1
|
Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022; 9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.
Collapse
Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Lei Lu
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Fei-yang Pu
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - De-rong Zhang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Fu-qiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Fu-qiang Xie
| |
Collapse
|
2
|
Insight towards the effect of the multi basic cleavage site of SARS-CoV-2 spike protein on cellular proteases. Virus Res 2022; 318:198845. [PMID: 35680004 PMCID: PMC9170277 DOI: 10.1016/j.virusres.2022.198845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/27/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection presents an immense global health problem. Spike (S) protein of coronavirus is the primary determinant of its entry into the host as it consists of both receptor binding and fusion domain. Besides tissue tropism, and host range, coronavirus pathogenesis are primarily controlled by the interaction of S protein with the cell receptor. Moreover, the proteolytic activation of S protein by host cell proteases plays a decisive role. The host-cell proteases have shown to be involved in the proteolysis of S protein and cleaving it into two functional subunits, S1 and S2, during the maturation process. In the present study, the interaction of the S protein of SARS-CoV-2 with different host proteases like furin, cathepsin B, and plasmin has been analyzed using molecular docking and molecular dynamics (MD) simulation. Incorporation of the furin cleavage site (R-R-A-R) in the S protein of SARS-CoV-2 has been studied by mutating the individual amino acid. MD simulation results suggest the polytropic nature of the S protein. Our analysis indicated that a single amino acid substitution in the polybasic cleavage site of S protein perturb the binding of cellular proteases. This mutation study might help to generate an attenuated SARS-CoV-2. Besides, targeting host proteases by inhibitors may result in a practical approach to stop the cellular spread of SARS-CoV-2 and develop its antiviral.
Collapse
|
3
|
Jia L, Liang B, Wu K, Wang R, Liu H, Di Liu, Chen Q. Circulation, genomic characteristics, and evolutionary dynamics of class I Newcastle disease virus in China. Virulence 2022; 13:414-427. [PMID: 35188866 PMCID: PMC8865265 DOI: 10.1080/21505594.2022.2037342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Lijia Jia
- Cas Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega- Chinese Academy of Sciences, Wuhan, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bilin Liang
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ke Wu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Runkun Wang
- Cas Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega- Chinese Academy of Sciences, Wuhan, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Quanjiao Chen
- Cas Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega- Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
4
|
Mechanism of Cross-Species Transmission, Adaptive Evolution and Pathogenesis of Hepatitis E Virus. Viruses 2021; 13:v13050909. [PMID: 34069006 PMCID: PMC8157021 DOI: 10.3390/v13050909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
Hepatitis E virus (HEV) is the leading cause of acute hepatitis worldwide. While the transmission in developing countries is dominated by fecal-oral route via drinking contaminated water, the zoonotic transmission is the major route of HEV infection in industrialized countries. The discovery of new HEV strains in a growing number of animal species poses a risk to zoonotic infection. However, the exact mechanism and the determinant factors of zoonotic infection are not completely understood. This review will discuss the current knowledge on the mechanism of cross-species transmission of HEV infection, including viral determinants, such as the open reading frames (ORFs), codon usage and adaptive evolution, as well as host determinants, such as host cellular factors and the host immune status, which possibly play pivotal roles during this event. The pathogenesis of hepatitis E infection will be briefly discussed, including the special forms of this disease, including extrahepatic manifestations, chronic infection, and fulminant hepatitis in pregnant women.
Collapse
|
5
|
Analysis of codon usage pattern in the viral proteins of chicken anaemia virus and its possible biological relevance. INFECTION GENETICS AND EVOLUTION 2019; 69:93-106. [DOI: 10.1016/j.meegid.2019.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
|
6
|
Das M, Kumar S. Analysis of codon usage pattern of infectious laryngotracheitis virus immunogenic glycoproteins and its biological implications. INFECTION GENETICS AND EVOLUTION 2018; 62:53-59. [PMID: 29654923 DOI: 10.1016/j.meegid.2018.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 11/29/2022]
Abstract
Infectious laryngotracheitis virus (ILTV) is a highly contagious acute respiratory poultry pathogen. Modified live ILTV vaccines are the only control against ILT infections. Reversions and establishment of latent infections are the major concerns imparting the need to develop safer vaccines against ILTV infection. ILTV glycoprotein B and D (gB and gD) are major protective immunogens. The factors shaping synonymous codon usage bias and nucleotide composition in ILTV glycoprotein genes have not yet been reported. In the present study, we have analyzed the synonymous codon usage indices of ILTV gB and gD genes. Variation in the codon usage was seen in both the glycoproteins majorly by mutational pressure. The pattern was determined using the correspondence analysis, effective number of codon (Nc), GC3 plot and correlation analyses among different indices. The study is a comprehensive analysis of the codon usage patterns of ILTV glycoprotein genes. This will be helpful in understanding the codon usage bias of ILTV and related DNA viruses which could further explore its biology.
Collapse
Affiliation(s)
- Moushumee Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam Pin-781039, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam Pin-781039, India.
| |
Collapse
|
7
|
Kumar CS, Kumar S. Synonymous codon usage of genes in polymerase complex of Newcastle disease virus. J Basic Microbiol 2017; 57:481-503. [PMID: 28387456 DOI: 10.1002/jobm.201600740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 11/10/2022]
Abstract
Newcastle disease virus (NDV) is pathogenic to both avian and non-avian species but extensively finds poultry as its primary host and causes heavy economic losses in the poultry industry. In this study, a total of 186 polymerase complex comprising of nucleoprotein (N), phosphoprotein (P), and large polymerase (L) genes of NDV was analyzed for synonymous codon usage. The relative synonymous codon usage and effective number of codons (ENC) values were used to estimate codon usage variation in each gene. Correspondence analysis (COA) was used to study the major trend in codon usage variation. Analyzing the ENC plot values against GC3s (at synonymous third codon position) we concluded that mutational pressure was the main factor determining codon usage bias than translational selection in NDV N, P, and L genes. Moreover, correlation analysis indicated, that aromaticity of N, P, and L genes also influenced the codon usage variation. The varied distribution of pathotypes for N, P, and L gene clearly suggests that change in codon usage for NDV is pathotype specific. The codon usage preference similarity in N, P, and L gene might be detrimental for polymerase complex functioning. The study represents a comprehensive analysis to date of N, P, and L genes codon usage pattern of NDV and provides a basic understanding of the mechanisms for codon usage bias.
Collapse
Affiliation(s)
- Chandra Shekhar Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| |
Collapse
|
8
|
Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1. INFECTION GENETICS AND EVOLUTION 2017; 50:28-37. [PMID: 28189889 DOI: 10.1016/j.meegid.2017.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 12/22/2022]
Abstract
In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank complete genome sequences, and compared codon usage of class I (CI-29 sequences containing 132,675 codons) and class II (CII-259 sequences containing 1,184,925 codons) APMV-1 genomes. We also compared available complete fusion protein gene sequences (CI-175 sequences containing 96,775 codons; CII-1166 sequences containing 644,798 codons). Adaptation to Gallus gallus was compared among the different classes of viruses, among different genomic regions based on transcriptional levels, or among the fusion gene. Interestingly, distinctive codon usage determined by differences in relative synonymous codon usage and by codon adaptation indexes was observed for the two APMV-1 classes and for different transcriptional regions within classes. Furthermore, differential use of the third codon position and preferential use of codon pairs were seen for the two different classes and for selected genotypes of class II despite the fact that there were no large differences in nucleotide composition. The data suggest that codon usage has changed significantly since the two APMV-1 classes diverged, however, these changes are not significantly pronounced among viruses of the same genotype, suggesting that codon adaptation in APMV-1 occurs through a slow evolutionary process.
Collapse
|
9
|
Synonymous codon usage pattern in glycoprotein gene of rabies virus. Gene 2016; 584:1-6. [DOI: 10.1016/j.gene.2016.02.047] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/20/2022]
|
10
|
Makhija A, Kumar S. Analysis of synonymous codon usage in spike protein gene of infectious bronchitis virus. Can J Microbiol 2015; 61:983-9. [PMID: 26452019 DOI: 10.1139/cjm-2015-0418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Infectious bronchitis virus (IBV) is responsible for causing respiratory, renal, and urogenital diseases in poultry. IBV infection in poultry leads to high mortality rates in affected flocks and to severe economic losses due to a drop in egg production and a reduced gain in live weight of the broiler birds. IBV-encoded spike protein (S) is the major protective immunogen for the host. Although the functions of the S protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the S gene have not been reported yet. In the present study, we analyzed the relative synonymous codon usage and effective number of codons (Nc) using the 53 IBV S genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of Nc values against GC3 as well as the correlation between base composition and codon usage bias suggest that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in the S gene. Interestingly, no association of aromaticity, degree of hydrophobicity, and aliphatic index was observed with the codon usage variation in IBV S genes. The study represents a comprehensive analysis of IBV S gene codon usage patterns and provides a basic understanding of the codon usage bias.
Collapse
Affiliation(s)
- Aditi Makhija
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| |
Collapse
|
11
|
Kumar CS, Hazarika NMJ, Kumar S. Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus. Arch Virol 2015; 160:2359-66. [DOI: 10.1007/s00705-015-2505-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
|