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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.
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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.
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Comparison of the pathogenic potential of highly pathogenic avian influenza (HPAI) H5N6, and H5N8 viruses isolated in South Korea during the 2016-2017 winter season. Emerg Microbes Infect 2018. [PMID: 29535296 PMCID: PMC5849756 DOI: 10.1038/s41426-018-0029-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Highly pathogenic avian influenza (HPAI) A(H5N6) and A(H5N8) virus infections resulted in the culling of more than 37 million poultry in the Republic of Korea during the 2016/17 winter season. Here we characterize two representative viruses, A/Environment/Korea/W541/2016 [Em/W541(H5N6)] and A/Common Teal/Korea/W555/2017 [CT/W555(H5N8)], and evaluate their zoonotic potential in various animal models. Both Em/W541(H5N6) and CT /W555(H5N8) are novel reassortants derived from various gene pools of wild bird viruses present in migratory waterfowl arising from eastern China. Despite strong preferential binding to avian virus–type receptors, the viruses were able to grow in human respiratory tract tissues. Em/W541(H5N6) was found to be highly pathogenic in both chickens and ducks, while CT/W555(H5N8) caused lethal infections in chickens but did not induce remarkable clinical illness in ducks. In mice, both viruses appeared to be moderately pathogenic and displayed limited tissue tropism relative to HPAI H5N1 viruses. Em/W541(H5N6) replicated to moderate levels in the upper respiratory tract of ferrets and was detected in the lungs, brain, spleen, liver, and colon. Unexpectedly, two of three ferrets in direct contact with Em/W541(H5N6)-infected animals shed virus and seroconverted at 14 dpi. CT/W555(H5N8) was less pathogenic than the H5N6 virus in ferrets and no transmission was detected. Given the co-circulation of different, phenotypically distinct, subtypes of HPAI H5Nx viruses for the first time in South Korea, detailed virologic investigations are imperative given the capacity of these viruses to evolve and cause human infections.
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Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus. Oncotarget 2017; 8:110337-110349. [PMID: 29299151 PMCID: PMC5746386 DOI: 10.18632/oncotarget.22738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/27/2017] [Indexed: 11/25/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. We also observed that gene function, evolution time and the different host species of the virus all contributed to the bias of MERS-CoV, to some extent. Additionally, the codon usage pattern of MERS-CoV isolates is different from other related Nidovirales viruses isolated from bats and hedgehogs. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.
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Chen Y, Shi Y, Deng H, Gu T, Xu J, Ou J, Jiang Z, Jiao Y, Zou T, Wang C. Characterization of the porcine epidemic diarrhea virus codon usage bias. INFECTION GENETICS AND EVOLUTION 2014; 28:95-100. [PMID: 25239728 PMCID: PMC7185563 DOI: 10.1016/j.meegid.2014.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 08/26/2014] [Accepted: 09/01/2014] [Indexed: 11/15/2022]
Abstract
Codon usage bias of porcine epidemic diarrhea virus is low. Mutational bias and natural selection pressure influence codon usage bias of porcine epidemic diarrhea virus. Natural selection plays an increasingly significant role during evolution of porcine epidemic diarrhea virus.
Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree.
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Affiliation(s)
- Ye Chen
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yuzhen Shi
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hongjuan Deng
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Ting Gu
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jian Xu
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jinxin Ou
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Zhiguo Jiang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yiren Jiao
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Tan Zou
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Chong Wang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China.
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Gutiérrez RA, Naughtin MJ, Horm SV, San S, Buchy P. A(H5N1) Virus Evolution in South East Asia. Viruses 2009; 1:335-61. [PMID: 21994553 PMCID: PMC3185531 DOI: 10.3390/v1030335] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 09/02/2009] [Accepted: 10/02/2009] [Indexed: 12/15/2022] Open
Abstract
Highly Pathogenic Avian Influenza (HPAI) H5N1 virus is an ongoing public health and socio-economic challenge, particularly in South East Asia. H5N1 is now endemic in poultry in many countries, and represents a major pandemic threat. Here, we describe the evolution of H5N1 virus in South East Asia, the reassortment events leading to high genetic diversity in the region, and factors responsible for virus spread. The virus has evolved with genetic variations affecting virulence, drug-resistance, and adaptation to new host species. The constant surveillance of these changes is of primary importance in the global efforts of the scientific community.
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Affiliation(s)
- Ramona Alikiiteaga Gutiérrez
- Institut Pasteur du Cambodge, Virology Unit, 5 Monivong boulevard, PO Box 983, Phnom Penh, Cambodia; E-Mails: (M.J.N.); (S.V.H.)
| | - Monica Jane Naughtin
- Institut Pasteur du Cambodge, Virology Unit, 5 Monivong boulevard, PO Box 983, Phnom Penh, Cambodia; E-Mails: (M.J.N.); (S.V.H.)
| | - Srey Viseth Horm
- Institut Pasteur du Cambodge, Virology Unit, 5 Monivong boulevard, PO Box 983, Phnom Penh, Cambodia; E-Mails: (M.J.N.); (S.V.H.)
| | - Sorn San
- National Veterinary Research Institute (NaVRI)/ Phum Trea, Sals Street # 371, Phnom Penh, Cambodia; E-Mail: (S.S.)
| | - Philippe Buchy
- Institut Pasteur du Cambodge, Virology Unit, 5 Monivong boulevard, PO Box 983, Phnom Penh, Cambodia; E-Mails: (M.J.N.); (S.V.H.)
- Author to whom correspondence should be addressed; E-mail: (P.B.); Tel.: +855-23-426-009, Fax: +855-23-725-606
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