Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

The PHA4GE Microbial Data-Sharing Accord: establishing baseline consensus microbial data-sharing norms to facilitate cross-sectoral collaboration

Microbial data sharing underlies evidence-based microbial research, as well as pathogen surveillance and analysis essential to public health. While the need for data sharing was highlighted during the SARS-CoV-2 pandemic, some concerns regarding secondary data use have also surfaced. Although general guidelines are available for data sharing, we note the absence of a set of established, universal, unambiguous and accessible principles to guide the secondary use of microbial data. Here, we propose the Public Health Alliance for Genomic Epidemiology (PHA4GE) Microbial Data-Sharing Accord to consolidate consensus norms and accepted practices for the secondary use of microbial data. The Accord provides a set of seven simple, baseline principles to address key concerns that may arise for researchers providing microbial datasets for secondary use and to guide responsible use by data users. By providing clear rules for secondary use of microbial data, the Accord can increase confidence in sharing by data providers and protect against data mis-use during secondary analyses.

The Vaccine World of COVID-19: India’s Contribution

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) eruption has left not only illness and mortality in its wake, but also an overwhelming threat to health policy, human regality, food security, and struggle worldwide. The accessibility and potential distribution of a protective and successful vaccination to communities throughout the world are being considered now not just, as a potential of overcoming these hurdles, but also as an example of human perseverance in the face of catastrophe. A vaccine is the only tool that can efficaciously deal with the COVID-19 catastrophe. Currently, more than 47 vaccines are permitted for emergency use in distinct parts of the world. India will play a significant role in the development of the high-priced Moderna shots and Pfizer Inc, therefore assisting in the immunization of a large portion of the world. Moreover, many of the internationally researched and developed vaccine laboratories seek manufacturing in Indian firms and companies for efficient and low-cost production of vaccines intending to provide to the world, hence, making India, a major role player during these pandemic times. This review highlights the Indian contribution to the globe for COVID-19 management.

Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era

Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral genotyping, metadata linkage, data reporting, and public health responses. Unfortunately, current limitations in each of these steps have compromised the overall effectiveness of these strategies. Biases from convenience-based sampling methods can obfuscate the true distribution of circulating variants. The lack of standardization in genotyping strategies and bioinformatic expertise can create bottlenecks in data processing and complicate interpretation. Limitations and inconsistencies in clinical and demographic data collection and sharing can slow the compilation and limit the utility of comprehensive datasets. This likewise can complicate data reporting, restricting the availability of timely data. Finally, gaps and delays in the implementation of genomic surveillance data in the public health sphere can prevent officials from formulating effective mitigation strategies to prevent outbreaks. In this review, we outline current SARS-CoV-2 global genomic surveillance methods and assess roadblocks at each step of the pipeline to identify potential solutions. Evaluating the current obstacles that impede effective surveillance can improve both global coordination efforts and pandemic preparedness for future outbreaks.

Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues

The main protease (M^pro) is a key enzyme responsible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication that causes the spread of the global pandemic novel coronavirus (nCOVID-19) infection. In the present study, multiple computational approaches such as docking, long-range molecular dynamics (MD) simulations, and binding free-energy (BFE) estimation techniques were employed to investigate the mechanistic basis of the high-affinity inhibitors─GC-376, Calpain XII, and Calpain II (hereafter Calpain as Cal) from the literature─binding to M^pro. Redocking GC-376 and docking Cal XII and Cal II inhibitors to M^pro were able to reproduce all crucial interactions like the X-ray conformation. Subsequently, the apo (ligand-free) and three holo (ligand-bound) complexes were subjected to extensive MD simulations, which revealed that the ligand binding did not alter the overall M^pro structural features, whereas the heatmap analysis showed that the residues located in subsites S1 and S2, the catalytic dyad, and the ⁴⁵TSEDMLN⁵¹ loop in M^pro exhibit a conformational deviation. Moreover, the BFE estimation method was used to elucidate the crucial thermodynamic properties, which revealed that Coulomb, solvation surface accessibility (Solv_SA), and lipophilic components contributed significant energies for complex formation. The decomposition of the total BFE to per-residue showed that H41, H163, M165, Q166, and Q189 residues contributed maximum energies. The overall results from the current investigation might be valuable for designing novel anti-M^pro inhibitors.

Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines

Background: The coronavirus disease 2019 (COVID-19) global pandemic required a rapid and effective response. This included ethical and legally appropriate sharing of data. The European Commission (EC) called upon the Research Data Alliance (RDA) to recruit experts worldwide to quickly develop recommendations and guidelines for COVID-related data sharing. Purpose: The purpose of the present work was to explore how the RDA succeeded in engaging the participation of its community of scientists in a rapid response to the EC request. Methods: A survey questionnaire was developed and distributed among RDA COVID-19 work group members. A mixed-methods approach was used for analysis of the survey data. Results: The three constructs of radical collaboration (inclusiveness, distributed digital practices, productive and sustainable collaboration) were found to be well supported in both the quantitative and qualitative analyses of the survey data. Other social factors, such as motivation and group identity were also found to be important to the success of this extreme collaborative effort. Conclusions: Recommendations and suggestions for future work were formulated for consideration by the RDA to strengthen effective expert collaboration and interdisciplinary efforts.