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1.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-320513

ABSTRACT

COVID-19 has created a global pandemic with high morbidity and mortality in 2020. Novel coronavirus (nCoV), also known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), is responsible for this deadly disease. International Committee on Taxonomy of Viruses (ICTV) has declared that nCoV is highly genetically similar to SARS-CoV epidemic in 2003 (89% similarity). Limited number of clinically validated Human-nCoV protein interaction data is available in the literature. With this hypothesis, the present work focuses on developing a computational model for nCoV-Human protein interaction network, using the experimentally validated SARS-CoV-Human protein interactions. Initially, level-1 and level-2 human spreader proteins are identified in SARS-CoV-Human interaction network, using Susceptible-Infected-Susceptible (SIS) model. These proteins are considered as potential human targets for nCoV bait proteins. A gene-ontology based fuzzy affinity function has been used to construct the nCoV-Human protein interaction network at 99.98% specificity threshold. This also identifies the level-1 human spreaders for COVID-19 in human protein-interaction network. Level-2 human spreaders are subsequently identified using the SIS model. The derived host-pathogen interaction network is finally validated using 7 potential FDA listed drugs for COVID-19 with significant overlap between the known drug target proteins and the identified spreader proteins.

2.
Methods ; 203: 488-497, 2022 07.
Article in English | MEDLINE | ID: covidwho-1559797

ABSTRACT

Novel coronavirus(SARS-CoV2) replicates the host cell's genome by interacting with the host proteins. Due to this fact, the identification of virus and host protein-protein interactions could be beneficial in understanding the disease transmission behavior of the virus as well as in potential COVID-19 drug identification. International Committee on Taxonomy of Viruses (ICTV) has declared that nCoV is highly genetically similar to the SARS-CoV epidemic in 2003 (∼89% similarity). With this hypothesis, the present work focuses on developing a computational model for the nCoV-Human protein interaction network, using the experimentally validated SARS-CoV-Human protein interactions. Initially, level-1 and level-2 human spreader proteins are identified in the SARS-CoV-Human interaction network, using Susceptible-Infected-Susceptible (SIS) model. These proteins are considered potential human targets for nCoV bait proteins. A gene-ontology-based fuzzy affinity function has been used to construct the nCoV-Human protein interaction network at a ∼99.98% specificity threshold. This also identifies 37 level-1 human spreaders for COVID-19 in the human protein-interaction network. 2474 level-2 human spreaders are subsequently identified using the SIS model. The derived host-pathogen interaction network is finally validated using six potential FDA-listed drugs for COVID-19 with significant overlap between the known drug target proteins and the identified spreader proteins.


Subject(s)
COVID-19 , SARS-CoV-2 , Computer Simulation , Humans , Protein Interaction Maps/genetics , Proteins , RNA, Viral , SARS-CoV-2/genetics
3.
Environ Chem Lett ; 20(3): 1539-1544, 2022.
Article in English | MEDLINE | ID: covidwho-1408890

ABSTRACT

SARS-CoV-2 pandemic continues with emergence of new variants of concerns. These variants are fueling the third and fourth waves of pandemic across many nations. Here we describe the new emerging variants of SARS-CoV-2 and why they have enhanced infectivity and possess the ability to evade immunity.

4.
PeerJ ; 9: e12117, 2021.
Article in English | MEDLINE | ID: covidwho-1395270

ABSTRACT

The entire world is witnessing the coronavirus pandemic (COVID-19), caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 promotes fatal chronic respiratory disease followed by multiple organ failure, ultimately putting an end to human life. International Committee on Taxonomy of Viruses (ICTV) has reached a consensus that SARS-CoV-2 is highly genetically similar (up to 89%) to the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), which had an outbreak in 2003. With this hypothesis, current work focuses on identifying the spreader nodes in the SARS-CoV-human protein-protein interaction network (PPIN) to find possible lineage with the disease propagation pattern of the current pandemic. Various PPIN characteristics like edge ratio, neighborhood density, and node weight have been explored for defining a new feature spreadability index by which spreader proteins and protein-protein interaction (in the form of network edges) are identified. Top spreader nodes with a high spreadability index have been validated by Susceptible-Infected-Susceptible (SIS) disease model, first using a synthetic PPIN followed by a SARS-CoV-human PPIN. The ranked edges highlight the path of entire disease propagation from SARS-CoV to human PPIN (up to level-2 neighborhood). The developed network attribute, spreadability index, and the generated SIS model, compared with the other network centrality-based methodologies, perform better than the existing state-of-art.

5.
Methods ; 203: 564-574, 2022 07.
Article in English | MEDLINE | ID: covidwho-1373306

ABSTRACT

With the gradual increase in the COVID-19 mortality rate, there is an urgent need for an effective drug/vaccine. Several drugs like Remdesivir, Azithromycin, Favirapir, Ritonavir, Darunavir, etc., are put under evaluation in more than 300 clinical trials to treat COVID-19. On the other hand, several vaccines like Pfizer-BioNTech, Moderna, Johnson & Johnson's Janssen, Sputnik V, Covishield, Covaxin, etc., also evolved from the research study. While few of them already gets approved, others show encouraging results and are still under assessment. In parallel, there are also significant developments in new drug development. But, since the approval of new molecules takes substantial time, drug repurposing studies have also gained considerable momentum. The primary agent of the disease progression of COVID-19 is SARS-CoV2/nCoV, which is believed to have ~89% genetic resemblance with SARS-CoV, a coronavirus responsible for the massive outbreak in 2003. With this hypothesis, Human-SARS-CoV protein interactions are used to develop an in-silico Human-nCoV network by identifying potential COVID-19 human spreader proteins by applying the SIS model and fuzzy thresholding by a possible COVID-19 FDA drugs target-based validation. At first, the complete list of FDA drugs is identified for the level-1 and level-2 spreader proteins in this network, followed by applying a drug consensus scoring strategy. The same consensus strategy is involved in the second analysis but on a curated overlapping set of key genes/proteins identified from COVID-19 symptoms. Validation using subsequent docking study has also been performed on COVID-19 potential drugs with the available major COVID-19 crystal structures whose PDB IDs are: 6LU7, 6M2Q, 6W9C, 6M0J, 6M71 and 6VXX. Our computational study and docking results suggest that Fostamatinib (R406 as its active promoiety) may also be considered as one of the potential candidates for further clinical trials in pursuit to counter the spread of COVID-19.


Subject(s)
COVID-19 , Drug Repositioning , Aminopyridines , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , ChAdOx1 nCoV-19 , Drug Repositioning/methods , Humans , Molecular Docking Simulation , Morpholines , Pyrimidines , RNA, Viral , SARS-CoV-2
6.
Open Forum Infect Dis ; 8(8): ofab328, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1370785

ABSTRACT

BACKGROUND: Health care personnel and patients are at risk to acquire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in health care settings, including in outpatient clinics and ancillary care areas. METHODS: Between May 1, 2020, and January 31, 2021, we identified clusters of 3 or more coronavirus disease 2019 (COVID-19) cases in which nosocomial transmission was suspected in a Veterans Affairs health care system. Asymptomatic employees and patients were tested for SARS-CoV-2 if they were identified as being at risk through contact tracing investigations; for 7 clusters, all personnel and/or patients in a shared work area were tested regardless of exposure history. Whole-genome sequencing was performed to determine the relatedness of SARS-CoV-2 samples from the clusters and from control employees and patients. RESULTS: Of 14 clusters investigated, 7 occurred in community-based outpatient clinics, 1 in the emergency department, 3 in ancillary care areas, and 3 on hospital medical/surgical wards that did not provide care for patients with known COVID-19 infection. Eighty-one of 82 (99%) symptomatic COVID-19 cases and 31 of 35 (89%) asymptomatic cases occurred in health care personnel. Sequencing analysis provided support for several transmission events between coworkers and in 2 cases supported transmission from health care personnel to patients. There were no documented transmissions from patients to personnel. CONCLUSIONS: Clusters of COVID-19 with nosocomial transmission predominantly involved health care personnel and often occurred in outpatient clinics and ancillary care areas. There is a need for improved measures to prevent transmission of SARS-CoV-2 by health care personnel in inpatient and outpatient settings.

7.
Environ Chem Lett ; 19(3): 1935-1944, 2021.
Article in English | MEDLINE | ID: covidwho-1092692

ABSTRACT

The novel coronavirus disease (COVID-19) has rapidly spread across the world and was subsequently declared as a pandemic in 2020. To overcome this public health challenge, comprehensive understanding of the disease transmission is urgently needed. Recent evidences suggest that the most common route of transmission for SARS-CoV-2 is likely via droplet, aerosol, or direct contact in a person-to-person encounter, although the possibility of transmission via fomites from surfaces cannot be ruled out entirely. Environmental contamination in COVID-19 patient rooms is widely observed due to viral shedding from both asymptomatic and symptomatic patients, and SARS-CoV-2 can survive on hospital surfaces for extended periods. Sequence of contact events can spread the virus from one surface to the other in a hospital setting. Here, we review the studies related to viral shedding by COVID-19 patients that can contaminate surfaces and survival of SARS-CoV-2 on different types of surfaces commonly found in healthcare settings, as well as evaluating the importance of surface to person transmission characteristics. Based on recent evidences from the literature, decontamination of hospital surfaces should constitute an important part of the infection control and prevention of COVID-19.

9.
Environ Chem Lett ; 19(3): 1945-1951, 2021.
Article in English | MEDLINE | ID: covidwho-1049674

ABSTRACT

The coronavirus disease COVID-19 has spread throughout the world and has been declared as a pandemic by the World Health Organization on March 11th, 2020. The COVID-19 is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). One possible mode of virus transmission is through surfaces in the healthcare settings. This paper reviews currently used disinfection strategies to control SARS-CoV-2 at the healthcare facilities. Chemical disinfectants include hypochlorite, peroxymonosulfate, alcohols, quaternary ammonium compounds, and hydrogen peroxide. Advanced strategies include no-touch techniques such as engineered antimicrobial surfaces and automated room disinfection systems using hydrogen peroxide vapor or ultraviolet light.

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