On the Complexity of Constrained Sequences Alignment Problems

This report showed some physicochemical properties and structural features about DPV-UL13 protein predicted by some software and online tools. The online analysis of the physicochemical properties demonstrates that the protein has thirty-four potential phosphorylation sites when the threshold of prediction score is above 0.5 and both the signal peptide and the transmembrance region are not found. In addition, the protein has hydrophilic amine acid districts more than hydrophobic districts and subcellular localization largely locates at mitochondrial with 43.5%. The secondary structure results revealed that random coils dominated among secondary structure elements followed by alpha helix and extended strand. The phylogenetic tree shows that DPV-UL13 protein has close evolutionary relationship with the genus Mardivirus. And the multiple sequences alignment of UL13 protein in 156-436 sequence among DPV, HSV-1 and Mardivirus genus suggests highly conserved characteristic. These analysis surpports the guess that DPV-UL13 product may be a Ser/Thr protein kinase. All the data will be a basis for the further functional study of the DPV-UL13 protein.

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Comparative Study on Molecular Epidemiology of Measles H1a Outbreak and Sporadic Cases in Shandong Province, 2013-2019

10.21203/rs.3.rs-1122872/v1 ◽

2021 ◽

Author(s):

Suting Wang ◽

Changyin Wang ◽

Xiaodong Liu ◽

Ping Xiong ◽

Yao Liu ◽

...

Keyword(s):

Measles Virus ◽

Subacute Sclerosing Panencephalitis ◽

Viral Disease ◽

Shandong Province ◽

Nucleotide Sequencing ◽

Genetic Characteristics ◽

N Protein ◽

Measles Elimination ◽

Sporadic Cases ◽

Sequences Alignment

Abstract Background: Measles caused by measles virus (MeV) is a highly contagious viral disease which has also been associated with complications including pneumonia, myocarditis, encephalitis, and subacute sclerosing panencephalitis. The current study collected33 strains from 2013 to 2019 in 13 cities of Shandong province and separate them into 2 group, outbreak cases and sporadic cases. Comparative of genetic characterization between 15 outbreak strains and 18 sporadic strains was made using nucleotide sequencing of the C-terminal region of the N protein gene(N-450). Results: The results showed that all 33 stains belonged to genotype H1a. The outbreak strains and sporadic strains distribute crossly in phylogenetic tree. Sequences alignment revealed some interesting G and A transversion, which change the amino acids, on sites 1317, 1422, 1543. The nucleotide sequence and amino acid homologies of 15 Shandong outbreak isolates were 98%–100% (0–10 nucleotide variation) and 97.7%–100%, for sporadic isolations, they are 97.3%–100% and 96.6%–100% respectively. The mean evolution rate of 15 outbreak isolations and 18 sporadic isolations was 4.73× 10-3 and 2.068× 10-3 substitutions per site per year separately, which is higher than the study made before 2002. Conclusions: This report compared epidemic and genetic characteristics of outbreak strains and sporadic strains, and raise evolutionary study of sporadic cases may be helpful for discovery of the possibility of outbreak, especially in the stage of measles elimination.

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The physicochemical and phylogenetic properties of twelve spike glycoprotein models for SARS-CoV-2 from China, Iran, and Tunisia

10.21203/rs.3.rs-63469/v1 ◽

2020 ◽

Author(s):

Samih A. Odhaib ◽

Hayder Al-Aubaidy

Keyword(s):

Surface Protein ◽

3D Models ◽

Physicochemical Characteristics ◽

Evolutionary Divergence ◽

Spike Glycoprotein ◽

Model Quality ◽

Cross Sectional ◽

Structural Surface ◽

Clustal Omega ◽

Sequences Alignment

Abstract Background The coronavirus spike glycoprotein is a trimeric structural surface protein that facilitates the viral adhesion through attaching receptors on the human cell surface. This study aims to analyse and compare the genomic and phylogenetic properties of these spike glycoproteins from China, Iran, and Tunisia. Methods This is a descriptive cross-sectional comparative study for the different properties of S glycoprotein from 12 SARS-CoV-2 specimens from GenBank. Clustal Omega was used to study model sequences alignment, residual conservation, phylogeny, and identity matrix. SWISS-MODEL developed and validated the 3D models for three protein sequences with the highest model quality. The different physicochemical characteristics of different models were assessed by ExPASy proteomics. Results The Chinese and the Iranian sequences share 100% identity, although they have a different amino acids number, and 25-29.27% identity to the Tunisian sequences. The 12 models are monophyletic, with varying stages of evolutionary divergence. There are six fully, three highly, and five lowly conserved residues across the sequences. The resulting three highly reliable 3D models were of different global qualities, being the lowest for the Tunisian, and the highest for the Iranian models. All the models are highly hydrophilic. The Tunisian models were unstable in comparison to the relatively stable other models with different physicochemical characteristics. Conclusion The models had different N-terminal residues and side groups polarity and charge. The S glycoproteins are not identical nor unique in model structure nor the physicochemical profiles in different parts of the world. The Tunisian models are drastically biodiverse from the Chinese and Iranian models.

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