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1.
International Journal of Infectious Diseases ; 130(Supplement 2):S1, 2023.
Article in English | EMBASE | ID: covidwho-2321671

ABSTRACT

Intro: Viruses, including SARS-CoV-2, which causes COVID-19, are constantly changing. These genetic changes (aka mutations) occur over time and can lead to the emergence of new variants that may have different characteristics. After the first SARS-CoV-2 genome was published in early 2020, scientists all over the world soon realized the immediate need to obtain as much genetic information from as many strains as possible. However, understanding the functional significance of the mutations harbored by a variant is important to assess its impact on transmissibility, disease severity, immune escape, and the effectiveness of vaccines and therapeutics. Method(s): Here in Canada, we have developed an interactive framework for visualizing and reporting mutations in SARS-CoV-2 variants. This framework is composed of three stand-alone yet connected components;an interactive visualization (COVID-MVP), a manually curated functional annotation database (pokay), and a genomic analysis workflow (nf-ncov-voc). Finding(s): COVID-MVP provides (i) an interactive heatmap to visualize and compare mutations in SARS-CoV-2 lineages classified across different VOCs, VOIs, and VUMs;(ii) mutation profiles including the type, impact, and contextual information;(iii) annotation of biological impacts for mutations where functional data is available in the literature;(iv) summarized information for each variant and/or lineage in the form of a surveillance report;and (v) the ability to upload raw genomic sequence(s) for rapid processing and annotating for real-time classification. Discussion(s): This comprehensive comparison allows microbiologists and public health practitioners to better predict how the mutations in emerging variants will impact factors such as infection severity, vaccine resistance, hospitalization rates, etc. Conclusion(s): This framework is cloud-compatible & standalone, which makes it easier to integrate into other genomic surveillance tools as well. COVID-MVP is integrated into the Canadian VirusSeq data portal (https://virusseqdataportal.ca) - a national data hub for SARS-COV-2 genomic data. COVID-MVP is also used by the CanCOGeN and CoVaRR networks in national COVID-19 genomic surveillance.Copyright © 2023

2.
Geographical Review ; 111(4):592-615, 2021.
Article in English | GIM | ID: covidwho-1747099

ABSTRACT

The uneven outcomes of the Covid-19 pandemic in the United States can be characterized by its patchwork patterns. Given a weak national coordinated response, state-level decisions offer an important frame for analysis. This article explores how such analysis invokes fundamental geographic challenges related to the modified a real unit problem, and results in scientific predictive models that behave differently in different states. We examined morbidity with respect to state-level policy decisions, by comparing the fit and significance of different types of predictive modeling using data from the first wave of 2020. Our research reflects upon public health literature, mathematical modeling, and geographic approaches in the wake of the underlying complex pattern of drivers, decisions, and their impact on public health outcomes state by state time line. Contemplating these findings, we discuss the need to improve integration of fundamental geographic concepts to creatively develop modeling and interpretations across disciplines that offer value for both informing and holding accountable decision makers of the jurisdictions in which we live.

3.
Geographical Review ; : 24, 2021.
Article in English | Web of Science | ID: covidwho-1349703

ABSTRACT

The uneven outcomes of the covid-19 pandemic in the United States can be characterized by its patchwork patterns. Given a weak national coordinated response, state-level decisions offer an important frame for analysis. This article explores how such analysis invokes fundamental geographic challenges related to the modified areal unit problem, and results in scientific predictive models that behave differently in different states. We examined morbidity with respect to state-level policy decisions, by comparing the fit and significance of different types of predictive modeling using data from the first wave of 2020. Our research reflects upon public health literature, mathematical modeling, and geographic approaches in the wake of the underlying complex pattern of drivers, decisions, and their impact on public health outcomes state by statetime line. Contemplating these findings, we discuss the need to improve integration of fundamental geographic concepts to creatively develop modeling and interpretations across disciplines that offer value for both informing and holding accountable decision makers of the jurisdictions in which we live. Keywords: Accountability, covid-19, decision-making, modeling, patchwork.

4.
Journal of Indian College of Cardiology ; 10(3):101-104, 2020.
Article in English | EMBASE | ID: covidwho-1024741

ABSTRACT

In a clinical bulletin published by American College of Cardiology in February 2020, it was revealed that the case fatality rate of coronavirus disease 2019 (COVID-19) pandemic for patients with cardiovascular disease is 10.5%. Heart failure (HF) is a global pandemic affecting at least 26 million people worldwide and is increasing in prevalence. Looking at the historical prospectus of practice of clinical cardiology in most countries, patients with left ventricular ejection fraction (LVEF) < 40% presented periodically to exhibit worsening signs and symptoms. The superimposition of novel respiratory tract pathogens like COVID-19 can have accelerated inflammatory injury. Immunosenescense, overactive immune response or direct viral toxicity are hypothetical mechanisms of cardiac injury. Undoubtedly, all countries have to proactively approach their cardiovascular disease (CVD) patient population due to high vulnerability from individual and epidemiological risk factors.

5.
Journal of Experimental Biology and Agricultural Sciences ; 8(Special Issue 1):S57-S65, 2020.
Article in English | Scopus | ID: covidwho-994748

ABSTRACT

The COVID-19 outbreak originated from Wuhan, China has spread over the world, causing a “Global Pandemic”. We analyzed daily confirmed cases and deaths from different countries to understand the progression of the ongoing pandemic in different parts around the world. The data indicated that the pandemic is in different stages in different countries, where they are either at the end of the second wave or middle or early phase of it or still in the middle of the first wave of infection, and they can be divided into four groups. Type 1 countries such as UK, France, Spain, and the Netherlands are currently witnessing the second wave of infection with an exponential increase in daily cases. Countries such as Australia, United States, Japan, and Poland are currently in the declining stage of second-wave, grouped as Type 2 countries. Type 3 countries such as Germany, Italy, Belgium, and Russia are recently seeing the second wave with slowly rising of confirmed cases. Type 4 countries including India, Brazil, Argentina, and Mexico are currently fighting against the first wave of COVID-19. These countries have a chance to learn from the countries which have overcome the second wave successfully. To be ahead of the epidemic curve and preventing it, countries need to make future plans on family, hospital, and community levels. Isolation of the highly vulnerable elderly people and young children, preventing social or public gathering, following the guidelines of COVID-19 prevention including wearing face masks regularly can save countries from devastating effects of the second wave of pandemic COVID-19. © 2020, Editorial board of Journal of Experimental Biology and Agricultural Sciences. All rights reserved.

6.
Journal of Pure and Applied Microbiology ; 14(3):1675-1679, 2020.
Article in English | EMBASE | ID: covidwho-891732
7.
Journal of Pure and Applied Microbiology ; 14(3):1663-1674, 2020.
Article in English | EMBASE | ID: covidwho-891731

ABSTRACT

Severe acute respiratory syndrome coronavirus – 2 (SARS-CoV-2), an emerging novel coronavirus causing coronavirus disease 2019 (COVID-19) pandemic, has now rapidly spread to more than 215 countries and has killed nearly 0.75 million people out of more than 20 million confirmed cases as of 10th August, 2020. Apart from affecting respiratory system, the virus has shown multiple manifestations with neurological affections and damaging kidneys. SARS-CoV-2 transmission mainly occurs through close contact of COVID-19 affected person, however air-borne route is also now considered as dominant route of virus spread. The virus has been implicated to have originated from animals. Apart from bats, pangolins and others being investigates to play role in transmitting SARS-CoV-2 as intermediate hosts, the recent reports of this virus infection in other animals (cats, dogs, tigers, lions, mink) suggest one health approach implementation along with adopting appropriate mitigation strategies. Researchers are pacing to develop effective vaccines and drugs, few reached to clinical trials also, however these may take time to reach the mass population, and so till then adopting appropriate prevention and control is the best option to avoid SARS-CoV-2 infection. This article presents an overview on this pandemic virus and the disease it causes, with few recent concepts and advances.

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