Virus evolution and reduced viral viability during treatment of persistent COVID-19 Omicron BA.5 infection in an immunocompromised host

We present the clinical course of a 72-year-old female with COVID-19 and a history of hematologic stem cell transplantation for acute myeloid leukemia. We performed serial analyses of viral load and whole-genome amplification. The virus growth was evaluated by a real-time polymerase chain reaction assay. Neutralizing activity was measured using a chemiluminescence reduction neutralizing test of SARS-CoV-2 pseudotyped virus. After neutralizing antibody therapy, the cycle threshold value of viral genome was 28. Viruses were no longer isolated in a cell culture. K129R, V722I, and V987F of amino acid mutation in spike protein region were identified, although they soon disappeared. Four months after symptom onset, E340K, K356R, R346T, and E484V mutations appeared and persisted. The viability of the virus decreased over time, with the virus at day 145 having a cycle threshold value of 24 and positive virus isolation, but at a slower growth rate. Neutralizing antibody activity for Omicron BA.5 finally appeared about 4 months after infection. In immunocompromised patients, persistent infection with amino acid mutations can occur without neutralizing antibodies. However, the production of neutralizing antibodies reduces the growth rate of the SARS-CoV-2. Moreover, infection control requires attention to viral dynamics and evolution under different conditions.

Scoring amino acid mutation to predict pandemic risk of avian influenza virus

BACKGROUND

Avian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. The pandemic risk of avian influenza viruses should be analyzed and a prediction model should be constructed for virology applications.

RESULTS

The 178 signature positions in 11 viral proteins were firstly screened as features by the scores of five amino acid factors and their random forest rankings. The Supporting Vector Machine algorithm achieved well performance. The most important amino acid factor (Factor 5) and the minimal range of signature positions (63 amino acid residues) were also explored. Moreover, human-origin avian influenza viruses with three or four genome segments from human virus had pandemic risk with high probability.

CONCLUSION

Using machine learning methods, the present paper scores the amino acid mutations and predicts pandemic risk with well performance. Although long evolution distances between avian and human viruses suggest that avian influenza virus in nature still need time to fix among human host, it should be notable that there are high pandemic risks for H7N9 and H9N2 avian viruses.

Discerning the composition of penetratin for safe penetration from cornea to retina

Delivery of biomacromolecules into the eye is greatly hindered by several protective barriers. The cell-penetrating peptide, penetratin, has been found to be an effective absorption enhancer for noninvasive intraocular gene delivery. To discern the composition of penetratin for safe penetration from cornea to retina, we designed a series of penetratin derivatives by varying the hydrophobicity and evaluated their potency for retina-targeted delivery. The hydrophilic amino acids of penetratin, excluding the conserved basic amino acid residues, were respectively replaced with tryptophan. Secondary structure of the resultant derivatives was analyzed by computer simulation and circular dichroism, exhibiting that the hydrophobic derivatives had a propensity to form high content of helix and entered corneal and conjunctival cells more easily than did penetratin. As expected, the hydrophobic derivatives showed improved permeability in excised rabbit cornea and sclera, and kept intact after penetration. When instilled topically in the conjunctival sac of mice eyes, the hydrophobic derivatives distributed safely and rapidly into both cornea and retina, with increased amount and prolonged retention time in comparison to penetratin. In conclusion, we demonstrated that the ocular permeability of penetratin derivatives closely correlated with their hydrophobicity, and introducing hydrophobic amino acids in penetratin was a feasible approach to develop more powerful ocular absorption enhancers.

STATEMENT OF SIGNIFICANCE

Due to the defensive barriers of the eye, efficient and safe absorption enhancers are indispensable for noninvasive delivery of exogenous biomacromolecules to the posterior segment. In this manuscript, we designed a series of penetratin derivatives and validated they had significantly improved penetration ability from cornea to retina than wild-type penetratin, without increasing toxicity. More importantly, we provided a sequence of solid evidences that the ocular permeability of penetratin derivatives closely correlated with their hydrophobicity, and introducing hydrophobic amino acids in penetratin was a feasible approach to develop more powerful ocular absorption enhancers. We also demonstrated that the penetratin derivatives permeated through cornea and sclera with intact structure, and might enter the eye by non-corneal pathway.

High-level expression and characterization of the Bacillus subtilis subsp. subtilis str. BSP1 YwaD aminopeptidase in Pichia pastoris

Aminopeptidases are widely used for creating protein hydrolysates and peptide sequencing. The ywaD gene from a new Bacillus isolate, named Bacillus subtilis subsp. subtilis str. BSP1, was cloned into the yeast expression vector pHBM905A and expressed and secreted by Pichia pastoris strain GS115. The deduced amino acid sequence of the aminopeptidase encoded by the ywaD gene shared up to 98% identity with aminopeptidases from B. subtilis strains 168 and zj016. The yield (3.81 g/l) and specific activity (788 U/mg) of recombinant YwaD in high-density fermentation were extremely high. And 829.83 mg of the purified enzyme (4089.72 U/mg) were harvested. YwaD was glycosylated, and its activity decreased after deglycosylation, which was similar to that of the aminopeptidase from B. subtilis strain zj016. YwaD was most active toward l-arginine-4-nitroanilide. Moreover, it exhibited high resistance to carbamide, which was not true for aminopeptidases from B. subtilis strains 168 and zj016, which could simplify the purification of YwaD. Moreover, the expression and parts of characterization of the aminopeptidase from B. subtilis strain 168 in Pichia pastoris were added as supplementary material. The sequence and other characteristics of YwaD were compared with those of aminopeptidases from B. subtilis strains 168 and zj016, and they will provide a solid foundation for further research on the influence of amino acid mutations on the function of aminopeptidases.