ORCID Profile
0000-0002-6086-0307
Current Organisation
University of Melbourne
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Communications engineering | Signal processing | Wireless communication systems and technologies (incl. microwave and millimetrewave) |
Publisher: Springer Science and Business Media LLC
Date: 17-06-2020
Publisher: Cold Spring Harbor Laboratory
Date: 26-08-2020
DOI: 10.1101/2020.08.26.267724
Abstract: Knowledge of the epitopes of SARS-CoV-2 that are targeted by T cells in convalescent patients is important for understanding T cell immunity against COVID-19. This information can aid the design, development and assessment of COVID-19 vaccines, and inform novel diagnostic technologies. Here we provide a unified description and meta-analysis of emerging data of SARS-CoV-2 T cell epitopes compiled from 15 independent studies of cohorts of convalescent COVID-19 patients. Our analysis demonstrates the broad ersity of T cell epitopes that have been collectively recorded for SARS-CoV-2, while also identifying a selected set of immunoprevalent epitopes that induced consistent T cell responses in multiple cohorts and in a large fraction of tested patients. The landscape of SARS-CoV-2 T cell epitopes that we describe can help guide future immunological studies, including those related to vaccines and diagnostics. A web-based platform has been developed to help complement these efforts.
Publisher: Cold Spring Harbor Laboratory
Date: 14-12-2021
DOI: 10.1101/2021.12.12.472315
Abstract: Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant.
Publisher: Wiley
Date: 08-01-2019
DOI: 10.1002/CPE.5121
Abstract: The growing popularity of Digital Social Networks (DSNs) among young students demands an introspection of its impact across different dimensions, such as students' academic performance and daily life. The results of the existing literature on the issue vary across societies due to differences in cultural and religious values. This research aims to examine the social network usage among students to analyze their bonding within their social and personal lives. As a case study, we selected Pakistani students as a convenient s le. Multiple social aspects like in‐person interaction of students with their family members, physical activities, religious knowledge, social capital, and level of students' trust in DSNs are considered. Considering the complex nature of the network, a Complex Adaptive System (CAS) approach is used to model the relationships between different nodes of the network. In addition, Linear Regression models are created to predict a node from the combination of different nodes based on their relationships.
Publisher: Elsevier BV
Date: 04-2021
Publisher: MDPI AG
Date: 03-09-2022
DOI: 10.3390/V14091960
Abstract: Beginning in May 2022, a novel cluster of monkeypox virus infections was detected in humans. This virus has spread rapidly to non-endemic countries, sparking global concern. Specific vaccines based on the vaccinia virus (VACV) have demonstrated high efficacy against monkeypox viruses in the past and are considered an important outbreak control measure. Viruses observed in the current outbreak carry distinct genetic variations that have the potential to affect vaccine-induced immune recognition. Here, by investigating genetic variation with respect to orthologous immunogenic vaccinia-virus proteins, we report data that anticipates immune responses induced by VACV-based vaccines, including the currently available MVA-BN and ACAM2000 vaccines, to remain highly cross-reactive against the newly observed monkeypox viruses.
Publisher: Springer Science and Business Media LLC
Date: 05-07-2020
Publisher: Elsevier BV
Date: 12-2011
Publisher: MDPI AG
Date: 25-02-2020
DOI: 10.3390/V12030254
Abstract: The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the 120 available SARS-CoV-2 sequences (as of 21 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2022
DOI: 10.1101/2022.06.23.497143
Abstract: Starting May 2022, a novel cluster of monkeypox virus infections was detected in humans. This has spread rapidly to non-endemic countries and sparked global concern. Vaccinia virus vaccines have demonstrated high efficacy against monkeypox viruses in the past and are considered an important outbreak control measure. Viruses observed in the current outbreak carry distinct genetic variation that have the potential to affect vaccine-induced immune recognition. Here, by investigating genetic variation with respect to orthologous immunogenic vaccinia-virus proteins, we report data that anticipates vaccine-induced immune responses to remain highly cross-reactive against the newly observed monkeypox viruses.
Publisher: IEEE
Date: 07-2010
Publisher: Cold Spring Harbor Laboratory
Date: 2022
DOI: 10.1101/2021.12.31.21268591
Abstract: New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could facilitate outbreak control efforts and highlight new variants that warrant further study. Here we develop an analytical epidemiological model that infers the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that strongly affect the transmission rate, both within and outside the Spike protein. We also quantify the effects of travel and competition between different lineages on the inferred transmission effects of mutations. Importantly, our model detects lineages with increased transmission as they arise. We infer significant transmission advantages for the Alpha and Delta variants within a week of their appearances in regional data, when their regional frequencies were only around 1%. Our model thus enables the rapid identification of variants and mutations that affect transmission from genomic surveillance data.
Publisher: IEEE
Date: 07-2007
Publisher: Public Library of Science (PLoS)
Date: 21-09-2020
Publisher: Wiley
Date: 06-07-2021
DOI: 10.1111/BPH.15582
Abstract: Emerging data show that pregnant women with COVID‐19 are at significantly higher risk of severe outcomes compared with non‐pregnant women of similar age. This review discusses the invaluable insight revealed from vaccine clinical trials in women who were vaccinated and inadvertently became pregnant during the trial period. It further explores a number of clinical avenues in their management and proposes a drug development strategy in line with clinical trials for vaccines and drug treatments for the drug development community. Little is known of the long‐term effects of COVID‐19 on the mother and the baby. Our hypothesis that COVID‐19 predisposes pregnant women to pre‐ecl sia or hypertensive disorders during pregnancy is supported by a clinical study, and this may also adversely impact a woman's cardiovascular disease risk later in life. It may also increase a woman's risk of pre‐ecl sia in subsequent pregnancy. This is an ever‐evolving landscape, and early knowledge for healthcare providers and drug innovators is offered to ensure benefits outweigh the risks. COVID‐19 mRNA vaccines appear to generate robust humoral immunity in pregnant and lactating women. This novel approach to vaccination also offers new ways to therapeutically tackle disorders of many unmet medical needs. This article is part of a themed issue on The second wave: are we any closer to efficacious pharmacotherapy for COVID 19? (BJP 75th Anniversary). To view the other articles in this section visit oi/10.1111/bph.v179.10/issuetoc
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2020
DOI: 10.1101/2020.02.03.933226
Abstract: The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the available SARS-CoV-2 sequences (as of 9 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.
Publisher: IEEE
Date: 09-2011
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 11-2015
Publisher: MDPI AG
Date: 02-01-2022
DOI: 10.3390/V14010079
Abstract: Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant.
Publisher: Cold Spring Harbor Laboratory
Date: 24-05-2020
DOI: 10.1101/2020.05.23.111385
Abstract: We introduce COVIDep ( COVIDep.ust.hk ), a web-based platform that provides immune target recommendations for guiding SARS-CoV-2 vaccine development. COVIDep implements a protocol that pools together publicly-available genetic data for SARS-CoV-2 and epitope data for SARS-CoV to identify B cell and T cell epitopes that present potential immune targets for SARS-CoV-2. Correspondences between outputs of COVIDep and immune responses recorded in COVID-19 patients and preclinical vaccine trials are also indicated. The platform is user-friendly, flexible, and based on up-to-date data. It may help guide vaccine designs and associated experimental studies for SARS-CoV-2.
Publisher: MDPI AG
Date: 31-03-2022
Abstract: Memory SARS-CoV-2-specific CD8+ T cell responses induced upon infection or COVID-19 vaccination have been important for protecting against severe COVID-19 disease while being largely robust against variants of concern (VOCs) observed so far. However, T cell immunity may be weakened by genetic mutations in future SARS-CoV-2 variants that lead to widespread T cell escape. The capacity for SARS-CoV-2 mutations to escape memory T cell responses requires comprehensive experimental investigation, though this is prohibited by the large number of SARS-CoV-2 mutations that have been observed. To guide targeted experimental studies, here we provide a screened list of potential SARS-CoV-2 T cell escape mutants. These mutants are identified as candidates for T cell escape as they lie within CD8+ T cell epitopes that are commonly targeted in in iduals and are predicted to abrogate HLA–peptide binding.
Publisher: IEEE
Date: 09-2011
Publisher: Oxford University Press (OUP)
Date: 28-06-2019
DOI: 10.1093/BIOINFORMATICS/BTZ524
Abstract: Patterns of mutational correlations, learnt from patient-derived sequences of human immunodeficiency virus (HIV) proteins, are informative of biochemically linked networks of interacting sites that may enable viral escape from the host immune system. Accurate identification of these networks is important for rationally designing vaccines which can effectively block immune escape pathways. Previous computational methods have partly identified such networks by examining the principal components (PCs) of the mutational correlation matrix of HIV Gag proteins. However, driven by a conservative approach, these methods analyze the few dominant (strongest) PCs, potentially missing information embedded within the sub-dominant (relatively weaker) ones that may be important for vaccine design. By using sequence data for HIV Gag, complemented by model-based simulations, we revealed that certain networks of interacting sites that appear important for vaccine design purposes are not accurately reflected by the dominant PCs. Rather, these networks are encoded jointly by both dominant and sub-dominant PCs. By incorporating information from the sub-dominant PCs, we identified a network of interacting sites of HIV Gag that associated very strongly with viral control. Based on this network, we propose several new candidates for a potent T-cell-based HIV vaccine. Accession numbers of all sequences used and the source code scripts for all analysis and figures reported in this work are available online at araz107/HIV-Gag-Immunogens. Supplementary data are available at Bioinformatics online.
Publisher: Elsevier BV
Date: 06-2021
Location: Saudi Arabia
Start Date: 2023
End Date: 12-2025
Amount: $425,000.00
Funder: Australian Research Council
View Funded Activity