scholarly journals Emergence of new SARS-CoV-2 variant under investigation in Saudi Arabia

2021 ◽  
Author(s):  
Majed F. ALGHORIBI ◽  
Abdulrahman ALSWAJI ◽  
Liliane OKDAH ◽  
Sadeem ALHAYLI ◽  
Zinab BU ALI ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Binding Domain ◽  
Surveillance Program ◽  
Original Strain ◽  
Receptor Binding Domain ◽  
Rapid Rise ◽  
N Protein ◽  
New Variant ◽  
Health Tracking ◽  
Medical City

Abstract Genomic surveillance helps public health tracking the path of a pandemic, understand its transmission route, and how quickly the virus is spreading and adapting through mutation and recombination. In late 2020, the Infectious Diseases Research Department (IDRD) at King Abdullah International Medical Research Center (KAIMRC) initiated a surveillance program focused on monitoring the dissemination of SARS-CoV-2 variants by sequencing the receptor-binding domain (RBD) of 20 to 32% of all community-acquired SARS-CoV-2 positive cases identified from November 2020 to February 2021 at King Abdulaziz Medical City (KAMC) in Riyadh. Sequence analysis detected among sequenced isolates a SARS-CoV-2 variant harboring an N501T substitution in the receptor-binding domain (RBD). COVID-19 cases linked to this new variant under investigation, first detected in isolates from November, grew exponentially in 2021 to account alone for more than 62 % (142/228) of all SARS-CoV-2 positive cases studied in February, thus suggesting that this variant might have increased transmissibility. Genome sequencing showed that this variant has evolved from the pangolin lineage B.1.1 and diverged from the original strain of Wuhan in China by ten amino acid changes located in ORF1a (P3359L and Q3729K), ORF1b (P314L), spike (S) protein (F157S, N501T, D614G), ORF6 (F2S) and nucleocapsid (N) protein (I84V, R203K and G204R). Isolates belonging to the new variant were further split into two sub-groups based on additional changes in the spike. Of these, one sub-group carried the Y144*, G257S, T859N and A899S variations combined, while one carried the H49Y variation alone. Patients infected with this new variant did not show any increase in the severity of infections. The rapid rise of the new variant among community-acquired SARS-CoV-2 cases suggests a national spread, although this needs to be further assessed carefully.

Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein

2021 ◽  
Author(s):  
Yuzhao Zhang ◽  
Xibing He ◽  
Viet Hoang Man ◽  
Jingchen Zhai ◽  
Beihong Ji ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Rna Virus ◽  
Md Simulations ◽  
Binding Domain ◽  
Spike Protein ◽  
World Health ◽  
Receptor Binding Domain ◽  
Binding Profile ◽  
New Variant ◽  
The World

<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 and has accumulated nearly a hundred million reported infections thereafter. This highly transmissible and pathogenic coronavirus has caused a pandemic of acute respiratory disease, coronavirus disease 2019 (COVID-19), which has caught extensive attention and greatly changed people’s lifestyles all over the world. As an RNA virus, SARS-CoV-2 mutates rapidly as the virus replicates. The world health organization is now closely monitoring the emergence of a new variant, N501Y, on the spike protein. This N501Y variant is found to have higher transmission ability and infectivity, and is believed to be related to the rapid increase of COVID-19 cases in December 2020 in the UK. It was recently reported that the N501Y variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies. The Tyr mutation at 501 is located at the receptor binding domain (RBD) of the spike protein, the area that directly contacts human ACE2 (hACE2). It’s urgent to figure out the driving force of the new mutant’s enhanced infectivity. Thus, a computational aided binding profile prediction is made to investigate the binding affinity alteration and potential structural change of the N501Y mutant. <a>The resulting structures of N501Y mutant from MD simulations could be used to develop drug inhibitors against hACE2/RBD binding. </a></p>

Receptor-binding domain–based immunoassays for serosurveillance differentiate efficiently between SARS-CoV2–exposed and non-exposed farmed mink

2021 ◽  
pp. 104063872110578
Author(s):  
Jorge Pulido ◽  
Marga García-Durán ◽  
Ricardo Fernández-Antonio ◽  
Carmen Galán ◽  
Lissette López ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Protein Microarray ◽  
Binding Domain ◽  
Health Concern ◽  
Receptor Binding Domain ◽  
Serum Samples ◽  
N Protein ◽  
International Agencies ◽  
Microarray Immunoassay ◽  
Nucleoprotein N

During the COVID-19 pandemic, infection of farmed mink has become not only an economic issue but also a widespread public health concern. International agencies have advised the use of strict molecular and serosurveillance methods for monitoring the SARS-CoV2 status on mink farms. We developed 2 ELISAs and a duplex protein microarray immunoassay (MI), all in a double-recognition format (DR), to detect SARS-CoV2 antibodies specific to the receptor-binding domain (RBD) of the spike protein and to the full-length nucleoprotein (N) in mink sera. We collected 264 mink serum samples and 126 oropharyngeal samples from 5 Spanish mink farms. In both of the ELISAs and the MI, RBD performed better than N protein for serologic differentiation of mink from SARS-CoV2–positive and –negative farms. Therefore, RBD was the optimal antigenic target for serosurveillance of mink farms.

scholarly journals The mRNA-1273 Vaccine Induces Cross-Variant Antibody Responses to SARS-CoV-2 With Distinct Profiles in Individuals With or Without Pre-Existing Immunity

2021 ◽  
Vol 12 ◽  
Author(s):  
Sonia Tejedor Vaquero ◽  
Leire de Campos-Mata ◽  
José María Ramada ◽  
Pilar Díaz ◽  
Juan Navarro-Barriuso ◽  
...  
Keyword(s):  
Antibody Response ◽  
Receptor Binding ◽  
Vaccine Dose ◽  
Binding Domain ◽  
Antibody Responses ◽  
Slight Reduction ◽  
Original Strain ◽  
Receptor Binding Domain ◽  
Wild Type ◽  
Compositional Patterns

mRNA-based vaccines effectively induce protective neutralizing antibodies against SARS-CoV-2, the etiological agent of COVID-19. Yet, the kinetics and compositional patterns of vaccine-induced antibody responses to the original strain and emerging variants of concern remain largely unknown. Here we characterized serum antibody classes and subclasses targeting the spike receptor-binding domain of SARS-CoV-2 wild type and α, β, γ and δ variants in a longitudinal cohort of SARS-CoV-2 naïve and COVID-19 recovered individuals receiving the mRNA-1273 vaccine. We found that mRNA-1273 vaccine recipients developed a SARS-CoV-2-specific antibody response with a subclass profile comparable to that induced by natural infection. Importantly, these antibody responses targeted both wild type SARS-CoV-2 as well as its α, β, γ and δ variants. Following primary vaccination, individuals with pre-existing immunity showed higher induction of all antibodies but IgG3 compared to SARS-CoV-2-naïve subjects. Unlike naïve individuals, COVID-19 recovered subjects did not mount a recall antibody response upon the second vaccine dose. In these individuals, secondary immunization resulted in a slight reduction of IgG1 against the receptor-binding domain of β and γ variants. Despite the lack of recall humoral response, vaccinees with pre-existing immunity still showed higher titers of IgG1 and IgA to all variants analyzed compared to fully vaccinated naïve individuals. Our findings indicate that mRNA-1273 vaccine triggered cross-variant antibody responses with distinct profiles in vaccinees with or without pre-existing immunity and suggest that individuals with prior history of SARS-CoV-2 infection may not benefit from the second mRNA vaccine dose with the current standard regimen.

scholarly journals Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein

2021 ◽  
Author(s):  
Yuzhao Zhang ◽  
Xibing He ◽  
Viet Hoang Man ◽  
Jingchen Zhai ◽  
Beihong Ji ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Rna Virus ◽  
Md Simulations ◽  
Binding Domain ◽  
Spike Protein ◽  
World Health ◽  
Receptor Binding Domain ◽  
Binding Profile ◽  
New Variant ◽  
The World

<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 and has accumulated nearly a hundred million reported infections thereafter. This highly transmissible and pathogenic coronavirus has caused a pandemic of acute respiratory disease, coronavirus disease 2019 (COVID-19), which has caught extensive attention and greatly changed people’s lifestyles all over the world. As an RNA virus, SARS-CoV-2 mutates rapidly as the virus replicates. The world health organization is now closely monitoring the emergence of a new variant, N501Y, on the spike protein. This N501Y variant is found to have higher transmission ability and infectivity, and is believed to be related to the rapid increase of COVID-19 cases in December 2020 in the UK. It was recently reported that the N501Y variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies. The Tyr mutation at 501 is located at the receptor binding domain (RBD) of the spike protein, the area that directly contacts human ACE2 (hACE2). It’s urgent to figure out the driving force of the new mutant’s enhanced infectivity. Thus, a computational aided binding profile prediction is made to investigate the binding affinity alteration and potential structural change of the N501Y mutant. <a>The resulting structures of N501Y mutant from MD simulations could be used to develop drug inhibitors against hACE2/RBD binding. </a></p>

scholarly journals Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein

2021 ◽  
Author(s):  
Yuzhao Zhang ◽  
Xibing He ◽  
Viet Hoang Man ◽  
Jingchen Zhai ◽  
Beihong Ji ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Rna Virus ◽  
Md Simulations ◽  
Binding Domain ◽  
Spike Protein ◽  
World Health ◽  
Receptor Binding Domain ◽  
Binding Profile ◽  
New Variant ◽  
The World

<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 and has accumulated nearly a hundred million reported infections thereafter. This highly transmissible and pathogenic coronavirus has caused a pandemic of acute respiratory disease, coronavirus disease 2019 (COVID-19), which has caught extensive attention and greatly changed people’s lifestyles all over the world. As an RNA virus, SARS-CoV-2 mutates rapidly as the virus replicates. The world health organization is now closely monitoring the emergence of a new variant, N501Y, on the spike protein. This N501Y variant is found to have higher transmission ability and infectivity, and is believed to be related to the rapid increase of COVID-19 cases in December 2020 in the UK. It was recently reported that the N501Y variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies. The Tyr mutation at 501 is located at the receptor binding domain (RBD) of the spike protein, the area that directly contacts human ACE2 (hACE2). It’s urgent to figure out the driving force of the new mutant’s enhanced infectivity. Thus, a computational aided binding profile prediction is made to investigate the binding affinity alteration and potential structural change of the N501Y mutant. <a>The resulting structures of N501Y mutant from MD simulations could be used to develop drug inhibitors against hACE2/RBD binding. </a></p>

Destabilizing the Structural Integrity of SARS-CoV2 Receptor Proteins by Curcumin Along with Hydroxychloroquine: An Insilco Approach for a Combination Therapy

2020 ◽  
Author(s):  
Akhileshwar Srivastava ◽  
Divya Singh
Keyword(s):  
Binding Energy ◽  
Combination Therapy ◽  
Receptor Binding ◽  
Structural Integrity ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Receptor Proteins ◽  
Main Protease ◽  
The Stability ◽  
Therapeutic Activities

Presently, an emerging disease (COVID-19) has been spreading across the world due to coronavirus (SARS-CoV2). For treatment of SARS-CoV2 infection, currently hydroxychloroquine has been suggested by researchers, but it has not been found enough effective against this virus. The present study based on in silico approaches was designed to enhance the therapeutic activities of hydroxychloroquine by using curcumin as an adjunct drug against SARS-CoV2 receptor proteins: main-protease and S1 receptor binding domain (RBD). The webserver (ANCHOR) showed the higher protein stability for both receptors with disordered score (<0.5). The molecular docking analysis revealed that the binding energy (-24.58 kcal/mol) of hydroxychloroquine was higher than curcumin (-20.47 kcal/mol) for receptor main-protease, whereas binding energy of curcumin (<a>-38.84</a> kcal/mol) had greater than hydroxychloroquine<a> (-35.87</a> kcal/mol) in case of S1 receptor binding domain. Therefore, this study suggested that the curcumin could be used as combination therapy along with hydroxychloroquine for disrupting the stability of SARS-CoV2 receptor proteins

Role of key point Mutations in Receptor Binding Domain of SARS-CoV-2 Spike Glycoprotein

2020 ◽  
Vol 20 ◽  
Author(s):  
Bipin Singh
Keyword(s):  
Receptor Binding ◽  
Point Mutations ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Angiotensin Converting Enzyme 2 ◽  
Recent Outbreak ◽  
Novel Coronavirus ◽  
Genomic Similarity

: The recent outbreak of novel coronavirus (SARS-CoV-2 or 2019-nCoV) and its worldwide spread is posing one of the major threats to human health and the world economy. It has been suggested that SARS-CoV-2 is similar to SARSCoV based on the comparison of the genome sequence. Despite the genomic similarity between SARS-CoV-2 and SARSCoV, the spike glycoprotein and receptor binding domain in SARS-CoV-2 shows the considerable difference compared to SARS-CoV, due to the presence of several point mutations. The analysis of receptor binding domain (RBD) from recently published 3D structures of spike glycoprotein of SARS-CoV-2 (Yan, R., et al. (2020); Wrapp, D., et al. (2020); Walls, A. C., et al. (2020)) highlights the contribution of a few key point mutations in RBD of spike glycoprotein and molecular basis of its efficient binding with human angiotensin-converting enzyme 2 (ACE2).

scholarly journals Ivermectin Docks to the SARS-CoV-2 Spike Receptor-binding Domain Attached to ACE2

In Vivo ◽  
2020 ◽  
Vol 34 (5) ◽  
pp. 3023-3026 ◽  
Author(s):  
STEVEN LEHRER ◽  
PETER H. RHEINSTEIN
Keyword(s):  
Receptor Binding ◽  
Binding Domain ◽  
Receptor Binding Domain
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