Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

Malik, Yashpal Singh; Ansari, Mohd Ikram; Kattoor, Jobin Jose; Kaushik, Rahul; Sircar, Shubhankar; Anbazhagan, Subbaiyan; Tiwari, Ruchi; Dhama, Kuldeep; Ghosh, Souvik; Tomar, Shailly; Zhang, Kam Y. J.

doi:10.1093/bib/bbaa383

Cited by 21 publications

(27 citation statements)

References 113 publications

(128 reference statements)

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“…In the case of Spike (S) protein, the CUB was found to be similar to that of other coronaviruses, with preferential use of A/U ending codons, and partly governed through the mutational pressure (27.35%) and majorly through natural selection and other factors (72.65%). In addition, CAI values for the S-gene indicated a relatively better adaptability in humans, when compared to other mammals [53]. The same bias was observed for ORF1ab, and it was reported that it was more pronounced in SARS-CoV-2 than in SARS-CoV [54].…”

Section: Introductionmentioning

confidence: 77%

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

Mogro

Bottero

Lozano

2021

Preprint

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SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.

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Section: Introductionmentioning

confidence: 77%

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

Mogro

Bottero

Lozano

2021

Preprint

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“…Multiple studies have been targeted at the investigation of codon usage patterns of SARS-CoV-2 till date (Alonso and Diambra, 2020;Dilucca et al, 2020;Gu et al, 2020;Kanduc, 2020;Malik et al, 2020;Saha et al, 2021). Recently, Tort et al (2020) reported a close relationship of SARS-CoV-2 with Bat-CoVs in comparison to SARS-CoV, MERS-CoV, and other coronaviruses isolated from civets and ferrets, based on a comparative codon usage analysis.…”

Section: Discussionmentioning

confidence: 99%

“…Since the emergence of SARS-CoV-2, extensive research has been undertaken to decipher its genomic features and riddles of its transmission, evolutionary dynamics, epidemiology, and mode of infection (Alonso and Diambra, 2020;Benvenuto et al, 2020b;Chen et al, 2020;Dilucca et al, 2020;Gu et al, 2020;Kames et al, 2020;Lam et al, 2020;Lu et al, 2020;Malik et al, 2020;Wang et al, 2020;Xiao et al, 2020;Zhou et al, 2020). However, the complexities of codon usage by SARS-CoV-2 and its impact on the adaptation and fitness of this virus to human hosts have not yet been addressed.…”

Section: Introductionmentioning

confidence: 99%

Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective

et al. 2021

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The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading rapidly all over the world and has raised grave concern globally. The present research aims to conduct a robust base compositional analysis of SARS-CoV-2 to reveal adaptive intricacies to the human host. Multivariate statistical analysis revealed a complex interplay of various factors including compositional constraint, natural selection, length of viral coding sequences, hydropathicity, and aromaticity of the viral gene products that are operational to codon usage patterns, with compositional bias being the most crucial determinant. UpG and CpA dinucleotides were found to be highly preferred whereas, CpG dinucleotide was mostly avoided in SARS-CoV-2, a pattern consistent with the human host. Strict avoidance of the CpG dinucleotide might be attributed to a strategy for evading a human immune response. A lower degree of adaptation of SARS-CoV-2 to the human host, compared to Middle East respiratory syndrome (MERS) coronavirus and SARS-CoV, might be indicative of its milder clinical severity and progression contrasted to SARS and MERS. Similar patterns of enhanced adaptation between viral isolates from intermediate and human hosts, contrasted with those isolated from the natural bat reservoir, signifies an indispensable role of the intermediate host in transmission dynamics and spillover events of the virus to human populations. The information regarding avoided codon pairs in SARS-CoV-2, as conferred by the present analysis, promises to be useful for the design of vaccines employing codon pair deoptimization based synthetic attenuated virus engineering.

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“…RSCU values of <0.6, 0.6–1.6, >1.6 indicate low, normal and over usage of the codon [ 46 ]. The average RSCU data of humans originated from work by Malik et al [ 48 ], while the mean RSCU values of HPV16 ORFs were calculated by R package SADEG v1.0.0. [ 44 ].…”

Section: Methodsmentioning

confidence: 99%

Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16

Liu

et al. 2021

Viruses

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Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.

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Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

Cited by 21 publications

References 113 publications

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective

Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16

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