Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus

Ma, Xiaoxia; Chang, Qiu-yan; Ma, Peilin; Li, Linjie; Zhou, Xiao-kai; Zhang, Derong; Li, Mingsheng; Cao, Xin; Ma, Zhiyong

doi:10.1016/j.gene.2017.09.045

Cited by 18 publications

(6 citation statements)

References 59 publications

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“…A strong body of research shows how synonymous codon usage can be biased by evolutionary and functional factors such as RNA stability, protein secondary structure, mutation pressure, and translational selection ( Bahir et al. 2009 ; Ma et al. 2017 ; Taylor, Dimitrov, and Afonso 2017 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Courcelle,

Salami,

Tounkara

et al. 2024

Virus Evolution

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Peste des petits ruminants virus (PPRV) causes a highly infectious disease affecting mainly goats and sheep in large parts of Africa, Asia, and the Middle East and has an important impact on the global economy and food security. Full genome sequencing of PPRV strains has proved to be critical to increasing our understanding of PPR epidemiology and to inform the ongoing global efforts for its eradication. However, the number of full PPRV genomes published is still limited and with a heavy bias towards recent samples and genetic Lineage IV (LIV), which is only one of the four existing PPRV lineages. Here, we generated genome sequences for twenty-five recent (2010–6) and seven historical (1972–99) PPRV samples, focusing mainly on Lineage II (LII) in West Africa. This provided the first opportunity to compare the evolutionary pressures and history between the globally dominant PPRV genetic LIV and LII, which is endemic in West Africa. Phylogenomic analysis showed that the relationship between PPRV LII strains was complex and supported the extensive transboundary circulation of the virus within West Africa. In contrast, LIV sequences were clearly separated per region, with strains from West and Central Africa branched as a sister clade to all other LIV sequences, suggesting that this lineage also has an African origin. Estimates of the time to the most recent common ancestor place the divergence of modern LII and LIV strains in the 1960s–80s, suggesting that this period was particularly important for the diversification and spread of PPRV globally. Phylogenetic relationships among historical samples from LI, LII, and LIII and with more recent samples point towards a high genetic diversity for all these lineages in Africa until the 1970s–80s and possible bottleneck events shaping PPRV’s evolution during this period. Molecular evolution analyses show that strains belonging to LII and LIV have evolved under different selection pressures. Differences in codon usage and adaptative selection pressures were observed in all viral genes between the two lineages. Our results confirm that comparative genomic analyses can provide new insights into PPRV’s evolutionary history and molecular epidemiology. However, PPRV genome sequencing efforts must be ramped up to increase the resolution of such studies for their use in the development of efficient PPR control and surveillance strategies.

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Section: Resultsmentioning

confidence: 99%

Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Courcelle,

Salami,

Tounkara

et al. 2024

Virus Evolution

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“…The nucleotide and codon usage composition showed a significant correlation with ENC, indicating its influence on CUB (Ma et al, 2017;Gu et al, 2020). The GC content (35.95%) characterizes ASFV as an AT-rich DNA virus.…”

Section: Discussionmentioning

confidence: 98%

Comprehensive codon usage analysis of the African Swine Fever Virus

Kanyema,

Cheng,

Luo

et al. 2023

Acta Virol.

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The non-uniform usage of synonymous codons occurs in genomes of all organisms, including DNA and RNA viruses. The preferential selection of a codon at the expense of other synonymous codons within the same group is known as Codon Usage Bias. The understanding of this bias assists in unveiling the factors driving molecular evolution, as defined by the selection-mutation-drift theory. According to this model, molecular evolution is predominantly driven by mutation, natural selection, and genetic drift. Nevertheless, elements like nucleotide composition, gene length, and protein secondary structure also contribute to this process. Comprehensive genomic analyses that highlight the codon usage preference of the African Swine Fever Virus (ASFV) are infrequent. ASFV, a hemorrhagic and highly contagious viral disease, almost invariably results in 100% fatality among infected pigs and wild boars. This study, therefore, embarked on a thorough examination of codon usage patterns in ASFV’s complete genomic sequences, an endeavor of great relevance to molecular evolution studies, complex transmission models, and vaccine research. For an exhaustive evaluation of ASFV’s whole-genome codon usage, we used parameters like ENC, RSCU, and CAI. A Principal Component Analysis was carried out to reaffirm the interconnected RSCU lineages based on the continent, and their evolutionary relationships were later elucidated through phylogenetic tree construction. ASFV emerged as a low-biased codon user (ENC = 52.8) that is moderately adapted to its host. Its genome has a high AT composition (64.05%), suggesting the impact of mutational pressure on genomic evolution. However, neutrality plot analysis revealed natural selection’s slight supremacy over mutational pressure. The low codon bias (>45) implies ASFV’s diverse usage of synonymous codons within a given codon family, allowing for effective translation and subsequent successful viral replication cycles. Its moderate adaptation (CAI = 0.56) permits the virus to infect a range of hosts, including reservoirs such as warthogs and bush pigs. To the best of our knowledge, this is the pioneering report providing a comprehensive examination of ASFV’s complete genomic sequences. Consequently, research focusing on viral gene expression and regulation, gene function prediction, parasite-host interaction, immune dysfunction, and drug and vaccine design may find this report to be a valuable resource.

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“…The synonymous codon usage pattern is crucial in modulating the efficiency and accuracy of viral protein translation and maintaining the viral protein amino acid sequence [11][12][13]. Synonymous codon usages in the viral genome can reflect the active cross-talk between viral infection and host immune response [14][15][16]. Currently, there have been two major models to account for synonymous codon usage bias, namely the neutral (or mutational) model and the natural selective (or the translation-related selection) model.…”

Section: Introductionmentioning

confidence: 99%

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

et al. 2022

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Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via V s calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (V s value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (V s < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (V s > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.

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Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus

Cited by 18 publications

References 59 publications

Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Comprehensive codon usage analysis of the African Swine Fever Virus

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

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