Design of putative T-cell epitope-based vaccine against SARS-CoV-2 : reverse vaccinology approach

Khaerunissa Anbar Istiadi1, Fadilah Fadilah1,2, Rafika Indah Paramita1,2, Linda Erlina1,2, Budi Wiweko3

1Bioinformatics Core Facilities – IMERI, Faculty of Medicine, Universitas Indonesia. Jalan Salemba Raya number 6, Jakarta, Indonesia

2Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia. Jalan Salemba Raya number 4, Jakarta, Indonesia

3Department of Obstetrics and Gynaecology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia

 

Late 2019, severe pneumonia cases were found in Wuhan, China. The cases then identified as COVID-19, caused by a novel Coronavirus, SARS-CoV-2. Until now, there has been no efficacious and approved therapy to control SARS-CoV-2 spread. The rapid global spread and vulnerability of infection made an urgency to produce drugs or vaccine, enhancing global immune system. Currently researchers and companies are working to develop a vaccine for SARS-CoV-2. Most of this vaccine target the Spike protein aim to elicit protective antibodies. S protein (S) might be used as target for vaccine development since it is the outer surface protein of SARS-CoV-2 which can be directly recognized by the immune system. Here an attempt has been made to design putative epitope-based vaccine for SARS-CoV-2, analyzing virus genome using reverse vaccinology approach based on SARS-CoV-2 virus spike protein sequence data. About 6000 sequences were downloaded from ViPR database and processed by AVANA to find conserved region. Based on predictions through the reverse vaccinology approach and molecular docking, HLA Class I putative epitope YQPYRVVVL which overlap with HLA Class II putative epitope NGVGYQPYRVVVLSF sequence was selected as potential peptide-vaccine candidates.

Keywords: HLA, Reverse vaccinology, SARS-CoV-2, Spike protein, T-cell epitope-based vaccine

COVID-19 eResearch Experiences and Collaborations in Australasia and Southeast Asia – Upskilling Support for Pandemic Response, Preparedness and Recovery

Dr Markus Buchhorn1, Sam Moskwa2, Dr Idris Sulaiman2,3, Rowland Mosbergen

1Asia-Pacific Advanced Network (APAN.net)

2Australasia eResearch Organisations (AeRO.edu.au)

3SE Asia Engagement

 

The Covid-19 pandemic is affecting countries in Southeast Asia and the broader Indo-Pacific region in ways that increasingly demand Australia and New Zealand’s collective attention since in fighting a global pandemic, no country can go it alone.

The ability to weather a crisis of this magnitude depends upon partnerships and collaboration around research capacity and infrastructure, public health capacity, economic, social and many other aspects.

This Birds of a Feather aims to provide participants the opportunity to consider potential topics that centre on the acceleration of upskilling and access to e-Research infrastructure and data sharing capabilities for the region. Disciplinary efforts to develop data-driven, timely and effective upskilling to the Pandemic as part of national and regional COVID-19 responses.

Objectives

To help address inequities in medical research capability and capacity by leveraging opportunities with the

Australasian research infrastructure providers and the wider research community.

Overview of emerging trends obtained from various stakeholders

* Extent of recognition that sharing data is important and worthwhile

* Requirements for greater capacity in computational infrastructure

* Extent of recognition that community-led infrastructure development is important

Agenda

* Introduction and Overview of eResearch experiences and constraints (10 minutes)

* Panel of speakers, discussants and general discusions(Lighting Talks & discussion: 40 min.)

* Possible Threads:

(1) Designing vaccines through High Performance Computing (HPC) and “big data” techniques

(2) Framework for Research Data Management and eResearch Community of Practice (CoP) Development

(3) Data Sharing Standards (such as Research Data Alliance COVID-19 Data Sharing Guidelines) (4) Role of Identity and Federated Access Management

* Wrap-up for take-aways (10 minutes)

* Possible extra time for networking at following break of eResConf (10 minutes, 14:30 – 14:40)

 

Multidisciplinary Big-Data Sharing, Analysis, and Policy Recommendations to Support COVID-19 Pandemic Response

Dr Damar Susilaradeya1, Dr Prasandhya Astagiri Yusuf1, Gina Anindyajati1 , Dr Ahmad Gamal2, Dr Adila Alfa Krisnadhi3, Dr Bagus  Takwin4, Jarot Mulyo Semedi5, Iwan Ariawan6, Rus’an Nasrudin7, Dr Hervita Diatri1, Ima Mayasari8, Prof Budi Wiweko1

1Faculty of Medicine Universitas Indonesia, Depok, Indonesia
2Faculty of Engineering Universitas Indonesia, Depok, Indonesia
3Faculty of Computer Sciences Universitas Indonesia, Depok, Indonesia
4Faculty of Psychology Universitas Indonesia, Depok, Indonesia
5Faculty of Mathematics and Natural Sciences Universitas Indonesia, Depok, Indonesia
6Faculty of Public Health Universitas Indonesia, Depok, Indonesia
7Faculty of Economics & Business Universitas Indonesia, Depok, Indonesia
8Faculty of Administrative Science Universitas Indonesia, Depok, Indonesia

Introduction

The COVID-19 pandemic requires massive actions across multiple disciplines to prevent extended consequences. Indonesia as a multi-cultural archipelago with more than 260 million population faces a unique challenge in addressing the pandemic. Universitas Indonesia formed a multidisciplinary research group analysing big data in collaboration with various academic, government, and industry partners to inform the national COVID-19 committee.

Methods

We analysed data related to the large-scale social restriction implemented by the government. We looked at COVID-19 cases, mobility data, mental health status, health-related, and economic behaviours. We performed spatial analysis using Geographical Information System (GIS) to map region-specific risks that require tailored government intervention.

Results and discussions

This multidisplinary approach allowed us to have a comprehensive and well-rounded view of the problem our nation is facing which was then translated into big-data driven policy recommendations. We faced several challenges during the process of this research utilising big-data from various resources, including variability (variety of data), validity (study design, power of study, statistics), reproducibility (transparency and open science), and responsibility (ethics, security, and privacy). These challenges need to be addressed in order to provide the government with accurate scientific COVID-19 advice. Moreover, joint collaborations providing the necessary human resources, software platforms and computational infrastructure during COVID-19 and beyond are needed specifically to be able to do responsible data sharing and data mining.


Biography:

Damar Susilaradeya is a researcher at the Medical Technology Cluster Indonesian Medical Education and Research Institute (IMERI) Faculty of Medicine Universitas Indonesia. She is also a lecturer at the Medical Physics Department at the Faculty of Medicine Universitas Indonesia. She is the coordinator of Universitas Indonesia Big-Data Synergy Against COVID-19 team.

Secure eResearch Platform to support research during COVID-19

Mr Mat Ishac1, Mr Jerico Revote1, Mr Daniel Waghorn1, Ms Komathy Padmanabhan1, Professor Belinda Gabbe1, Mr Chris Mac Manus1, Ms Anitha Kannan1

1Monash University, Melbourne, Australia

Monash SeRP is a secure research platform that enables the storage, analysis and sharing of research data, in a well governed environment. During the COVID-19 pandemic researchers are working remotely due to site closures and physical distancing.

The Secure eResearch Platform (SeRP) has been developed by Swansea University and is the gold standard for managing, sharing and collaborating over sensitive data. Monash has collaborated with Swansea University to adapt SeRP for the Australian context and this is being operated as Monash SeRP.

Prof Belinda Gabbe has been an early adopter of Monash SeRP through three key research projects; the NHMRC funded VIBES-Junior study, population linkage of state-based trauma datasets, and an international bench-marking study of trauma outcomes. Each of these projects has had critical reporting deadlines to key funders and stakeholders.

The availability of Monash SeRP and other remote tools for collaboration have ensured continuity during the COVID-19 pandemic. The availability of this platform has provided access to high capacity computing for complex analytics by multiple analysts in Australia and internationally, with exceptional security and data custodian control.  Monash SeRP has accelerated analysis of complex data, and collaboration between analysts, in a time-frame that would not otherwise be possible.

Monash SeRP has been approved for hosting de-identified data and certification for hosting identified and re-identifiable data is in progress, and is envisaged to support a significant proportion of research at Monash University that require secure collaboration environments for sensitive research data.


Biography:

Mathew Ishac is Project Support Officer at Helix, Monash University with a background in facilitating the implementation and training of new technology within hospital and health research fields.

Galaxy Australia’s role in responding to the COVID-19 pandemic

Mr Simon Gladman1, Dr Nicholas Rhodes2, Dr Gareth Price2, Professor Andrew Lonie3

1University of Melbourne, Carlton, Australia
2QCIF Facility for Advanced Bioinformatics, St Lucia, Australia
3Australian BioCommons, Carlton, Australia

Introduction

The global Galaxy Project responded to the urgent need for insight into the SARS-COV-2 virus through its global partners to help build a truly global, democratised, reproducible and transparent multifaceted approach to systematic analyses of the virus. Galaxy Australia contributed to this effort through deployment of specific SARS-COV-2 analytical workflows at the Pawsey Supercomputing, for access to all Australian researchers.

Methods

Galaxy Australia in conjunction with the Pawsey Supercomputing centre were able to deploy a Galaxy Pulsar (Galaxy remote deployment) on the NIMBUS cloud, complete with tools and workflows for analysis of DNA sequencing data from SARS-COV-2 samples. Galaxy Australia was configured to prioritise user requests for tools associated with SARS-COV-2 workflows to be directed to Pawsey for rapid analysis turnaround.

Results

This talk will describe the deployment at Pawsey, the linkages and complementary analysis established at Galaxy Australia, Galaxy Main (USA) and Galaxy Europe, highlighting Galaxy Australia’s role in enabling research into a global problem. Up to date details of the utilisation of the workflows will also be presented.

Conclusion

In response to a global need, Galaxy Australia and Pawsey Supercomputing centre were able to demonstrate agility and timeliness to the growing threat of SARS-COV-2. The workflows deployed on Galaxy Australia were complemented by additional workflows on the partner usegalaxy.* global platforms, demonstrating the power of open source democratised science.


Biography:

Simon Gladman works at Melbourne Bioinformatics and is Chief Engineering of Galaxy Australia. Simon has contributed actively to the global Galaxy community for 10 years and helps shape the direction and support Australian researchers garner from their use of the national Galaxy Australia platform.

COVID-19 Collaboration Network

Mr Melroy Almeida1, Dr  Amir  Aryani2, Dr Jingbo Wang3

1Australian Access Federation, Brisbane , Australia
2Swinburne University of Technology , Hawthorn, Australia
3Australian National University , Canberra, Australia

The global pandemic has changed the focus of researchers around the world to COVID-19 impact and recovery. In this work, we leverage ORCID and the connected graph of scholarly communications to look at how organisations and countries are collaborating towards finding a pathway to COVID-19 recovery.

Persistent identifiers (PIDs) allow us to link different entities like people, organisations, datasets and publications by precisely identifying the participants within a research project. PIDs enable research provenance and attribution by accurately linking research entities.  PIDs are not just a technical capability, but a community effort that is also collaborative in nature. This work uses persistent identifiers like ORCID IDs, DoI’s and org ids (organisational identifiers) to establish connections such as

DoI, PMID -> ORCID-> ORG ID (ISNI, GRID, ROR)

Using these links and leveraging the interconnectedness of the different identifiers, we report on the formation of a collaboration network that captures connections between researchers, research datasets, publications and grants. Using this newly formed collaboration network, we demonstrate how COVID19 research collaboration has formed since late 2019.

This presentation will touch on the following topics

  • A time series visualisation on how the international community collaborates on COVID-19 research
  • The top countries publishing articles on COVID-19
  • The most bilateral engagement between universities in this space

Biography:

‘Bio to come’

Modelling COVID-19 Spike Protein Interactions on CSIRO’s Bracewell GPU Cluster

Dr Michael Kuiper1, Dr Tim Ho2

1CSIRO, Docklands, Australia
2CSIRO, Clayton, Australia

The coronavirus SARS-CoV-2 (COVID-19) attaches to human cell through its spike (S) protein receptor binding domain (RBD) to ACE2 proteins to begin the infectious process.

We used molecular dynamics to model the RBD binding to ACE2 protein to better understand the key interactions between residues. Additionally, we built a larger spike model, complete with its glycosylation pattern to help our researchers visualize effects of mutations and better understand interactions of other host proteins, such as the protease furin, which is important for viral infectivity.

CSIRO’s Bracewell GPU cluster was key to quickly initiating and performing this work. Having rapid access allows for quick prototyping and troubleshooting with the simulations. Earlier on in the pandemic little structural information was available. However, as the worldwide research effort gained pace, we were able to incorporate new findings into our developing models. As a new dominant strain was being recorded, (D614G) we were able to incorporate this into our models and, with experimental validation from the Australian Center for Disease Prevention (ACDP), able to assess the effects of the mutation. Fortunately, this strain does not appear to resist vaccine responses, however, work by others indicates it is a more efficient spreader.


Biography:

Dr Michael Kuiper is a computational research scientist at CSIRO’s Dat61 specialising in bio-molecular simulations and visualisation. He contributes to many varied collaborative projects enabling researchers in biological science to utilise high-performance computing (HPC) and has a keen interest in using Virtual Reality to visualize molecular complexes. Currently he is focused on COVID-19 research as well as microbial plastics degradation and antimicrobial resistance. Michael previously worked at other HPC centres including the VLSCI and has spent time in Antarctica studying antifreeze proteins in fish with the United States Antarctic Program.

eResearch Community Continuity During a Pandemic: The MeRC Community Cohesion Strategy

Mrs Jane Frazier1, Ms Ai-Lin Soo1

1Monash eResearch Centre, Melbourne, Australia

The transition to an increasingly remote workplace due to the COVID-19 pandemic highlighted the need to rapidly mitigate three key risks in the Monash eResearch Centre (MeRC) to ensure cohesive team operations and undisrupted support to researchers:

  1. The absence of common, remote internal communication channels to effectively replicate the coordination of operations in-office in a timely manner;
  2. The absence of a centre-wide channel for external key stakeholder and user communication to ensure standardised and timely notifications; and
  3. The inability to “self-serve” accurate stakeholder and user contact information for communication purposes across the centre.

As a result, a Community Cohesion Strategy and Team were established to address gaps that emerged in the operational management of MeRC as staff transitioned to a remote working environment, and to facilitate the rapid dissemination of key centre and operational updates to stakeholders. This drastic change in working environments provided a unique opportunity to implement a framework by which working-from-home arrangements and wellbeing of partially or fully remote teams might be supervised successfully.

In this presentation, we highlight the elements that were implemented to address these gaps, in accordance with a number of principal purposes. The strategies were a mixture of social and cultural changes as well as technological solutions.

The implementation of the Community Cohesion Strategy within MeRC resulted in the successful transition to a remote workforce supporting researchers at an unreduced capacity, and has improved operational management and preserved team culture that will extend beyond the initial duration of remote working.


Biography:

https://orcid.org/0000-0002-2374-4964

Jane Frazier is Senior Research Community Manager at Monash eResearch Centre and Project Manager for the Australian Characterisation Commons at Scale. Jane has extensive experience in the metadata and ontologies space, and has focused her career on building solutions to facilitate the description, storage, discovery, and use of data across a range of industries and sectors, including employment, research and e-commerce. Jane was part of the team that built the world’s first national controlled vocabulary and ontology management and sharing platform, and is most interested in creating data-driven solutions and supporting research capability.

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