Evolutionary and genetic analysis of the VP2 gene of canine parvovirus
BMC Genomics volume 18, Article number: 534 (2017)
Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness.
Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution.
There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.
Canine parvovirus (CPV) belongs to the genus Protoparvovirus and causes severe intestinal disease and leukopenia among carnivores, especially in canines and felines [1, 2]. CPV is a non-enveloped DNA virus with an approximately 5000-nucleotide, single-stranded DNA genome including two open reading frames (ORFs). The first ORF encodes two non-structural proteins (NS1 and NS2) and the second ORF encodes two structural proteins (VP1 and VP2) . VP2 is the most abundant structural protein, accounting for 90% of the viral capsid, and is able to self-assemble to make virus like particles (VLPs) . VP2 is a major antigenic determinant and plays a critical role in determining viral tissue tropism and host range [5, 6]. Notably, only a few amino acid substitutions in its sequence can alter relevant biological characteristics of the virus . NS1, is a pleiotropic nuclear phosphoprotein that is important for viral replication and is responsible for inducing apoptosis [8, 9]. Canine parvovirus (also known as CPV type 2) emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity . The virus experiences continuous genetic variation. CPV-2a, CPV-2b, and CPV-2c are the current three main antigenic variants of CPV . Amino-acid substitutions at specific VP2 residues are the basis for the classification of CPV type 2 viruses into variants CPV-2a, CPV-2b and CPV-2c [12, 13].
Group of codons that encode the same amino acid are generally referred to as ‘synonymous’ codons, although their corresponding tRNAs may be different from their relative abundance in cells and the ribosome recognition speed. Notably, the usage of synonymous codons is a non-random selection process. Some codons are used more often than others [14, 15], a phenomenon referred to as “codon usage bias” that can be found in numerous species, such as prokaryotes, eukaryotes, and viruses . Previous studies revealed that codon usage patterns are influenced by natural selection and mutation bias [17, 18]. The differential usage of synonymous codons (among other aspects of genome evolution) might be crucial to the understanding of viral biology, especially the interplay between viruses and the immune response. Genome-wide mutational pressure is the most important factor shaping patterns of codon usage bias in DNA viruses [19, 20]. Thus, understanding the codon usage of viruses can provide information about the mechanisms driving molecular evolution and expand our understanding of the regulation of viral gene expression. This will ultimately improve live attenuated vaccine antigenicity due to more efficient viral gene expression.
Compared with RNA viruses, DNA viruses have a lower mutation rate, thus, until now there has been very little research focusing on codon usage bias of animal DNA viruses. Of note, although CPV is a DNA virus, the genomic substitution rate of CPV is approximate to 10−4 per site per year, similar to RNA viruses . Previous studies showed that mutation pressure constrained by nucleotide composition and natural selection are two decisive forces driving the codon usage of DNA virus. To describe the genetic features of the VP2 gene of CPV, we analyzed in detail the genetic evolution, the codon usage pattern, and the evolutionary patterns of VP2 of CPV.
Phylogenetic analysis and amino acid mutant site analysis
To analyze the genetic diversity and evolution dynamics of CPV, we collected 424 full-length VP2 sequences of CPV obtained over a period of 38 years (from 1979 to 2016) from 21 countries that reported CPV epidemics and the phylogeny of the full-length VP2 gene (1755 base pairs) was reconstructed (Fig. 1). Based on the phylogeny, nucleotide identity (less than 99.7%) and Bayesian posterior probabilities, we identified six clades: GI to GVI. Group GI includes the earliest two CPV sequences from the USA from 1979 and 1980 and the earliest sequences from China from 1983; it also includes several recent origin CPV-2 isolates, suggesting that the early CPV-2 strain has re-emerged in canine populations in India and China. Sequences belonging to group GII are mainly from China, Thailand, and India from 2008 to 2011. Group GIII mainly consists of the early CPV-2a sequences from epidemics in Brazil in 1980, while group GIV mainly consists of sequences from the USA.
Sequences in group GV can be divided into four subgroups: GVa, GVb, GVc and GVd. GVa comprises CPV-2a strains from an epidemic in Brazil. Sequences in GVb and GVd have mainly circulated in Asia from 1995 to date, including China, Japan, India, South Korea, et. These sequences include different genotypes of CPV in these countries. Sequences in GVc are mainly from the USA, except for one from China. Similarly to group GV, group GVI can also be divided into four subgroups: GVIa, GVIb, GVIc and GVId. GVIa and GVIb mainly consist of sequences belonging to CPV-2a. GVIc is mainly composed of genotype CPV-2b sequences and almost all CPV-2c sequences form another independent subgroup, group GVId. Overall, early CPV 2a sequences mainly belong to Group GI and GII. CPV 2a is classified into clades GIII, GVd, GVIa and GVIb. CPV 2b sequences cluster with clades of GVd, and GVIc, while CPV-2c is mainly clusters with the GVId group in this study.
Interestingly, analysis of the amino acid alignments (Table 1) revealed universal substitution of amino acid sites: K80R, K93 N, V103A, D323N, N564S, and A568G. In addition, mutant sites discovered in special genotype: M87 L, I101T, A300G, and D305Y in CPV-2a; N426D substitution in CPV-2b in 1984; and N426E substitution in CPV-2c. Moreover, new CPV-2a and CPV-2b carrying a S297A substitution were identified. Other potential important substitutions were also found in CPV isolates: F267Y, Y324I, and T440A (Table 1). The detailed numbers of the three sites of the 424 sequences are listed in the Additional file 1: Table S1. Additionally, a Q370R change was found in some CPV-2c strains isolated from China.
Composition of the CPV VP2 gene
The nucleotide content of the analyzed sequences were calculated (Additional file 1: Table S2). The A%, T%, C%, and G% were 34.98 ± 0.118, 29.15 ± 0.66, 15.79 ± 0.113, and 19.8 ± 0.093 (mean ± standard deviation; mean ± SD) respectively. This indicates that all the selected sequences are A/T rich with subtle differences among the CPV VP2 sequences. Additionally, the codon composition at the third position including A3, G3, T3, C3, and GC3 were calculated with mean ± SD of 56.69 ± 0.4086, 8.97 ± 0.3638, 53.68 ± 0.3296, 5.91 ± 0.3346, and 32.62 ± 0.4391 further suggesting that A/T terminated codons might be more abundant than G/C terminated codons. Accordingly, the GC composition of CPV VP2 was low, ranging from 34.9% to 36.75% (mean 35.67%, SD ± 0.1672) compared with other vertebrate DNA viruses.
Synonymous codon usage bias among CPV VP2 genes
The various RSCU of synonymous codons of the CPV VP2 gene were calculated to decrypt the degree of preferred A/T-terminated codons (Table 2). Among the eighteen most abundant codons, all were A/T terminated codons including ten T-terminated codons (TGT for Cys, GAT for Asp, TTT for Phe, GGT for Gly, CAT for His, ATT for IIe, AAT for Asn, TAT for Tyr, GTT for Val, and TCT for Ser) and eight A-terminated codons (GCA for Ala, GAA for Glu, AAA for Lys, TTA for Leu, CCA for Pro, CAA for Gln, AGA for Arg, and ACA for Thr). This indicates codon usage bias in synonymous codons. This together with the nucleotide composition analysis indicates that the usage of optional codons might be influenced by compositional constraints resulting in the presence of mutational pressure.
Moreover, the effective number of codons (ENC) values were calculated to quantify the extent of codon usage bias of the CPV VP2 gene. ENC values ranged from 31.85 to 34.83 with an average value of 32.62 and a SD of 0.43 indicating a high codon usage bias.
Mutational pressure shaping codon usage bias
ENC plots were constructed according to the geographical distribution and isolation time (Fig. 2a and b respectively). The ENC plots show that not all the different sequences are positioned on the standard curve, indicating that mutational pressure is not the sole factor shaping codon usage bias but other forces, including geographical distribution, could play a role too. Additionally, sequences isolated from different countries and years clustered together with slight fluctuation except for sequences isolated from Germany in 1995. This result is consistent with the small SD of the ENC.
To explain the influence of mutational pressure on synonymous codon usage bias in-depth, correlation analyses was performed between the nucleotide compositions (A%, T%, G%, C%, and GC%) and codon compositions (A3s, T3s, G3s, C3s, and GC3s) and the ENC values (Additional file 1: Table S3). The nucleotide contents correlated with composition (p < 0.01), excluding the relationship between T% and the A3 and C3, and GC% with the A3, G3. These results indicate that nucleotide composition constrains synonymous codon usage bias and hence mutational pressure.
To analyze the variation of codon usage in the CPV VP2 gene, CoA analysis—a multivariable method—was employed  (Fig. 3a). The analysis suggested that the first four principal axes accounted for 60.56% of the total variation with the first, second, third, and fourth principal axis accounting for 23.17%, 14.65%, 13.2%, and 9.55%, respectively, suggesting that the variation of RSCU of synonymous codons were contributed by the first and second axis, this phenomenon regarded as the tendency of codon usage bias. To understand the distribution of synonymous codons, the first and second axes values were plotted against each other. The CoA-RSCU analysis revealed that all of the eighteen frequently employed codons—ending with A/T—clustered near the origin with slightly deviation from each other. Additionally, the remarkable correlation between the first axis and codon compositions demonstrated that nucleotide composition contributed to codon usage.
Evolutionary rate analysis
The evolutionary rate of the CPV2 gene in the five continents was estimated (Fig. 3b) revealing that the substitution rates of strains isolated from Asia and Europe descend over time (−1.17 × 10−5 and −3.4 × 10−5 respectively). However, sequences collected from Oceania, South America, and North America increased with rates of 7.8 × 10−6, 1.9 × 10−6, and 2.6 × 10−6 respectively. Additionally, the Asian and European sequences experienced wider substitution ranges, not falling within the regression lines.
The role of natural selection in shaping codon usage bias
To determine the role of natural selection in shaping codon usage of CPV VP2, the correlations between codon usage composition (A3s, T3s, G3s, C3s, GC3s) and Gravy and Aroma were calculated (Additional file 1: Table S3). The result shows that both Gravy and Aroma were significantly correlated with codon usage composition (p < 0.01) while Gravy correlated with T3 s with a higher p value (0.01 < p < 0.05), revealing that translational selection is one factor affecting codon usage during the evolution of CPV.
The role of dinucleotide abundance driving the codon usage of CPV VP2
Analysis of the sixteen dinucleotides (Additional file 1: Table S4) showed that no dinucleotide frequency equaled to the expected value, thus no dinucleotide was randomly used. Over-represented dinucleotides were TpG, GpG, CpA, while under-represented dinucleotides were CpG and TpC. The most under-represented dinucleotide was CpG, in accordance with the fact of GC being the lowest nucleotide composition and that none of the eighteen most frequently used synonymous codons ended in G/C. This indicates that the dinucleotide frequency shapes the codon usage of the CPV VP2 gene.
The decisive factor in shaping codon usage bias—Mutational pressure vs. natural selection
Based on the analysis above, it can be concluded that the codon usage pattern was influenced not only by mutational pressure but also by natural selection. Therefore, to determine the decisive one shaping codon usage bias, neutrality analysis was performed (Fig. 4a). The neutrality analysis showed that the GC12 value did not correlate with the GC3 value (R2 = 0.003261). The slope of the regression line was −0.02745 ± 0.02336, with p > 0.01, indicating no correlation between GC3s and GC12s. Thus, natural selection dominates directional mutation pressure in driving the codon usage pattern.
Moreover, the evolutionary rate was plotted by GC12s or GC3s against evolution time (Fig. 4b). The plot shows that GC12 is negatively correlated with year of isolation, while the GC3 is positively correlated with year of isolation, suggesting that the role of mutational pressure is increasing with CPV evolution.
Other factors shaping codon usage bias
Previous studies have shown that geographical distribution also contributes to codon usage patterns . To investigate if this is the case for the CPV VP2 gene, the CoA according to isolated areas were analyzed (Fig. 5). We found that different sequences isolated from different countries diverged from each other, in particular sequences isolated from China, France, and Russia. Notably, isolates from the same country did not cluster together, such that the Chinese sequences exhibited a significant distribution, indicating that the CPV VP2 gene experienced mutation during its evolution.
Since the emergence of canine parvovirus, there has been a lack of systematic genomic analysis on the evolution of CPV type 2 VP2 gene. This study represents a large-scale comprehensive analysis, as phylogenetic analysis and mutant analysis combined with codon usage analysis was performed.
CPV VP2 is a main structural protein, which determines the major mutations during the evolution of CPV. CPV has some persistent genetic variations and at present CPV-2a, CVP-2b, and CPV-2c are the three major antigenic variants of origin CPV type 2 [13, 23]. The phylogenetic analysis performed here showed that CPV VP2 diverged into 6 clades: GI, GII, GIII, GIV, GV, GVI and there are no differences in the geographical distribution of the sequences.
The phylogeny revealed that the GI, GII, and GIII group mainly include the early CPV-2a sequences. The genotype of the CPV-2b antigenic variant mainly belongs to the GVIc group worldwide. Almost all the CPV-2c strains formed another independent subgroup, named group GVId. It is important to note that the CPV-2a, CPV-2b, and CPV-2c variants do not cluster into to the same clades based on the phylogeny. This is because the classification into genotypes is based on mutation sites while the phylogeny is reconstructed based on nucleotide relationships. Nowadays, CPV-2a and CPV-2b are predominant in Asian countries including Korea, China, Thailand, Japan, Taiwan, and India. Outside of Asia, CPV-2a and 2b isolates are common in the United States, whereas CPV-2c is more widespread in Uruguay, Brazil, and Argentina . The phylogenetic analysis demonstrated the evolution of CPV VP2 from a macro-perspective, while the detailed changes were analyzed by amino acid mutant analysis and codon usage analysis. It is considered that CPV, as the original type 2 (origin CPV type 2), emerged in 1978 and is a specific variant of feline panleukopenia virus . Several amino acid mutations (M87 L, I101T, A300G, D305Y) in CPV 2a  as well as the N426D mutation in VP2 of CPV-2b  result in biological differences between CPV-2 and CPV-2a, CPV 2b, respectively, including antigenic reactivity to monoclonal antibodies, binding affinity to the feline transferrin receptor, and the ability to replicate in cats [27,28,29]. In addition, a third variant carrying a N426E mutation, that is critical to distinguish CPV-2a, CPV-2b and CPV-2c strains (Table 1), was discovered in Italy in 2000 .
New variants discovered in CPV-2a and CPV-2b carrying substitutions on site 297 were previously identified and designated as new CPV-2a and new CPV-2b, respectively [30, 31]. This site is under strong positive selection and may have had a remarkable influence on the process of host adaptation . This site is defined as a marker in identifying the new CPV-2a and new CPV-2b variants. Except for these mutations, a Q370R mutation was only found in some CPV-2c strains isolated from China and Taiwan. Previous studies have suggested that this is evidence of a potential CPV-2c variant or new CPV-2c. Further studies regarding the potential variant CPV-2c strains should be conducted to understand the relationship between the Q370R substitution and viral pathogenicity .
In addition, we found other mutations (F267Y, Y324I and T440A) in genotype new CPV 2a and 2b, which had been previously described. These may contribute to virus immune escape via antigenic drift and consequent vaccine failure [33,34,35,36]. Among the non-synonymous mutations, amino acid residue 267 is not exposed on the capsid surface and thus substitutions in this position may not affect the antigenicity of the virus . The T324I mutation in CPV-2a strains may be a common amino acid alteration in Asian countries, especially in China  and in South America. Mutations at amino acid residue 324 may have an impact on parvovirus host range  and it was also been demonstrated that the T324I mutation occurs in regions referring to potentially important antigenic epitopes. This substitution might have a direct influence on viral biology . The T440A mutation is also important for CPV because residue 440 is located on the top of the three-fold spike of the VP2 protein on the surface of the capsid, the main viral antigenic site [39, 40]. Therefore, resulting in the emergence of further antigenic variants. Overall, further studies on the effects of the F267Y, Y324I, and T440A mutations on CPV VP2 are imperative. Additionally, we found amino acid substitutions: K80R, K93 N, V103A and D323N, in agreement with previous studies [27, 41, 42].
Our study has several limitations. Firstly, not all CPV sequences were included. For example, sequences collected from Oceania are not complete and thus not included, which might impair the correct characterization of the geographical distribution of CPV in New Zealand in comparison with the study of Ohneiser et al. . Secondly, the sequences analyzed are very similar to each other with 99.7% identity. Since the sequences were obtained from GenBank and probably obtained by PCR amplification, we have no information on the levels of fidelity of the enzymes that were used and measures to control for PCR bias.
The evolutionary rate of the CPV VP2 gene was estimated for the first time according to the geographical distribution in different continents, which revealed that the evolutionary rate of CPV VP2 in Asia and Europe decreased.
Furthermore, to understand the molecular evolution of CPV from 1979 to 2016, the codon usage of the 424 coding sequences of the CPV type 2 VP2 gene were analyzed. Previous studies demonstrated that the degree of codon usage bias is different among the different species, even for genes belonging to the same species [44,45,46,47]. It is considered that mutation pressure [48, 49] or natural selection [50, 51] are the two major factors affecting codon usage bias, as well as other factors such as secondary mRNA structure , tRNA abundance , geographical distribution , and external environment . To date, most studies on codon usage bias focus on RNA viruses and their complete genomes. There are few studies on DNA viruses and in single genes. Here, we firstly analyzed the nucleotide composition of CPV VP2 and we found that the A/T content was higher than the G/C content and that A/T terminated codons were preferred than G/C terminated codons. Furthermore, most of the eighteen most frequently used codons ended in A/T. Altogether this indicates that there is codon usage bias in the CPV VP2 gene.
Here ENC analysis was employed to evaluate the codon usage bias of the VP2 gene of CPV. Compared with previously reported DNA viruses such as porcine circovirus  (mean value 56.80), human herpesvirus  (range from 39.47 ± 4.81 to 54.92 ± 3.26), duck plague virus UL35 gene  (mean value 47.55), duck enteritis virus UL24 gene  (range from 40.10 to 60.44), and iridovirus  (range from 35.87 to 51.81), canine parvovirus  exhibits high codon usage bias (36.46), in accordance with the study of Shackelton et al. . Interestingly, we found that among the above-mentioned DNA viruses, porcine circovirus exhibits lower codon usage while CPV exhibits much higher codon usage bias. This might be the result of small DNA viruses replicating in cells that are mitotically active  and the CPV having a strict host range, for example, the origin CPV type 2 is only infectious in dogs, while CPV 2a and CPV 2b infect both dogs and felines.
In this study, the ENC-plot analysis showed that all points representing different sequences were lower than the theoretical curve, which is suggestive of mutation pressure contributing to the codon usage pattern and also revealing that other factors also influence the codon usage of the CPV VP2 gene. Mutation pressure and natural selection were proven to be the two main factors shaping codon usage bias. To explore the role of mutation pressure, the correlation between nucleotide content and codon composition was analyzed and showed a strong correlation. However, the relationship between T%, A3s and C3 indicated that the codon usage pattern was influenced by mutation pressure. Further, the CoA based on RSCU analysis demonstrated the role of mutation pressure. Thus, mutation pressure is essential in shaping the codon usage of the VP2 gene of CPV in accordance with previous studies showing that mutational bias is important in shaping the codon usage pattern of DNA viruses .
To demonstrate the possible role of natural selection, a strong correlation between nucleotide content and Gravy/Aroma was revealed, suggesting that natural selection is more important shaping the codon usage than mutation pressure. This was significantly demonstrated by neutrality analysis in which the natural selection constrains the codon usage bias (97.25% coverage). In conclusion, high codon usage bias was observed for the VP2 gene of CPV, which was mainly caused by natural selection, in contrast to porcine circovirus that is mainly driven by mutation pressure . In addition, the results reveal that the suppression of CpG in CPV VP2, which might due to the innate immune system of host treatment of unmethylated CpGs, is a pathogen characteristic. Also, geographical distribution is correlated with the codon usage pattern of VP2 by CoA analysis based on the country of isolation. Thus, codon usage analysis, natural selection, mutation pressure, dinucleotide abundance and geographical distribution are essential.
In conclusion, a total of 424 sequences of the CPV type 2 were analyzed and new viewpoints regarding phylogenetic relationships, amino acid mutations, and codon usage were discovered including: CPV VP2 sequences can be classified into six clades GI, GII, GIII, GIV, GV, and GVI; the origin CPV type 2 sequences mainly belong to Group GI and GII; genotype CPV 2a cluster into clades GIII, GVd, GVIa and GVIb; CPV 2b sequences cluster into clades GVd, and GVIc; and CPV-2c cluster into group GVId. Additionally, the substitution rates of sequences isolated from Asia and Europe descended over time. Most importantly, natural selection is the force that has the biggest impact in driving the codon usage of CPV. These new results regarding CPV evolution will greatly serve future CPV research.
Materials and methods
A total of 424 reference sequences were extracted from the National Center for Biotechnological Information (NCBI) website (https://www.ncbi.nlm.nih.gov/) including 744,120 codons. The complete coding sequences (CDS) of CPV type 2 VP2 were 1755 bp in length, representing 21 countries across the world and isolated from 1979 to 2016. Detailed information is listed in Additional file 1: Table S5.
Phylogenetic and amino acid analysis
Maximum clade credibility (MCC) trees were inferred using Bayesian evolutionary analysis by sampling trees (BEAST, version 1.8.4, http://beast.bio.ed.ac.uk) using HKY as the nucleotide substitution model with gamma-distributed rate heterogeneity and a relaxed molecular clock. The Markov chain Monte Carlo (MCMC) algorithm was run for 100-million generations; 10 % of the chain was removed as burn-in. The time to the most recent common ancestor (tMRCA) was estimated. It is essential to note that the value of the Bayesian posterior probabilities indicate the support value of each node. Bayesian posterior probability >0.5 of the relative clades were displayed in the tree. The posterior probability of clades GVId was 0.23, while the GVI clade with value less than 0.1, due to the similarity of the relative sequences. Amino acid mutations and mutation sites were analyzed using the DNASTAR software.
Evolutionary rate of the CPV VP2 gene
The evolutionary rate was calculated as the number of substitutions per site per year. The evolutionary rate of the sequences derived from each continent was analyzed and compared to the earliest identified sequence for that continent, respectively. The substituted sites were aligned by method of Align by ClustalW using the MEGA7.0 software. Linear regression was calculated using Graph Pad Prism 6.0.
Codon usage measurement indices
The frequencies of the related coding sequences for nucleotide content (A%, C%, T%, and G%) were analyzed using BioEdit. The synonymous codons on the third position (A3%, C3%, T3%, and G3%) were calculated using the CodonW (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::CodonW) without confusing the amino acid composition or the overall G + C at the third codon positions. In addition, cusp (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::cusp) was employed to measure the G + C at the first and second positions of the synonymous codons.
The effective codon usage statistic-ENC
The magnitude of codon usage of relative viruses were reflected by the ENC . ENC values range from 20 to 61, with a score of 20 signifying severe bias (only one codon being employed in each synonymous codon) and a score of 61 denoting no bias (the frequency of all employed codons are equal in coding amino acids). The ENC was calculated as the given formula:
In the i-fold degenerate amino acids, F (i = 2,3,4,6) represents Fi values of them. An ENC value less than 35 is considered a stronger indication of codon usage bias .
The ENC-plot is an absolute statistic to evaluate the decisive factor in shaping codon usage bias. ENC values were taken into account for the background of the GC3s . If codon usage is constrained only by G + C mutation bias, the expected ENC values would simply lie on or around the standard curve. Alternatively, other factors such as natural selection may play a major role in shaping codon usage bias. The ENC plots were calculated using the following formula:
where s is the GC content at the third codon position, namely the GC3s.
Relative synonymous codon usage analysis
Relative synonymous codon usage (RSCU) was previously employed to estimate the codon usage bias of a particular gene or genome , using the ratio of observed frequency to theoretical frequency , with the formula given below:
It’s essential to note that g ij represent the i th codon of the j th amino acid, and n i represent the kinds of synonymous codons . All codons, except Met, Trp, and termination codons were used equally for the corresponding amino acid. Without the influence of the amino acid frequency, the RSCU matrix was considered the preferred method. In contrast to the ENC, larger RSCU values indicate stronger codon usage bias, such that RSCU values equal to 1, means no bias, more than 1 indicates positive codon usage bias, otherwise, negative codon usage bias.
General average hydrophobicity (Gravy) and aromaticity (Aroma) analysis
The Gravy and Aroma scores represent a particular amino acid usage, which result from translation selection, namely natural selection. Both the Gravy and Aroma scores were calculated using CondoW (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::CodonW) . The hydrophobicity of each amino acid is denoted by the Gravy index . Similarly, the occurrence of aromatic amino acids (Phe, Trp and Tyr) is revealed by the Aroma value.
Multifactor variable-CoA analysis
To analyze the variation of codon usage data, CoA analysis—a multivariable method—was employed . The RSCU of all the selected sequences was used to measure the synonymous codon usage pattern. The RSCU values of all codons were distributed into a 59-dimension space (excluding for three terminated codons, Met and Trp) and transformed into unrelated factors. Therefore, the factors affecting codon usage bias were detected [69, 70]. In this study, excluding the influence of unequal usage of amino acid, the axes were reduced to 40, even though the synonymous codons were 59 . In this analysis, CoA was plotted against RSCU. Moreover, CoA based on the isolated locations was analyzed.
Neutral evolution analysis
To differentiate the varying role of mutation pressure and natural selection, neutral analysis was employed . Neutrality plots represent the GC12s against the GC3s. Each independent dot represents a selected sequence. The regression line was employed to explain the major role of mutation pressure as opposed to natural selection. In addition, the evolutionary rate was explained by GC12s or GC3s plotted against an isolated year which was drawn using Graph Pad Prism 6.0.
Dinucleotide frequency analysis
Dinucleotide abundance correlates with codon usage bias , therefore, the sixteen dinucleotide compositions of the coding sequences of VP2 representing 424 sequences were calculated using the software DAMBE using the following formula as previously described :
f x , f y represent the occurance of the nucleotide X, Y respectively, while f xy denotes the observed occurrence of dinucleotide XY. f x f y denote the expected occurance of dinucleotide XY. It is considered that P xy > 1.23 suggests over-represented while P xy <0.78 suggests under-represented.
Correlation analysis of nucleotide composition with A3s, T3s, G3s, C3s, GC3s, Aroma, Gravy, ENC, 1st axis and 2nd axis were calculated using Graph Pad Prism 6.0.
Canine parvovirus type 2
Effective number of codons
Principal component analysis
The relative synonymous codon usage
Decaro N, Desario C, Parisi A, Martella V, Lorusso A, Miccolupo A, Mari V, Colaianni ML, Cavalli A, Di Trani L, et al. Genetic analysis of canine parvovirus type 2c. Virology. 2009;385(1):5–10.
Wang J, Lin P, Zhao H, Cheng Y, Jiang Z, Zhu H, Wu H, Cheng S. Continuing evolution of canine parvovirus in China: isolation of novel variants with an Ala5Gly mutation in the VP2 protein. Infection Genetics & Evolution Journal of Molecular Epidemiology & Evolutionary Genetics in Infectious Diseases. 2015;38:73–8.
Cotmore SF, Tattersall P. The autonomously replicating parvoviruses of vertebrates. Adv Virus Res. 1987;33:91–174.
Ja LDT, Cortés E, Martínez C. Ruiz dYR, Simarro I, Vela C, Casal I: Recombinant vaccine for canine parvovirus in dogs. J Virol. 1992;66(5):2748.
Hueffer K, Parker JS, Weichert WS, Geisel RE, Sgro JY, Parrish CR. The natural host range shift and subsequent evolution of canine parvovirus resulted from virus-specific binding to the canine transferrin receptor. J Virol. 2003;77(3):1718–26.
Nelson CD, Palermo LM, Hafenstein SL, Parrish CR. Different mechanisms of antibody-mediated neutralization of parvoviruses revealed using the fab fragments of monoclonal antibodies. Virology. 2007;361(2):283–93.
Parrish CR, Carmichael LE. Characterization and recombination mapping of an antigenic and host range mutation of canine parvovirus. Virology. 1986;148(1):121–32.
Saxena L, Kumar GR, Saxena S, Chaturvedi U, Sahoo AP, Singh LV, Santra L, Palia SK, Desai GS, Tiwari AK. Apoptosis induced by NS1 gene of canine parvovirus-2 is caspase dependent and p53 independent. Virus Res. 2013;173(2):426–30.
Gilbert L, Valilehto O, Kirjavainen S, Tikka PJ, Mellett M, Kapyla P, Oker-Blom C, Vuento M. Expression and subcellular targeting of canine parvovirus capsid proteins in baculovirus-transduced NLFK cells. FEBS Lett. 2005;579(2):385–92.
Meunier PC, Cooper BJ, Appel MJ, Slauson DO. Pathogenesis of canine parvovirus enteritis: the importance of viremia. Vet Pathol. 1985;22(1):60–71.
Decaro N, Buonavoglia C. Canine parvovirus--a review of epidemiological and diagnostic aspects, with emphasis on type 2c. Vet Microbiol. 2012;155(1):1–12.
Buonavoglia C, Martella V, Pratelli A, Tempesta M, Cavalli A, Buonavoglia D, Bozzo G, Elia G, Decaro N, Carmichael L. Evidence for evolution of canine parvovirus type 2 in Italy. J Gen Virol. 2001;82(Pt 12):3021–5.
Decaro N, Martella V, Desario C, Bellacicco AL, Camero M, Manna L, d'Aloja D, Buonavoglia C. First detection of canine parvovirus type 2c in pups with haemorrhagic enteritis in Spain. J Vet Med B Infect Dis Vet Public Health. 2006;53(10):468–72.
Grantham R, Gautier C, Gouy M, Mercier R, Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980;8(1):r49–62.
Marin A, Bertranpetit J, Oliver JL, Medina JR. Variation in G + C-content and codon choice: differences among synonymous codon groups in vertebrate genes. Nucleic Acids Res. 1989;17(15):6181–9.
Liu YS, Zhou JH, Chen HT, Ma LN, Pejsak Z, Ding YZ, Zhang J. The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern. Infect Genet Evol. 2011;11(5):1168–73.
Gu W, Zhou T, Ma J, Sun X, Lu Z. Analysis of synonymous codon usage in SARS coronavirus and other viruses in the Nidovirales. Virus Res. 2004;101(2):155–61.
Shi SL, Jiang YR, Liu YQ, Xia RX, Qin L. Selective pressure dominates the synonymous codon usage in parvoviridae. Virus Genes. 2013;46(1):10–9.
Moratorio G, Iriarte A, Moreno P, Musto H, Cristina J. A detailed comparative analysis on the overall codon usage patterns in West Nile virus. Infection Genetics & Evolution. 2013;14(1):396–400.
Shackelton LA, Parrish CR, Holmes EC. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol. 2006;62(5):551–63.
Shackelton LA, Parrish CR, Truyen U, Holmes EC. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc Natl Acad Sci U S A. 2005;102(2):379–84.
Singh NK, Tyagi A, Kaur R, Verma R, Gupta PK. Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus. Virus Res. 2016;221:58–65.
Hogezand RAV, Bänffer D, Zwinderman AH, Mccloskey EV, Griffioen G, Hamdy NAT. Antigenic analysis of canine parvovirus strains isolated in Italy. New Microbiol. 2000;23(1):93–6.
Amrani N, Desario C, Kadiri A, Cavalli A, Berrada J, Zro K, Sebbar G, Colaianni ML, Parisi A, Elia G, et al. Molecular epidemiology of canine parvovirus in Morocco. Infect Genet Evol. 2016;41:201–6.
Simpson AA, Chandrasekar V, Hébert BT, Sullivan GM, Rossmann MG, Parrish CR. Host range and variability of calcium binding by surface loops in the capsids of canine and feline parvoviruses 1. J Mol Biol. 2000;300(3):597–610.
Pérez R, Bianchi P, Calleros L, Francia L, Hernández M, Maya L, Panzera Y, Sosa K, Zoller S: Recent spreading of a divergent canine parvovirus type 2a (CPV-2a) strain in a CPV-2c homogenous population. Vet Microbiol 2012, 155(2–4):214–219.
Parrish CR. Mapping specific functions in the capsid structure of canine parvovirus and feline panleukopenia virus using infectious plasmid clones. Virology. 1991;183(1):195–205.
Parrish CR, Aquadro CF, Strassheim ML, Evermann JF, Sgro JY, Mohammed HO. Rapid antigenic-type replacement and DNA sequence evolution of canine parvovirus. J Virol. 1992;65(12):6544–52.
Truyen U, Gruenberg A, Chang SF, Obermaier B, Veijalainen P, Parrish CR. Evolution of the feline-subgroup parvoviruses and the control of canine host range in vivo. J Virol. 1995;69(8):4702–10.
Truyen U. Evolution of canine parvovirus--a need for new vaccines? Vet Microbiol. 2006;117(1):9–13.
Ohshima T, Hisaka M, Kawakami K, Kishi M, Tohya Y, Mochizuki M. Chronological analysis of canine parvovirus type 2 isolates in Japan. J Vet Med Sci. 2008;70(8):769.
Pereira CA, Leal ES, Durigon EL. Selective regimen shift and demographic growth increase associated with the emergence of high-fitness variants of canine parvovirus. Infect Genet Evol. 2007;7(3):399–409.
Geng Y, Guo D, Li C, Wang E, Wei S, Wang Z, Yao S, Zhao X, Su M, Wang X. Co-circulation of the rare CPV-2c with unique Gln370Arg substitution, new CPV-2b with unique Thr440Ala substitution, and new CPV-2a with high prevalence and variation in Heilongjiang Province. Northeast China PLoS One. 2012;10(9):e0137288.
Lin CN, Chien CH, Chiou MT, Chueh LL, Hung MY, Hsu HS: Genetic characterization of type 2a canine parvoviruses from Taiwan reveals the emergence of an Ile324 mutation in VP2. Virol J 2014, 11(1):1–7.
Han SC, Guo HC, Sun SQ, Shu L, Wei YQ, Sun DH, Cao SZ, Peng GN, Liu XT. Full-length genomic characterizations of two canine parvoviruses prevalent in Northwest China. Arch Microbiol. 2015;197(4):621–6.
Jeoung SY, Ahn SJ, Kim D. Genetic analysis of VP2 gene of canine parvovirus isolates in Korea. J Vet Med Sci. 2008;70(7):719–22.
Agbandje M, Parrish CR, Rossmann MG. The recognition of parvovirus capsids by antibodies. Semin Virol. 1995;6(6):219–31.
Nookala M, Mukhopadhyay HK, Sivaprakasam A, Balasubramanian B, Antony PX, Thanislass J, Srinivas MV, Pillai RM. Full-length VP2 gene analysis of canine parvovirus reveals emergence of newer variants in India. Acta Microbiol Immunol Hung. 2016;63(4):411–26.
Battilani M, Ciulli S, Tisato E, Prosperi S. Genetic analysis of canine parvovirus isolates (CPV-2) from dogs in Italy. Virus Res. 2002;83(2):149–57.
Tsao J, Chapman MS, Agbandje M, Keller W, Smith K, Wu H, Luo M, Smith TJ, Rossmann MG, Compans RW. The three-dimensional structure of canine parvovirus and its functional implications. Science. 1991;251(5000):1456–64.
Truyen U, Evermann JF, Vieler E, Parrish CR. Evolution of canine parvovirus involved loss and gain of feline host range. Virology. 1996;215(2):186–9.
Kelly WR. An enteric disease of dogs reselmbing feline panleucopaenia. Aust Vet J. 1978;54(12):593.
Ohneiser SA, Hills SF, Cave NJ, Passmore D, Dunowska M. Canine parvoviruses in New Zealand form a monophyletic group distinct from the viruses circulating in other parts of the world. Vet Microbiol. 2015;178(3–4):190–200.
Chen R, Yan H, Zhao KN, Martinac B, Liu GB. Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage. Mitochondrial DNA. 2007;18(4):269–78.
Jenkins GM, Holmes EC. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 2003;92(1):1–7.
Selva KC, Nair RR, Sivaramakrishnan KG, Ganesh D, Janarthanan S, Arunachalam M, Sivaruban T. Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects. Mitochondrial DNA. 2012;23(6):447–60.
Wong EH, Smith DK, Rabadan R, Peiris M, Poon LL. Codon usage bias and the evolution of influenza a viruses. Codon usage biases of influenza virus. BMC Evol Biol. 2010;10(1):1–14.
Liu W, Jie Z, Zhang Y, Zhou J, Chen H, Ma L, Ding Y, Liu Y. Compare the differences of synonymous codon usage between the two species within cardiovirus. Virol J. 2011;8(1):1–8.
Jenkins GM, Pagel M, Gould EA, Pm DAZ, Holmes EC. Evolution of base composition and codon usage bias in the genus Flavivirus. J Mol Evol. 2001;52(4):383–90.
Peixoto L, Zavala A, Romero H, Musto H. The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti. Gene. 2003;320(1):109–16.
Romero H, Zavala A, Musto H, Bernardi G. The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene. 2003;317(317):141–7.
Zama M. Codon usage and secondary structure of mRNA. Nucleic Acids Symp Ser. 1990;22:93.
Rocha EP. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 2004;14(11):2279–86.
Chen Y, Shi Y, Deng H, Gu T, Xu J, Ou J, Jiang Z, Jiao Y, Zou T, Wang C. Characterization of the porcine epidemic diarrhea virus codon usage bias. Infect Genet Evol. 2014;28:95–100.
Lynn DJ, Singer GAC, Hickey DA. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 2002;30(19):4272–7.
Liu XS, Zhang YG, Fang YZ, Wang YL. Patterns and influencing factor of synonymous codon usage in porcine circovirus. Virol J. 2012;9:68.
Fu M. Codon usage bias in herpesvirus. Arch Virol. 2010;155(3):391–6.
Cai M-S, Cheng A-C, Wang M-S, Zhao L-C, Zhu D-K, Luo Q-H, Liu F, Chen X-Y. Characterization of synonymous codon usage bias in the duck plague virus UL35 gene. Intervirology. 2009;52(5):266–78.
Jia R, Cheng A, Wang M, Xin H, Guo Y, Zhu D, Qi X, Zhao L, Ge H, Chen X. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes. 2009;38(1):96–103.
Tsai CT, Lin CH, Chang CY. Analysis of codon usage bias and base compositional constraints in iridovirus genomes. Virus Res. 2007;126(1–2):196–206.
Wang G, Liu Y, Qiao J, Meng Q, Yang H, Zhihao HE, Peng Y, Xie K, Chen C. Analysis of synonymous codon preference of the major protein genes of canine parvovirus. Journal of Shihezi University. 2013;
Liu XS, Zhang YG, Fang YZ, Wang YL. Patterns and influencing factor of synonymous codon usage in porcine circovirus. Virol J. 2012;9(1):1–9.
Wright F. The 'effective number of codons' used in a gene. Gene. 1990;87(1):23–9.
Comeron JM, Aguadé M. An evaluation of measures of synonymous codon usage bias. J Mol Evol. 1998;47(3):268–74.
Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol. 1986;24(1):28–38.
Peden J. Analysis of codon usage. PhD dissertation: University of Nottingham; 1999.
Nasrullah I, Butt AM, Tahir S, Idrees M, Tong Y. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution. BMC Evol Biol. 2015;15(1):1–15.
Lobry JR, Gautier C. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 1994;22(15):3174–80.
Sau K, Gupta SK, Sau S, Mandal SC, Ghosh TC. Factors influencing synonymous codon and amino acid usage biases in Mimivirus. Biosystems. 2006;85(2):107–13.
Ewens WJ, Grant G. Statistical methods in bioinformatics. Technometrics. 2006;44(1):101–49.
Greenacre MJ: Theory and applications of correspondence analysis. J Am Stat Assoc 1985, 80(392).
Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci U S A. 1988;85(8):2653–7.
Chiusano ML, Alvarez-Valin F, Di GM, D'Onofrio G, Ammirato G, Colonna G, Bernardi G: Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 2000, 261(1):63.
Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics Tig. 1995;11(7):283.
This paper was supported in part by the National Key Research and Development Program of China (2017YFD0500101); the National Natural Science Foundation of Jiangsu Province (Grant no.BK20170721); the Fundamental Research Funds for the Central Universities Y0201600147 and the Priority Academic Program Development of Jiangsu Higher Education Institutions.
Availability of data and materials
The datasets and materials used during the current study were obtained from National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/). The detailed accession numbers included in this study were in Additional file 1: Table S2. All sequence/date used in phylogenetic analysis were also achieved from NCBI (accession number were shown in Additional file 1: Table S2) .
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Table S1. The detail numbers of the three discovered mutation sites of the 424 sequences. Table S2. The nucleotide contents of the selected sequences and the mean ± SD values of the A%,T%,G%,C%,respectively. Table S3. The correlation analysis of codon usage indices. *Signifies 0.05 > p > 0.01; **signifies p < 0.01. Table S4. The abundance of the 16 dinucleotides. Table S5. The detail information of the 424 sequences. (DOCX 96 kb)
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Li, G., Ji, S., Zhai, X. et al. Evolutionary and genetic analysis of the VP2 gene of canine parvovirus. BMC Genomics 18, 534 (2017). https://doi.org/10.1186/s12864-017-3935-8