dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.

The relationship between time to a high COVID-19 response level and timing of peak daily incidence: an analysis of governments' Stringency Index from 148 countries.

BACKGROUND: The transmission dynamics and severity of coronavirus disease 2019 (COVID-19) pandemic is different across countries or regions. Differences in governments' policy responses may explain some of these differences. We aimed to compare worldwide government responses to the spread of COVID-19, to examine the relationship between response level, response timing and the epidemic trajectory. METHODS: Free publicly-accessible data collected by the Coronavirus Government Response Tracker (OxCGRT) were used. Nine sub-indicators reflecting government response from 148 countries were collected systematically from January 1 to May 1, 2020. The sub-indicators were scored and were aggregated into a common Stringency Index (SI, a value between 0 and 100) that reflects the overall stringency of the government's response in a daily basis. Group-based trajectory modelling method was used to identify trajectories of SI. Multivariable linear regression models were used to analyse the association between time to reach a high-level SI and time to the peak number of daily new cases. RESULTS: Our results identified four trajectories of response in the spread of COVID-19 based on when the response was initiated: before January 13, from January 13 to February 12, from February 12 to March 11, and the last stage-from March 11 (the day WHO declared a pandemic of COVID-19) on going. Governments' responses were upgraded with further spread of COVID-19 but varied substantially across countries. After the adjustment of SI level, geographical region and initiation stages, each day earlier to a high SI level (SI > 80) from the start of response was associated with 0.44 (standard error: 0.08, P < 0.001, R2 = 0.65) days earlier to the peak number of daily new case. Also, each day earlier to a high SI level from the date of first reported case was associated with 0.65 (standard error: 0.08, P < 0.001, R2 = 0.42) days earlier to the peak number of daily new case. CONCLUSIONS: Early start of a high-level response to COVID-19 is associated with early arrival of the peak number of daily new cases. This may help to reduce the delays in flattening the epidemic curve to the low spread level.