homo sapiens）和埃及果蝠（Rousettus aegyptiacus）——等多种因素的影响。
结果. 核苷酸组成与相对同义密码子使用度（relative synonymous codon usage, RSCU）分析表明，马尔堡病毒存在突变偏性，且偏好使用以尿嘧啶（U）和腺嘌呤（A）结尾的密码子编码氨基酸。有效密码子数（effective number of codons）分析结果显示，马尔堡病毒基因组的整体密码子使用仅存在轻微偏性。奇偶规则2（Parity Rule 2）绘图分析显示，鸟嘌呤-胞嘧啶（GC）与腺嘌呤-尿嘧啶（AU）核苷酸的使用比例不均衡，这证实了自然选择的存在。研究同时发现，马尔堡病毒的密码子使用模式会受到宿主的影响，这提示马尔堡病毒已进化出适配其两类宿主的特异性密码子使用模式。此外，相较于智人的选择压力，埃及果蝠对马尔堡病毒相对同义密码子使用模式施加的选择压力占主导地位。总体而言，突变压力是塑造马尔堡病毒密码子使用模式的最关键且占主导地位的进化动力。
结论. 据我们所知，本研究是首个针对马尔堡病毒开展的系统性密码子使用分析，拓展了学界对马尔堡病毒密码子使用模式及其进化机制的认知。