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1.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-322717

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes are at risk of the disease. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include, membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N) and the spike protein (S). The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein. The M protein of SARS-CoV-2 is 98.6% similar to the M protein of bat SARS-CoV, maintains 98.2% homology with pangolin SARS-CoV, and has 90% homology with M protein of SARS-CoV;whereas, the similarity was only 38% with the M protein of MERS-CoV. In silico analyses showed that the M protein of SARS-CoV-2 has a triple helix bundle, form a single 3-transmembrane domain (TM), and are homologous to the prokaryotic sugar transport protein semiSWEET. SemiSWEETs are related to the PQ-loop family that function as cargo receptors in vesicle transport, mediates movement of basic amino acids across lysosomal membranes, and is also involved in phospholipase flippase function. The advantage and role of the M protein having a sugar transport-like structure is not clearly understood. The M protein of SARS-CoV-2 interacts with S, E and N protein. The S protein of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein influences glycosylation of the S protein. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the semiSWEET sugar transporter-like structure of the M protein may be involved in multiple functions that may aid in the rapid proliferation, replication and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the semiSWEET sugar transporter.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-322716

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the disease COVID-19 has wreaked havoc on the health and economy of humanity. In addition, the disease is observed in domestic and wild animals. The disease has impacted directly and indirectly every corner of the planet. Currently, there are no vaccines and effective therapies for COVID-19. SARS-CoV-2 is an enveloped virus with a single-stranded RNA genome of 29.8 kb. More than two-thirds of the genome comprises Orf1ab encoding 16 non-structural proteins (nsps) followed by mRNAs encoding structural proteins, spike (S), envelop (E), membrane (M), and nucleocapsid (N). These genes are interspaced with several accessory genes (open reading frames [Orf] 3a, 3b, 6, 7a, 7b, 8, 9b, 9c and 10). The functions of these proteins are of particular interest for understanding the pathogenesis of SARS-CoV-2. Several of the nsps (nsp3, nsp4, nsp6) and Orf3a are transmembrane proteins involved in regulating the host immunity, modifying host cell organelles for viral replication and escape and hence considered drug targets. In this paper we report mapping the transmembrane structure of the non-structural proteins of SARS-CoV-2.

3.
Methods Mol Biol ; 2410: 3-25, 2022.
Article in English | MEDLINE | ID: covidwho-1575758

ABSTRACT

The COVID-19 pandemic of 2020-2021 has highlighted the importance of vaccines and vaccination in human health. The pandemic has resulted in social distancing, travel restrictions, decreased trade, high unemployment, commodity price decline, and financial stress that has impacted the global economy. Since December 2020, a massive vaccination campaign is undergoing in every country on the planet to protect against SARS-CoV-2. Vaccination is the cheapest health-care interventions that can save more lives than any other drugs or therapies. Some of the common diseases of the twentieth century including smallpox and polio are seldom reported due to intense vaccination programs that eradicated it. Smallpox is completely eradicated globally; whereas, polio is confined to only a couple of countries. Vaccination has not only improved the health of man but also improved food security by preventing diseases in farm animals and aquacultured fish. Awareness of the principles of immunology and novel vaccines has led to effective vaccination strategies. Climate change could lead to generation of new strains of infectious microorganisms that would require development of novel vaccines. Recent years have seen the increase in incidence of brain-eating amoeba and flesh-eating bacteria (necrotizing fasciitis). There are no vaccines for these diseases. Though vaccination programs have eradicated several diseases and increased the quality of life, there are several diseases that have no effective vaccines. Currently there are no vaccines for cancer, neurodegenerative diseases, autoimmune diseases, as well as infectious diseases like tuberculosis, AIDS, and parasitic diseases including malaria. Spontaneous evolution of pathogenic microorganisms may lead to pandemics that impact the health of not only humanity but also other animals. Hence, the challenge to vaccinologists is the development of novel vaccines and vaccination strategies within limited time period and using minimum resources. In addition, the vaccine developed should be administered globally within a short duration so as to prevent generation of pathogenic variants more lethal than the parent strain.


Subject(s)
Vaccination , Vaccines , Animals , COVID-19 , Humans , Pandemics , Quality of Life
4.
Methods Mol Biol ; 2410: 131-146, 2022.
Article in English | MEDLINE | ID: covidwho-1575757

ABSTRACT

Knowledge in the fields of biochemistry, structural biology, immunological principles, microbiology, and genomics has all increased dramatically in recent years. There has also been tremendous growth in the fields of data science, informatics, and artificial intelligence needed to handle this immense data flow. At the intersection of wet lab and data science is the field of bioinformatics, which seeks to apply computational tools to better understanding of the biological sciences. Like so many other areas of biology, bioinformatics has transformed immunology research leading to the discipline of immunoinformatics. Within this field, many new databases and computational tools have been created that increasingly drive immunology research, in many cases drawing upon artificial intelligence and machine learning to predict complex immune system behaviors, for example, prediction of B cell and T cell epitopes. In this book chapter, we provide an overview of computational tools and artificial intelligence being used for protein modeling, drug screening, vaccine design, and highlight how these tools are being used to transform approaches to pandemic countermeasure development, by reference to the current COVID-19 pandemic.


Subject(s)
Artificial Intelligence , Drug Design , COVID-19 , Humans , Pandemics
5.
Methods Mol Biol ; 2410: 111-129, 2022.
Article in English | MEDLINE | ID: covidwho-1575756

ABSTRACT

Infectious diseases are a leading cause of death worldwide, and vaccines are the cheapest and efficient approach to preventing diseases. Use of conventional vaccination strategies such as live, attenuated, and subunit has limitations as it does not fully provide protection against many infectious diseases. Hence, there was a need for the development of a new vaccination strategy. Use of nucleic acids-DNA and RNA-has emerged as promising alternative to conventional vaccine approaches. Knowledge of mRNA biology, chemistry, and delivery systems in recent years have enabled mRNA to become a promising vaccine candidate. One of the advantages of a mRNA vaccine is that clinical batches can be generated after the availability of a sequence encoding the immunogen. The process is cell-free and scalable. mRNA is a noninfectious, nonintegrating molecule and there is no potential risk of infection or mutagenesis. mRNA is degraded by normal cellular processes, and its in vivo half-life can be regulated by different modifications and delivery methods. The efficacy can be increased by modifications of the nucleosides that can make mRNA more stable and highly translatable. Efficient in vivo delivery can be achieved by formulating mRNA into carrier molecules, allowing rapid uptake and expression in the cytoplasm. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread globally, prompting an international effort to accelerate development of a vaccine. The spike (S) glycoprotein mediates host cell attachment and is required for viral entry; it is the primary vaccine target for many candidate SARS-CoV-2 vaccines. Development of a lipid nanoparticle encapsulated mRNA vaccine that encodes the SARS-CoV-2 S glycoprotein stabilized in its prefusion conformation conferred 95% protection against Covid-19.


Subject(s)
Viral Vaccines , COVID-19/prevention & control , COVID-19 Vaccines , Humans , Liposomes , Nanoparticles , Spike Glycoprotein, Coronavirus , Viral Vaccines/genetics
6.
Methods Mol Biol ; 2410: 265-272, 2022.
Article in English | MEDLINE | ID: covidwho-1575755

ABSTRACT

COVID-19 caused by SARS-CoV-2, an RNA coronavirus has impacted the health and economy of all the countries. The virus has wide host adaptability and causes severe diseases in humans and animals. The major structural proteins of SARS-CoV-2 include spike (S), envelop (E), membrane (M), and nucleocapsid (N). The current vaccines are based on the S protein. The emergence of variants of SARS-CoV-2 has renewed interest in the use of additional structural proteins for the development of diagnostics and vaccines. Knowledge of B cell epitopes and MHC-I binding regions of the structural proteins of SARS-CoV-2 is essential in the development of effective diagnostics and therapies. This chapter provides information on the epitopes of the structural proteins of SARS-CoV-2.


Subject(s)
Coronavirus Envelope Proteins/immunology , Epitopes, B-Lymphocyte , Epitopes, T-Lymphocyte , Spike Glycoprotein, Coronavirus/immunology , Viral Matrix Proteins/immunology , Animals , COVID-19 , COVID-19 Vaccines , Humans , SARS-CoV-2
7.
Methods Mol Biol ; 2410: 93-108, 2022.
Article in English | MEDLINE | ID: covidwho-1575754

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. Lack of a voice on how to handle the pandemic impacted the management of the disease globally. Publication of the importance of masks and social distancing in preprint servers reduced the spread of the disease and deaths associated with it. Very few countries have invested in science and research and development and that has impacted the development of therapies for the pandemic. Though vaccination against COVID-19 started in December 2020, slower rate of immunizations has resulted in rapid spread of the mutant strains of SARS-CoV-2. Lack of transparency and accountability coupled with anergic leadership was responsible for the high incidence of disease and death associated with the COVID-19 pandemic.


Subject(s)
COVID-19 Vaccines , COVID-19 , Pandemics , Animals , COVID-19/epidemiology , Humans , Masks , Pandemics/prevention & control , Physical Distancing , SARS-CoV-2
8.
J Comput Biol ; 28(9): 909-921, 2021 09.
Article in English | MEDLINE | ID: covidwho-1286546

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the disease coronavirus-19 disease (COVID-19) has wreaked havoc on the health and economy of humanity. In addition, the disease is observed in domestic and wild animals. The disease has impacted directly and indirectly every corner of the planet. Currently, there are no effective therapies for the treatment of COVID-19. Vaccination to protect against COVID-19 started in December 2020. SARS-CoV-2 is an enveloped virus with a single-stranded RNA genome of 29.8 kb. More than two-thirds of the genome comprise Orf1ab encoding 16 nonstructural proteins (nsps) followed by mRNAs encoding structural proteins, spike (S), envelop (E), membrane (M), and nucleocapsid (N). These genes are interspaced with several accessory genes (open reading frames [Orfs] 3a, 3b, 6, 7a, 7b, 8, 9b, 9c, and 10). The functions of these proteins are of particular interest for understanding the pathogenesis of SARS-CoV-2. Several of the nsps (nsp3, nsp4, and nsp6) and Orf3a are transmembrane proteins involved in regulating the host immunity, modifying host cell organelles for viral replication and escape and hence considered drug targets. In this paper, we report mapping the transmembrane structure of the nsps of SARS-CoV-2.


Subject(s)
SARS-CoV-2/genetics , Viral Nonstructural Proteins/chemistry , Protein Conformation , SARS-CoV-2/chemistry , Viral Nonstructural Proteins/genetics
9.
J Am Med Inform Assoc ; 27(12): 1913-1920, 2020 12 09.
Article in English | MEDLINE | ID: covidwho-1060085

ABSTRACT

OBJECTIVE: India reported its first coronavirus disease 2019 (COVID-19) case in the state of Kerala and an outbreak initiated subsequently. The Department of Health Services, Government of Kerala, initially released daily updates through daily textual bulletins for public awareness to control the spread of the disease. However, these unstructured data limit upstream applications, such as visualization, and analysis, thus demanding refinement to generate open and reusable datasets. MATERIALS AND METHODS: Through a citizen science initiative, we leveraged publicly available and crowd-verified data on COVID-19 outbreak in Kerala from the government bulletins and media outlets to generate reusable datasets. This was further visualized as a dashboard through a front-end Web application and a JSON (JavaScript Object Notation) repository, which serves as an application programming interface for the front end. RESULTS: From the sourced data, we provided real-time analysis, and daily updates of COVID-19 cases in Kerala, through a user-friendly bilingual dashboard (https://covid19kerala.info/) for nonspecialists. To ensure longevity and reusability, the dataset was deposited in an open-access public repository for future analysis. Finally, we provide outbreak trends and demographic characteristics of the individuals affected with COVID-19 in Kerala during the first 138 days of the outbreak. DISCUSSION: We anticipate that our dataset can form the basis for future studies, supplemented with clinical and epidemiological data from the individuals affected with COVID-19 in Kerala. CONCLUSIONS: We reported a citizen science initiative on the COVID-19 outbreak in Kerala to collect and deposit data in a structured format, which was utilized for visualizing the outbreak trend and describing demographic characteristics of affected individuals.


Subject(s)
COVID-19/epidemiology , Citizen Science , Computer Graphics , Datasets as Topic , Pandemics , Adolescent , Adult , Aged , Aged, 80 and over , Child , Female , Humans , India/epidemiology , Male , Middle Aged , User-Computer Interface , Young Adult
10.
PLoS One ; 15(12): e0242536, 2020.
Article in English | MEDLINE | ID: covidwho-965821

ABSTRACT

Retinoic acid (RA) has been shown to improve epithelial and endothelial barrier function and development and even suppress damage inflicted by inflammation on these barriers through regulating immune cell activity. This paper thus sought to determine whether RA could improve baseline barrier function and attenuate TNF-α-induced barrier leak in the human bronchial epithelial cell culture model, 16HBE14o- (16HBE). We show for the first time that RA increases baseline barrier function of these cell layers indicated by an 89% increase in transepithelial electrical resistance (TER) and 22% decrease in 14C-mannitol flux. A simultaneous, RA-induced 70% increase in claudin-4 attests to RA affecting the tight junctional (TJ) complex itself. RA was also effective in alleviating TNF-α-induced 16HBE barrier leak, attenuating 60% of the TNF-α-induced leak to 14C-mannitol and 80% of the leak to 14C-inulin. Interleukin-6-induced barrier leak was also reduced by RA. Treatment of 16HBE cell layers with TNF-α resulted in dramatic decrease in immunostaining for occludin and claudin-4, as well as a downward "band-shift" in occludin Western immunoblots. The presence of RA partially reversed TNF-α's effects on these select TJ proteins. Lastly, RA completely abrogated the TNF-α-induced increase in ERK-1,2 phosphorylation without significantly decreasing the TNF-driven increase in total ERK-1,2. This study suggests RA could be effective as a prophylactic agent in minimizing airway barrier leak and as a therapeutic in preventing leak triggered by inflammatory cascades. Given the growing literature suggesting a "cytokine storm" may be related to COVID-19 morbidity, RA may be a useful adjuvant for use with anti-viral therapies.


Subject(s)
Bronchi/drug effects , Respiratory Mucosa/drug effects , Tretinoin/pharmacology , Tumor Necrosis Factor-alpha/metabolism , Anti-Inflammatory Agents/pharmacology , Bronchi/cytology , Bronchi/metabolism , Cell Line , Humans , Inflammation/drug therapy , Inflammation/metabolism , Permeability/drug effects , Respiratory Mucosa/cytology , Respiratory Mucosa/metabolism , Tight Junctions/drug effects , Tight Junctions/metabolism
11.
Pathog Immun ; 5(1): 342-363, 2020.
Article in English | MEDLINE | ID: covidwho-914901

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes are at risk of the disease. As yet we do not know why the virus has been highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N), and the spike protein (S). METHODS: The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein, is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein. RESULTS: The M protein of SARS-CoV-2 is 98.6% similar to the M protein of bat SARS-CoV, maintains 98.2% homology with pangolin SARS-CoV, and has 90% homology with the M protein of SARS-CoV; whereas, the similarity is only 38% with the M protein of MERS-CoV. In silico analyses showed that the M protein of SARS-CoV-2 has a triple helix bundle, forms a single 3-trans-membrane domain, and is homologous to the prokaryotic sugar transport protein SemiSWEET. SemiSWEETs are related to the PQ-loop family whose members function as cargo receptors in vesicle transport, mediate movement of basic amino acids across lysosomal membranes, and are also involved in phospholipase flippase function. CONCLUSIONS: The advantage and role of the M protein having a sugar transporter-like structure is not clearly understood. The M protein of SARS-CoV-2 interacts with S, E, and N protein. The S protein of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein influences glycosylation of the S protein. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the SemiSWEET sugar transporter-like structure of the M protein may be involved in multiple functions that may aid in the rapid proliferation, replication, and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the SemiSWEET sugar transporter.

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