Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

Signal Transduction and Targeted Therapy, Год журнала: 2022, Номер 7(1)

Опубликована: Апрель 26, 2022

Abstract The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns variants include possible recombinants, as genome recombination an important evolutionary mechanism for the emergence and re-emergence human viral pathogens. In this study, we identified diverse events between two major subvariants (BA.1 BA.2) other concern (VOCs) interest (VOIs), suggesting that co-infection subsequent play roles in ongoing evolution SARS-CoV-2. Through scanning high-quality completed spike gene sequences, 18 core mutations BA.1 (frequency >99%) 27 BA.2 (nine than BA.1) were identified, which 15 are specific to Omicron. share nine common amino acid (three protein with most VOCs, a origin from these VOCs. There three Alpha-related BA.2, phylogenetically closer Alpha Revertant found some dominant >95%) BA.1. Most notably, multiple characteristic Delta have been also “Deltacron”-like Variants isolated since November 11, 2021 South Africa, implies occurring Monitoring evolving SARS-CoV-2 genomes especially critically recognition abrupt changes attributes including its epitopes may call vaccine modifications.

Язык: Английский

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Evolutionary dynamics of SARS‐CoV‐2 nucleocapsid protein and its consequences

Journal of Medical Virology, Год журнала: 2020, Номер 93(4), С. 2177 - 2195

Опубликована: Окт. 23, 2020

Abstract The emerged novel coronavirus severe acute respiratory syndrome 2 (SARS‐CoV‐2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis, containment. Here, we explored 61,485 sequences nucleocapsid (N) protein, potent diagnostic prophylactic target, identifying mutations to review their roles in real‐time polymerase chain reaction based diagnosis observe consequent impacts. Compared Wuhan reference strain, total 1034 unique nucleotide were identified mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including 3′‐end mismatch primer‐pair 11 well‐characterized sets. Noteworthily, CDC (USA) recommended N2 set contained lower than other Moreover, 684 amino acid (aa) substitutions located across 317 (75.66% aa) positions 82, 21, 83 those RNA N‐terminal domain (NTD), SR‐rich region, C‐terminal dimerization domain, respectively. in‐frame deletions, mostly ( 10) within highly flexible linker revealed, rest was NTD region. Furthermore, predicted possible consequence high‐frequency (≥20) deletions on tertiary structure N protein. Remarkably, observed high frequency (67.94% mutated sequences) co‐occuring (R203K G204R) destabilized decreased overall structural flexibility. protein SARS‐CoV‐2 comprises average 1.2 per strain compared 4.4 0.4 Middle East syndrome‐related SARS‐CoV, Despite being proposed as alternative target spike vaccine therapeutics, ongoing evolution may challenge endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required tracing interventions.

Язык: Английский

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V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity

Journal of Virology, Год журнала: 2021, Номер 95(16)

Опубликована: Июнь 13, 2021

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused the pandemic of COVID-19. The origin SARS-CoV-2 was associated with zoonotic infections.

Язык: Английский

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Assessing and controlling infection risk with Wells-Riley model and spatial flow impact factor (SFIF)

Sustainable Cities and Society, Год журнала: 2021, Номер 67, С. 102719 - 102719

Опубликована: Янв. 18, 2021

Язык: Английский

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V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2020, Номер unknown

Опубликована: Март 17, 2020

The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. SARS-CoV-2 spike protein receptor-binding domain (RBD) the critical determinant viral tropism and infectivity. To investigate whether naturally occurring mutations in RBD have altered receptor binding affinity infectivity, firstly we analyzed silico dynamics between mutated RBDs human ACE2 receptor. Among 1609 genomes strains isolated during early transmission phase, 32 non-synonymous mutants were identified found clustered into nine mutant types under high positive selection pressure. Applying molecular simulations, three (V367F, W436R, N354D/D364Y) displayed higher to ACE2, likely due enhanced structural stabilization beta-sheet scaffold. increased infectivity one (V367F) circulating worldwide was further validated performing receptor-ligand ELISA, surface plasmon resonance, pseudotyped virus assays. Genome phylogenetic analysis V367F showed that most more closely with prototype strain than dual-mutation variants (V367F + D614G), which emerged later formed distinct sub-cluster. provides insights evolutionary trajectory pressure supports continuing surveillance aid development drugs vaccines.

Язык: Английский

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Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Chemical Reviews, Год журнала: 2022, Номер 122(13), С. 11287 - 11368

Опубликована: Май 20, 2022

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component combating disease 2019 (COVID-19) due to their low cost, efficiency, fact that they are free from safety ethical constraints. Additionally, mechanism governs global transmission SARS-CoV-2 cannot be revealed individual experiments was discovered by integrating genotyping massive viral sequences, biophysical modeling protein-protein deep mutational data, learning, advanced mathematics. There exists a tsunami literature on molecular modeling, simulations, predictions related developments drugs, vaccines, antibodies, diagnostics. To provide readers with quick update about this literature, we present comprehensive systematic methodology-centered review. Aspects such as biophysics, bioinformatics, cheminformatics, machine mathematics discussed. review will beneficial researchers who looking ways contribute those interested status field.

Язык: Английский

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COVID-19 and urban spaces: A new integrated CFD approach for public health opportunities

Building and Environment, Год журнала: 2021, Номер 204, С. 108131 - 108131

Опубликована: Июль 12, 2021

Язык: Английский

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Prevalence and genetic evolution of porcine reproductive and respiratory syndrome virus in commercial fattening pig farms in China

Porcine Health Management, Год журнала: 2024, Номер 10(1)

Опубликована: Янв. 22, 2024

Abstract Background To investigate the prevalence and evolution of Porcine Reproductive Respiratory Syndrome Virus (PRRSV) at commercial fattening pig farms, a total 1397 clinical samples were collected from single cycle seven farms in five provinces China 2020 to 2021. Results The RT‒PCR results revealed that PRRSV was present on all percentage PRRSV-positive individuals 17.54–53.33%. A 344 partial NSP2 gene sequences 334 complete ORF5 obtained positive samples. statistical showed PRRSV-2 PRRSV-1 only one farm. six subtypes detected, had two or more subtypes. L1.8 (L1C) dominant epidemic strain farms. Sequence analysis different its consistency across varied substantially. amino acid alignment demonstrated there 131 aa discontinuous deletions between strains GP5 mutation mainly concentrated peptide signal region T-cell epitopes. Selection pressure use MLV vaccine no significant episodic diversifying effect PRRSV. Conclusion infection is common China, high. There are multiple China. main circulating detected exhibited substantial differences but similar molecular characteristics. may not be directly related vaccines.

Язык: Английский

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Vision of China’s future urban construction reform: In the perspective of comprehensive prevention and control for multi disasters

Sustainable Cities and Society, Год журнала: 2020, Номер 64, С. 102511 - 102511

Опубликована: Сен. 26, 2020

Язык: Английский

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Social distancing enhanced automated optimal design of physical spaces in the wake of the COVID-19 pandemic

Sustainable Cities and Society, Год журнала: 2021, Номер 68, С. 102791 - 102791

Опубликована: Фев. 21, 2021

Язык: Английский

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