The importance of accessory protein variants in the pathogenicity of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) with an estimated fatality rate of less than 1%. The SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 possess putative functions to manipulate host immune mechanisms. These involve interferons, which appear as a consensus function, immune signaling receptor NLRP3 (NLR family pyrin domain-containing 3) inflammasome, and inflammatory cytokines such as interleukin 1ß (IL-1ß) and are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins were observed across six continents of all complete SARS-CoV-2 proteomes based on the data reported before November 2020. A decreasing order of percentage of unique variations in the accessory proteins was determined as ORF3a > ORF8 > ORF7a > ORF6 > ORF10 > ORF7b across all continents. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. These findings suggest that the wide variations in accessory proteins seem to affect the pathogenicity of SARS-CoV-2.

Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution.

Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least 500 in each SARS-CoV-2 protein, we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frame (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in the ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2.

Molecular phylogeny and missense mutations at envelope proteins across coronaviruses.

Envelope (E) protein is one of the structural viroporins (76-109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the ß-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV-2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.

SARS-CoV2 envelope protein: non-synonymous mutations and its consequences.

In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus domains in 15 (0.414%) genomes among 3617 SARS-CoV2 genomes, analyzed. More precisely, 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contained the missense mutations over the E-protein of SARS-CoV2 genomes. The C-terminus motif DLLV has been to DFLV and YLLV in the proteins from QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.

Missense mutations in SARS-CoV2 genomes from Indian patients.

The genetic diversity of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) in several countries sums up to worldwide genetic diversity. In this present study, variations in terms of missense mutations among the SARS-CoV2 genomes from 128 Indian patients, as of May 2020, are accounted and thereby some key findings with some hypotheses were made. These mutations across various genes of these genomes show wide genetic variations in sequence and rapid evolution of SARS-CoV2 virus. The presence of unique mutations in the studied SARS-CoV2 genomes may led to their attenuation. Few Genes such as ORF6, ORF10 are free from any mutations in the Indian context of 339 genomes observed as of 14th July 2020. Further, E protein contains only one mutation. This may suggest that designing a therapeutic approach against ORF6, ORF10 and E genes may have a beneficial effect in controlling COVID-19 pandemic especially in India.

Molecular conservation and differential mutation on ORF3a gene in Indian SARS-CoV2 genomes.

A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory protein in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty-two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2's virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservation of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2.

Ranking and clustering of Drosophila olfactory receptors using mathematical morphology.

This article introduces an alignment-free clustering method in order to cluster all the 66 DORs sequentially diverse protein sequences. Two different methods are discussed: one is utilizing twenty standard amino acids (without grouping) and another one is using chemical grouping of amino acids (with grouping). Two grayscale images (representing two protein sequences by order pair frequency matrices) are compared to find the similarity index using morphology technique. We could achieve the correlation coefficients of 0.9734 and 0.9403 for without and with grouping methods respectively with the ClustalW result in the ND5 dataset, which are much better than some of the existing alignment-free methods. Based on the similarity index, the 66 DORs are clustered into three classes - Highest, Moderate and Lowest - which are seen to be best fitted for 66 DORs protein sequences. OR83b is the distinguished olfactory receptor expressed in divergent insect population which is substantiated through our investigation.

Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features.

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22-42, aa 79-84, and aa 330-393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.

Spectroscopic Study of a Photoactive Antibacterial Agent: 2,3-Distyrylindole.

Optical properties and fluorescence decay dynamics of a photoactive indole based antibacterial chromophore system, 2,3-distyrylindole (23DSI), were investigated using various spectroscopic characterization techniques. Experimental studies were done by utilizing steady-state UV-vis spectroscopy, steady-state fluorescence spectroscopy, time-resolved fluorescence upconversion spectroscopy, and time-correlated single-photon counting spectroscopy. Our studies show that the 23DSI molecule has a multiphoton absorption property as indicated by two- and three-photon absorption in the both the solution and the solid phases. The ultrafast time-resolved fluorescence upconversion studies show that this molecule undergoes a fast decay process with an average time constant of 34 ps, a single exponential decay, and an average fluorescence lifetime of 1 ns. The compound 23DSI did not show any signs of singlet oxygen production. The density functional theory (DFT) calculations showed that the 23DSI molecule has conjugated electron densities that are responsible for multiphoton absorption. The chlorine-substituted styryl groups, attached to the central indole ring facilitate the excellent electron delocalization within the molecule. This optimal electron delocalization, combined with the good electron conjugation in the 23DSI molecule is important for efficient multiphoton absorption and is in excellent agreement with experimental observations. Both the optical spectrum and emission spectrum using DFT calculations are also surprisingly well matched with the experimentally measured UV-vis spectrum and the emission spectrum, respectively. Combined experimental and theoretical studies suggest that excited electrons initially relax to the singlet state (S1) by internal conversion (IC) and subsequently relax back to their ground state by emitting absorbed energy as fluorescence emission. The outstanding multiphoton absorption capabilities of this 23DSI molecule support its potential application in both biological imaging and photodynamic inactivation (PDI).

Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane.

Graphane functionalized with hydroxyl groups is shown to rapidly conduct protons under anhydrous conditions through a contiguous network of hydrogen bonds. Density functional theory calculations predict remarkably low barriers to diffusion of protons along a 1D chain of surface hydroxyls. Diffusion is controlled by the local rotation of hydroxyl groups, a mechanism that is very different from that found in 1D water wires in confined nanopores or in bulk water. The proton mean square displacement in the 1D chain was observed to follow Fickian diffusion rather than the expected single-file mobility. A charge analysis reveals that the charge on the proton is essentially equally shared by all hydrogens bound to oxygens, effectively delocalizing the proton.

Publisher's Note: Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane [Phys. Rev. Lett. 118, 186101 (2017)].

This corrects the article DOI: 10.1103/PhysRevLett.118.186101.

In Situ Observation of Initial Stage in Dielectric Growth and Deposition of Ultrahigh Nucleation Density Dielectric on Two-Dimensional Surfaces.

Several proposed beyond-CMOS devices based on two-dimensional (2D) heterostructures require the deposition of thin dielectrics between 2D layers. However, the direct deposition of dielectrics on 2D materials is challenging due to their inert surface chemistry. To deposit high-quality, thin dielectrics on 2D materials, a flat lying titanyl phthalocyanine (TiOPc) monolayer, deposited via the molecular beam epitaxy, was employed to create a seed layer for atomic layer deposition (ALD) on 2D materials, and the initial stage of growth was probed using in situ STM. ALD pulses of trimethyl aluminum (TMA) and H2O resulted in the uniform deposition of AlOx on the TiOPc/HOPG. The uniformity of the dielectric is consistent with DFT calculations showing multiple reaction sites are available on the TiOPc molecule for reaction with TMA. Capacitors prepared with 50 cycles of AlOx on TiOPc/graphene display a capacitance greater than 1000 nF/cm(2), and dual-gated devices have current densities of 10(-7)A/cm(2) with 40 cycles.

Plasmon assisted synthesis of TiN-supported single-atom nickel catalysts.

We report the deposition of single atom nickel catalyst on refractory plasmonic titanium nitride (TiN) nanomaterials supports using the wet synthesis method under visible light irradiation. TiN nanoparticles efficiently absorb visible light to generate photoexcited electrons and holes. Photoexcited electrons reduce nickel precursor to deposit Ni atoms on TiN nanoparticles' surface. The generated hot holes are scavenged by the methanol. We studied the Ni deposition on TiN nanoparticles by varying light intensity, light exposure time, and metal precursor concentration. These studies confirmed the photodeposition method is driven by hot electrons and helped us to find optimum synthesis conditions for single atoms deposition. We characterized the nanocatalysts using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), energy dispersive X-ray spectroscopy (EDX), and X-ray photoelectron spectroscopy (XPS). We used density functional theory (DFT) calculations to predict favorable deposition sites and aggregation energy of Ni atoms on TiN. Surface defect sites of TiN are most favorable for single nickel atoms depositions. Interestingly, the oxygen sites on native surface oxide layer of TiN also exhibit strong binding with the single Ni atoms. Plasmon enhanced synthesis method can facilitate photodeposition of single atom catalysts on a wide class of metallic supports with plasmonic properties.

Chemical characterizations of neurotransmission receptors of human and plant to unfold the evolutionary relationships among them.

Vertebrates have very well defined nervous systems. A group of researchers hypothesize that plant also has an alternative sort of sensitive nervous system. They find a close relationship of the neurotransmission mechanism of animal with that of the plant and suspect a close relationship in amino acid transport mechanism among both the organisms. Although the protein structure is conserved more than molecular sequences, but the 3D structure of protein is largely influenced by the amino acid residues in the interior part of it. The constituents of a primary protein sequence have a variety of biochemical information which control the structure, function and stability of the protein. Hence, in this present study it is tried for characterization and comparison of neurotransmission receptors associated with human and plant to unfold the evolutionary relationships among them in bio-molecular level based on the chemical properties of the amino acids. The protein sequences of ionotropic glutamate receptor and GABA receptor of human (from vertebrate) and Arabidopsis thaliana (from plant) are considered as datasets. The 20 standard amino acids are classified into 8 chemical groups and are identified by specific numeric values. Alignment-based methods are used to identify the identical and similar amino acids among the aligned sequences.The common pattern finding procedure finds some conserved regions in the receptor protein sequences of both the species. The proximity between the protein sequences are calculated based on the distribution of each chemical group (in percentage) in them and phylogenetic trees are constructed to show the evolutionary relationships of neurotransmission receptors of both the species. The conventional multiple sequence alignment (MSA) method is also applied on the datasets and the results are compared. The analysis is further extended to structural level to understand the extent to which the animal and plant proteins are similar.

Reduced protein sequence patterns in identifying key structural elements of dissimilatory sulfite reductase homologs.

Methanogenic archaea carry homologs of dissimilatory sulfite reductase (Dsr), called Dsr Like proteins (DsrLP). Dsr reduces sulfite to sulfide, a key step in an Earth's ancient metabolic process called dissimilatory sulfate reduction. The DsrLPs do not function as Dsr, and a computational approach is needed to develop hypotheses for guiding wet bench investigations on DsrLP's function. To make the computational analysis process efficient, the DsrLP amino acid sequences were transformed using only eight alphabets functionally representing twenty amino acids. The resultant reduced amino acid sequences were analyzed to identify conserved signature patterns in DsrLPs. Many of these patterns mapped on critical structural elements of Dsr and some were associated tightly with particular DsrLP groups. A search into the UniProtKB database identified several proteins carrying DsrLP's signature patterns; cysteine desulfurase, nucleosidase, and uroporphyrinogen III methylase were such matches. These outcomes provided clues to the functions of DsrLPs and highlighted the utility of the computational approach used.

Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function.

The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made targeting the COVID-19 pandemic a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in lung tissue. Mutations and co-occurring mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, we highlight 128 single mutations and 35 co-occurring mutations in the unique SARS-CoV-2 ORF10 variants. The possible predicted effects of these mutations and co-occurring mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-occurring mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.

Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin.

Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.

An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2.

Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs.

Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence" hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.