Evolving Patterns in COVID-19: the Virus, Its Variants and Infectivity-Cum-Virulence
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Molecular Analysis of SARS-Cov-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level
pathogens Article Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level Malik Sallam 1,2,* and Azmi Mahafzah 1,2 1 Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; [email protected] 2 Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan * Correspondence: [email protected]; Tel.: +962-79-184-5186 Abstract: The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, Citation: Sallam, M.; Mahafzah, A. the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a Molecular Analysis of SARS-CoV-2 deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the Genetic Lineages in Jordan: Tracking synonymous mutation C22444T. -
Leveraging Artificial Intelligence to Analyze the COVID-19 Distribution Pattern Based on Socio-Economic Determinants
Leveraging Artificial Intelligence to Analyze the COVID-19 Distribution Pattern based on Socio-economic Determinants Mohammadhossein Ghahramania,<, Francesco Pillaa aSpatial Dynamics Lab, University College Dublin, Ireland ARTICLEINFO ABSTRACT Keywords: The spatialization of socioeconomic data can be used and integrated with other sources of information Geodemographic analysis to reveal valuable insights. Such data can be utilized to infer different variations, such as the dynamics Big Data of city dwellers and their spatial and temporal variability. This work focuses on such applications to Dimensionality Reduction explore the underlying association between socioeconomic characteristics of different geographical Neural Network regions in Dublin, Ireland, and the number of confirmed COVID cases in each area. Our aim is to implement a machine learning approach to identify demographic characteristics and spatial patterns. Spatial analysis was used to describe the pattern of interest in Electoral Divisions (ED), which are the legally defined administrative areas in the Republic of Ireland for which population statistics are published from the census data. We used the most informative variables of the census data to model the number of infected people in different regions at ED level. Seven clusters detected by implementing an unsupervised neural network method. The distribution of people who have contracted the virus was studied. 1. Introduction Different inequality issues can also make it difficult to main- tain social distancing [37]. Hence, it is essential to under- In March 11th, 2020, the Republic of Ireland’s govern- stand the existed relation between socio-economic inequal- ment launched a national action plan in response to COVID- ities and the pandemic. As discussed, such inequalities can 19, a widespread lock-down in order to minimize the risk threaten public health by making it difficult to enforce pro- of illness. -
Arxiv:2104.01215V1 [Cs.SI] 2 Apr 2021 Agreement on Ambiguous Statements
The Coronavirus is a Bioweapon: Analysing Coronavirus Fact-Checked Stories Lynnette Hui Xian Ng1 ID and Kathleen M. Carley1 ID CASOS, Institute for Software Research Carnegie Mellon University, Pittsburgh, PA 15213 fhuixiann, [email protected] Abstract. The 2020 coronavirus pandemic has heightened the need to flag coronavirus-related misinformation, and fact-checking groups have taken to verifying misinformation on the Internet. We explore stories reported by fact-checking groups PolitiFact, Poynter and Snopes from January to June 2020, characterising them into six story clusters before then analyse time-series and story validity trends and the level of agree- ment across sites. We further break down the story clusters into more granular story types by proposing a unique automated method with a BERT classifier, which can be used to classify diverse story sources, in both fact-checked stories and tweets. Keywords: Coronavirus · Fact Checking · Misinformation 1 Introduction The 2020 coronavirus pandemic has prompted major fact-checking groups like PolitiFact, Poynter and Snopes to verify misinformation on the Internet. Since fact-checking influences citizens' reactions [5], coronavirus-related fact checking is crucial in informing the public and reducing panic. Previous works compared election-related misinformation from fact-checking sites. While Amazeen con- clude a high level of agreement [1], Lim augmented the result [8], finding rare arXiv:2104.01215v1 [cs.SI] 2 Apr 2021 agreement on ambiguous statements. Hossain et. al trained word representations of manually classified COVID-19 tweets before performing automatic classifica- tion using ROBERTa and BERTScore [6]. This paper classifies coronavirus-related fact-checks into story clusters and empirically analyse their characteristics. -
REALM Research Briefing: Vaccines, Variants, and Venitlation
Briefing: Vaccines, Variants, and Ventilation A Briefing on Recent Scientific Literature Focused on SARS-CoV-2 Vaccines and Variants, Plus the Effects of Ventilation on Virus Spread Dates of Search: 01 January 2021 through 05 July 2021 Published: 22 July 2021 This document synthesizes various studies and data; however, the scientific understanding regarding COVID-19 is continuously evolving. This material is being provided for informational purposes only, and readers are encouraged to review federal, state, tribal, territorial, and local guidance. The authors, sponsors, and researchers are not liable for any damages resulting from use, misuse, or reliance upon this information, or any errors or omissions herein. INTRODUCTION Purpose of This Briefing • Access to the latest scientific research is critical as libraries, archives, and museums (LAMs) work to sustain modified operations during the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. • As an emerging event, the SARS-CoV-2 pandemic continually presents new challenges and scientific questions. At present, SARS-CoV-2 vaccines and variants in the US are two critical areas of focus. The effects of ventilation-based interventions on the spread of SARS-CoV-2 are also an interest area for LAMs. This briefing provides key information and results from the latest scientific literature to help inform LAMs making decisions related to these topics. How to Use This Briefing: This briefing is intended to provide timely information about SARS-CoV-2 vaccines, variants, and ventilation to LAMs and their stakeholders. Due to the evolving nature of scientific research on these topics, the information provided here is not intended to be comprehensive or final. -
COVID-19 Weekly Epidemiological Update
COVID-19 Weekly Epidemiological Update Edition 45, published 22 June 2021 In this edition: • Global overview • Special focus: Update on SARS-CoV-2 Variants of Interest and Variants of Concern • Special focus: Global Consultation on SARS-CoV-2 Variants of Concern and their Impact on Public Health Interventions • WHO regional overviews • Key weekly updates Global overview Data as of 20 June 2021 Global numbers of cases and deaths continued to decrease over the past week (14-20 June 2021) with over 2.5 million new weekly cases and over 64 000 deaths, a 6% and a 12% decrease respectively, compared to the previous week (Figure 1). While the number of cases reported globally now exceeds 177 million, last week saw the lowest weekly case incidence since February 2021. This week, the Americas and Western Pacific Regions reported numbers of new weekly cases similar to the previous week, while the South-East Asia and the European Regions reported a decline in the number of new cases. The African Region recorded a marked increase in the number of weekly cases as compared to the previous week (Table 1). Globally, mortality remains high with more than 9000 deaths reported each day over the past week, however, the number of new deaths reported in the past week decreased across all Regions except for the Eastern Mediterranean and the African Regions. Figure 1. COVID-19 cases reported weekly by WHO Region, and global deaths, as of 20 June 2021** 6 000 000 120 000 Americas South-East Asia 5 000 000 100 000 Europe Eastern Mediterranean 4 000 000 Africa -
Effectiveness of COVID-19 Vaccines Against Variants of Concern, Canada
medRxiv preprint doi: https://doi.org/10.1101/2021.06.28.21259420; this version posted July 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Effectiveness of COVID-19 vaccines against variants of concern, Canada Authors: Sharifa Nasreen PhD1, Siyi He MSc1, Hannah Chung MPH1, Kevin A. Brown PhD1,2,3, Jonathan B. Gubbay MD MSc3, Sarah A. Buchan PhD1,2,3,4, Sarah E. Wilson MD MSc1,2,3,4, Maria E. Sundaram PhD1,2, Deshayne B. Fell PhD1,5,6, Branson Chen MSc1, Andrew Calzavara MSc1, Peter C. Austin PhD1,7, Kevin L. Schwartz MD MSc1,2,3, Mina Tadrous PharmD PhD1,8, Kumanan Wilson MD MSc9, and Jeffrey C. Kwong MD MSc1,2,3,4,10,11 on behalf of the Canadian Immunization Research Network (CIRN) Provincial Collaborative Network (PCN) Investigators Affiliations: 1 ICES, Toronto, ON 2 Dalla Lana School of Public Health, University of Toronto, Toronto, ON 3 Public Health Ontario, ON 4 Centre for Vaccine Preventable Diseases, University of Toronto, Toronto, ON 5 School of Epidemiology and Public Health, University of Ottawa, ON 6 Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON 7 Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON 8 Women’s College Hospital, Toronto, ON 9 Department of Medicine, University of Ottawa, Ottawa and Bruyere Hospital Research Institutes, Ottawa, ON 10 Department of Family and Community Medicine, University of Toronto, Toronto, ON 11 University Health Network, Toronto, ON Corresponding author: 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
Evolution of Disease Transmission During the COVID-19
www.nature.com/scientificreports OPEN Evolution of disease transmission during the COVID‑19 pandemic: patterns and determinants Jie Zhu & Blanca Gallego* Epidemic models are being used by governments to inform public health strategies to reduce the spread of SARS‑CoV‑2. They simulate potential scenarios by manipulating model parameters that control processes of disease transmission and recovery. However, the validity of these parameters is challenged by the uncertainty of the impact of public health interventions on disease transmission, and the forecasting accuracy of these models is rarely investigated during an outbreak. We ftted a stochastic transmission model on reported cases, recoveries and deaths associated with SARS‑CoV‑2 infection across 101 countries. The dynamics of disease transmission was represented in terms of the daily efective reproduction number ( Rt ). The relationship between public health interventions and Rt was explored, frstly using a hierarchical clustering algorithm on initial Rt patterns, and secondly computing the time‑lagged cross correlation among the daily number of policies implemented, Rt , and daily incidence counts in subsequent months. The impact of updating Rt every time a prediction is made on the forecasting accuracy of the model was investigated. We identifed 5 groups of countries with distinct transmission patterns during the frst 6 months of the pandemic. Early adoption of social distancing measures and a shorter gap between interventions were associated with a reduction on the duration of outbreaks. The lagged correlation analysis revealed that increased policy volume was associated with lower future Rt (75 days lag), while a lower Rt was associated with lower future policy volume (102 days lag). -
Understanding Variants COVID-19 Vaccine Astrazeneca
Understanding Variants COVID-19 Vaccine AstraZeneca Latest data released Summary of the variant data for COVID-19 Vaccine AstraZeneca It is well known that viruses constantly change through mutation, which can lead to the emergence of new variants. Only those that demonstrate increased transmission or virulence are considered variants of concern. Globally, there are currently four such variants: • B.1.1.7, also known as the UK, or Kent variant • P.1, also known as the Brazilian variant • B.1.351, also known as the South African variant • B.1.617.2, also known as the Indian Variant We now have data – from non-clinical, pre-clinical, and clinical studies, as well as emerging real- world evidence – that demonstrate the effectiveness of COVID-19 Vaccine AstraZeneca against these new variants. No variants have emerged that significantly undermine efficacy of our vaccine against severe disease and hospitalisation. • Clinical studies confirmed the vaccine is effective against the Kent (B.1.1.7) variant, with comparable efficacy to the predominant global strain (the Victoria strain) (VE: 74.6%; CI: 1 The impact of virus variants 41.6% to 88.9%). • In vitro analyses using sera from convalescent individuals that received COVID-19 Vaccine When a virus is circulating widely in a AstraZeneca demonstrate that antibodies from vaccinated individuals were able to neutralise population, it has a greater opportunity to the Brazil (P.1.) variant and the Indian variant (B.1.617.2) to a similar extent as the Victoria replicate. With this, the likelihood that the 2 strain. virus will change a bit, or that variants will 6 • In addition, an early real-world analysis shows for the first time that two doses of COVID-19 appear, also increases. -
COVID-19 Clinical Update
COVID-19 Clinical Update Jonathan Vilasier Iralu, MD, FACP Indian Health Service Chief Clinical Consultant for Infectious Diseases Disclosures Virology: Denmark Cluster 5 Variant WHO Outbreak News November 6, 2020 214 human cases of COVID-19 associated with farmed minks 12 cases had unique “Cluster 5” variant with new mutations not seen before. Cluster 5 has decreased sensitivity to neutralizing antibodies. Human impact is being studied. 17 million minks were to be culled https://www.who.int/csr/don/06-november-2020-mink-associated-sars-cov2-denmark/en/ Immunology Humoral Response to SARS-CoV-2 in Iceland: (Gudbjartsson et al, NEJM. 10/129/2020) Studied sera from 30,576 people in Iceland with 6 assays: pan-Ig assays: nucleoprotein and receptor binding domain of spike protein. (IgM, IgG, IgA) IgG/IgM against N, IgG/IgA against S1 spike protein 1797 patients recovered from COVID-19, 4222 were under quarantine and 23,452 had no exposure 91% of recovered patients still had antibody two months after the diagnosis by PCR and remained positive up to 4 months Risk of death in Iceland was only 0.03% Serology results show and estimated 44% of people with SARS-CoV-2 infection were not diagnosed by PCR https://www.nejm.org/doi/full/10.1056/NEJMoa2026116 Epidemiology SARS CoV-2 seroprevalence and transmission risk factors among high-risk close contacts (Ng et al, Lancet 11/2/2020) Retrospective cohort study of all close contacts of COVID cases in Singapore January-April 2020 Identified 7770 Close Contacts. (1863 household, 2319 work, -
COVID-19 Situation and Strategic Response
COVID-19 Situation and Strategic Response REPORT TO THE EXECUTIVE BOARD GLOBAL EPIDEMIOLOGICAL TREND As of 17 Jan 2021 6 000 000 100 000 Americas South-East Asia 90 000 5 000 000 Europe 80 000 Eastern Mediterranean 70 000 4 000 000 Africa Western Pacific 60 000 3 000 000 Deaths 50 000 Cases Deaths 40 000 2 000 000 30 000 20 000 1 000 000 10 000 0 0 30-Dec 20-Jan 10-Feb 02-Mar 23-Mar 13-Apr 04-May 25-May 15-Jun 06-Jul 27-Jul 17-Aug 07-Sep 28-Sep 19-Oct 09-Nov 30-Nov 21-Dec 11-Jan Reported week commencing 28 Oct: 5th IHR EC; 5 Nov: TORs for Global ~43 million cases, Study of Origins of 14 Dec: UK 18 Dec: RSA 1.16 million deaths SARS-CoV-2 published; highlights concern 31 Dec: WHO issue first emergency 18 Jan: report detection Denmark report new over variant VOC use validation of COVID-19 vaccine 12 Jan: International 93 million cases, of new variant mink-associated variant 202012/01 (Pfizer/BioNTech Comirnaty) mission on virus >2 million deaths 501Y.V2 origins travels to China * Data are incomplete for the current week. Cases depicted by bars; deaths depicted by line. WEEKLY SITUATION BY WHO REGION As of 17 Jan 2021 COVID Data Source: World Health Organization | United Nations Population Division (Population Prospect 2020) AGE & GENDER DISTRIBUTION: CASES & DEATHS COVID Gender Female Male Age groups Cases Deaths Cases 49% 51% 0-4 1.4% 0.10% Deaths 43% 57% 5-14 3.8% 0.05% 15-24 11.7% 0.21% 25-64 63.2% 16,16% 65-84 20% 83.48% AGE DISTRIBUTION OF CASES & DEATHS OVER TIME COVID Cases Deaths Data Source: World Health Organization case report -
SARS-Cov-2 Genome Surveillance in Mainz, Germany, Reveals Convergent Origin of the N501Y Spike Mutation in a Hospital Setting
medRxiv preprint doi: https://doi.org/10.1101/2021.02.11.21251324; this version posted February 12, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . SARS-CoV-2 genome surveillance in Mainz, Germany, reveals convergent origin of the N501Y spike mutation in a hospital setting Lemmermann NA1,2#$, Lieb B3#, Laufs T3, Renzaho A2, Runkel S1,4, Kohnen W1,5, Linke M1,6, Gerber S1,6, Schweiger S1,6, Michel A1,7, Bikar S-E1,3*, Plachter B1,2*§, Hankeln T1,8* 1 SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 2 Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 3 StarSEQ GmbH, Mainz, Germany 4 Transfusion Unit & Test Center, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 5 Department of Hygiene and Infection Prevention, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 6 Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 7 Medical Management Department, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany 8 Faculty of Biology, Institute of Organismal and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany * joint senior authors # equal contribution $ correspondence to NL: [email protected] Niels A. -
COVID-19 Weekly Epidemiological Update
COVID-19 Weekly Epidemiological Update Edition 54, published 24 August 2021 In this edition: • Global overview • Special focus: Update on SARS-CoV-2 Variants of Interest and Variants of Concern • WHO regional overviews • Key weekly updates Global overview Data as of 22 August 2021 With over 4.5 million new cases reported this week (16-22 August), the number of new cases reported globally seems to be stable after increasing for nearly two months (since mid-June) (Figure 1). The Regions of Western Pacific and Americas continue to report increases in new cases, with increases of 20% and 8% respectively as compared to last week. The South-East Asia and Eastern Mediterranean regions reported decreases in weekly incidence of 16% and 10% respectively. The European and African Regions reported case incidence rates similar to those reported last week. The number of deaths reported globally this week remains similar to last week, with over 68 000 new deaths reported. Two Regions including Europe and Americas reported increases in new deaths of 11% and 10% respectively. The African and South-East Asia Regions reported decreases in new deaths of 11% and 10% respectively, whereas the numbers of deaths reported in the Eastern Mediterranean and Western Pacific Regions were similar to the numbers reported last week. The cumulative number of cases reported globally is now over 211 million and the cumulative number of deaths is just over 4.4 million. Figure 1. COVID-19 cases reported weekly by WHO Region, and global deaths, as of 22 August 2021** 6 000