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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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Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, Clark TG, Campino S. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasit Vectors 2021; 14:332. [PMID: 34174947 PMCID: PMC8235865 DOI: 10.1186/s13071-021-04828-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
Mosquitoes of the genus Aedes are the main vectors of many viruses, e.g. dengue and Zika, which affect millions of people each year and for which there are limited treatment options. Understanding how Aedes mosquitoes tolerate high viral loads may lead to better disease control strategies. Elucidating endogenous viral elements (EVEs) within vector genomes may give exploitable biological insights. Previous studies have reported the presence of a large number of EVEs in Aedes genomes. Here we investigated if flavivirus EVEs are conserved across populations and different Aedes species by using ~ 500 whole genome sequence libraries from Aedes aegypti and Aedes albopictus, sourced from colonies and field mosquitoes across continents. We found that nearly all flavivirus EVEs in the Ae. aegypti reference genome originate from four separate putative viral integration events, and that they are highly conserved across geographically diverse samples. By contrast, flavivirus EVEs in the Ae. albopictus reference genome originate from up to nine distinct integration events and show low levels of conservation, even within samples from narrow geographical ranges. Our analysis suggests that flaviviruses integrated as long sequences and were subsequently fragmented and shuffled by transposable elements. Given that EVEs of Ae. aegypti and Ae. albopictus belong to different phylogenetic clades and have very differing levels of conservation, they may have different evolutionary origins and potentially different functional roles.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Lara Ferrero Gomez
- Unidade de Ciências da Natureza, da Vida e do Ambiente, Universidade Jean Piaget de Cabo Verde, Praia, Cabo Verde
| | - Fady Mohareb
- School of Water, Energy and Environment, Cranfield University, Bedford, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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Alonso-Palomares LA, Moreno-García M, Lanz-Mendoza H, Salazar MI. Molecular Basis for Arbovirus Transmission by Aedes aegypti Mosquitoes. Intervirology 2019; 61:255-264. [PMID: 31082816 DOI: 10.1159/000499128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/17/2019] [Indexed: 11/19/2022] Open
Abstract
Mosquitoes are considered the most important vectors for the transmission of pathogens to humans. Aedes aegypti is a unique species, not only by its highly anthropophilic and peridomestic habits but also because it can transmit an important variety of pathogenic viruses. Examples are dengue, yellow fever, chikungunya, Zika, and Mayaro viruses. After ingesting viremic blood, a wide range of mechanisms are activated in the mosquito to counteract viral infection. Nevertheless, these arboviruses possess strategies to overcome barriers in the mosquito and eventually reach the salivary glands to continue the transmission cycle. However, the infection and eventual transmission of arbovirus depends on multiple factors. The current review focuses in detail on the anatomic, physiological, and molecular characteristics of the mosquito A. aegypti that participate in response to a viral infection. In the past decades, the awareness of the importance of this mosquito as a disease vector and its impact on human health was largely recognized. We need to improve our comprehension of molecular mechanisms that determine the outcome of successful virus replication or control of infection for each arbovirus in the vector; this could lead to the design of effective control strategies in the future.
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Affiliation(s)
- Luis A Alonso-Palomares
- Laboratorio de Virología e Inmunovirología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Unidad Profesional "Lázaro Cárdenas", Mexico City, Mexico.,Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (CISEI-INSP), Cuernavaca, Mexico
| | - Miguel Moreno-García
- Centro Regional de Control de Vectores, Secretaría de Salud (CERECOVE-SS), Panchimalco, Mexico
| | - Humberto Lanz-Mendoza
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (CISEI-INSP), Cuernavaca, Mexico
| | - Ma Isabel Salazar
- Laboratorio de Virología e Inmunovirología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Unidad Profesional "Lázaro Cárdenas", Mexico City, Mexico,
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Tahir Ul Qamar M, Maryam A, Muneer I, Xing F, Ashfaq UA, Khan FA, Anwar F, Geesi MH, Khalid RR, Rauf SA, Siddiqi AR. Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus. Sci Rep 2019; 9:1433. [PMID: 30723263 PMCID: PMC6363786 DOI: 10.1038/s41598-018-38450-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Emergence of Dengue as one of the deadliest viral diseases prompts the need for development of effective therapeutic agents. Dengue virus (DV) exists in four different serotypes and infection caused by one serotype predisposes its host to another DV serotype heterotypic re-infection. We undertook virtual ligand screening (VLS) to filter compounds against DV that may inhibit inclusively all of its serotypes. Conserved non-structural DV protein targets such as NS1, NS3/NS2B and NS5, which play crucial role in viral replication, infection cycle and host interaction, were selected for screening of vital antiviral drug leads. A dataset of plant based natural antiviral derivatives was developed. Molecular docking was performed to estimate the spatial affinity of target compounds for the active sites of DV’s NS1, NS3/NS2B and NS5 proteins. The drug likeliness of the screened compounds was followed by ADMET analysis whereas the binding behaviors were further elucidated through molecular dynamics (MD) simulation experiments. VLS screened three potential compounds including Canthin-6-one 9-O-beta-glucopyranoside, Kushenol W and Kushenol K which exhibited optimal binding with all the three conserved DV proteins. This study brings forth novel scaffolds against DV serotypes to serve as lead molecules for further optimization and drug development against all DV serotypes with equal effect against multiple disease causing DV proteins. We therefore anticipate that the insights given in the current study could be regarded valuable towards exploration and development of a broad-spectrum natural anti-dengue therapy.
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Affiliation(s)
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Feng Xing
- College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Faheem Ahmed Khan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education China, Huazhong Agricultural University, Wuhan, P.R. China
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Mohammed H Geesi
- Department of Chemistry, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia.
| | - Rana Rehan Khalid
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadaf Abdul Rauf
- Department of Computer Science, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
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Lin D, Li L, Xie T, Yin Q, Saksena N, Wu R, Li W, Dai G, Ma J, Zhou X, Chen X. Codon usage variation of Zika virus: The potential roles of NS2B and NS4A in its global pandemic. Virus Res 2018; 247:71-83. [PMID: 29428601 DOI: 10.1016/j.virusres.2018.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive demonstration of Zika virus (ZIKV) molecular evolution is essential for understanding its adaptation and expansion in its recent pandemics. Despite several studies on mutations and codon usage in ZIKVs, the variations in codon usage patterns across individual genes and their biological implication remains unclear. Here, we performed a gene-by-gene comparison of the codon usage variation in ZIKVs of the African and Asian lineages. We found that besides the evidence of positive selection (Ka/Ks >1) in the Asian lineage of the ZIKV genome, codon usage patterns were gene-specific and codon usage variation of ZIKV genes, was possibly constrained by their individual functional features, such as transmembrane domains, or antigenicity. In particular, the NS2B and NS4A genes showed distinct codon usage patterns, clearly separating them from the clusters of other genes in the correspondence analysis (CA). In the Asian lineage, the NS2B and NS4A genes showed the highest codon usage bias (ENC values: 51.01 ± 0.72 and 48.89 ± 0.99 respectively), and were subjected to the highest translation selection (ENCobs/ENCexp ratio: 0.847 ± 0.0297 and 0.828 ± 0.0233 respectively) in comparison to the African lineages of ZIKV. The CpG frequency of the NS2B showed a gradual ascending trend in the Asian ZIKV lineages, while in NS4A it was constrained along with the expansion of the Asian lineage. Furthermore, between the African and Asian lineages, differentiated and specific over-represented codons were more prominent in the NS2B and NS4A. Together, our study implies that ZIKVs are in the process of evolutionary fine tuning their codon as seen in the recent pandemics, and NS2B and NS4A could have played a potential role in the molecular evolution of the Asian lineage and their establishment.
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Affiliation(s)
- Dechun Lin
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China; BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Liqiang Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Tian Xie
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Qingqing Yin
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Nitin Saksena
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Rangke Wu
- The School of Foreign Studies, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Wanyu Li
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Geyang Dai
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xiaohong Zhou
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Xiaoguang Chen
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
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