Analysis of synonymous codon usage in 11 human bocavirus isolates

The prevalence, genetic diversity and evolutionary analysis of cachavirus firstly detected in northeastern China

Canine cachavirus is a novel parvovirus belonging to the genus Chaphamaparvovirus that was first detected in dogs in the United States. However, our knowledge of the prevalence and genetic characteristics of cachavirus is relatively limited. In this study, 325 canine fecal specimens collected from healthy and diarrheic dogs in northeastern China were screened with PCR. Twenty-two of the 325 (6.8%) samples were positive for cachavirus. The diarrhea samples showed high viral coinfection rates, and we detected coinfections with canine astrovirus (CaAstV) and cachavirus for the first time. A sequence analysis revealed that the Chinese cachavirus strains have point mutations in four consecutive amino acid codons relative to the original American strain. A codon usage analysis of the VP1 gene showed that most preferred codons in cachavirus were A- or T-ending codons, as in traditional canine parvovirus 2. A co-evolutionary analysis showed that cachavirus has undergone cospeciation with its hosts and has been transmitted among different host species. Our findings extend the limited cachavirus sequences available, and provide detailed molecular characterization of the strains in northeastern China. Further epidemiological surveillance is required to determine the significance and evolution of cachavirus.

Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host

In the present analysis, codon usage strategies and base distribution of Horseshoe bat hepatitis B virus (HBHBV) were analyzed and compared with its host Rhinolophus sinicus, as no work was yet reported. The magnitude of synonymous codon usage bias (CUB) in the virus and its host was low with higher proportion of the base C. Notably, 21 more frequently used codons, 19 less frequently used codons and 3 underrepresented codons (TCG, ACG and GCG) were found to be similar in both virus and its host coding sequences. Neutrality plot analysis reported greater role of natural selection in HBHBV (67.84%) and R. sinicus (76.90%) over mutation pressure. Base skewness and protein properties also influenced the CUB of genes. Further, codon usage analysis depicted, HBHBV and R. sinicus had many similarities in codon usage patterns that might reflect viral adaptation to its host.

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.

Genome-wide analysis of codon usage pattern in herpesviruses and its relation to evolution

The preferential use of a specific codon, out of a group of synonymous codons encoding the same amino acid, in a gene transcript results from the bias in codon choice. Various evolutionary forces namely mutation pressure and natural selection influence the pattern of codon usage i.e. distinct for each gene/genome. We investigated the pattern of codon usage of eight human herpesvirus genomes and compared them with two other herpesvirus genomes namely murine herpesvirus 68 and bovine herpesvirus type 1.1 to elucidate its compositional features, pattern of codon usage across the genomes and report the differences of codon usage pattern of human herpesviruses from that of other two other viruses. We also identified the similarity of the codon usage of human herpesviruses with its host (human). The genes were found to be CG rich in HHV2, HHV3, HHV4, HHV6, HHV7 and BH genomes while TA rich in HHV1, HHV5, HHV8 and MH genomes. The codon usage bias (CUB) of genes was low. A highly significant correlation was found among compositional contents depicting the role of mutational pressure along with natural selection in framing CUB. Several more frequently used codons as well as less frequently used codons were identified to be similar between each human virus and its host (human), while murine herpesvirus 68 and bovine herpesvirus type 1.1 genomes did not possess similar adaptation strategy as human herpesviruses to human (host), thus we could conclude that viral CUB might have been shaped as per their host's nature for better surveillance. Neutrality plot revealed mutational pressure mostly influenced the CUB of HHV1, HHV8 and MH viruses, while natural selection had a major impact in the CUB of HHV2, HHV3, HHV4, HHV5, HHV6, HHV7 and BH genomes.

CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2

In December 2019, the Chinese city of Wuhan was the center of origin of a pneumonia-like disease outbreak with an unknown causative pathogen. The CDC, China, managed to track the source of infection to a novel coronavirus (2019-nCoV; SARS-CoV-2) that shares approximately 79.6% of its genome with SARS-CoV. The World Health Organization (WHO) initially declared COVID-19 as a Public Health Emergency of International Concern (PHEIC) and later characterized it as a global pandemic on March 11, 2020. Due to the novel nature of this virus, there is an urgent need for vaccines and therapeutics to control the spread of SARS-CoV-2 and its associated disease, COVID-19. Global efforts are underway to circumvent its further spread and treat COVID-19 patients through experimental vaccine formulations and therapeutic interventions, respectively. In the absence of any effective therapeutics, we have devised h bioinformatics-based approaches to accelerate global efforts in the fight against SARS-CoV-2 and to assist researchers in the initial phase of vaccine and therapeutics development. In this study, we have performed comprehensive meta-analyses and developed an integrative resource, “CoronaVR” (http://bioinfo.imtech.res.in/manojk/coronavr/). Predominantly, we identified potential epitope-based vaccine candidates, siRNA-based therapeutic regimens, and diagnostic primers. The resource is categorized into the main sections “Genomes,” “Epitopes,” “Therapeutics,” and Primers.” The genome section harbors different components, viz, genomes, a genome browser, phylogenetic analysis, codon usage, glycosylation sites, and structural analysis. Under the umbrella of epitopes, sub-divisions, namely cross-protective epitopes, B-cell (linear/discontinuous), T-cell (CD4⁺/CD8⁺), CTL, and MHC binders, are presented. The therapeutics section has different sub-sections like siRNA, miRNAs, and sgRNAs. Further, experimentally confirmed and designed diagnostic primers are earmarked in the primers section. Our study provided a set of shortlisted B-cell and T-cell (CD4⁺ and CD8⁺) epitopes that can be experimentally tested for their incorporation in vaccine formulations. The list of selected primers can be used in testing kits to identify SARS-CoV-2, while the recommended siRNAs, sgRNAs, and miRNAs can be used in therapeutic regimens. We foresee that this resource will help in advancing the research against coronaviruses.

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.

Detection, genetic, and codon usage bias analyses of the VP2 gene of mink bocavirus

Mink bocavirus 1 (MiBoV1), a novel virus detected from the feces of domestic minks in China in 2016, may be related to gastrointestinal diseases. However, its prevalence and genetic characteristics are poorly described. In this study, we examined 192 samples collected from minks in the major mink industry province from northern China. PCR results showed that 10 samples (5.2%) were positive for MiBoV1, and 60% of MiBoV1-positive samples were co-infected with Aleutian mink disease virus or mink circovirus. MiBoV1 was detected in six serum samples. Sequence analysis demonstrated that the VP2 gene of MiBoV1 was highly conserved and had low viral diversity over the VP2 region and unique nucleotide mutations. Phylogenetic analysis of the VP2 sequence demonstrated that MiBoV1 strains formed two clades and were grouped with California sea lion bocavirus, Canine bocavirus, and Feline bocavirus. Codon usage analysis revealed that most of the preferentially used codons in MiBoV1 were A- or U-ended codons, and no evident codon usage bias was found. This study provides evidence that MiBoV1 has a low prevalence in Jilin and Hebei provinces in China. Moreover, it contributes information regarding the expansion of the limited mink bocavirus sequence and determines the codon usage bias of the VP2 gene for the first time. Epidemiological surveillance is necessary to understand the importance and evolution of MiBoV1.

Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code

Motivation

Understanding how viruses co-evolve with their hosts and adapt various genomic level strategies in order to ensure their fitness may have essential implications in unveiling the secrets of viral evolution, and in developing new vaccines and therapeutic approaches. Here, based on a novel genomic analysis of 2625 different viruses and 439 corresponding host organisms, we provide evidence of universal evolutionary selection for high dimensional ‘silent’ patterns of information hidden in the redundancy of viral genetic code.

Results

Our model suggests that long substrings of nucleotides in the coding regions of viruses from all classes, often also repeat in the corresponding viral hosts from all domains of life. Selection for these substrings cannot be explained only by such phenomena as codon usage bias, horizontal gene transfer and the encoded proteins. Genes encoding structural proteins responsible for building the core of the viral particles were found to include more host-repeating substrings, and these substrings tend to appear in the middle parts of the viral coding regions. In addition, in human viruses these substrings tend to be enriched with motives related to transcription factors and RNA binding proteins. The host-repeating substrings are possibly related to the evolutionary pressure on the viruses to effectively interact with host's intracellular factors and to efficiently escape from the host's immune system.

Supplementary information

Supplementary data are available at Bioinformatics online.

Novel Primate Bocaparvovirus Species 3 Identified in Wild Macaca Mulatta in China

Primate bocaparvovirus (BOV) is a possible cause of respiratory disorders and gastroenteritis in humans. However, the diversity and evolution of these viruses remain largely unknown, despite the identification of a growing number of BOVs in non-human primates (NHPs). Here, we report the identification of a novel BOV (provisionally named Macaca mulatta bocaparvovirus [MmBOV]) in the feces of wild Macaca mulatta in China by viral metagenomic analysis. Seven of 400 fecal samples from Macaca mulatta were positive for MmBOV. An almost complete genome sequence of 4,831 nucleotides was obtained, which had genomic organization and protein motifs similar to human bocaviruses (HOBVs), and shared characteristically low G/C content and weak codon usage bias. Sequence analyses of NS1, NP1, and VP1 revealed that MmBOV was most closely related to HBOV4 of Primate bocaparvovirus 2 (approximately 68.4%/70.6%, 73.3%/67.6%, and 70.4%/73.1% nucleotide/amino acid identities, respectively). Additionally, phylogenetic analysis revealed that MmBOV formed an independent peripheral branch, but clustered closely with those of the Primate bocaparvovirus species in the BOV genus (particularly HBOV4). These data strongly suggest that HBOV4 originated from NHP bocaparvoviruses around 200-300 years ago, and that NHPs may act as HBOV reservoirs. Following the International Committee of Taxonomy for Viruses guidelines, we propose MmBOV as a new species (tentatively named Primate bocaparvovirus 3) in the genus Bocaparvovirus, which is the first report of a novel species of primate BOV. Our data facilitate future research on the genetic diversity and evolution of primate bocaparvoviruses and highlight the importance of bocaparvovirus surveys in wild NHPs.

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Background

Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses.

Results

The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others).

Conclusions

All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

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

Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low. Mutational pressure acted as an increasingly dominant factor for the evolution of the virus compared with the natural selection. Notably, codon usage bias was also affected by the geographic distribution and isolated time. The first systemic analysis on the codon usage bias of the SVA provides important information for the understanding of the evolution of the SVA and has fundamental and theoretical benefits.

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus

The classical swine fever virus (CSFV), circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC) showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA) and translational selection-correlation analysis between the general average hydropathicity (Gravy) and aromaticity (Aroma), and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s). Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV.

Codon usage bias in the N gene of rabies virus

Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure. Additionally, we found that dinucleotide bias partly contributed to RABV codon usage bias. On the other hand, based on the clades of phylogenetic tree, we found that the evolutionary rate of the Africa 2 clade was the highest with a mean value of 3.75×10^-3 substitutions per site per year. Above all, our results regarding N gene of RABV codon usage will serve future RABV evolution research.

Genome-wide analysis of codon usage bias in Bovine Coronavirus

BACKGROUND

Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host's immune system and evolution.

METHODS

We performed a comprehensive analysis of codon usage and composition of BCoV.

RESULTS

The global codon usage among BCoV strains is similar. Significant differences of codon preferences in BCoV genes in relation to codon usage of Bos taurus host genes were found. Most of the highly frequent codons are U-ending. G + C compositional constraint and dinucleotide composition also plays a role in the overall pattern of BCoV codon usage.

CONCLUSIONS

The results of these studies revealed that mutational bias is a leading force shaping codon usage in this virus. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern.

Analysis of the codon usage of the ORF2 gene of feline calicivirus

Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role. Our results reveal part of the mechanisms driving FCV evolution, which will lay foundation for the further research of FCV.

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The codon usage of the ORF2 gene of FCV was first analysed in this study.

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The ORF2 gene of FCV shows a low codon usage bias.

Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host

Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future.

Characterization of the porcine epidemic diarrhea virus codon usage bias

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Codon usage bias of porcine epidemic diarrhea virus is low.

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Mutational bias and natural selection pressure influence codon usage bias of porcine epidemic diarrhea virus.

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Natural selection plays an increasingly significant role during evolution of porcine epidemic diarrhea virus.

Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree.

Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1

Two species of the DNA virus Torque teno sus virus (TTSuV), TTSuV1 and TTSuV2, have become widely distributed in pig-farming countries in recent years. In this study, we performed a comprehensive analysis of synonymous codon usage bias in 41 available TTSuV2 coding sequences (CDS), and compared the codon usage patterns of TTSuV2 and TTSuV1. TTSuV codon usage patterns were found to be phylogenetically conserved. Values for the effective number of codons (ENC) indicated that the overall extent of codon usage bias in both TTSuV2 and TTSuV1 was not significant, the most frequently occurring codons had an A or C at the third codon position. Correspondence analysis (COA) was performed and TTSuV2 and TTSuV1 sequences were located in different quadrants of the first two major axes. A plot of the ENC revealed that compositional constraint was the major factor determining the codon usage bias for TTSuV2. In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. Finally, the comparison of RSCU for TTSuV2, TTSuV1 and the corresponding host sequence indicated that the codon usage pattern of TTSuV2 was similar to that of TTSuV1. However the similarity was low for each virus and its host. These conclusions provide important insight into the synonymous codon usage pattern of TTSuV2, as well as better understangding of the molecular evolution of TTSuV2 genomes.

A detailed comparative analysis on the overall codon usage patterns in West Nile virus

West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments.

Patterns of synonymous codon usage on human metapneumovirus and its influencing factors

Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity.

Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1)

Torque teno sus virus 1 (TTSuV1) is a novel virus that has been found widely distributed in the swine population in recent years. Analysis of codon usage can reveal much about the molecular evolution of TTSuV1. In this study, synonymous codon usage patterns and the key determinants in the coding region of 29 available complete TTSuV1 genome sequences were examined. By calculating the nucleotide content and relative synonymous codon usage (RSCU) of TTSuV1 coding sequences, we found that the preferentially used codons were mostly those ending with A or C nucleotides; less-used codons were mostly codons ending with U or G nucleotides, and these were mainly affected by composition constraints. Although there was a variation in codon usage bias among different TTSuV1 genomes, the codon usage bias and GC content in the TTSuV1 coding region was lower, which was mainly determined by the base composition in the third codon position and the effective number of codons (ENC) value. Moreover, the results of correspondence analysis (COA) indicated that the codon usage patterns of TTSuV1 isolated from different countries varied greatly and had significant differences. In addition, Spearman’s rank correlation analysis and an ENC plot revealed that apart from mutation pressure, which was critical in determining the codon usage pattern, other factors were involved in shaping the evolution of codon usage bias in TTSuV1, such as natural selection. Those results suggested that synonymous codon usage patterns of TTSuV1 genomes were the result of interaction between mutation pressure and natural selection. The information from this study not only provides important insights into the synonymous codon usage pattern of TTSuV1, but also helps to identify the main factors affecting codon usage by this virus.

Selective pressure dominates the synonymous codon usage in parvoviridae

Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence's composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family.

Patterns and influencing factor of synonymous codon usage in porcine circovirus

Background

Analysis of codon usage can reveal much about the molecular evolution of the viruses. Nevertheless, little information about synonymous codon usage pattern of porcine circovirus (PCV) genome in the process of its evolution is available. In this study, to give a new understanding on the evolutionary characteristics of PCV and the effects of natural selection from its host on the codon usage pattern of the virus, Patterns and the key determinants of codon usage in PCV were examined.

Methods

We carried out comprehensive analysis on codon usage pattern in the PCV genome, by calculating relative synonymous codon usage (RSCU), effective number of codons (ENC), dinucleotides and nucleic acid content of the PCV genome.

Results

PCV genomes have relatively much lower content of GC and codon preference, this result shows that nucleotide constraints have a major impact on its synonymous codon usage. The results of the correspondence analysis indicate codon usage patterns of PCV of various genotypes, various subgenotypes changed greatly, and significant differences in codon usage patterns of Each virus of Circoviridae.There is much comparability between PCV and its host in their synonymous codon usage, suggesting that the natural selection pressure from the host factor also affect the codon usage patterns of PCV. In particular, PCV genotype II is in synonymous codon usage more similar to pig than to PCV genotype I, which may be one of the most important molecular mechanisms of PCV genotype II to cause disease. The calculations results of the relative abundance of dinucleotides indicate that the composition of dinucleotides also plays a key role in the variation found in synonymous codon usage in PCV. Furthermore, geographic factors, the general average hydrophobicity and the aromaticity may be related to the formation of codon usage patterns of PCV.

Conclusion

The results of these studies suggest that synonymous codon usage pattern of PCV genome are the result of interaction between mutation pressure and natural selection from its host. The information from this study may not only have theoretical value in understanding the characteristics of synonymous codon usage in PCV genomes, but also have significant value for the molecular evolution of PCV.

The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern

BACKGROUND

Hepatitis B virus (HBV) infection is one of the main human health problem and causes a large-scale of patients chronic infection worldwide.. As the replication of HBV depends on its host cell system, codon usage pattern for the viral gene might be susceptible to two main selections, namely mutation pressure and translation selection. In this case, a deeper investigation between HBV evolution and host adaptive response might assist control this disease.

RESULT

Relative synonymous codon usage (RSCU) values for the whole HBV coding sequence were studied by Principal component analysis (PCA). The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i) genotyps A and E, (ii) genotype B, (iii) genotypes C, D and G.

CONCLUSION

Codon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

In this study, an abundant (A + U)% and low codon bias were revealed in duck hepatitis virus type 1 (DHV-1) and the new serotype strains isolated from Taiwan, South Korea and Mainland China (DHV-N). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in these samples. By comparative analysis of the codon usage patterns of 40 ORFs of DHV, we found that all of DHV-1 strains grouped in genotype C; the DHV-N strains isolated in South Korea and China clustered into genotypes B; and the DHV-N strains isolated from Taiwan clustered into genotypes A. The findings revealed that more than one subtype of DHV-1 circulated in East Asia. Furthermore, the results of phylogenetic analyses based on RSCU values and Clustal W method indicated obvious phylogenetic congruities. This suggested that better genome consistency of DHV may exist in nature and phylogenetic analyses based on RSCU values maybe a good method in classifying genotypes of the virus. Our work might give some clues to the features and some evolutionary information of DHV.

Analysis of synonymous codon usage in hepatitis A virus

BACKGROUND

Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined.

RESULTS

The overall extent of codon usage bias in HAV is high in Picornaviridae. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.

CONCLUSIONS

HAV presents a higher codon usage bias than other members of Picornaviridae. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.

A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus

Hepatitis A virus (HAV) is a hepatotropic member of the family Picornaviridae. HAV has several unique biological characteristics that distinguish it from other members of this family. Recent and previous studies revealed that codon usage plays a key role in HAV replication and evolution. In this study, the patterns of synonymous codon usage in HAV have been studied through multivariate statistical methods on 30 complete open reading frames (ORFs) from the available 30 full-length HAV sequences. Effective number of codons (ENC) indicates that the overall extent of codon usage bias in HAV genomes is significant. The relative dinucleotide abundances suggest that codon usage in HAV can also be strongly influenced by underlying biases in dinucleotide frequencies. These factors strongly correlated with the first major axis of correspondence analysis (COA) on relative synonymous codon usage (RSCU). The distribution of the HAV ORFs along the plane defined by the first two major axes in COA showed that different genotypes are located at different places in the plane, suggesting that HAV codon usage is also reflecting an evolutionary process. It has been very recently described that fine-tuning translation kinetics selection also contributes to codon usage bias of HAV. The results of these studies suggest that HAV genomic biases are the result of the co-evolution of genome composition, controlled translation kinetics and probably the ability to escape the antiviral cell responses.

The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern

To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. The characteristics of the synonymous codon usage patterns and nucleotide contents of EV71 and the comparison between ENC values for the whole coding sequence of EV71 and that of coding sequences for viral proteins of EV71 all indicate that the interaction between mutation pressure from virus and natural selection from host exists in the processes of evolution of EV71. The synonymous codon usage pattern of EV71 is a mixture of coincidence and antagonism to that of host cell. In addition, the genetic diversity of EV71 strains and the preferential selection of some synonymous codons in EV71 strains based on the different epidemic areas were observed, suggesting that geographic and social factors may play roles in influencing the evolution of this virus.

Analysis of human P[4]G2 rotavirus strains isolated in Brazil reveals codon usage bias and strong compositional constraints

The Rotavirus genus belongs to the family Reoviridae and its genome consist of 11 segments of double-stranded RNA. Group A rotaviruses (RV-A) are the main etiological agent of acute viral gastroenteritis in infants and young children worldwide. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. However, the factors shaping synonymous codon usage bias and nucleotide composition in human RV-A are currently unknown. In order to gain insight into these matters, we analyzed the codon usage and base composition constraints on the two genes that codify the two outer capsid proteins (VP4 [VP8*] and VP7) of 58 P[4]G2 RV-A strains isolated in Brazil and investigated the possible key evolutionary determinants of codon usage bias. The results of these studies revealed that the frequencies of codon usage in both RV-A proteins studied are significantly different than the ones used by human cells. In order to observe if similar trends of codon usage are found when RV-A complete genomes are considered, we compare these results with results found using a dataset of 10 reference strains for whom the complete codes of the 11 segments are known. Similar results were obtained using capsid proteins or complete genomes. The general correlations found between the position of each sequence on the first axis generated by correspondence analysis and the relative dinucleotide abundances indicate that codon usage in RV-A can also be strongly influenced by underlying biases in dinucleotide frequencies. CpG and GpC containing codons are markedly suppressed. Thus, the results of this study suggest that RV-A genomic biases are the result of the evolution of genome composition in relation to host adaptation and the ability to escape antiviral cell responses.

Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences

Viruses have to exploit host transcription and translation mechanisms to replicate in a hostile host cellular environment, and therefore, it is likely that the infected host may impose pressure on viral evolution. In this study, we investigated differences in codon usage preferences among the highly mutable single strain RNA viruses which infect vertebrate or invertebrate hosts, respectively. We incorporate principal component analysis (PCA) and k-mean methods to clustering viruses infected with different type of hosts. The relative synonymous codon usage (RSCU) indices of all genes in 32 RNA viruses were calculated, and the correlation of the RSCU indices among different viruses was analyzed by the PCA. Our results show a positive correlation in codon usage preferences among viruses that target the same host category. Results of k-means clustering analysis further confirmed the statistical significance of this study, demonstrating that viruses infecting vertebrate hosts have different codon usage preferences to those of invertebrate viruses. Based on the analysis of the effective number of codons (ENC) in relation to the GC-content at the synonymous third codon position (GC3s), we further identified that mutational pressure was the dominant evolution driving force in making the different codon usage preferences. This study suggests a new and effective way to characterize host-dependent RNA viruses based on the codon usage pattern.

Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus

In this study, we calculated the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to implement a comparative analysis of codon usage pattern of open reading frames (ORFs) which belong to the two main genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By analysis of synonymous codon usage values in each ORF of PRRSV, the optimal codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in different ORFs of PRRSV were different and genetically conserved. Among them, ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main serotypes (EU and US). Due to mutational pressure, compositional constraint played an important role in shaping the synonymous codon usage pattern in different ORFs, and the synonymous codon usage diversity in ORFs was correlated with gene function. The degree of CUB for some particular amino acids under strong selection pressure probably served as a potential genetic marker for each ORF in PRRSV. However, gene length and translational selection in nature had no effect on the synonymous codon usage pattern in PRRSV. These conclusions could not only offer an insight into the synonymous codon usage pattern and differentiation of gene function, but also assist in understanding the discrepancy of evolution among ORFs in PRRSV.

Di-codon usage for classification of genes

Genes are often classified into biologically related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying genes by using di-codon usage as features. The method is illustrated on 1841 HLA sequences which are classified into two major classes, HLA-I and HLA-II, and further classified into the subclasses of major classes. By using both codon and di-codon features, we show near perfect accuracies in the classification of HLA molecules into major classes and their sub-classes.

Analysis of synonymous codon usage in classical swine fever virus

Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.

Comparison of correspondence analysis methods for synonymous codon usage in bacteria

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.