Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development.

The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected from patients. Sequence analysis reveals that the codon adaptation index (CAI) values of viral sequences have decreased over time but with occasional fluctuations. Through evolution modeling, it is found that this phenomenon may result from the virus's mutation preference during transmission. Using dual-luciferase assays, it is further discovered that the deoptimization of codons in the viral sequence may weaken protein expression during virus evolution, indicating that codon usage may play an important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccines, it is designed several codon-optimized Omicron BA.2.12.1, BA.4/5, and XBB.1.5 spike mRNA vaccine candidates and experimentally validated their high levels of expression. This study highlights the importance of codon usage in virus evolution and provides guidelines for codon optimization in mRNA and DNA vaccine development.

Surface-enhanced Raman scattering as a potential strategy for wearable flexible sensing and point-of-care testing non-invasive medical diagnosis.

As a powerful and effective analytical tool, surface-enhanced Raman scattering (SERS) has attracted considerable research interest in the fields of wearable flexible sensing and non-invasive point-of-care testing (POCT) medical diagnosis. In this mini-review, we briefly summarize the design strategy, the development progress of wearable SERS sensors and its applications in this field. We present SERS substrate analysis of material design requirements for wearable sensors and highlight the benefits of novel plasmonic particle-in-cavity (PIC)-based nanostructures for flexible SERS sensors, as well as the unique interfacial adhesion effect and excellent mechanical properties of natural silk fibroin (SF) derived from natural cocoons, indicating promising futures for applications in the field of flexible electronic, optical, and electrical sensors. Additionally, SERS wearable sensors have shown great potential in the fields of different disease markers as well as in the diagnosis testing for COVID-19. Finally, the current challenges in this field are pointed out, as well as the promising prospects of combining SERS wearable sensors with other portable health monitoring systems for POCT medical diagnosis in the future.

Knowledge, Attitudes, and Practices toward COVID-19 and Vaccines among Chinese Small-Town Residents: A Cross-sectional Study.

China has basically controlled the COVID-19 epidemic as a result of widespread vaccination and other containment strategies, despite localized outbreaks, as of September 2021. This study investigates the knowledge, attitudes, and practices (KAP) of COVID-19 and COVID-19 vaccines among Chinese small-town residents to provide suggestions for public health policy. Residents who were vaccinated against COVID-19 were asked to complete a paper questionnaire on KAP in Xidian, Zhejiang. The knowledge questionnaire consisted of 12 questions regarding COVID-19 and 12 questions regarding COVID-19 vaccines. Attitude and practice evaluation included agreement on the eventual control of COVID-19 and having recently worn a mask outside. Of 405 survey responders, 52.3% were male, 71.4% had middle school education or less, and 59.0% engaged in physical labor as an occupation. The correct answer rates of the COVID-19 section and the vaccine section were 79.2% and 71.7%, respectively. Age groups of 18 to 29 years and > 50 years, occupations of physical labor and unemployment, and primary school education and less were associated with lower knowledge scores. The majority of participants (91.6%) believed that COVID-19 will eventually be controlled, whereas women, students, and patients with chronic held relatively negative attitudes toward epidemic control. Most participants (87.4%) wore masks outside recently. In conclusion, Chinese small-town residents have a medium level of knowledge regarding COVID-19 and vaccines, hold positive attitudes, and have appropriate practices. Health education should be provided to the target populations to enrich their knowledge of COVID-19 and vaccines, and to improve their attitudes toward epidemic control.

Functional coupling between TRPV4 channel and TMEM16F modulates human trophoblast fusion.

TMEM16F, a Ca2+-activated phospholipid scramblase (CaPLSase), is critical for placental trophoblast syncytialization, HIV infection, and SARS-CoV2-mediated syncytialization, however, how TMEM16F is activated during cell fusion is unclear. Here, using trophoblasts as a model for cell fusion, we demonstrate that Ca2+ influx through the Ca2+ permeable transient receptor potential vanilloid channel TRPV4 is critical for TMEM16F activation and plays a role in subsequent human trophoblast fusion. GSK1016790A, a TRPV4 specific agonist, robustly activates TMEM16F in trophoblasts. We also show that TRPV4 and TMEM16F are functionally coupled within Ca2+ microdomains in a human trophoblast cell line using patch-clamp electrophysiology. Pharmacological inhibition or gene silencing of TRPV4 hinders TMEM16F activation and subsequent trophoblast syncytialization. Our study uncovers the functional expression of TRPV4 and one of the physiological activation mechanisms of TMEM16F in human trophoblasts, thus providing us with novel strategies to regulate CaPLSase activity as a critical checkpoint of physiologically and disease-relevant cell fusion events.

The Effect of Reading Leaflets During the Observation Period After Vaccination on Knowledge of COVID-19 and Vaccines Among Chinese Small Town Residents: A Randomized Controlled Trial.

Background: Public health education is essential for epidemic prevention and control in the post-COVID-19 era. This randomized controlled trial (RCT) aims to evaluate the effect of reading leaflets during the observation period after vaccination on knowledge of COVID-19 disease and vaccines in Chinese small town residents and to provide suggestions for public health education. Methods: Residents were recruited during the observation period after getting vaccinated against COVID-19 in Xidian and were randomly divided into an education group and a control group. The education group was asked to complete the questionnaire after reading a leaflet, whereas the control group directly completed the questionnaire. The questionnaire comprised two sections on COVID-19 knowledge and vaccine knowledge, and the scores were used to assess the resident's knowledge. Results: A total of 142 participants in the education group and 154 participants in the control group were enrolled. The rates of correct knowledge in the education group and the control group were 90.7 and 83.1%, respectively. The scores of the two sections and the aggregate knowledge score of the education group were significantly higher than those of the control group (P < 0.001). The rates of correct responses to questions on clinical manifestations and transmission routes of COVID-19 and indications and contraindications of vaccines significantly increased after reading the leaflets (P < 0.05). Knowledge of different groups of genders, ages, marital statuses, education levels and occupations all improved (P < 0.05), and the 18-29-year-old and never-married group revealed a higher growth rate of correct responses. Conclusion: Chinese small town residents have a median level of knowledge regarding COVID-19 disease and vaccines. Reading leaflets during the observation period after vaccination effectively improved their knowledge. This low-cost and efficient health education approach can be widely applied.

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant.

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping. The molecular spectrum of mutations (i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process.

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA. Although the molecular spectrum of de novo mutations-the relative rates at which various base substitutions occur-are widely recognized as informative toward understanding the evolution of a viral genome, little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus. Here, we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines, enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes. We find that de novo mutations are generated in a replication-independent manner, typically on the genomic strand, and highly dependent on mutagenic mechanisms specific to the host cellular environment. De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution, in an asymmetric manner favoring specific mutation types. Consequently, similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13, which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans. Collectively, our findings provide data-driven support for the natural origin of SARS-CoV-2.