Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

Ata, Galal; Wang, Hao; Bai, Haoxiang; Yao, Xiaoting; Tao, Shiheng

doi:10.3389/fmicb.2021.699788

Cited by 13 publications

(6 citation statements)

References 71 publications

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“…The total AT and GC compositions were found to be 73.42 and 26.57%, respectively, suggesting that LSDV strains have strong AT ( Figure 1C ). This finding is similar to the previous research on Porcine astrovirus ( 18 ), Hantaan virus ( 36 ), and Bluetongue virus ( 12 ) which were enriched with A and T. However, the biological significance of this condition still needs to be clarified, and therefore, it is essential to explore the causes for increased AT contents and decreased GC contents in the virus genomes ( 37 ).…”

Section: Resultssupporting

confidence: 88%

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Rahman¹,

Rehman²,

Rahman³

et al. 2022

Front. Vet. Sci.

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Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.

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Section: Resultssupporting

confidence: 88%

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Rahman¹,

Rehman²,

Rahman³

et al. 2022

Front. Vet. Sci.

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“…Our results agreed with those of a previous report [23]. Similar CUB was also observed in other viruses, such as HTNV (47.52) [26] and PEDV (48.1) [27]. Such low CUB might facilitate their survival and replication within the host via minimizing the protein synthesize resource competition between the host and inner viruses [18,28].…”

Section: Discussionsupporting

confidence: 92%

Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak

Zhou¹,

Wang²,

Zhu³

et al. 2023

IJMS

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The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the monkeypox virus (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.

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“…ASFV's preference for using AT nucleotides over GC nucleotides in all its coding sequences has been observed in a comparative genomics analysis of ASFV (Pu et al, 2023). Other viruses with a similar AT nucleotide composition include Hantaan viruses (Ata et al, 2021), Hepadnaviridae (Deb et al, 2020), Flaviviridae (Yao et al, 2019), lyssaviruses (Zhang et al, 2018), PEDV (Chen et al, 2014), PDCoV (He et al, 2019), and SARS-CoV-2 (Hou, 2020).…”

Section: Discussionmentioning

confidence: 93%

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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Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

Cited by 13 publications

References 71 publications

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak

Comprehensive codon usage analysis of the African Swine Fever Virus

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