Analysis of Nipah Virus Codon Usage and Adaptation to Hosts

Khandia, Rekha; Singhal, Shailja; Kumar, Utsang; Ansari, Afzal; Tiwari, Ruchi; Dhama, Kuldeep; Das, Jayashankar; Munjal, Ashok; Singh, Raj Kumar

doi:10.3389/fmicb.2019.00886

Cited by 120 publications

(150 citation statements)

References 84 publications

(96 reference statements)

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“…When evaluated in terms of their ENc value, the 44 viral genomes all lacked a strong codon bias. This result is consistent with the codon usage in most RNA viruses, such as the Citrus tristeza virus [35], Enterovirus [36], Hendra virus [37], and Nipah virus [38], in that they all lacked a strong codon bias. A possible explanation for the weak codon bias is that it is advantageous for efficient replication, re-adaption, and survival in host cells [39,40].…”

Section: Discussionsupporting

confidence: 82%

“…A possible explanation for the weak codon bias is that it is advantageous for efficient replication, re-adaption, and survival in host cells [39,40]. The similarity index R(A,B) has been widely used to represent the degree of similarity between a virus and its host, with respect to their overall codon usage patterns, and to further evaluate the potential role of the overall codon usage patterns of the host in the formation of the overall codon usage of a virus [25,38]. We used this index to infer the similarity between host-taxa-groups and found that all of the similarity values were at higher levels.…”

Section: Discussionmentioning

confidence: 99%

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Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Sheng

Xia

2019

Viruses

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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.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Sheng

Xia

2019

Viruses

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“…The higher the CAI value the higher the gene expression, and vice versa. The 13 SARS-CoV-2 isolates used in the analysis showed an overall average CAI value of 0.54 ± 0.0003 for the complete coding region, which is comparatively slightly lower than the CAI values of viruses from other studies in relation to Homo sapiens, indicating moderate SARS-CoV-2 adaptation to Homo sapiens (Butt et al, 2016;Khandia et al, 2019;Kumar et al, 2018). However, at the individual genes level, different CAI values have been observed.…”

Section: Moderate Adaptation Of Sars-cov-2 To Homo Sapiensmentioning

confidence: 77%

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Khodary

Anwar

2020

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In the present study, we analyzed genome-wide codon usage patterns in 13 SARS-CoV-2 isolates from different geo-locations (countries) by utilizing different CUB measurements. Nucleotide and di-nucleotide compositions displayed bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Relative Synonymous Codon Usage (RSCU) analysis revealed 8 common putative preferred codons among all the 13 isolates.Interestingly, all of the latter codons are A/U-ended (U-ended: 7, A-ended: 1). Cluster analysis (based on RSCU values) was performed and showed comparable results to the phylogenetic analysis (based on their whole genome sequences) indicating that the CUB pattern may reflect the evolutionary relationship between the tested isolates. To investigate the force (mutation and/or selection) influencing the pattern of CUB in SARS-CoV-2 coding sequences, we employed the following; (i). Effective number of codons (ENc), (ii). ENc-GC3 plot, (iii). Neutrality plot, and (iv) Codon adaptation index (CAI). According to their results, natural selection and/or other factors (not investigated in this study) may be the dominant force driving SARS-CoV-2 CUB. It is also worth mentioning that, by using the most expressed genes in human lung tissues as a reference set, some viral genes such as Nucleocapsid phosphoprotein, ORF7a protein, and surface glycoprotein had high CAI values which may indicate for selection force acting on their codon usage, as they play important roles in viral assembly and may help viruses avoid the host immune system. The outcome of our study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 viruses, and the interactions with their host. Also, it may aid in vaccine design strategies.

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“…Codon usage vari-ation occurs may be due to natural selection and/or mutation pressure for accurate and efficient translation in various organisms [19,20]. Differences in the frequency of occurrence on synonymous codons in coding DNA is termed as synonymous codon usage bias [32].…”

Section: Data Acquisition and Processingmentioning

confidence: 99%

Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions

Das

Chakraborty

Roy

2020

Preprint

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Understanding the molecular mechanism of COVID19 disease pathogenesis helps in the rapid development of therapeutic targets. Usually, viral protein targets host proteins in an organized fashion. The pathogen may target cell signaling pathways to disrupt the pathway genes’ regular activities, resulting in disease. Understanding the interaction mechanism of viral and host proteins involved in different signaling pathways may help decipher the attacking mechanism on the signal transmission during diseases, followed by discovering appropriate therapeutic solutions.The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploiting the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the codon usage pattern similarity (and dissimilarity), we propose a computational scheme to recreate the hostviral protein interaction network (HVPPI). We use seventeen (17) essential signaling pathways for our current work and study the possible targeting mechanism of SARS-CoV2 viral proteins on such pathway proteins. We infer both negatively and positively interacting edges in the network. We can find a relationship where one host protein may target by more than one viral protein.Extensive analysis performed to understand the network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins, mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among non-structural proteins, NSP3 and structural protein, Spike (S) protein, are the most influential proteins in interacting multiple host proteins. In ranking the most affected pathways, MAPK pathways observe to be worst affected during the COVID-19 disease. A good number of targeted proteins are highly central in host protein interaction networks. Proteins participating in multiple pathways are also highly connected in their own PPI and mostly targeted by multiple viral proteins.

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Analysis of Nipah Virus Codon Usage and Adaptation to Hosts

Cited by 120 publications

References 84 publications

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions

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