Search

In comparison to previously known severe respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, the newly emerged Omicron (B.1.1.529) variant shows higher infectivity in humans. Exceptionally high infectivity of this variant raises concern of its possible transmission via other intermediate hosts. The SARS-CoV-2 infectivity is established via the association of spike (S) protein receptor binding domain (RBD) with host angiotensin I converting enzyme 2 (hACE2) receptor. In the course of this study, we investigated the interaction between Omicron S protein RBD with the ACE2 receptor of 143 mammalian hosts including human by protein-protein interaction analysis. The goal of this study was to forecast the likelihood that the virus may infect other mammalian species that coexist with or are close to humans in the household, rural, agricultural, or zoological environments. The Omicron RBD was found to interact with higher binding affinity with the ACE2 receptor of 122 mammalian hosts via different amino acid residues from the human ACE2 (hACE2). The rat (Rattus rattus) ACE2 was found to show the strongest interaction with Omicron RBD with a binding affinity of -1393.6 kcal/mol. These distinct strong binding affinity of RBD of Omicron with host ACE2 indicates a greater potential of new host transmissibility and infection via intermediate hosts. Though expected but the phylogenetic position of the mammalian species may not dictate the Omicron RBD binding to the host ACE2 receptor suggesting an involvement of multiple factors in guiding host divergence of the variant., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), which first appeared in December 2019. Angiotensin I converting enzyme 2 ( ACE2 ) receptor, present on the host cells, interacts with the receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 and facilitates the viral entry into host cells., Methods: Non-synonymous single nucleotide polymorphisms (nsSNPs) in the ACE2 gene may have an impact on the protein's stability and its function. The deleterious or harmful nsSNPs of the ACE2 gene that can change the strength as well as the pattern of interaction with the RBD of S protein were selected for this study., Results: The ACE2 :RBD interactions were analyzed by protein-protein docking study. The missense mutations A242V, R708W, G405E, D292N, Y633C, F308L, and G405E in ACE2 receptor were found to interact with RBD of Omicron subvariants with stronger binding affinity. Among the other selected nsSNPs of human ACE2 (h ACE2 ), R768W, Y654S, F588S, R710C, R710C, A191P, and R710C were found to have lower binding affinity for RBD of Omicron subvariants., Conclusion: The findings of this study suggest that the nsSNPs present in the human ACE2 gene alter the structure and function of the protein and, consequently, the susceptibility to Omicron subvariants., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: The SARS-CoV-2 infection has spread at an alarming rate with many places showing multiple peaks in incidence. Present study analyzes a total of 332 SARS-CoV-2 genome sequences from 114 asymptomatic and 218 deceased patients from twenty-one different countries to assess the mutation profile therein in order to establish the correlation between the clinical status and the observed mutations., Methods: The mining of mutations was carried out using the GISAID CoVSurver (www.gisaid.org/epiflu-applications/covsurver-mutations-app) with the reference sequence 'hCoV-19/Wuhan/WIV04/2019' present in NCBI with Accession number NC-045512.2. The impact of the mutations on SARS-CoV-2 proteins mutation was predicted using PredictSNP1(loschmidt.chemi.muni.cz/predictsnp1) which is a meta-server integrating six predictor tools: SIFT, PhD-SNP, PolyPhen-1, PolyPhen-2, MAPP and SNAP. The iStable integrated server (predictor.nchu.edu.tw/iStable) was used to predict shifts in the protein stability due to mutations., Results: A total of 372 variants were observed in the 332 SARS-CoV-2 sequences with several variants present in multiple patients accounting for a total of 1596 incidences. Asymptomatic and deceased specific mutants constituted 32% and 62% of the repertoire respectively indicating their partial exclusivity. However, the most prevalent mutations were those present in both. Though some parts of the genome are more variable than others but there was clear difference between incidence and prevalence. Non-structural protein 3 (NSP3) with 68 variants had a total of only 105 incidences whereas Spike protein had 346 incidences with just 66 variants. Amongst the Deleterious variants, NSP3 had the highest incidence of 25 followed by NSP2 (16), ORF3a (14) and N (14). Spike protein had just 7 Deleterious variants out of 66., Conclusion: Deceased patients have more Deleterious than Neutral variants as compared to the asymptomatic ones. Further, it appears that the Deleterious variants which decrease protein stability are more significant in pathogenicity of SARS-CoV-2., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Mutational status of SARS-CoV-2 genomes from India along with their impact on proteins was ascertained through multiple tools including MEGA, Genome Detective, SIFT, PROVEAN and ws-SNPs&GO. Excluding gaps and ambiguous sequences, 493 variable sites (152 parsimony informative and 341 singleton) were observed. NSP3 had the highest incidence of 101 sites followed by S protein (74), NSP12b (43) and ORF3a (31). Average mutations per sample for males and females was 2.56 and 2.88 respectively. Non-uniform geographical distribution of mutations suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 Neutral and 83 Disease) affecting amino acid sequence. NSP13 has a maximum of 14 Disease variants followed by S protein and ORF3a with 13 each. Disease mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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&#95;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&#95;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., (© 2021 Laskar and Ali.)

In the era of 2019 the most dangerous disease that have affected more than 200 countries is Covid-19 (i.e. corona virus disease 2019) spread by the virus (i.e. novel coronavirus) which is transmitted from susceptible person to survivors in his surroundings. Such an epidemicity occurs first time in the world and number of cases are in excess of normal expectancy for the different areas that's why it is not easy to overcome this pandemic circumstances immediately. However, it is a challenge to develop anti-virus drugs for the suspected patients at global level. The scientists are interested in detailed experiments on Chloroquine (CQ) and Hydroxychloroquine (HCQ) as one of the unique substance used in the manufacturing for an anti virus drugs. For instance the Hydroxychloroquine conjugated molecular structure became an interesting chemical by the scientist. The significance of both substances can be examine by the number of publications which are leading us to introduce an effective treatment. In this paper, we are interested to discussed physcio-chemical properties of Hydroxychloroquine structure and computational work for the specific topological descriptors named as the F-co-index, first Zagreb co-index and first multiplicative Zagreb co-index, second Zagreb co-index and second multiplicative Zagreb co-index. [ABSTRACT FROM AUTHOR]

The newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARSCoV- 2) has steered concerns across the world due to the possession of a large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in spike (S) protein alone. The viral infectivity is determined mainly by the ability of S protein Receptor Binding Domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARSCoV- 2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. This unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants. [ABSTRACT FROM AUTHOR]