1
|
Fan P, Sun M, Zhang X, Zhang H, Liu Y, Yao Y, Li M, Fang T, Sun B, Chen Z, Chi X, Chen L, Peng C, Chen Z, Zhang G, Ren Y, Liu Z, Li Y, Li J, Li E, Guan W, Li S, Gong R, Zhang K, Yu C, Chiu S. A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer. Nat Commun 2024; 15:4330. [PMID: 38773072 PMCID: PMC11109247 DOI: 10.1038/s41467-024-48601-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) glycoproteins required for virus entry remains unclear. Here, we isolate a panel of Macaca-derived G-specific antibodies that cross-neutralize HNVs via multiple mechanisms. The most potent antibody, 1E5, confers adequate protection against the Nipah virus challenge in female hamsters. Crystallography demonstrates that 1E5 has a highly similar binding pattern to the receptor. In cryo-electron microscopy studies, the tendency of 1E5 to bind to the upper or lower heads results in two distinct quaternary structures of G. Furthermore, we identify the extended outer loop β1S2-β1S3 of G and two pockets on the apical region of fusion (F) glycoprotein as the essential sites for G-F interactions. This work highlights promising drug candidates against HNVs and contributes deeper insights into the viruses.
Collapse
Grants
- the Defense Industrial Technology Development Program, Grant No. JCKY2020802B001
- the Ministry of Science and Technology of China,Grant No. 2022YFC2303700; the Fundamental Research Funds for the Central Universities, Grant No. WK9100000032
- Hubei Jiangxia Laboratory, Grant No. JXBS002
- the Ministry of Science and Technology of China,Grant No. 2022YFC2303700, Grant No. 2022YFA1302700; the Strategic Priority Research Program of the Chinese Academy of Sciences, Grant No. XDB0490000; the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Grant No. QYPY20220019; the Fundamental Research Funds for the Central Universities, Grant No. WK9100000044
- the Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB0490000
Collapse
Affiliation(s)
- Pengfei Fan
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China.
| | - Mengmeng Sun
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xinghai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Huajun Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yujiao Liu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yanfeng Yao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ting Fang
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Bingjie Sun
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Zhengshan Chen
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Xiangyang Chi
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Li Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zhen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Guanying Zhang
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yi Ren
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Zixuan Liu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yaohui Li
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Jianmin Li
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wuxiang Guan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rui Gong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Changming Yu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China.
| |
Collapse
|
2
|
Aktürk Dizman Y. Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses. Virology 2024; 593:110030. [PMID: 38402641 DOI: 10.1016/j.virol.2024.110030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.
Collapse
Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Türkiye.
| |
Collapse
|
3
|
Pouresmaeil M, Azizi-Dargahlou S. Investigation of CaMV-host co-evolution through synonymous codon pattern. J Basic Microbiol 2024; 64:e2300664. [PMID: 38436477 DOI: 10.1002/jobm.202300664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/20/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
Collapse
Affiliation(s)
- Mahin Pouresmaeil
- Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Seed and Plant Certification and Registration Institute, Ardabil Agricultural and Natural Resources Research Center, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| |
Collapse
|
4
|
Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms 2024; 12:696. [PMID: 38674640 PMCID: PMC11052288 DOI: 10.3390/microorganisms12040696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.
Collapse
Affiliation(s)
- Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Naveen Kumar
- Diagnostics and Vaccines Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462021, Madhya Pradesh, India;
| | - Pragya Yadav
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Shubhankar Sircar
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Anita Shete-Aich
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Thomas Launey
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, Punjab, India
| |
Collapse
|
5
|
Lu M, Wan W, Li Y, Li H, Sun B, Yu K, Zhao J, Franzo G, Su S. Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability. Int J Biol Macromol 2023; 253:127319. [PMID: 37820917 DOI: 10.1016/j.ijbiomac.2023.127319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.
Collapse
Affiliation(s)
- Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Wenbo Wan
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Yuxing Li
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Haipeng Li
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Kang Yu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro 35020, PD, Italy
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China.
| |
Collapse
|
6
|
Guo F, Yang J, Abd El-Aty AM, Wang R, Ju X. Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation. Poult Sci 2023; 102:103029. [PMID: 37713803 PMCID: PMC10511809 DOI: 10.1016/j.psj.2023.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Goose astroviruses (GoAstVs) are causative agents that account for fatal infection of goslings characterized by visceral urate deposition, resulting in severe economic losses in major goose-producing regions in China since 2017. In this study, we sought to unravel the intrinsic properties associated with adaptation and evolution in the host environment of GoAstVs. Consistent results from phylogenetic analysis and correspondence analysis performed on the codon usage patterns (CUPs) reveal 2 clusters of GoAstVs, namely, GoAstV-1 and GoAstV-2. However, multiple similar compositional characteristics were found, despite the high divergence between GoAstV-1 and GoAstV-2. Studies on the base composition of GoAstVs reveal an A/U bias, indicating a compositional constraint, while natural selection prevailed in determining the CUPs in the virus genome based on our neutrality plot analysis, reflecting high adaptive pressure to fit the host environment. Codon adaptation index (CAI) analysis revealed a higher degree of fitness to the CUPs of the corresponding host for GoAstVs than avian influenza virus and betacoronaviruses, which may be a favorable factor contributing to the high pathogenicity and wide distribution of GoAstVs in goslings. In addition, GoAstVs were less adapted to ducks and chickens, with significantly lower CAI values than to geese, which may be a reason for the different prevalence of GoAstVs among these species. Extensive investigations on dinucleotide distribution revealed a significant suppression of the CpG and UpA motifs in the virus genome, which may facilitate adaptation to the host's innate immune system by evading surveillance. In addition, our study reported the trends of increasing fitness to the host's microenvironment for GoAstVs through increasing adaptation to host CUPs and ongoing reduction of CpG motifs in the virus genome. The present analysis deepens our understanding of the basic biology, pathogenesis, adaptation and evolutionary pattern of GoAstVs, and contributes to the development of novel antiviral strategies.
Collapse
Affiliation(s)
- Fucheng Guo
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jinjin Yang
- Technology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Ruichen Wang
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing 102206, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Marine Medical Research and Development Centre, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China.
| |
Collapse
|
7
|
Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023; 104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Poxviruses (family Poxviridae) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
Collapse
Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (Univ Montpellier CNRS, IRD), Centre National de la Recherche Scientifique, Montpellier, France
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| |
Collapse
|
8
|
Lu Y, Wang W, Liu H, Li Y, Yan G, Franzo G, Dai J, He WT. Mutation and codon bias analysis of the spike protein of Omicron, the recent variant of SARS-CoV-2. Int J Biol Macromol 2023; 250:126080. [PMID: 37536405 DOI: 10.1016/j.ijbiomac.2023.126080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is a heavily mutated virus and designated as a variant of concern. To investigate the codon usage pattern of this new variant, we performed mutation and codon bias analysis for Omicron as well as for its sub-lineages BA.1 and BA.2 and compared them with the original SARS-CoV-2 and the Delta variant sequences obtained in this study. Our results indicate that the sub-lineage BA.1 and BA.2 have up to 23 sites of difference on the spike protein, which have minimal impact on function. The Omicron variant and its sub-lineages have similar codon usage patterns and A/U ending codons appear to be preferred over G/C ending codons. The Omicron has a lower degree of codon usage bias in spite of evidence that natural selection, mutation pressure and dinucleotide abundance shape the codon usage bias of Omicron, with natural selection being more significant on BA.2 than the other sub-lineages of Omicron. The codon usage pattern of Omicron variant that we explored provides valid information for a clearer understanding of Omicron and its sub-lineages, which could find application in vaccine development and optimization.
Collapse
Affiliation(s)
- Yunbiao Lu
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China
| | - Weixiu Wang
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China
| | - Hao Liu
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China
| | - Yue Li
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China
| | - Ge Yan
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro 35020, PD, Italy
| | - Jianjun Dai
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
| |
Collapse
|
9
|
Gurjar P, Karuvantevida N, Rzhepakovsky IV, Khan AA, Khandia R. A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons. Vaccines (Basel) 2023; 11:vaccines11020487. [PMID: 36851364 PMCID: PMC9967482 DOI: 10.3390/vaccines11020487] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes' spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes.
Collapse
Affiliation(s)
- Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (A.A.K.); or (R.K.)
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah Universty, Bhopal 462026, India
- Correspondence: (A.A.K.); or (R.K.)
| |
Collapse
|
10
|
Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022; 12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.
Collapse
Affiliation(s)
- Yu Fan
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Duan Guo
- Department of Palliative Medicine, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu, China
- Palliative Medicine Research Center, West China−Peking Union Medical College, Chen Zhiqian (PUMC C.C). Chen Institute of Health, Sichuan University, Chengdu, China
| | - Shangping Zhao
- Department of Urology, West China School of Nursing and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| | - Tao Lin
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| |
Collapse
|
11
|
Ayolabi CI, Olusola BA, Lawal AA, Chibuike AD, Nzekwue BN. Detection of novel paramyxoviruses in Chaerephon bat species in Nigeria and phylogenetics of paramyxoviruses co-evolution with bats in Africa. Zoonoses Public Health 2021; 69:117-135. [PMID: 34817117 DOI: 10.1111/zph.12900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
Bat paramyxoviruses (PmV) are a diverse group of viruses and include zoonotic viruses such as henipaviruses. Members of this group in other continents have been associated with severe respiratory and neurological infections in animals and humans. Furthermore, despite the richness of diverse bat species that can transmit this virus in African countries like Nigeria, there is very scanty information as to the presence and co-evolution of paramyxoviruses in bats. There is a need for continuous surveillance of zoonotic viruses and their biological reservoirs as this will help in the prevention and management of pathogens' spillovers. This study detected novel paramyxoviruses in Chaerephon nigeriae bat species found in Badagry, Lagos. Phylogenetic analyses of paramyxovirus sequences' co-evolution with frugivorous and insectivorous bats circulating in African countries were also performed using sequences of African origin available in the Database of Bat-Associated Viruses (DBatVir: http://www.mgc.ac.cn/DBatVir/). Oral swabs (n = 18) and blood samples (n = 32) were collected from C. nigeriae bats in Badagry, Lagos. The L gene of bat paramyxovirus was detected in all oral swabs using PCR techniques. Six of the amplicons were successfully sequenced. Estimated phylogenies placed the sequences in close relationship with those isolated from insectivorous bats. Phylogenetic analyses of previously sequenced isolates in the African region showed the likelihood of different co-evolution mechanisms of paramyxoviruses with frugivorous bats compared with insectivorous bats. This may be due to codon usage bias of the L gene. Spatial distribution of paramyxoviruses in African countries showed limited ongoing surveillance of this virus in the continent, especially in southern and northern countries. Extensive surveillance of paramyxoviruses with possible zoonotic potentials among bat species in the continent is recommended. This will provide further insights into co-evolution as well as prevent possible spillover into the human population.
Collapse
|
12
|
Si F, Jiang L, Yu R, Wei W, Li Z. Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype. Front Microbiol 2021; 12:738082. [PMID: 34733253 PMCID: PMC8558211 DOI: 10.3389/fmicb.2021.738082] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.
Collapse
Affiliation(s)
- Fusheng Si
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ruisong Yu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhen Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
13
|
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Mishra A, Sood R, Srivastava P, Tripathi M, Zhang KYJ, Bhatia S. Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species. Viruses 2021; 13:1847. [PMID: 34578428 PMCID: PMC8473330 DOI: 10.3390/v13091847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
Many viruses that cause serious diseases in humans and animals, including the betacoronaviruses (beta-CoVs), such as SARS-CoV, MERS-CoV, and the recently identified SARS-CoV-2, have natural reservoirs in bats. Because these viruses rely entirely on the host cellular machinery for survival, their evolution is likely to be guided by the link between the codon usage of the virus and that of its host. As a result, specific cellular microenvironments of the diverse hosts and/or host tissues imprint peculiar molecular signatures in virus genomes. Our study is aimed at deciphering some of these signatures. Using a variety of genetic methods we demonstrated that trends in codon usage across chiroptera-hosted CoVs are collaboratively driven by geographically different host-species and temporal-spatial distribution. We not only found that chiroptera-hosted CoVs are the ancestors of SARS-CoV-2, but we also revealed that SARS-CoV-2 has the codon usage characteristics similar to those seen in CoVs infecting the Rhinolophus sp. Surprisingly, the envelope gene of beta-CoVs infecting Rhinolophus sp., including SARS-CoV-2, had extremely high CpG levels, which appears to be an evolutionarily conserved trait. The dissection of the furin cleavage site of various CoVs infecting hosts revealed host-specific preferences for arginine codons; however, arginine is encoded by a wider variety of synonymous codons in the murine CoV (MHV-A59) furin cleavage site. Our findings also highlight the latent diversity of CoVs in mammals that has yet to be fully explored.
Collapse
Affiliation(s)
- Naveen Kumar
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; (R.K.); (K.Y.J.Z.)
| | - Chandana Tennakoon
- Bioinformatics, Sequencing & Proteomics Group, The Pirbright Institute, Woking GU24 0NF, UK;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center ‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’, Moscow Region, 142290 Pushchino, Russia
| | - Anamika Mishra
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| | - Richa Sood
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| | - Pratiksha Srivastava
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| | - Meghna Tripathi
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; (R.K.); (K.Y.J.Z.)
| | - Sandeep Bhatia
- Zoonotic Diseases Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, India; (A.M.); (R.S.); (P.S.); (M.T.); (S.B.)
| |
Collapse
|
14
|
Identification and molecular characterization of H9N2 viruses carrying multiple mammalian adaptation markers in resident birds in central-western wetlands in India. INFECTION GENETICS AND EVOLUTION 2021; 94:105005. [PMID: 34293481 DOI: 10.1016/j.meegid.2021.105005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/03/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022]
Abstract
We report here a targeted risk-based study to investigate the presence of influenza A viruses at the migratory-wild-domestic bird interface across the major wetlands of central India's Maharashtra state during the winter migration season. The H9N2 viruses have been isolated and confirmed in 3.86% (33/854) of the fecal samples of resident birds. To investigate the genetic pools of H9N2 circulating in resident birds, we sequenced two isolates of H9N2 from distant wetlands. Sequence and phylogenetic analyses have shown that these viruses are triple reassortants, with HA, NA, NP, and M genes belonging to G1 sub-lineage (A/quail/Hong Kong/G1/1997), PB2, PB1, and NS genes originating from the prototype Eurasian lineage (A/mallard/France/090360/2009) and PA gene deriving from Y439/Korean-like (A/duck/Hong Kong/Y439/97) sub-lineage. It was confirmed not only that four of their gene segments had a high genetic association with the zoonotic H9N2 virus, A/Human/India/TCM2581/2019, but also that they had many molecular markers associated with mammalian adaptation and enhanced virulence in mammals including the unique multiple basic amino acids, KSKR↓GLF at the HA cleavage site, and analog N-and O-glycosylation patterns on HA with that of the zoonotic H9N2 virus. Furthermore, future experiments would be to characterize these isolates biologically to address the public health concern. Importantly, due to the identification of these viruses at a strategic geographical location in India (a major stop-over point in the Central Asian flyway), these novel viruses also pose a possible threat to be exported to other regions via migratory/resident birds. Consequently, systematic investigation and active monitoring are a prerequisite for identifying and preventing the spread of viruses of zoonotic potential by enforcing strict biosecurity measures.
Collapse
|
15
|
Das JK, Roy S. Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns. Genomics 2021; 113:2177-2188. [PMID: 34019999 PMCID: PMC8131179 DOI: 10.1016/j.ygeno.2021.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023]
Abstract
The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.
Collapse
Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, MD, USA.
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
| |
Collapse
|
16
|
Deb B, Uddin A, Chakraborty S. Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host. Virology 2021; 561:69-79. [PMID: 34171764 DOI: 10.1016/j.virol.2021.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
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.
Collapse
Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, 788150, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788150, Assam, India.
| |
Collapse
|
17
|
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Brief Bioinform 2021; 22:6231751. [PMID: 33866372 DOI: 10.1093/bib/bbab145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered regions/proteins (IDRs) are abundant across all the domains of life, where they perform important regulatory roles and supplement the biological functions of structured proteins/regions (SRs). Despite the multifunctionality features of IDRs, several interrogations on the evolution of viral genomic regions encoding IDRs in diverse viral proteins remain unreciprocated. To fill this gap, we benchmarked the findings of two most widely used and reliable intrinsic disorder prediction algorithms (IUPred2A and ESpritz) to a dataset of 6108 reference viral proteomes to unravel the multifaceted evolutionary forces that shape the codon usage in the viral genomic regions encoding for IDRs and SRs. We found persuasive evidence that the natural selection predominantly governs the evolution of codon usage in regions encoding IDRs by most of the viruses. In addition, we confirm not only that codon usage in regions encoding IDRs is less optimized for the protein synthesis machinery (transfer RNAs pool) of their host than for those encoding SRs, but also that the selective constraints imposed by codon bias sustain this reduced optimization in IDRs. Our analysis also establishes that IDRs in viruses are likely to tolerate more translational errors than SRs. All these findings hold true, irrespective of the disorder prediction algorithms used to classify IDRs. In conclusion, our study offers a novel perspective on the evolution of viral IDRs and the evolutionary adaptability to multiple taxonomically divergent hosts.
Collapse
Affiliation(s)
- Naveen Kumar
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Moscow region, Pushchino 142290, Russia
| | - Sonia Longhi
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sandeep Bhatia
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| |
Collapse
|
18
|
Malik YS, Ansari MI, Kattoor JJ, Kaushik R, Sircar S, Subbaiyan A, Tiwari R, Dhama K, Ghosh S, Tomar S, Zhang KYJ. Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Brief Bioinform 2021; 22:1006-1022. [PMID: 33377145 PMCID: PMC7953982 DOI: 10.1093/bib/bbaa383] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.
Collapse
Affiliation(s)
| | | | | | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Japan
| | | | | | - Ruchi Tiwari
- Department of Vet erinary Microbiology, DUVASU, Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Souvik Ghosh
- Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | | | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Japan
| |
Collapse
|
19
|
Huang W, Guo Y, Li N, Feng Y, Xiao L. Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 89:104736. [PMID: 33516969 PMCID: PMC7843097 DOI: 10.1016/j.meegid.2021.104736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/28/2020] [Accepted: 01/22/2021] [Indexed: 12/25/2022]
Abstract
Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans.
Collapse
Affiliation(s)
- Wanyi Huang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| |
Collapse
|
20
|
Abstract
The development of safe and effective vaccines against viruses is central to disease control. With advancements in DNA synthesis technology, the production of synthetic viral genomes has fueled many research efforts that aim to generate attenuated viruses by introducing synonymous mutations. Elucidation of the mechanisms underlying virus attenuation through synonymous mutagenesis is revealing interesting new biology that can be exploited for vaccine development. Here, we review recent advancements in this field of synthetic virology and focus on the molecular mechanisms of attenuation by genetic recoding of viruses. We highlight the action of the zinc finger antiviral protein (ZAP) and RNase L, two proteins involved in the inhibition of viruses enriched for CpG and UpA dinucleotides, that are often the products of virus recoding algorithms. Additionally, we discuss current challenges in the field as well as studies that may illuminate how other host functions, such as translation, are potentially involved in the attenuation of recoded viruses.
Collapse
|
21
|
Dimonaco NJ, Salavati M, Shih BB. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses 2020; 13:E49. [PMID: 33396801 PMCID: PMC7823979 DOI: 10.3390/v13010049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international "CoronaHack" in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene-gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.
Collapse
Affiliation(s)
- Nicholas J. Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales SY3 3FL, UK
| | - Mazdak Salavati
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Barbara B. Shih
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| |
Collapse
|
22
|
Nambou K, Anakpa M. Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104471. [PMID: 32707288 PMCID: PMC7374176 DOI: 10.1016/j.meegid.2020.104471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has caused thousands of deaths worldwide and has become an urgent public health concern. The extraordinary interhuman transmission of this disease has urged scientists to examine the various facets of its pathogenic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, based on publicly available genomic data, we analyzed the codon usage co-adaptation profiles of SARS-CoV-2 and other respiratory coronaviruses (CoVs) with their human host, identified CoV-responsive human genes and their functional roles on the basis of both the relative synonymous codon usage (RSCU)-based correlation of viral genes with human genes and differential gene expression analysis, and predicted potential drugs for COVID-19 treatment based on these genes. The relatively high codon adaptation index (CAI) values (>0.70) signposted the gene expressivity efficiency of CoVs in human. The ENc-GC3 plot indicated that SARS-CoV-2 genome was under strict selection pressure while SARS-CoV and MERS-CoV were under selection and mutational pressures. The RSCU-based correlation analysis indicated that the viral genomes shared similar codons with a panoply of human genes. The merging of RSCU-based correlation data and SARS-CoV-2-responsive differentially expressed genes allowed the identification of human genes potentially affected by SARS-CoV-2 infection. Functional enrichment analysis indicated that these genes were enriched in biological processes and pathways related to host response to viral infection and immune response. Using the drug-gene interaction database, we screened a list of drugs that could target these genes as potential COVID-19 therapeutics. Our findings not only will contribute in vaccine development but also provide a useful set of drugs that could guide practitioners in strategical monitoring of COVID-19. We recommend practitioners to scrupulously screen this list of predicted drugs in order to authenticate those qualified for treating COVID-19 symptoms.
Collapse
Affiliation(s)
- Komi Nambou
- Shenzhen Nambou1 Biotech, 506, Block B, West Silicon Valley, 5010 Baoan Avenue, Baoan District, Shenzhen, China.
| | - Manawa Anakpa
- Key Laboratory of Trustworthy Distributed Computing and Service, Ministry of Education, School of Sofware, Beijing University of Posts and Telecommunications, 10 Xitucheng Road, Haidian District, Beijing 100876, China
| |
Collapse
|
23
|
Sun J, Zhao W, Wang R, Zhang W, Li G, Lu M, Shao Y, Yang Y, Wang N, Gao Q, Su S. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. Int J Mol Sci 2020; 21:ijms21197129. [PMID: 32992529 PMCID: PMC7583936 DOI: 10.3390/ijms21197129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/17/2022] Open
Abstract
Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus.
Collapse
|
24
|
Silverj A, Rota-Stabelli O. On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus. Virus Res 2020; 286:198097. [DOI: 10.1016/j.virusres.2020.198097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
|
25
|
Khodary SM, Anwar AM. Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.01.019463. [PMID: 34013275 PMCID: PMC8132235 DOI: 10.1101/2020.04.01.019463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens . Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.
Collapse
|
26
|
Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. INFECTION GENETICS AND EVOLUTION 2020; 84:104399. [PMID: 32512206 DOI: 10.1016/j.meegid.2020.104399] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 01/06/2023]
Abstract
Mycobacterium lepromatosis was identified as a causative agent for leprosy in the year 2008 in the United States and later more cases were identified in Canada, Singapore, Brazil, and Myanmar. It is known to cause diffuse lepromatosis leprosy among humans. Since it is invasive, the mortality rates are higher in comparison to the M. leprae. At genomic level, there exists 90.9% similarity between M. lepromatosis and M. leprae. Codon usage analysis based on analyses of 228 coding sequences (CDSs) of M. lepromatosis, revealed that the genome is GC rich. Among the total 16 dinucleotides, CpG dinucleotide possesses the highest dinucleotide frequency in M. lepromatosis, that is strikingly an unobvious observation since higher CpG is associated with higher proinflammatory cytokine production and NF-κB activation that eventually leads to high pathogenicity. To evade immune response, CpG content is generally less in pathogens. The unusually high CpG content can be explained by the fact that the nucleotide composition of M. lepromatosis is CG rich. Various forces interplay to shape codon usage pattern of any organism including selection; mutation, nucleotide composition as well as GC biased gene conversion. To understand the interplay between various forces; neutrality, parity, Nc-GC3 (Effective number of codons-GC content at 3rd position of the codon), aromaticity (AROMO) and the general average hydropathicity score (GRAVY) analyses have been carried out. The analyses revealed that selection force is the major contributory force. Along with the selection; mutation, nucleotide composition as well as GC biased gene conversion also play role in shaping codon usage bias in M. lepromatosis. This is the first report on the codon usage in M. lepromatosis.
Collapse
|
27
|
Nunes A, Ribeiro DR, Marques M, Santos MAS, Ribeiro D, Soares AR. Emerging Roles of tRNAs in RNA Virus Infections. Trends Biochem Sci 2020; 45:794-805. [PMID: 32505636 DOI: 10.1016/j.tibs.2020.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Viruses rely on the host cell translation machinery for efficient synthesis of their own proteins. Emerging evidence highlights different roles for host transfer RNAs (tRNAs) in the process of virus replication. For instance, different RNA viruses manipulate host tRNA pools to favor viral protein translation. Interestingly, specific host tRNAs are used as reverse transcription primers and are packaged into retroviral virions. Recent data also demonstrate the formation of tRNA-derived fragments (tRFs) upon infection to facilitate viral replication. Here, we comprehensively discuss how RNA viruses exploit distinct aspects of the host tRNA biology for their benefit. In light of the recent advances in the field, we propose that host tRNA-related pathways and mechanisms represent promising cellular targets for the development of novel antiviral strategies.
Collapse
Affiliation(s)
- Alexandre Nunes
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Diana Roberta Ribeiro
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Daniela Ribeiro
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Ana Raquel Soares
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| |
Collapse
|
28
|
Tian HF, Hu QM, Xiao HB, Zeng LB, Meng Y, Li Z. Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus. INFECTION GENETICS AND EVOLUTION 2020; 84:104379. [PMID: 32497680 DOI: 10.1016/j.meegid.2020.104379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/29/2022]
Abstract
The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.
Collapse
Affiliation(s)
- Hai-Feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Qiao-Mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Han-Bing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Ling-Bing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| |
Collapse
|
29
|
Singh RK, Dhama K, Chakraborty S, Tiwari R, Natesan S, Khandia R, Munjal A, Vora KS, Latheef SK, Karthik K, Singh Malik Y, Singh R, Chaicumpa W, Mourya DT. Nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies - a comprehensive review. Vet Q 2019; 39:26-55. [PMID: 31006350 PMCID: PMC6830995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 10/20/2023] Open
Abstract
Nipah (Nee-pa) viral disease is a zoonotic infection caused by Nipah virus (NiV), a paramyxovirus belonging to the genus Henipavirus of the family Paramyxoviridae. It is a biosafety level-4 pathogen, which is transmitted by specific types of fruit bats, mainly Pteropus spp. which are natural reservoir host. The disease was reported for the first time from the Kampung Sungai Nipah village of Malaysia in 1998. Human-to-human transmission also occurs. Outbreaks have been reported also from other countries in South and Southeast Asia. Phylogenetic analysis affirmed the circulation of two major clades of NiV as based on currently available complete N and G gene sequences. NiV isolates from Malaysia and Cambodia clustered together in NiV-MY clade, whereas isolates from Bangladesh and India clusterered within NiV-BD clade. NiV isolates from Thailand harboured mixed population of sequences. In humans, the virus is responsible for causing rapidly progressing severe illness which might be characterized by severe respiratory illness and/or deadly encephalitis. In pigs below six months of age, respiratory illness along with nervous symptoms may develop. Different types of enzyme-linked immunosorbent assays along with molecular methods based on polymerase chain reaction have been developed for diagnostic purposes. Due to the expensive nature of the antibody drugs, identification of broad-spectrum antivirals is essential along with focusing on small interfering RNAs (siRNAs). High pathogenicity of NiV in humans, and lack of vaccines or therapeutics to counter this disease have attracted attention of researchers worldwide for developing effective NiV vaccine and treatment regimens.
Collapse
Affiliation(s)
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, West Tripura, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Senthilkumar Natesan
- Biomac Life Sciences Pvt Ltd., Indian Institute of Public Health Gandhinagar, Gujarat, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Kranti Suresh Vora
- Wheels India Niswarth (WIN) Foundation, Maternal and Child Health (MCH), University of Canberra, Gujarat, India
| | - Shyma K. Latheef
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Devendra T. Mourya
- National Institute of Virology, Ministry of Health and Family Welfare, Govt of India, Pune, India
| |
Collapse
|
30
|
Ismail SNFB, Baharum SN, Fazry S, Low CF. Comparative genome analysis reveals a distinct influence of nucleotide composition on virus-host species-specific interaction of prawn-infecting nodavirus. JOURNAL OF FISH DISEASES 2019; 42:1761-1772. [PMID: 31637743 DOI: 10.1111/jfd.13093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
Collapse
Affiliation(s)
| | | | - Shazrul Fazry
- Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Bangi, Malaysia
| | - Chen Fei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| |
Collapse
|
31
|
Shi SL, Xia RX. Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa. Viruses 2019; 11:E1087. [PMID: 31766648 PMCID: PMC6950266 DOI: 10.3390/v11121087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st-2nd codon positions are more biased than those at the 2nd-3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.
Collapse
Affiliation(s)
| | - Run-Xi Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China;
| |
Collapse
|
32
|
Affiliation(s)
- Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
33
|
Li L, Cao X, Wu J, Dou Y, Meng X, Liu D, Liu Y, Shang Y, Liu X. Epidemic and evolutionary characteristics of peste des petits ruminants virus infecting Procapra przewalskii in Western China. INFECTION GENETICS AND EVOLUTION 2019; 75:104004. [PMID: 31415822 DOI: 10.1016/j.meegid.2019.104004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/14/2022]
Abstract
Due to the migration or transboundary spread of domestic and wild animals, peste des petits ruminants virus posed a high potential threat to them. In this study, we initially detected that a class of animal named Procapra przewalskii was infected with peste des petits ruminants virus (PPRV ChinaGS2018) in Gansu province. According to phylogenetic relationships analysis, we found that ChinaGS2018 comprised of 15,954 nucleotides and was classified into IV genotypes. In addition, indirect immunofluorescence assay (IFA) showed that ChinaGS2018 could infect isolated primary goat tracheal epithelium cells (GTC). Comparing with full-length genome sequences revealed that ChinaGS2018 strain has high identity to the reference complete genomes (87.16-99.55%) at the nucleotide level. Multiple sequence alignment showed that F protein has the highest identity of 99.8%, and H protein has the highest nucleotide substitution ratio. Our study also suggested this strain may be transmitted from Xinjiang, China. Along with the migratory of Procapraprzewalskii, this wild ruminant infected with PPRV can pose a huge threat to other wild ruminants and domestic ones. This is the first report describing infected with PPRV which will provide insights into the epidemiology and pathogenesis of this important virus.
Collapse
Affiliation(s)
- Lingxia Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Jinyan Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xuelian Meng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Dan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| |
Collapse
|
34
|
Singh RK, Dhama K, Chakraborty S, Tiwari R, Natesan S, Khandia R, Munjal A, Vora KS, Latheef SK, Karthik K, Singh Malik Y, Singh R, Chaicumpa W, Mourya DT. Nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies - a comprehensive review. Vet Q 2019. [PMID: 31006350 PMCID: PMC6830995 DOI: 10.1080/01652176.2019.1580827] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Nipah (Nee-pa) viral disease is a zoonotic infection caused by Nipah virus (NiV), a paramyxovirus belonging to the genus Henipavirus of the family Paramyxoviridae. It is a biosafety level-4 pathogen, which is transmitted by specific types of fruit bats, mainly Pteropus spp. which are natural reservoir host. The disease was reported for the first time from the Kampung Sungai Nipah village of Malaysia in 1998. Human-to-human transmission also occurs. Outbreaks have been reported also from other countries in South and Southeast Asia. Phylogenetic analysis affirmed the circulation of two major clades of NiV as based on currently available complete N and G gene sequences. NiV isolates from Malaysia and Cambodia clustered together in NiV-MY clade, whereas isolates from Bangladesh and India clusterered within NiV-BD clade. NiV isolates from Thailand harboured mixed population of sequences. In humans, the virus is responsible for causing rapidly progressing severe illness which might be characterized by severe respiratory illness and/or deadly encephalitis. In pigs below six months of age, respiratory illness along with nervous symptoms may develop. Different types of enzyme-linked immunosorbent assays along with molecular methods based on polymerase chain reaction have been developed for diagnostic purposes. Due to the expensive nature of the antibody drugs, identification of broad-spectrum antivirals is essential along with focusing on small interfering RNAs (siRNAs). High pathogenicity of NiV in humans, and lack of vaccines or therapeutics to counter this disease have attracted attention of researchers worldwide for developing effective NiV vaccine and treatment regimens.
Collapse
Affiliation(s)
- Raj Kumar Singh
- a ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Sandip Chakraborty
- c Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry , West Tripura , India
| | - Ruchi Tiwari
- d Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences , Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Senthilkumar Natesan
- e Biomac Life Sciences Pvt Ltd. , Indian Institute of Public Health Gandhinagar , Gujarat , India
| | - Rekha Khandia
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Ashok Munjal
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Kranti Suresh Vora
- g Wheels India Niswarth (WIN) Foundation, Maternal and Child Health (MCH) , University of Canberra , Gujarat , India
| | - Shyma K Latheef
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kumaragurubaran Karthik
- h Central University Laboratory , Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Yashpal Singh Malik
- i Division of Biological Standardization , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Rajendra Singh
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Wanpen Chaicumpa
- j Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Devendra T Mourya
- k National Institute of Virology , Ministry of Health and Family Welfare, Govt of India , Pune , India
| |
Collapse
|
35
|
Immune System Modulation and Viral Persistence in Bats: Understanding Viral Spillover. Viruses 2019; 11:v11020192. [PMID: 30813403 PMCID: PMC6410205 DOI: 10.3390/v11020192] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/18/2022] Open
Abstract
Bats harbor a myriad of viruses and some of these viruses may have spilled over to other species including humans. Spillover events are rare and several factors must align to create the “perfect storm” that would ultimately lead to a spillover. One of these factors is the increased shedding of virus by bats. Several studies have indicated that bats have unique defense mechanisms that allow them to be persistently or latently infected with viruses. Factors leading to an increase in the viral load of persistently infected bats would facilitate shedding of virus. This article reviews the unique nature of bat immune defenses that regulate virus replication and the various molecular mechanisms that play a role in altering the balanced bat–virus relationship.
Collapse
|