Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

Genomic and transcriptomic analysis of the recent Mpox outbreak

The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.

The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus

Recent studies show that newly sampled monkeypox virus (MPXV) genomes exhibit mutations consistent with Apolipoprotein B mRNA Editing Catalytic Polypeptide-like3 (APOBEC3)-mediated editing compared to MPXV genomes collected earlier. It is unclear whether these single-nucleotide polymorphisms (SNPs) result from APOBEC3-induced editing or are a consequence of genetic drift within one or more MPXV animal reservoirs. We develop a simple method based on a generalization of the General-Time-Reversible model to show that the observed SNPs are likely the result of APOBEC3-induced editing. The statistical features allow us to extract lineage information and estimate evolutionary events.

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

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.

Human mpox: Biology, epidemiology, therapeutic options, and development of small molecule inhibitors

Although monkeypox (mpox) has been endemic in Western and Central Africa for 50 years, it has not received sufficient prophylactic and therapeutical attention to avoid evolving into an epidemic. From January 2022 to January 2023, more than 84,000 of mpox cases were reported from 110 countries worldwide. Case numbers appear to be rising every day, making mpox an increasing global public health threat for the foreseeable future. In this perspective, we review the known biology and epidemiology of mpox virus, together with the latest therapeutic options available for mpox treatment. Further, small molecule inhibitors against mpox virus and the future directions in this field are discussed as well.

An overview on monkeypox virus: Pathogenesis, transmission, host interaction and therapeutics

Orthopoxvirus is one of the most notorious genus amongst the Poxviridae family. Monkeypox (MP) is a zoonotic disease that has been spreading throughout Africa. The spread is global, and incidence rates are increasing daily. The spread of the virus is rapid due to human-to-human and animals-to-human transmission. World Health Organization (WHO) has declared monkeypox virus (MPV) as a global health emergency. Since treatment options are limited, it is essential to know the modes of transmission and symptoms to stop disease spread. The information from host-virus interactions revealed significantly expressed genes that are important for the progression of the MP infection. In this review, we highlighted the MP virus structure, transmission modes, and available therapeutic options. Furthermore, this review provides insights for the scientific community to extend their research work in this field.

Evolution of codon usage in Taenia saginata genomes and its impact on the host

The beef tapeworm, also known as Taenia saginata, is a zoonotic tapeworm from the genus Taenia in the order Cyclophyllidea. Taenia saginata is a food-borne zoonotic parasite with a worldwide distribution. It poses serious health risks to the host and has a considerable negative socioeconomic impact. Previous studies have explained the population structure of T. saginata within the evolutionary time scale and adaptive evolution. However, it is still unknown how synonymous codons are used by T. saginata. In this study, we used 90 T. saginata strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in the genome of T. saginata. Further low CUB was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection was involved in the structuring of CUB in T. saginata. Further analysis showed that T. saginata has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Generally, both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in T. saginata. This study is important because it characterized the codon usage pattern in the T. saginata genomes and provided the necessary data for a basic evolutionary study on them.

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

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.

Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus

Recent monkeypox (MPX) outbreaks are major ones in non-endemic countries. The present study analyzed molecular phylogenetics, divergence, epidemiology, the geographical distribution, entropy diversity of genome, mutational landscape, and evolution of the monkeypox virus (MPXV) genome and the current MPXV is entitled "hMPXV1." We used different in-silico and statistical methods to study our objectives. The developed phylogram from molecular phylogenetics describes the origin and evolution of hMPXV1 of A, A.1, A.1.1, A.2, and B.1 lineages. The microevolution of B.1 lineage shows its evolution from May to August 2022. B.1 lineage is further adapting and showing more mutation and sub-lineages. The scatter plot of all lineages shows the clustering pattern of lineages and the divergence. We also developed two statistical models of confirmed cases and a diagram of the age-related pattern of infected cases to illustrate the epidemiology of the MPX outbreaks. The entropy diversity and mutational landscape of the hMPXV1 genome were analyzed in nucleotide and codon contexts. Our study has shown the in-depth evolution pattern of different lineages of the hMPXV1. We found B.1 lineage is associated with the current outbreaks. The mutational landscape informs about the slow mutation of the virus. Finally, the study might assists the new therapeutic development considering all the above points and would help the researcher to set up their future research directions.

Monkeypox: An emerging zoonotic pathogen

Monkeypox virus (MPXV), which belongs to the orthopoxvirus genus, causes zoonotic viral disease. This review discusses the biology, epidemiology, and evolution of MPXV infection, particularly cellular, human, and viral factors, virus transmission dynamics, infection, and persistence in nature. This review also describes the role of recombination, gene loss, and gene gain in MPXV evol-vement and the role of signal transduction in MPXV infection and provides an overview of the current access to therapeutic options for the treatment and prevention of MPXV. Finally, this review highlighted gaps in knowledge and proposed future research endeavors to address the unresolved questions.

Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Sesamum indicum is an ancient oil crop grown in tropical and subtropical areas of the world. We have analyzed 23,538 coding sequences (CDS) of S. indicum to understand the factors shaping codon usage in this important oil crop plant. We identified eleven highly preferred codons in S. indicum that have AT-endings. The slope of a neutrality plot was less than one while effective number of codons (ENC) plot showed distribution above and below the standard curve. There is a significant relationship between protein length and relative synonymous codon usage (RSCU) at the primary axis while there is a weak correlation between protein length and Nc values. Correspondence analysis conducted on RSCU values differentiated CDS based on their GC content and their characteristic feature and showed a discrete distribution. Moreover, by determining codon usage, we found out that majority of the lignan biosynthesis related genes showed a weaker codon usage bias. These results provide insights into understanding codon evolution in sesame.

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.

Analysis of codon usage bias of classical swine fever virus

Background and Aim:

Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5’ and 3’ end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern.

Materials and Methods:

The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern.

Results:

The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias.

Conclusion:

The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints

Background

Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium.

Methods

Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons.

Results

The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC₃ content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection.

Discussions

Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.

Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.

A Crosstalk on Codon Usage in Genes Associated with Leukemia

Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.

Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 virus genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 virus genomes. The proposed method combines supervised machine learning with digital signal processing (MLDSP) for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman's rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp, including the 29 COVID-19 virus sequences available on January 27, 2020. Our results support a hypothesis of a bat origin and classify the COVID-19 virus as Sarbecovirus, within Betacoronavirus. Our method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.