scholarly journals Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from India

2021 ◽  
Vol 4 (5) ◽  
pp. e202000925
Author(s):  
Rezwanuzzaman Laskar ◽  
Safdar Ali
Keyword(s):  
Viral Evolution ◽  
Reference Sequence ◽  
The Novel ◽  
Accession Number ◽  
Global Epidemic ◽  
The Core ◽  
Link Type ◽  
Ncbi Accession ◽  
Novel Coronavirus ◽  
Ncbi Accession Number

The novel coronavirus (SARS-CoV-2) from Wuhan China discovered in December 2019 has since developed into a global epidemic. Presently, we constructed and analyzed the phylo-geo-network of SARS-CoV-2 genomes from across India to understand the viral evolution in the country. A total of 611 full-length genomes from different states of India were extracted from the EpiCov repository of GISAID initiative on 6 June, 2020. Their alignment with the reference sequence (Wuhan, NCBI accession number NC_045512.2) uncovered 270 parsimony informative sites. Furthermore, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. Remaining haplogroups had <10 identical sequences across a maximum of three states. Some states with fewer samples had more haplogroups. Forty-one haplogroups were localized exclusively to any one state. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. Because the pandemic is still emerging, the observations need to be monitored.

scholarly journals Phylo-geo-network and haplogroup analysis of 611 novel Coronavirus (nCov-2019) genomes from India

2020 ◽  
Author(s):  
Rezwanuzzaman Laskar ◽  
Safdar Ali
Keyword(s):  
Viral Evolution ◽  
Final Outcome ◽  
Full Length ◽  
Reference Sequence ◽  
The Novel ◽  
Global Epidemic ◽  
The Core ◽  
Evolution Of Viruses ◽  
Novel Coronavirus

AbstractThe novel Coronavirus from Wuhan China discovered in December 2019 (nCOV-2019) has since developed into a global epidemic with major concerns about the possibility of the virus evolving into something even more sinister. In the present study we constructed the phylo-geo-network of nCOV-2019 genomes from across India to understand the viral evolution in the country. A total of 611 full length genomes were extracted from different states of India from the EpiCov repository of GISAID initiative and NCBI. Their alignment uncovered 270 parsimony informative sites. Further, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. The rest were having not more than ten identical sequences across not more than three locations. Interestingly, some locations with fewer samples have more haplogroups and most haplogroups (41) are localized exclusively to any one state only, suggesting the local evolution of viruses. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. However, since the pandemic is still emerging, the final outcome will be clear later only.

scholarly journals Identification and Diagnostic Utility of Leishmania infantum Proteins Found in Urine Samples from Patients with Visceral Leishmaniasis

2012 ◽  
Vol 19 (6) ◽  
pp. 935-943 ◽  
Author(s):  
Claudia Abeijon ◽  
Suely S. Kashino ◽  
Fernando O. Silva ◽  
Dorcas L. Costa ◽  
Ricardo T. Fujiwara ◽  
...  
Keyword(s):  
Visceral Leishmaniasis ◽  
Leishmania Infantum ◽  
Antigen Detection ◽  
Enzyme Linked Immunosorbent Assay ◽  
Accession Number ◽  
Content Type ◽  
Link Type ◽  
Detection Assay ◽  
Ncbi Accession ◽  
Ncbi Accession Number

ABSTRACTDespite the clear need to control visceral leishmaniasis (VL), the existing diagnostic tests have serious shortcomings. Here, we introduce an innovative approach to directly identifyLeishmania infantumantigens producedin vivoin humans with VL. We combined reverse-phase high-performance liquid chromatography (RP-HPLC) with mass spectrometry and categorized three distinctL. infantumproteins presumably produced in bone marrow/spleen/liver and excreted in the urine of patients with VL. The genes coding for these proteins (L. infantumiron superoxide dismutase, NCBI accession numberXP_001467866.1;L. infantumtryparedoxin, NCBI accession numberXP_001466642.1; andL. infantumnuclear transport factor 2, NCBI accession numberXP_001463738.1) were cloned, and the recombinant molecules were produced inEscherichia coli. Antibodies to these proteins were produced in rabbits and chickens and were used to develop a capture enzyme-linked immunosorbent assay (ELISA) designed to detect theseL. infantumantigens in the urine of VL patients. Specificity of the antibodies was confirmed by a Western blot analysis using both recombinant proteins and whole parasite extract. Importantly, a urinary antigen detection assay assembled with pairs of antibodies specific for each of these antigens identified 17 of 19 patients with VL. These results indicate that an improved antigen detection assay based onL. infantumproteins present in the urine of patients with VL may represent an important new strategy for the development of a specific and accurate diagnostic test that has the potential to both distinguish active VL from asymptomatic infection and serve as an important tool to monitor therapy efficacy.

scholarly journals OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources

2021 ◽  
Vol 18 (1) ◽  
pp. 9-17 ◽  
Author(s):  
Md. Asif Ahsan ◽  
Yongjing Liu ◽  
Cong Feng ◽  
Ralf Hofestädt ◽  
Ming Chen
Keyword(s):  
Clinical Research ◽  
Human Health ◽  
Clinical Data ◽  
The Novel ◽  
Web Portal ◽  
Vast Amount ◽  
Link Type ◽  
Other Information ◽  
Novel Coronavirus ◽  
The Web

Abstract Outbreaks of COVID-19 caused by the novel coronavirus SARS-CoV-2 is still a threat to global human health. In order to understand the biology of SARS-CoV-2 and developing drug against COVID-19, a vast amount of genomic, proteomic, interatomic, and clinical data is being generated, and the bioinformatics researchers produced databases, webservers and tools to gather those publicly available data and provide an opportunity of analyzing such data. However, these bioinformatics resources are scattered and researchers need to find them from different resources discretely. To facilitate researchers in finding the resources in one frame, we have developed an integrated web portal called OverCOVID (http://bis.zju.edu.cn/overcovid/). The publicly available webservers, databases and tools associated with SARS-CoV-2 have been incorporated in the resource page. In addition, a network view of the resources is provided to display the scope of the research. Other information like SARS-CoV-2 strains is visualized and various layers of interaction resources is listed in distinct pages of the web portal. As an integrative web portal, the OverCOVID will help the scientist to search the resources and accelerate the clinical research of SARS-CoV-2.

scholarly journals How to Dispose of Medical Waste Caused by COVID-19? A Case Study of China

2021 ◽  
Vol 18 (22) ◽  
pp. 12127
Author(s):  
Min Su ◽  
Qiang Wang ◽  
Rongrong Li
Keyword(s):  
Waste Disposal ◽  
Medical Waste ◽  
Chinese Government ◽  
The Novel ◽  
Global Epidemic ◽  
Medical Institutions ◽  
Process System ◽  
The Government ◽  
Novel Coronavirus ◽  
And Control

The rapid increase in novel coronavirus (COVID-19) patients also means a rapid increase in medical waste that could carry the novel coronavirus (SARS-CoV-2). How to safely dispose of medical waste caused by COVID-19 is a huge challenge that needs to be solved urgently. The outbreak of the COVID-19 has led to a significant increase in the daily generation of medical waste in China and has placed a severe test on the Chinese medical waste disposal system. Unlike ordinary wastes and garbage, medical waste that is untreated or incompletely treated will not only cause environmental pollution, but also directly or indirectly cause infections and endanger people’s health. Faced with difficulties, the Chinese government formulated a policy for medical waste management and a response plan for the epidemic, which provides policy guarantee for the standardized disposal of epidemic medical waste. In addition, the government and medical institutions at all levels formed a comprehensive, refined, and standardized medical treatment process system during research and practice. China has increased the capacity of medical waste disposal in various places by constructing new centralized disposal centers and adding mobile disposal facilities. China has achieved good results in the fight against COVID-19, and the pressure on medical waste disposal has been relieved to a certain extent. However, the global epidemic situation is severe. How to ensure the proper and safe disposal of medical waste is related to the prevention and control of the epidemic situation. This study summarizes China’s experience in the disposal of medical waste in the special case of COVID-19 and hopes to provide some reference for other countries in the disposal of medical waste.

scholarly journals Whole-Genome Sequence of an Indian Group A Streptococcus emm Type 1-2 Strain Isolated from a Blood Sample in North India

2020 ◽  
Vol 9 (19) ◽  
Author(s):  
Vivek Sagar ◽  
Anuradha Chakraborti ◽  
Rajesh Kumar
Keyword(s):  
Partial Information ◽  
Group A Streptococcus ◽  
North India ◽  
Whole Genome Sequence ◽  
Accession Number ◽  
Genetic Characteristics ◽  
Ncbi Accession ◽  
Group A ◽  
Ncbi Accession Number

Group A Streptococcus emm type 1-2 is more prevalent than emm type 1 in India. Only partial information is available about the genetic characteristics of this type. Here, genome sequencing of emm type 1-2 strain 1085 (from blood) was conducted. A contig 2,010,300 bp long, with a total of 1,877 annotated proteins, was obtained (NCBI accession number CP047120, assembly accession number ASM983284v1).

scholarly journals Endogenous viral mutations, evolutionary selection, and containment policy design

2022 ◽  
Author(s):  
Patrick Mellacher
Keyword(s):  
Policy Design ◽  
Viral Evolution ◽  
The Novel ◽  
Agent Based ◽  
Evolutionary Selection ◽  
Long Run ◽  
Evolutionary Advantage ◽  
Short Run ◽  
Containment Policy ◽  
Novel Coronavirus

AbstractHow will the novel coronavirus evolve? I study a simple epidemiological model, in which mutations may change the properties of the virus and its associated disease stochastically and antigenic drifts allow new variants to partially evade immunity. I show analytically that variants with higher infectiousness, longer disease duration, and shorter latent period prove to be fitter. “Smart” containment policies targeting symptomatic individuals may redirect the evolution of the virus, as they give an edge to variants with a longer incubation period and a higher share of asymptomatic infections. Reduced mortality, on the other hand, does not per se prove to be an evolutionary advantage. I then implement this model as an agent-based simulation model in order to explore its aggregate dynamics. Monte Carlo simulations show that a) containment policy design has an impact on both speed and direction of viral evolution, b) the virus may circulate in the population indefinitely, provided that containment efforts are too relaxed and the propensity of the virus to escape immunity is high enough, and crucially c) that it may not be possible to distinguish between a slowly and a rapidly evolving virus by looking only at short-term epidemiological outcomes. Thus, what looks like a successful mitigation strategy in the short run, may prove to have devastating long-run effects. These results suggest that optimal containment policy must take the propensity of the virus to mutate and escape immunity into account, strengthening the case for genetic and antigenic surveillance even in the early stages of an epidemic.

scholarly journals Tracking and Classifying Global COVID-19 Cases by using 1D Deep Convolution Neural Networks

2020 ◽  
Author(s):  
Mark Amo-Boateng
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Time Series Data ◽  
Sequence Data ◽  
Series Data ◽  
The Novel ◽  
Response Curves ◽  
Convolution Neural Networks ◽  
Link Type ◽  
Novel Coronavirus

ABSTRACTThe novel coronavirus disease (COVID-19) and pandemic has taken the world by surprise and simultaneously challenged the health infrastructure of every country. Governments have resorted to draconian measures to contain the spread of the disease despite its devastating effect on their economies and education. Tracking the novel coronavirus 2019 disease remains vital as it influences the executive decisions needed to tighten or ease restrictions meant to curb the pandemic. One-Dimensional (1D) Convolution Neural Networks (CNN) have been used classify and predict several time-series and sequence data. Here 1D-CNN is applied to the time-series data of confirmed COVID-19 cases for all reporting countries and territories. The model performance was 90.5% accurate. The model was used to develop an automated AI tracker web app (AI Country Monitor) and is hosted on https://aicountrymonitor.org. This article also presents a novel concept of pandemic response curves based on cumulative confirmed cases that can be use to classify the stage of a country or reporting territory. It is our firm believe that this Artificial Intelligence COVID-19 tracker can be extended to other domains such as the monitoring/tracking of Sustainable Development Goals (SDGs) in addition to monitoring and tracking pandemics.

scholarly journals Genome Characterization and Potential Risk Assessment of the Novel SARS-CoV-2 Variant Omicron (B.1.1.529)

Zoonoses ◽  
2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Si Qin ◽  
Mengnan Cui ◽  
Siqi Sun ◽  
Jiyang Zhou ◽  
Zongmin Du ◽  
...  
Keyword(s):  
Sharp Increase ◽  
World Health ◽  
The Novel ◽  
Receptor Binding Domain ◽  
Global Epidemic ◽  
New Variant ◽  
The World ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Global Population

As the novel coronavirus SARS-CoV-2 spread around the world, multiple waves of variants emerged, thus leading to local or global population shifts during the pandemic. A new variant named Omicron (PANGO lineage B.1.1.529), which was first discovered in southern Africa, has recently been proposed by the World Health Organization to be a Variant of Concern. This variant carries an unusually large number of mutations, particularly on the spike protein and receptor binding domain, in contrast to other known major variants. Some mutation sites are associated with enhanced viral transmission, infectivity, and pathogenicity, thus enabling the virus to evade the immune protective barrier. Given that the emergence of the Omicron variant was accompanied by a sharp increase in infection cases in South Africa, the variant has the potential to trigger a new global epidemic peak. Therefore, continual attention and a rapid response are required to decrease the possible risks to public health.

scholarly journals In Silico Analysis of Bioactive Peptides Released from Giant Grouper (Epinephelus lanceolatus) Roe Proteins Identified by Proteomics Approach

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2910 ◽  
Author(s):  
Fenny Panjaitan ◽  
Honey Gomez ◽  
Yu-Wei Chang
Keyword(s):  
In Silico ◽  
Bioactive Peptides ◽  
In Silico Analysis ◽  
Epinephelus Coioides ◽  
Accession Number ◽  
Inhibitory Peptides ◽  
Dpp Iv ◽  
Ncbi Accession ◽  
Silico Analysis ◽  
Ncbi Accession Number

Major proteins contained in dried giant grouper roe (GR) such as vitellogenin (from Epinephelus coioides; NCBI accession number: AAW29031.1), apolipoprotein A-1 precursor (from Epinephelus coioides; NCBI accession number: ACI01807.1) and apolipoprotein E (from Epinephelus bruneus; NCBI accession number: AEB31283.1) were characterized through compiled proteomics techniques (SDS-PAGE, in-gel digestion, mass spectrometry and on-line Mascot database analysis). These proteins were subjected to in silico analysis using BLAST and BIOPEP-UWM database. Sequence similarity search by BLAST revealed that the aligned vitellogenin sequences from Epinephelus coioides and Epinephelus lanceolatus share 70% identity, which indicates that the sequence sample has significant similarity with proteins in sequence databases. Moreover, prediction of potential bioactivities through BIOPEP-UWM database resulted in high numbers of peptides predominantly with dipeptidyl peptidase-IV (DPP-IV) and angiotensin-I-converting enzyme (ACE-I) inhibitory activities. Pepsin (pH > 2) was predicted to be the most promising enzyme for the production of bioactive peptides from GR protein, which theoretically released 82 DPP-IV inhibitory peptides and 47 ACE-I inhibitory peptides. Overall, this work highlighted the potentiality of giant grouper roe as raw material for the generation of pharmaceutical products. Furthermore, the application of proteomics and in silico techniques provided rapid identification of proteins and useful prediction of its potential bioactivities.

scholarly journals Identification of Glucoamylase cDNA Sequence of Saccharomycopsis (Syn. Endomycopsis) bubodii 2066

KIMIKA ◽  
2016 ◽  
Vol 27 (2) ◽  
pp. 14-27
Author(s):  
Joel H. G. Tolentino ◽  
Kevin L. Labrador ◽  
Jennifer P. Fronteras ◽  
Lani L. R. Bullo ◽  
Leslie P. M. Cancio ◽  
...  
Keyword(s):  
Cdna Sequence ◽  
Gene Sequence ◽  
Direct Conversion ◽  
Sago Starch ◽  
Accession Number ◽  
Base Pairs ◽  
Raw Starch ◽  
Ncbi Accession ◽  
Glucoamylase Gene ◽  
Ncbi Accession Number

Saccharomycopsis (Syn. Endomycopsis) bubodii 2066 is an isolate from bubod, a starter used in making rice wine in northern Philippines. We have shown that the yeast has amylolytic activity on raw sago starch. In our attempt to identify the putative raw starch-digesting amylase in S. bubodii, we determined the cDNA sequence of a glucoamylase gene. One primer pair that was designed based on a glucoamylase of Saccharomycopsis fibuligera HUT7212 (GLU1, NCBI Accession Number L25641.1) produced a sequence of 1234 base pairs. To obtain a wider coverage, a primer walking strategy was carried out using four primer pairs designed based on GLU1 gene. The generated sequence of 1535 base pairs shows 98.7 to 100% homology when aligned with glucoamylase genes from four strains of S. fibuligera suggesting that this glucoamylase is highly conserved between the Saccharomycopsis species. This work further reports a gene sequence of glucoamylase derived from Philippine-isolated yeast. The sequence is deposited in GenBank and assigned the accession number KP068007.1. The gene may be heterologously expressed in Saccharomyces cerevisiae for possible utilization in the direct conversion of raw sago starch to bioethanol.

Sign in / Sign up

Export Citation Format

Share Document