Samira Mubareka's research while affiliated with University of Toronto and other places

Publications (198)

Article
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Low-pathogenicity avian influenza viruses (AIV) of the H9N2 subtype can infect and cause disease in chickens. Little is known about the efficacy of immune-based strategies for reducing the transmission of these viruses. The present study investigated the efficacy of Toll-like receptor (TLR) ligands (CpG ODN 2007 and poly(I:C)) to reduce H9N2 AIV tr...
Article
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Given the enormous global impact of the COVID-19 pandemic, outbreaks of highly pathogenic avian influenza in Canada, and manifold other zoonotic pathogen activity, there is a pressing need for a deeper understanding of the human-animal-environment interface and the intersecting biological, ecological, and societal factors contributing to the emerge...
Chapter
Coexistence of humans and bats in cities requires mitigation of two key sources of human-bat conflict: risk of zoonotic disease transmission and human concerns about cleanliness. Bats can transmit infectious diseases to humans, and mitigating this risk is an important challenge for both public health and bat conservation. Bat colonies in buildings...
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Background The spread of carbapenemase-producing Enterobacterales (CPE) is global threat. Numerous outbreaks of CPE have been reported during the COVID-19 pandemic. We describe the impact of of the SARS-CoV-2 pandemic on the emergence of CPE in south-central Ontario, Canada. Incidence of clinical isolates of CPE and isolates with different CPE gene...
Preprint
BACKGROUND With the growing volume and complexity of laboratory repositories, it has become tedious to parse unstructured data into structured and tabulated formats for secondary uses such as decision support, quality assurance, and outcome analysis. However, advances in Natural Language Processing (NLP) approaches have enabled efficient and automa...
Article
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SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRI...
Preprint
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Background: With the growing volume and complexity of laboratory repositories, it has become tedious to parse unstructured data into structured and tabulated formats for secondary uses such as decision support, quality assurance, and outcome analysis. However, advances in Natural Language Processing (NLP) approaches have enabled efficient and autom...
Preprint
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Background: We investigate the effects of remdesivir (RDV) treatment on intra-host SARS-CoV-2 diversity and low-frequency mutations in moderately ill hospitalized COVID-19 patients and compare them to patients without RDV treatment. Methods: Sequential collections of nasopharyngeal and mid-turbinate swabs were obtained from 16 patients with and 31...
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Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral variants that can emerge to infect humans. In North America, there is phylogenomic evidence of continual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (Odocoileus virginianus) through unknow...
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Unlabelled: Cases of vaccine breakthrough, especially in variants of concern (VOCs) infections, are emerging in coronavirus disease (COVID-19). Due to mutations of structural proteins (SPs) (e.g., Spike proteins), increased transmissibility and risk of escaping from vaccine-induced immunity have been reported amongst the severe acute respiratory s...
Preprint
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SARS-CoV-2, the causative agent of COVID-19, has been responsible for a global pandemic. Monoclonal antibodies have been used as antiviral therapeutics, but have been limited in efficacy by viral sequence variability in emerging variants of concern (VOCs), and in deployment by the need for high doses. In this study, we leverage the MULTI-specific,...
Article
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Lower viral loads were observed in the upper respiratory tract of patients infected with the BA.1 whereas patients infected with BA.2 and BA.5 had comparable viral loads to those seen with Alpha or Delta. This suggests viral loads are not likely responsible for the increased transmission of the Omicron lineages.
Article
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The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike glycoprotein (S) binds to angiotensin-converting enzyme 2 (ACE2) to mediate membrane fusion via two distinct pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In this study, we found that SARS-CoV-2 S has a wider protease...
Article
Objectives: SARS-CoV-2 shedding has changed as new variants have emerged. It is important to understand the trajectory of PCR positivity due to Omicron in vaccinated populations. Methods: Double- or triple-vaccinated adult household contacts of individuals with COVID-19 self-collected oral-nasal swabs for 14 days. A hierarchical linear model estima...
Article
The development of robust biosensing strategies that can be easily implemented in everyday life remains a challenge for the future of modern biosensor research. While several reagentless approaches have attempted to address this challenge, they often achieve user-friendliness through sacrificing sensitivity or universality. While acceptable for cer...
Preprint
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from wildlife origins has raised concerns about spillover from humans to animals, the establishment of novel wildlife reservoirs, and the potential for future outbreaks caused by variants of wildlife origin. Norway rats ( Rattus norvegicus ) are abundant in urban areas an...
Article
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Migratory birds are major reservoirs for avian influenza viruses (AIV), which can be transmitted to poultry and mammals. The H9N2 subtype of AIV has become prevalent in poultry over the last two decades. Despite that, there is a scarcity of detailed information on how this virus can be transmitted. The current study aimed to establish a direct cont...
Article
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The emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) was met with rapid development of robust molecular-based detection assays. Many SARS-CoV-2 molecular tests target multiple genetic regions of the virus to maximize detection and protect against diagnostic escape. Despite the relatively moderate mutational rate of SARS-CoV-2...
Article
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Cell-mediated immunity is critical for long-term protection against most viral infections, including coronaviruses. We studied 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected survivors over a 1-year post-symptom onset (PSO) interval by ex vivo cytokine enzyme-linked immunosorbent spot assay (ELISpot) assay. All subjects dem...
Article
Among outpatients with COVID-19 due to the Delta variant who did and did not receive two vaccine doses at 7 days post symptom onset there was no difference in viral shedding (cycle threshold difference 0.59, 95% CI -4.68–3.50; p=0.77) with SARS-CoV-2 cultured from 7% (2/28) and 4% (1/26), respectively.
Article
SARS-CoV-2 is a novel respiratory virus that has quickly spread across the globe. The virus uses a protein called Spike and its associated receptor binding domain (RBD) to interact with angiotensin converting enzyme-2 (ACE-2) on the surface of epithelial cells in the respiratory tract. Although a definite correlate of protection against COVID-19 ha...
Article
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Although SARS-CoV-2 infects the upper respiratory tract, we know little about the amount, type, and kinetics of antibodies (Ab) generated in the oral cavity in response to COVID-19 vaccination. We collected serum and saliva samples from participants receiving two doses of mRNA COVID-19 vaccines and measured the level of anti-SARS-CoV-2 Ab. We detec...
Article
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Background SARS-CoV-2 omicron variant of concern (VOC) has evolved multiple mutations within the spike protein, raising concerns of increased antibody evasion. In this study, we assessed the neutralization potential of COVID-19 convalescent sera and sera from vaccinated individuals against ancestral SARS-CoV-2 and VOCs. Methods The neutralizing ac...
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Background For both the current and future pandemics, there is a need for high-throughput drug screening methods to identify existing drugs with potential preventative and/or therapeutic activity. Epidemiologic studies could complement lab-focused efforts to identify possible therapeutic agents. Methods We performed a pharmacopeia-wide association...
Article
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Objectives: Antibody testing against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in detecting previous exposures and analyzing vaccine-elicited immune responses. Here, we describe a scalable solution to detect and quantify SARS-CoV-2 antibodies, discriminate between natural infection- and vaccination-induced...
Article
Purpose The rapid emergence and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has sparked concerns of spillover to naïve wildlife populations and it is unclear if wildlife could ultimately serve as a reservoir for the virus. Evidence of SARS-CoV-2 has been detected in captive and wild animals (e.g., mink, tiger, lion). More...
Preprint
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Wildlife reservoirs of SARS-CoV-2 can lead to viral adaptation and spillback from wildlife to humans (Oude Munnink et al., 2021). In North America, there is evidence of spillover of SARS-CoV-2 from humans to white-tailed deer ( Odocoileus virginianus ), but no evidence of transmission from deer to humans (Hale et al., 2021; Kotwa et al., 2022; Kuch...
Article
We provide an update to the Association of Medical Microbiology and Infectious Disease Canada seasonal influenza foundation guideline on the use of antiviral drugs for influenza for the upcoming 2021–2022 influenza season in Canada. Peramivir and baloxavir marboxil were licensed in Canada in 2017 and 2020, respectively, but neither is currently mar...
Preprint
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To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent path...
Article
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Microfluidic polymeric blood vessel captures the adverse effects of SARS-CoV-2 on vasculature and enables identification of a therapeutic peptide that abolished virus induced cytokine storm orchestrated by the immune cells.
Article
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Since the vast majority of species solely rely on innate immunity for host defense, it stands to reason that a critical evolutionary trait like immunological memory evolved in this primitive branch of our immune system. There is ample evidence that vaccines such as Bacillus Calmette-Guerin (BCG) induce protective innate immune memory responses (tra...
Preprint
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White-tailed deer are susceptible to SARS-CoV-2 and represent a relevant species for surveillance. We investigated SARS-CoV-2 infection in white-tailed deer in Québec, Canada. In November 2021, 251 nasal swabs and 104 retropharyngeal lymph nodes from 258 deer were analyzed for SARS-CoV-2 RNA, whole genome sequencing and virus isolation and 251 thor...
Preprint
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Cellular-mediated immunity is critical for long-term protection against most viral infections, including coronaviruses. We studied 23 SARS-CoV-2-infected survivors over a one year post symptom onset (PSO) interval by ex vivo cytokine ELISpot assay. All subjects demonstrated SARS-CoV-2-specific IFN-γ, IL-2, and Granzyme B (GzmB) T cell responses at...
Preprint
The omicron variant of concern (VOC) of SARS-CoV-2 was first reported in November 2021 in Botswana and South Africa. Omicron variant has evolved multiple mutations within the spike protein and the receptor binding domain (RBD), raising concerns of increased antibody evasion. Here, we isolated infectious omicron from a clinical specimen obtained in...
Article
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces T cell, B cell, and Ab responses that are detected for several months in recovered individuals. Whether this response resembles a typical respiratory viral infection is a matter of debate. In this study, we followed T cell and Ab responses in 24 mainly nonhospitalized human subjec...
Article
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Background Several factors have been associated with severity of COVID-19 disease, but there remains a paucity of data surrounding whether the nature of exposure is impactful. Evidence demonstrating the correlation between initial viral exposure dose and disease severity exists for many viral infections. Observational studies have suggested that th...
Preprint
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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic, is capable of infecting a variety of wildlife species. Wildlife living in close contact with humans are at an increased risk of SARS-CoV-2 exposure and if infected have the potential to become a reservoir for the pathogen, maki...
Article
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Background The ongoing COVID-19 pandemic has resulted in 185 million recorded cases and over 4 million deaths worldwide. Several COVID-19 vaccines have been approved for emergency use in humans and are being used in many countries. However, all the approved vaccines are administered by intramuscular injection and this may not prevent upper airway i...
Article
Background We determined the burden of SARS-CoV-2 in air and on surfaces in rooms of patients hospitalized with COVID-19 and investigated patient characteristics associated with SARS-CoV-2 environmental contamination. Methods Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at six acute car...
Article
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Background We determined the burden of SARS-CoV-2 in air and on surfaces in rooms of patients hospitalized with COVID-19 and investigated patient characteristics associated with SARS-CoV-2 environmental contamination. Methods Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at six acute ca...
Article
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The evaluation of humoral protective immunity against SARS-CoV-2 remains crucial in understanding both natural immunity and protective immunity conferred by the several vaccines implemented in the fight against COVID-19. The reference standard for the quantification of antibodies capable of neutralizing SARS-CoV-2 is the plaquereduction neutralizat...
Article
Objective It is unclear whether supplemental oxygen and noninvasive ventilation respiratory support devices increase the dispersion of potentially infectious bioaerosols in a pressurized air medical cabin. This study quantitatively compared particle dispersion from respiratory support modalities in an air medical cabin during flight. Methods Dispe...
Article
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The golden hamster model of SARS-CoV-2 infection recapitulates key characteristics of COVID-19. In this work we examined the influence of the route of exposure, sex, and age on SARS-CoV-2 pathogenesis in hamsters. We report that delivery of SARS-CoV-2 by a low versus high volume intranasal or intragastric route results in comparable viral titers in...
Preprint
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OBJECTIVES Antibody testing against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in detecting previous exposures and analyzing vaccine-elicited immune responses. Here, we describe a scalable solution to detect and quantify SARS-CoV-2 antibodies, discriminate between natural infection- and vaccination-induced re...
Article
Background: Most individuals with coronavirus disease 2019 (COVID-19) experience mild symptoms and are managed in the outpatient setting. The aim of this study was to determine whether self-reported symptoms at the time of diagnosis can identify patients at risk of clinical deterioration. Methods: This was a retrospective cohort study of 671 out...
Article
Rationale Severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) was declared a pandemic on March 11, 2020. Countries entered lockdown, restricting medical activities to essential services. Pulmonary function tests (PFT) are crucial for management of lung diseases. With limited data regarding aerosol generation and the risk of disea...
Preprint
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The first line of defense against SARS-CoV-2 is the upper respiratory tract, yet we know little about the amount, type, and kinetics of mucosal anti-Spike antibodies (Ab) in response to intramuscular (i.m.) COVID-19 vaccination. We analyzed salivary Ab against SARS-CoV-2 Spike following mRNA/mRNA and adenovirus (Ad)/mRNA regimes. While anti-Spike/R...
Article
Background The COVID-19 pandemic highlighted the need for evidence-based approaches to decontamination and reuse of N95 filtering facepiece respirators (FFRs). We sought to determine whether vapourized hydrogen peroxide (VHP) reduced SARS-CoV-2 bioburden on FFRs without compromising filtration efficiency. We also investigated coronavirus HCoV-229E...
Preprint
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SARS-CoV-2, depends on host cell components for replication, therefore the identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection. Such host factors may be necessary for infection and replication of SARS-CoV-2 and, if druggable, presents an attractive strategy for anti-viral therapy. We...
Article
Full-text available
SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Usin...
Poster
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COVID-19 patients with respiratory distress require additional oxygen support. Some of the respiratory support devices used in intensive care units could increase the dispersion of infectious viral particles placing healthcare workers at increased risk of infection. The goal was to compare viral aerosol dispersion from invasive and non-invasive res...
Preprint
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The emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resultant pandemic of coronavirus disease 2019 (COVID-19) has led to over one hundred million confirmed infections, greater than three million deaths, and severe economic and social disruption. Animal models of SARS-CoV-2 are critical tools for the pre-clinical ev...
Preprint
SARS-CoV-2 induces T cell, B cell and antibody responses that are detected for several months in recovered individuals. Whether this response resembles a typical respiratory viral infection is a matter of debate. Here we followed T cell and antibody responses in 24 mainly non-hospitalized SARS-CoV-2 recovered subjects at two time points (median of...
Preprint
Full-text available
Background The aim of this prospective cohort study was to determine the burden of SARS-CoV-2 in air and on surfaces in rooms of patients hospitalized with COVID-19, and to identify patient characteristics associated with SARS-CoV-2 environmental contamination. Methods Nasopharyngeal swabs, surface, and air samples were collected from the rooms of...
Preprint
Safe and effective vaccines are needed to end the COVID-19 pandemic caused by SARS-CoV-2. Here we report the preclinical development of a lipid nanoparticle (LNP) formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutra...
Article
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Genome-wide variation in SARS-CoV-2 reveals evolution and transmission dynamics which are critical considerations for disease control and prevention decisions. Here, we review estimates of the genome-wide viral mutation rates, summarize current COVID-19 case load in the province of Ontario, Canada (5 January 2021), and analyze published SARS-CoV-2...
Article
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Objective We identified public sentiments and opinions toward the COVID-19 vaccines based on the content of Twitter. Materials and Methods We retrieved 4,552,652 publicly available tweets posted within the timeline of January 2020 to January 2021. Following extraction, we identified vaccine sentiments and opinions of tweets and compared their prog...
Article
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The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), calls for prompt and accurate diagnosis and rapid turnaround time for test results to limit transmission. Here, we evaluated two independent molecular assays, the Biomeme SARS-CoV-2 test, and the Precision Biomonitoring TripleLo...
Article
Patients infected with SARS‐CoV‐2 and influenza display similar symptoms but treatment requirements are different. Clinicians need to accurately distinguish SARS‐CoV‐2 from influenza in order to provide appropriate treatment. Here we show that the naked eye can differentiate between patients infected with SARS‐CoV‐2 and influenza A using a nucleic...
Article
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The ongoing COVID-19 pandemic has posed a severe threat to public health worldwide. In this study, we aimed to evaluate several digital data streams as early warning signals of COVID-19 outbreaks in Canada, the US and their provinces and states. Two types of terms including symptoms and preventive measures were used to filter Twitter and Google Tre...
Preprint
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The COVID-19 pandemic has affected more than 120 million people and resulted in over 2.8 million deaths worldwide. Several COVID-19 vaccines have been approved for emergency use in humans and are being used in many countries. However, all of the approved vaccines are administered by intramuscular injection and this may not prevent upper airway infe...
Article
Full-text available
New variants of concern (VOCs) now account for 67% of all Ontario SARS-CoV-2 infections. Compared with early variants of SARS-CoV-2, VOCs are associated with a 63% increased risk of hospitalization, a 103% increased risk of intensive care unit (ICU) admission and a 56% increased risk of death due to COVID-19. VOCs are having a substantial impact...
Article
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Background: Data on the outcomes of noninfluenza respiratory virus (NIRV) infections among hospitalized adults are lacking. We aimed to study the burden, severity and outcomes of NIRV infections in this population. Methods: We analyzed pooled patient data from 2 hospital-based respiratory virus surveillance cohorts in 2 regions of Canada during...