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SARS-CoV-2 proteins

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SARS-CoV-2 Proteins
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    Applying high throughput and comprehensive immunoinformatics approaches to design a trivalentsubunit vaccine forinduction of immune response against human emerging coronaviruses SARS-CoV, MERS-CoV and SARS-CoV2

    Authors: Abolfazl Rahmani; Masoud Baee; Kiarash Saleki; Saead Moradi; Hamid Reza Nouri

    doi:10.21203/rs.3.rs-92515/v1 Date: 2020-10-14 Source: ResearchSquare

    Background Coronaviruses (CoV) cause diseases MESHD such as severe acute respiratory syndrome MESHD (SARS), Middle East respiratory syndrome MESHD ( MERS MESHD) and Coronavirus disease 2019 MESHD ( COVID-19 MESHD). Therefore, this study was conducted to contrast a trivalent subunit vaccine against SARS, MERS MESHD and COVID-19 MESHD. The CTL, HTL MESHD, MHC I, and IFN-γ epitopes were predicted. Moreover, to stimulate strong helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) was used. Also, for boosting immune response, β-defensin 2 was added to the construct as an adjuvant. Furthermore, TAT was applied in the vaccine to facilitate the intracellular delivery.Results Based on the predicted epitopes, a trivalent multi-epitope vaccine with a molecular weight of 74.8 kDa as a strong antigen, a non-allergenic, and soluble protein was constructed. Furtheremore, analyses validated the stability of the proposed vaccine. The binding affinity of the vaccine construct with the TLR3 was confirmed by molecular docking and, stability of the docked complex was simulated. The predicted epitopes demonstrated strong potential to stimulate T and B-cell mediated immune responses. Furthermore, codon optimization and in silico cloning guaranteed increased expression.Conclusions In this work, immunoinformatics investigations demonstrated that this next-generation approach may provide a new horizon for the development of a highly immunogenic vaccine against SARS-CoV MESHD, MERS MESHD‐CoV, and SARS-CoV-2.

    Ensemble Machine Learning of Factors Influencing COVID-19 MESHD Across US Counties

    Authors: David McCoy; Whitney Mgbara; Nir Horvitzc; Wayne M. Getz; Alan Hubbard

    doi:10.21203/rs.3.rs-90547/v1 Date: 2020-10-09 Source: ResearchSquare

    Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causal agent for COVID-19 MESHD, is a communicable disease spread through close contact. It is known to disproportionately infect MESHD certain communities due to both biological susceptibility and inequitable exposure. In this study, we investigate the most important health, social, and environmental factors impacting both the early and later phases of COVID-19 MESHD transmission and mortality in US counties.Methods: We aggregate county-level physical and mental health, environmental pollution, access to health care, demographic characteristics, vulnerable population scores, and other epidemiological data to create a large feature set to analyze COVID-19 MESHD outcomes. Because of the high-dimensionality and multicollinearity of the data, we use ensemble machine learning and marginal prediction methods to identify the most salient factors associated with several COVID-19 MESHD outbreak measures.Findings: Our variable importance results show that measures of ethnicity, public transportation and preventable diseases are the strongest drivers for both incidence and mortality. Specifically, the CDC measures for minority populations, CDC measures for limited English, and proportion of Black/African-American individuals in a county were the most important features for COVID-19 MESHD cases at day 25 and to date. For mortality at day 100 and total to date, we find that public transportation use and proportion of Black/African-American individuals in a county are the strongest predictors. The methods predict that, keeping all other factors fixed, a 10% increase in public transportation use increases mortality at day 100 by 2012 (95% CI [1972, 2356]) and likewise a 10% increase in the proportion of Black/African-American individuals in a county increases total deaths to date by 2067 (95% CI [1189, 2654]). In terms of cases to date, ethnicity turns out to almost twice as important as the next most important factors, which are location, disease prevalence, and transit factors.Interpretations: Our findings indicate that a more focused approach should be taken when managing COVID-19 MESHD, by considering features of the economy most responsible for transmission and sectors of society most vulnerable to infection and mortality. In particular, our results strongly reinforce others pointing to the disproportionate impact of COVID-19 MESHD on minority populations. They also suggests that mitigation measures, including rolling out vaccinations as they become available, will be most efficacious for the US population as a whole when, beyond healthcare workers and first responders, are focused first on the highest-risk communities.Funding: UC Berkeley, Biomedical Big Data Training Fellowship; NSF Grant 2032264 to WMG and AH MESHD.

    Significance between Air pollutants, Meteorological Factors and COVID-19 MESHD Infections: Probable Evidences in India

    Authors: Mrunmayee M Sahoo

    doi:10.21203/rs.3.rs-73771/v1 Date: 2020-09-07 Source: ResearchSquare

    SARS-CoV-2 (Coronavirus) disease represents the causative agent with a potentially fatal risk which is having great global human health concern. Earlier studies suggested that air pollutants and meteorological factors were considered as the risk factors for acute respiratory infection MESHD, which carries harmful pathogens and affects the immunity. The study intended to explore the correlation between air pollutants, meteorological factors and the daily reported infection cases caused by novel coronavirus in India. The daily positive infected cases, air pollution and meteorological factors in 288 districts were collected from January 30, 2020 to April 23, 2020 in India. Speraman’s correlation and generalised additive model were applied to investigate the correlations of four air pollutants (PM2.5, PM10, NO2 and SO2) and eight meteorological factors (Temp, DTR, RH, AH MESHD, AP, RF, WS MESHD and WD MESHD) with COVID-19 MESHD infected cases. The study indicated that a 10 µg/m3 increase during (Lag0-14) in PM2.5, PM10 and NO2 was resulted in 2.21% (95%CI: 1.13 to 3.29), 2.67% (95% CI: 0.33 to 5.01) and 4.56 (95% CI: 2.22 to 6.90) increase in daily counts of COVID 19 infected cases respectively. However, only 1 unit increase in meteorological factor levels in case of daily mean temperature and DTR during (Lag0-14) associated with 3.78% (95%CI: 1.81 to 5.75) and 1.82% (95% CI: -1.74 to 5.38) rise of COVID-19 MESHD infected cases respectively. In addition, SO2 and relative humidity were negatively associated with COVID-19 MESHD infected cases at Lag0-14 with decrease of 7.23% (95% CI: -10.99 to -3.47) and 1.11% (95% CI: -3.45 to 1.23) for SO2 and for relative humidity respectively. The study recommended that there is significant relationship between air pollutants and meteorological factors with COVID-19 MESHD infected cases, which substantially explain the effect of national lockdown and suggested positive implications for control and prevention of the spread of SARS-CoV-2 disease MESHD

    Will COVID-19 pandemic MESHD COVID-19 pandemic MESHD diminish by summer-monsoon in India? Lesson from the first lockdown

    Authors: Sarvan Kumar

    doi:10.1101/2020.04.22.20075499 Date: 2020-04-25 Source: medRxiv

    The novel Coronavirus (2019-nCoV) was identified in Wuhan, Hubei Province, China, in December 2019 and has created a medical emergency worldwide. It has spread rapidly to multiple countries and has been declared a pandemic by the World Health Organization. In India, it is already reported more than 18 thousand cases and more than 600 deaths due to Coronavirus disease 2019 MESHD ( COVID-19 MESHD) till April 20, 2020. Previous studies on various viral infections like influenza have supported an epidemiological hypothesis that the cold and dry (low absolute humidity) environments favor the survival and spread of droplet-mediated viral diseases. These viral transmissions found attenuated in warm and humid (high absolute humidity) environments. However, the role of temperature, humidity, and absolute humidity in the transmission of COVID-19 MESHD has not yet been well established. Therefore the study to investigate the meteorological condition for incidence and spread of COVID-19 MESHD infection, to predict the epidemiology of the infectious disease MESHD, and to provide a scientific basis for prevention and control measures against the new disease is required for India. In this work, we analyze the local weather patterns of the Indian region affected by the COVID-19 MESHD virus for March and April months, 2020. We have investigated the effect of meteorological parameters like Temperature, relative humidity, and absolute humidity on the rate of spread of COVID-19 MESHD using daily confirm cases in India. We have used daily averaged meteorological data for the last three years (2017-2019) for March and April month and the same for the year 2020 for March 1 HGNC to April 15. We found a positive association (Pearsons r=0.56) between temperature and daily COVID-19 MESHD cases over India. We found a negative association of humidity (RH and AH MESHD) with daily COVID-19 MESHD Cases (Persons r=-0.62, -0.37). We have also investigated the role of aerosol in spreading the pandemic across India because its possible airborne nature. For this, we have investigated the association of aerosols (AOD) and other pollutions (NO2) with COVID-19 MESHD cases during the study period and also during the first lockdown period (25 March-15 April) in India. We found a negative association in March when there were few cases, but in April, it shows positive association when the number of cases is more (for AOD it was r=-0.41 and r=0.28 respectively). During the lockdown period, aerosols (AOD) and other pollutants (NO2; an indicator of PM2.5) reduced sharply with a percentage drop of about 36 and 37, respectively. This reduction may have reduced the risk for COVID-19 MESHD through air transmission due to the unavailability of aerosol particles as a base. HYSPLIT forward trajectory model also shows that surface aerosols may travel up to 4 km according to wind and direction within three h of its generation. If coronavirus becomes airborne as suggested by many studies, then it may have a higher risk of transmission by aerosols particles. So relaxing in the lockdown and environmental rules in terms of pollutant emissions from power plants, factories, and other facilities would be a wrong choice and could result in more COVID-19 MESHD incidences and deaths in India. Therefore the current study, although limited, suggests that it is doubtful that the spread of COVID-19 MESHD would slow down in India due to meteorological factors, like high temperature and high humidity. Because a large number of cases have already been reported in the range of high Tem, high Relative, and high absolute humidity regions of India. Thus our results in no way suggest that COVID-19 MESHD would not spread in warm, humid regions or during summer/monsoon. So effective public health interventions should be implemented across India to slow down the transmission of COVID-19 MESHD. If COVID-19 MESHD is indeed sensitive to environmental factors, it could be tested in the coming summer-monsoon for India. So the only summer is not going to help India until monsoon is coming. Only government mitigations strategies would be helpful, whether its lockdown, aggressive and strategic testing, medical facilities, imposing social distancing, encouraging to use face mask or monitoring by a mobile application (Aarogya Setu).

    Structural basis to design multi-epitope vaccines against Novel Coronavirus 19 ( COVID19 MESHD) infection, the ongoing pandemic emergency: an in silico approach

    Authors: Sukrit Srivastava; Sonia Verma; Mohit Kamthania; Rupinder Kaur; Ruchi Kiran Badyal; Ajay Kumar Saxena; Ho-Joon Shin; Michael Kolbe; Kailash Pandey

    doi:10.1101/2020.04.01.019299 Date: 2020-04-03 Source: bioRxiv

    The 2019 novel coronavirus ( COVID19 MESHD / Wuhan coronavirus), officially named as Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2), is a positive-sense single-stranded RNA coronavirus. SARS-CoV-2 causes the contagious COVID19 MESHD disease also known as 2019-nCoV acute respiratory disease MESHD and has led to the ongoing 2019-20 pandemic COVID19 MESHD outbreak. The effective counter measures against SARS-CoV-2 infection MESHD require the design and development of specific and effective vaccine candidate. In the present study, we have screened and shortlisted 38 CTL, 33 HTL MESHD and 12 B cell epitopes from the eleven Protein sequences of SARS-CoV-2 by utilizing different in silico tools. The screened epitopes were further validated for their binding with their respective HLA allele binders and TAP HGNC ( Transporter associated with antigen processing) HGNC molecule by molecular docking. The shortlisted screened epitopes were further utilized to design novel two multi-epitope vaccines (MEVs) composed of CTL, HTL MESHD and B cell epitopes overlaps with potential to elicit humoral as well as cellular immune response against SARS-CoV-2. To enhance the immune response for our vaccine design, truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has been utilized as an adjuvant at N terminal of both the MEVs. Further molecular models for both the MEVs were prepared and validated for their stable molecular interactions with Toll-Like Receptor 3 HGNC ( TLR 3 HGNC). The codon-optimized cDNA of both the MEVs were further analyzed for their potential of high level of expression in a human cell line. The present study is very significant in terms of molecular designing of prospective CTL and HTL MESHD vaccine against SARS-CoV-2 infection MESHD with the potential to elicit cellular as well as humoral immune response. (SARS-CoV-2), Coronavirus, Human Transporter associated with antigen processing (TAP) HGNC, Toll-Like Receptor (TLR), Epitope, Immunoinformatics, Molecular Docking, Molecular dynamics simulation, Multi-epitope Vaccine Graphical abstractThe designed CTL (Cytotoxic T lymphocyte) and HTL (Helper T lymphocyte) multi-epitope vaccines (MEV) against COVID19 MESHD infection. Both the CTL and HTL MEV models show a very stable and well fit conformational complex formation tendency with the Toll like receptor 3 HGNC. CTL and HTL MEVs: ribbon; Toll like receptor 3 HGNC: gray cartoon; Adjuvant [truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1]: orange ribbon regions; Epitopes: cyan ribbons regions; 6xHis Tag: magenta ribbon regions. O_FIG O_LINKSMALLFIG WIDTH=87 HEIGHT=200 SRC="FIGDIR/small/019299v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@6cb749org.highwire.dtl.DTLVardef@1752d54org.highwire.dtl.DTLVardef@1f2fc16org.highwire.dtl.DTLVardef@18415a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

    Design of a Peptide-Based Subunit Vaccine against Novel Coronavirus SARS-CoV-2

    Authors: Parismita Kalita; Aditya K. Padhi; Kam Y.J. Zhang; Timir Tripathi

    id:10.20944/preprints202003.0433.v1 Date: 2020-03-29 Source: Preprints.org

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is an emerging infectious disease MESHD that was first reported in Wuhan, China and has subsequently spread worldwide. In the absence of any antiviral or immunomodulatory therapies, the disease is spreading at an alarming rate. 5 to 10% of recovered patients in Wuhan test positive again; this suggest that for controlling COVID-19 MESHD, vaccines may be better option than drugs. A clinical trial to evaluate an anti- COVID-19 MESHD vaccine has started recently. However, its efficacy and potency have to be evaluated and validated. As an alternative, we are presenting a first-of-its-kind, designed multi-peptide subunit based epitope vaccine against COVID-19 MESHD. The vaccine construct comprise an adjuvant, CTL, HTL MESHD, and B-cell epitopes joined by linkers. The vaccine is non-toxic, non-allergenic, thermostable and immunogenic with the capability to elicit a humoral and cell-mediated immune response. The findings are validated with high-end computation-based methods. This unique vaccine is made up of 33 highly antigenic epitopes from three proteins that have a prominent role in host receptor recognition, viral entry, and pathogenicity. We advocate this vaccine must be synthesized and tested urgently as public health priority.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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