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

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.

Apoetic Life: Perec, Poetry, Pneumatology

For much of his life, it seems Georges Perec spurned poetry, identifying it with the sort of bourgeois sentimentalism that his own writing was constitutionally against. Once, however, he had been convinced by friends such as Harry Mathews that poetry was also exemplary of forms of compositional constraint, he returned to it with a vengeance — to the extent that his later work can even be seen to have received a new and decisive impetus from this realization. This chapter examines fragments from Shakespeare’s King Lear, Raymond Queneau’s oeuvre, and several works of Perec’s in order to identify key sets of operational constraints across their work. The differences and similarities between these operations are discussed, and consequences are drawn for contemporary poetry.

Compositional Constraint Is the Key Force in Shaping Codon Usage Bias in Hemagglutinin Gene in H1N1 Subtype of InfluenzaAVirus

It is vital to unravel the codon usage bias in order to gain insights into the evolutionary forces dictating the viral evolution process. InfluenzaAvirus has attracted attention of many investigators over the years due to high mutation rate and being cross-specific shift operational in the viral genome. Several authors have reported that the codon usage bias is low in influenzaAviruses, citing mutational pressure as the decisive force shaping up the codon usage in these viruses. In this study, complete coding sequences of hemagglutinin genes for H1N1 subtype of influenzaAvirus have been explored for the possible codon usage bias acting upon these genes. The results indicate overall low bias with peaking ENC values. The GC content is found to be substantially low as against AT content in the silent codon sites. Significant correlations were observed in between the compositional parameters versus AT3, implying the possible role of the latter in shaping codon usage profile in the viral hemagglutinin. The data showed conspicuously that the sequences wereAredundant with most codons preferring nucleotideAover others in the third synonymous codon site. The results indicated the pivotal role of compositional pressure affecting codon usage in this virus.

Characterization of Synonymous Codon Usage Bias in the UL1 Gene of Duck Plague Virus

In this study, we calculated the codon usage bias in DPV CHv UL1 gene and performed a comparative analysis of synonymous codon patterns in UL1 of DPV CHv strain and other 19 reference herpesviruses. The results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL1 gene of DPV CHv. G + C compositional constraint was the main factor that determined the codon usage bias in UL1 gene. In addition, the codon usage bias of DPV CHv UL1 gene was compared with those of E. coli, yeast and human. There are 25 codons showing distinct usage differences between DPV and E. coli, 26 codons between DPV and yeast, and 21 codons between DPV and human. Therefore, the Human expression system is more suitable for heterologous expression of the DPV UL1 gene.

Analysis of Synonymous Codon Usage in the US5 Gene of Duck Plague Virus

The Duck Plague Virus (DPV) US5 gene was identified by constructing the DPV genomic library, the synonymous codon usage in the US5 gene of DPV and 11 reference herpesviruses have been investigated by using the CodonW 1.4 program, CUSP (create a codon usage table) program and CHIPS (calculated ENC value) of EMBOSS (The European Molecular Biology Open Software Suite). The results reveals that the synonymous codons with A and T at the third codon positon have widely usage in the codon of US5 gene of DPV. G + C compositional constraint is the main factor that determines the codon usage bias in US5 gene. In addition, rare condons analysis showed that there are 75 rare condons (13.9%) in the ORF of the DPV US5 gene on line (http//:www.kazusa.or.jp/codon), There were 20 codons showing distinct usage differences between DPV with Escherichia coli, 19 between DPV and yeast, 25 between DPV and Human. Therefore the yeast expression system may be suitable for the expression of DPV US5 gene.