Spatial Transcriptomics and Single Cell-RNASeq Reveals Cellular Heterogeneity of SARS-CoV-2 in Lung Tissues and Global Mutational Patterns in COVID-19 Patients.

RNA viruses have high mutation frequency, quick generation periods and vast population numbers, which promote fast evolution and host environment adaptation. We integrated scRNA-seq and spatial transcriptomics to profile immune cells and viral gene expression in COVID-19. Cell types and interactions were identified using Seurat-based tools.

Artificial intelligence in metalloprotein binding site prediction: A systematic review bridging bioinformatics and biotechnology.

Metalloproteins, accounting for nearly half of all known proteins, are fundamental to biological processes and applications, including catalysis, electron transport and pharmaceutical engineering. Accurately predicting metal-binding sites is critical for elucidating molecular interactions and advancing innovations in the biotechnology and pharmaceutical industries. Traditional sequence- and structure-based prediction methods often struggle with the complexity and diversity of metalloprotein datasets.

Intersecting SARS-CoV-2 spike mutations and global vaccine efficacy against COVID-19.

In line with encountering the world with the emergence of vaccine-resistance variants of SARS-CoV-2, 15,669,529 samples that received COVID-19 vaccines until April 2023 were investigated as two doses in the first phase and booster vaccinations in the second phase. The analysis shows that D614G and P681 mutations occurred in both phases. The E484 and Y655 mutations significantly emerged during the second phase.

The Geographical Distribution of Global Biobanks.

This study aimed to comprehensively review the global biobanks to visualize their geographical distribution. The protocol for this review consisted of the following steps: i. Developing a search strategy to identify biobanks from each continent, ii.

Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new emerging coronavirus that caused coronavirus disease 2019 (COVID-19). Whole-genome tracking of SARS-CoV-2 enhanced our understanding of the mechanism of the disease, control, and prevention of COVID-19.

Methods: we analyzed 3368 SARS-CoV-2 protein sequences from Iran and compared them with 15.

Global landscape of SARS-CoV-2 mutations and conserved regions.

Background: At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths.

Mutations in SARS-CoV-2 structural proteins: a global analysis.

Background: Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally.

Methods: We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022.

analysis of the substitution mutations and evolutionary trends of the SARS-CoV-2 structural proteins in Asia.

Objectives: To address a highly mutable pathogen, mutations must be evaluated. SARS-CoV-2 involves changing infectivity, mortality, and treatment and vaccination susceptibility resulting from mutations.

Materials And Methods: We investigated the Asian and worldwide samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the announcement of the new coronavirus 2019 (COVID-19) up to January 2022.

SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents.

Objective: Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it.

SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents.

Unlabelled: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the . This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus.

The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends.

The high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown.

Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods.

Background: Moonlighting proteins (MPs) are a subclass of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Identification of unknown cellular processes, understanding novel protein mechanisms, improving the prediction of protein functions, and gaining information about protein evolution are the main reasons to study MPs. They also play an important role in disease pathways and drug-target discovery.