scholarly journals Corona virus (CoVid19) genome: genomic and biochemical analysis revealed its possible synthetic origin

2020 ◽  
Vol 7 (5) ◽  
pp. 200-213
Author(s):  
Tapan Kumar Mohanta
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Proteome Analysis ◽  
The United States ◽  
Surface Glycoprotein ◽  
Steam Treatment ◽  
Origin And Evolution ◽  
Corona Virus ◽  
Global Pandemic ◽  
German Isolate

The Severe acute respiratory syndrome (SARS) corona virus 2 SARS-CoV-2 mediated epidemic is a global pandemic. It has evolved as a curse to the human civilization and at the present situation, where most of the cities in the world are on lockdown. The first genome sequence data of SARS-CoV-2 (CoVid19) and their reports that followed concluded that it was a member of the genus Betacoronavirus and has a bat reservoir. To understand its origin and evolution, we conducted a deep comparative study by comparing the genomes of bat SARS CoV and other SARS CoVs (including human SARS CoV of German isolate). Results revealed that CoVid19 genomes from isolates of China, India, Italy, Nepal, and the United States of America has sequence similarity of 79-80% only with the bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV of German isolate. Whereas, the sequence similarity within the CoVid19 genomes of these countries was 99-100%. If the SARS CoV infection happened to human through the SARS CoV of bat origin, it should have sequence similarity of more than 99% which was absent in this case. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV of China, India, Italy, Nepal, and USA isolates. The genome analysis revealed the presence of multiple microsatellite repeats sequences. Proteome analysis revealed, the melting temperature (Tm) of surface glycoprotein was less than 55oC, suggesting the steam treatment can be an ideal preventative measure to destabilize the CoVid19, and thus it’s spreading

Corona Virus (CoVid19) Genome: Genomic and Evolutionary Analysis Point Towards Its Possible Synthetic Origin

2020 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Yugal Kishore Mohanta ◽  
Ahmed Al-Harrasi
Keyword(s):  
Natural Selection ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
The United States ◽  
Evolutionary Analysis ◽  
Corona Virus ◽  
New Genotype ◽  
Meat Market ◽  
German Isolate

The Severe acute respiratory syndrome (SARS) corona virus (CoV) 2 SARS-CoV-2 mediated epidemic is a global pandemic. The first genome sequence data of SARS-CoV-2 (CoVid19) concluded that it has a bat reservoir and bat was the immediate donor. Andersen et al., (2020) has reported that it is improbable to do laboratory manipulation of SARS CoV [1]. But, Lau et al., (2010) has already reported the generation of recombinant bat SARS CoV and they had reported three recombinant genotypes. Hence laboratory based manipulation has already completed long before[2]. A deep comparative study of bat SARS CoV with other SARS CoVs (including human SARS CoV of German isolate) revealed, human SARS CoV-2 genomes (isolates of China, India, Italy, Nepal, and the United States of America) had sequence similarity of 79-80% only with bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV (German isolate). The presence of large genomic dissimilarity of bat SARS CoV genome with human SARS CoV-2 cannot be considered as an immediate donor to human SARS CoV-2. However, the genomic sequence similarity within the SARS CoV-2 isolates of China, India, Italy, Nepal, and USA shared 99-100% similarity. This suggests that human SARS CoV-2 did not undergo heavy mutation to generate immediate new genotype. If the SARS CoV-2 infection happened to the human through the SARS CoV of bat from Wuhan meat market, it should have sequence similarity of more than 99% which was not found in the study. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV-2 of China, India, Italy, Nepal, and USA isolates. This suggests that bat SARS CoV has genomic and evolutionary dissimilarity and cannot be considered as immediate and direct donor of human SARS CoV-2. The natural selection of bat genome before transfer to the zoonotic organism is a time-consuming process and natural selection in human post zoonotic transfer is also time-consuming event. Therefore, concept mentioned by Andersen et al., (2020)[1] regarding its transfer from a bat of Wuhan meat market is irrefutably incorrect. Sequence alignment revealed the presence of inserted codons in human SARS CoV-2 and synteny analysis corroborated with the presence of extra nucleotides/codons in the human SARS CoV-2. Relative time tree analysis revealed it origin before 0.00 million year ago, suggesting its recent synthetic/modified origin.

Unique nCoV-2019 (COVID 19) spike glycoprotein processing by host protease: Analysis and Implication on infection

2020 ◽  
Vol 17 ◽  
Author(s):  
Ajoy Basak ◽  
Sarmistha Basak
Keyword(s):  
World Health ◽  
Spike Glycoprotein ◽  
Binding Domains ◽  
Corona Virus ◽  
Global Pandemic ◽  
High Infection ◽  
Crucial Information ◽  
Glycoprotein Processing ◽  
Health Organization ◽  
Host Reservoir

: The current global pandemic outbreak of a novel type of corona virus termed by World Health Organization as COVID-19 became an grave concern and worry to human health and world economy. Intense research efforts are now underway worldwide to combat and prevent the spread of this deadly disease. This zoonotic virus, a native to bat population is most likely transmitted to human via a host reservoir. Due to its close similarity to previously known SARS CoV (Severe Acute Respiratory Syndrome Corona Virus) of 2002 and related MERS CoV (Middle East Respiratory Syndrome Corona Virus) of 2012, it is also known as SARS CoV2. But unlike them it is far too infectious, virulent and lethal. Among its various proteins, the surface spike glycoprotein “S” has drawn significant attention because of its implication in viral recognition and host-virus fusion process. A detail comparative analysis of “S” proteins of SARS CoV (now called SARS CoV1), SARS CoV2 (COVID-19) and MERS CoV based on structure, sequence alignment, host cleavage sites, receptor binding domains, potential glycosylation and Cys-disulphide bridge locations has been performed. It revealed some key features and variations that may elucidate the high infection and virulence character of COVID-19. Moreover this crucial information may become useful in our quest for COVID-19 therapeutics and vaccines.

scholarly journals Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health

2020 ◽  
Vol 12 (s1) ◽  
Author(s):  
Rami Kantor ◽  
John P. Fulton ◽  
Jon Steingrimsson ◽  
Vladimir Novitsky ◽  
Mark Howison ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Sequence Data ◽  
The United States ◽  
Viral Sequence ◽  
Transmission Networks ◽  
New Methods ◽  
Hiv Epidemic ◽  
The World

AbstractGreat efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.

scholarly journals Influenza vaccination and the risk of COVID-19 infection and severe illness in older adults in the United States

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kelly Huang ◽  
Shu-Wen Lin ◽  
Wang-Huei Sheng ◽  
Chi-Chuan Wang
Keyword(s):  
Immune Responses ◽  
Influenza Vaccine ◽  
Influenza Vaccination ◽  
The United States ◽  
Cross Sectional Study ◽  
Severe Illness ◽  
Cross Sectional ◽  
Global Pandemic ◽  
Study Population ◽  
Health Database

AbstractThe coronavirus disease of 2019 (COVID-19) has caused a global pandemic and led to nearly three million deaths globally. As of April 2021, there are still many countries that do not have COVID-19 vaccines. Before the COVID-19 vaccines were developed, some evidence suggested that an influenza vaccine may stimulate nonspecific immune responses that reduce the risk of COVID-19 infection or the severity of COVID-19 illness after infection. This study evaluated the association between influenza vaccination and the risk of COVID-19 infection. We conducted a retrospective cross-sectional study with data from July 1, 2019, to June 30, 2020 with the Claims data from Symphony Health database. The study population was adults age 65 years old or older who received influenza vaccination between September 1 and December 31 of 2019. The main outcomes and measures were odds of COVID-19 infection and severe COVID-19 illness after January 15, 2020. We found the adjusted odds ratio (aOR) of COVID-19 infection risk between the influenza-vaccination group and no-influenza-vaccination group was 0.76 (95% confidence interval (CI), 0.75–0.77). Among COVID-19 patients, the aOR of developing severe COVID-19 illness was 0.72 (95% CI, 0.68–0.76) between the influenza-vaccination group and the no-influenza-vaccination group. When the influenza-vaccination group and the other-vaccination group were compared, the aOR of COVID-19 infection was 0.95 (95% CI, 0.93–0.97), and the aOR of developing a severe COVID-19 illness was 0.95 (95% CI, 0.80–1.13). The influenza vaccine may marginally protect people from COVID-19 infection.

scholarly journals 130. increase in Multidrug Resistance (2011–2018) and the Emergence of Extensive Drug Resistance (2020) in shigella Sonnei in the United States

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S195-S195
Author(s):  
Naeemah Z Logan ◽  
Beth E Karp ◽  
Kaitlin A Tagg ◽  
Claire Burns-Lynch ◽  
Jessica Chen ◽  
...  
Keyword(s):  
United States ◽  
Multidrug Resistance ◽  
Disease Surveillance ◽  
Sequence Data ◽  
The United States ◽  
Multidrug Resistant ◽  
Shigella Sonnei ◽  
Short Read ◽  
Men 2 ◽  
The Us

Abstract Background Multidrug-resistant (MDR) Shigella sonnei infections are a serious public health threat, and outbreaks are common among men who have sex with men (MSM). In February 2020, Australia’s Department of Health notified CDC of extensively drug-resistant (XDR) S. sonnei in 2 Australian residents linked to a cruise that departed from Florida. We describe an international outbreak of XDR S. sonnei and report on trends in MDR among S. sonnei in the United States. Methods Health departments (HDs) submit every 20th Shigella isolate to CDC’s National Antimicrobial Resistance Monitoring System (NARMS) laboratory for susceptibility testing. We defined MDR as decreased susceptibility to azithromycin (MIC ≥32 µg/mL) with resistance to ampicillin, ciprofloxacin, and cotrimoxazole, and XDR as MDR with additional resistance to ceftriaxone. We used PulseNet, the national subtyping network for enteric disease surveillance, to identify US isolates related to the Australian XDR isolates by short-read whole genome sequencing. We screened these isolates for resistance determinants (ResFinder v3.0) and plasmid replicons (PlasmidFinder) and obtained patient histories from HDs. We used long-read sequencing to generate closed plasmid sequences for 2 XDR isolates. Results NARMS tested 2,781 S. sonnei surveillance isolates during 2011–2018; 80 (2.9%) were MDR, including 1 (0.04%) that was XDR. MDR isolates were from men (87%), women (9%), and children (4%). MDR increased from 0% in 2011 to 15.3% in 2018 (Figure). In 2020, we identified XDR isolates from 3 US residents on the same cruise as the Australians. The US residents were 41–42 year-old men; 2 with available information were MSM. The US and Australian isolates were highly related (0–1 alleles). Short-read sequence data from all 3 US isolates mapped to the blaCTX-M-27 harboring IncFII plasmids from the 2 Australian isolates with >99% nucleotide identity. blaCTX-M-27 genes confer ceftriaxone resistance. Increase in Percentage of Shigella sonnei Isolates with Multidrug Resistance* in the United States, 2011–2018† Conclusion MDR S. sonnei is increasing and is most often identified among men. XDR S. sonnei infections are emerging and are resistant to all recommended antibiotics, making them difficult to treat without IV antibiotics. This outbreak illustrates the alarming capacity for XDR S. sonnei to disseminate globally among at-risk populations, such as MSM. Disclosures All Authors: No reported disclosures

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

Amidst pandemic and racial upheaval: Where Asian Americans Fit

2020 ◽  
pp. 1-17
Author(s):  
Whitney Hua ◽  
Jane Junn
Keyword(s):  
United States ◽  
Asian Americans ◽  
Racial Inequality ◽  
White Supremacy ◽  
The United States ◽  
Structural Racism ◽  
Global Pandemic ◽  
American Capitalism ◽  
Racial History ◽  
History Of

Abstract As racial tensions flare amidst a global pandemic and national social justice upheaval, the centrality of structural racism has renewed old questions and raised new ones about where Asian Americans fit in U.S. politics. This paper provides an overview of the unique racial history of Asians in the United States and analyzes the implications of dynamic racialization and status for Asian Americans. In particular, we examine the dynamism of Asian Americans' racial positionality relative to historical shifts in economic-based conceptions of their desirability as workers in American capitalism. Taking history, power, and institutions of white supremacy into account, we analyze where Asian Americans fit in contemporary U.S. politics, presenting a better understanding of the persistent structures underlying racial inequality and developing a foundation from which Asian Americans can work to enhance equality.

Foundation News: Impact of the pandemic on the GWB drinking water project in the Nepal Himalaya region

2021 ◽  
Vol 40 (4) ◽  
pp. 242-243
Author(s):  
Kirsten Nicholson ◽  
Klaus Neumann ◽  
Subodh Sharma ◽  
Lakpa Thering Sherpa
Keyword(s):  
Water Quality ◽  
Drinking Water ◽  
National Park ◽  
The United States ◽  
High Mountain ◽  
Geologic Mapping ◽  
Global Pandemic ◽  
Vulnerability To Climate Change ◽  
Sagarmatha National Park ◽  
Water Vulnerability

In 2019, after almost a decade of working on water quality in the Himalayas, we submitted a proposal to Geoscientists Without Borders® (GWB) titled “Understanding high mountain aquifers to source drinking water in Sagarmatha National Park.” The project involves a combination of water-quality and quantity measurements, geologic mapping, and an electrical resistivity tomography survey. The goal of the project is to help two communities (Phortse and Lobuche within Sagarmatha National Park in Nepal) minimize their water vulnerability to climate change and earthquakes. The project team includes researchers and students from the United States and Nepal, as well as nongovernmental organizations, government agencies, and community councils. In the proposal, we identified physical health and altitude as the primary risks that could hinder the success of the project. Like everyone else in early 2019, we had no way to foresee the events of 2020, which would almost completely derail our project. Health has turned out to be the major hinderance. The irony of the global pandemic is how much it has impacted the work of the U.S.-based team and how little it has impacted the necessity of the project.

Impacts of Social Distancing on Pedestrian Behavior and Risk Perception

2021 ◽  
Vol 65 (1) ◽  
pp. 1302-1306
Author(s):  
Kyra B. Phillips ◽  
Kelly N. Byrne ◽  
Branden S. Kolarik ◽  
Audra K. Krake ◽  
Young C. Bui ◽  
...  
Keyword(s):  
United States ◽  
Risk Perception ◽  
Perceived Risk ◽  
Close Contact ◽  
The United States ◽  
Survey Study ◽  
Pedestrian Behavior ◽  
Social Distancing ◽  
Global Pandemic ◽  
Over Time

Since COVID-19 transmission accelerated in the United States in March 2020, guidelines have recommended that individuals wear masks and limit close contact by remaining at least six feet away from others, even while outdoors. Such behavior is important to help slow the spread of the global pandemic; however, it may require pedestrians to make critical decisions about entering a roadway in order to avoid others, potentially creating hazardous situations for both themselves and for drivers. In this survey study, we found that while overall patterns of self-reported pedestrian activity remained largely consistent over time, participants indicated increased willingness to enter active roadways when encountering unmasked pedestrians since the COVID-19 pandemic began. Participants also rated the risks of encountering unmasked pedestrians as greater than those associated with entering a street, though the perceived risk of passing an unmasked pedestrian on the sidewalk decreased over time.

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