Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice DOI Creative Commons
Zhen Zhang, Qianyun Liu, Yingming Sun

и другие.

Emerging Microbes & Infections, Год журнала: 2021, Номер 10(1), С. 1626 - 1637

Опубликована: Янв. 1, 2021

Coronaviruses (CoVs) can infect a variety of hosts, including humans, livestock and companion animals, pose serious threat to human health the economy. The current COVID-19 pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed millions people. Unfortunately, effective treatments for CoVs infection are still lacking, suggesting importance vaccines. Our previous work showed that CoV nonstuctural protein 14 (nsp14) functions as (guanine-N7)-methyltransferase (N7-MTase), involved in RNA cap formation. Moreover, we found N7-MTase well conserved among different universal target developing antivirals against CoVs. Here, show be an ideal designing live attenuated Using murine hepatitis virus strain A59 (MHV-A59), representative well-studied model coronaviruses, constructed N7-MTase-deficient recombinant MHV D330A Y414A. These two mutants highly mice exhibit similar replication efficiency wild-type (WT) cell culture. Furthermore, single dose immunization or Y414A induce long-term humoral immune responses robust CD4+ CD8+ T responses, provide full protection challenge lethal-dose MHV-A59. Collectively, this study provides strategy design vaccines abolishing viral activity. This approach may apply other viruses encode their own conservative N7-methyltransferase.

Язык: Английский

Structures and functions of coronavirus replication–transcription complexes and their relevance for SARS-CoV-2 drug design DOI Creative Commons
Brandon Malone, Nadya Urakova, Eric J. Snijder

и другие.

Nature Reviews Molecular Cell Biology, Год журнала: 2021, Номер 23(1), С. 21 - 39

Опубликована: Ноя. 25, 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome ~30 kb. They express RNA-dependent polymerase a cohort other replication enzymes supporting factors transcribe replicate their genomes. The proteins performing these essential processes prime antiviral drug targets, but discovery is hindered by our incomplete understanding synthesis processing. In infected cells, the must coordinate viral host produce both mRNAs new Recent research aiming decipher contextualize structures, functions interplay subunits SARS-CoV-2 transcription complex burgeoned. this Review, we discuss recent advancements in molecular basis complexity RNA-synthesizing machinery. Specifically, outline mechanisms regulation translation, transcription. We also composition complexes suitability as targets for therapy. coronaviruses rely on specialized studies have improved transcription, offer therapeutic targets.

Язык: Английский

Процитировано

397

SARS-CoV-2: from its discovery to genome structure, transcription, and replication DOI Creative Commons
Ayslan Castro Brant, Wei Tian, Vladimır Majerčiak

и другие.

Cell & Bioscience, Год журнала: 2021, Номер 11(1)

Опубликована: Июль 19, 2021

Abstract SARS-CoV-2 is an extremely contagious respiratory virus causing adult atypical pneumonia COVID-19 with severe acute syndrome (SARS). has a single-stranded, positive-sense RNA (+RNA) genome of ~ 29.9 kb and exhibits significant genetic shift from different isolates. After entering the susceptible cells expressing both ACE2 TMPRSS2, directly functions as mRNA to translate two polyproteins ORF1a ORF1b region, which are cleaved by viral proteases into sixteen non-structural proteins (nsp1-16) initiate replication transcription. The also encodes four structural (S, E, M N) up six accessory (3a, 6, 7a, 7b, 8, 9b) proteins, but their translation requires newly synthesized individual subgenomic RNAs (sgRNA) in infected cells. Synthesis full-length genomic (gRNA) sgRNAs conducted inside double-membrane vesicles (DMVs) transcription complex (RTC), comprises nsp7, nsp8, nsp9, nsp12, nsp13 short primer. To produce sgRNAs, RTC starts synthesis highly structured gRNA 3' end switches template at various regulatory sequence (TRS B ) sites along body probably mediated long-distance RNA–RNA interaction. TRS motif 5' leader L responsible for interaction upstream each ORF skipping between them sgRNAs. Abundance depend on location read-through efficiency . Although more studies needed, unprecedented pandemic taught world painful lesson that invest proactively prepare future emergence other types coronaviruses any possible biological horrors.

Язык: Английский

Процитировано

225

SARS-CoV-2 biology and host interactions DOI
Silvio Steiner, Annika Kratzel, G. Tuba Barut

и другие.

Nature Reviews Microbiology, Год журнала: 2024, Номер 22(4), С. 206 - 225

Опубликована: Янв. 15, 2024

Язык: Английский

Процитировано

92

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli DOI Open Access
Felix Grünberger, Sébastien Ferreira-Cerca, Dina Grohmann

и другие.

RNA, Год журнала: 2021, Номер 28(3), С. 400 - 417

Опубликована: Дек. 14, 2021

High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, full-length transcripts based on the single-molecule platform from Oxford Nanopore Technologies (ONT) was introduced is widely used to sequence eukaryotic viral RNAs. However, experimental approaches implementing this technique prokaryotic transcriptomes remain scarce. Here, we present an bioinformatic workflow ONT RNA-seq bacterial model organism Escherichia coli , which can be applied any microorganism. Our study highlights critical steps library preparation computational analysis compares results gold standards field. Furthermore, comprehensively evaluate applicability advantages different ONT-based protocols, including direct RNA, cDNA, PCR-cDNA. We find that (PCR)-cDNA-seq offers improved yield accuracy compared sequencing. Notably, suitable quantitative measurements readily simultaneous accurate detection transcript 5′ 3′ boundaries, transcriptional units, heterogeneity. In summary, comprehensive study, show nanopore a ready-to-use tool allowing rapid, cost-effective, annotation multiple transcriptomic features. Thereby holds potential become valuable alternative method prokaryotes.

Язык: Английский

Процитировано

73

SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives DOI Creative Commons

Samuel Long

Viruses, Год журнала: 2021, Номер 13(10), С. 1923 - 1923

Опубликована: Сен. 24, 2021

SARS-CoV-2, the etiologic agent at root of ongoing COVID-19 pandemic, harbors a large RNA genome from which tiered ensemble subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation these products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes recent progress on sgRNA identification, characterization, application as viral replication marker. The significance findings potential future research areas interest discussed.

Язык: Английский

Процитировано

60

Role of genomics in combating COVID-19 pandemic DOI

K.A. Saravanan,

Manjit Panigrahi, Harshit Kumar

и другие.

Gene, Год журнала: 2022, Номер 823, С. 146387 - 146387

Опубликована: Март 4, 2022

Язык: Английский

Процитировано

54

Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences DOI Creative Commons
Young Seok Lee, Peter A. C. Wing, Dalia Gala

и другие.

eLife, Год журнала: 2022, Номер 11

Опубликована: Янв. 20, 2022

Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is urgent need to understand stages and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) quantify positive sense RNA genomes 95% detection efficiency, while simultaneously visualising negative genomes, subgenomic RNAs, proteins. Our absolute quantification RNAs factories revealed that SARS-CoV-2 genomic long-lived after entry, suggesting it avoids degradation by cellular nucleases. Moreover, we observed highly variable between cells, only a small cell population displaying high burden RNA. Unexpectedly, B.1.1.7 variant, first identified UK, exhibits significantly slower kinetics than Victoria strain, novel mechanism contributing its higher transmissibility important implications.

Язык: Английский

Процитировано

52

Nanopore sequencing technology and its applications DOI Creative Commons

Peijie Zheng,

Chuntao Zhou,

Yuemin Ding

и другие.

MedComm, Год журнала: 2023, Номер 4(4)

Опубликована: Июль 10, 2023

Abstract Since the development of Sanger sequencing in 1977, technology has played a pivotal role molecular biology research by enabling interpretation biological genetic codes. Today, nanopore is one leading third‐generation technologies. With its long reads, portability, and low cost, widely used various scientific fields including epidemic prevention control, disease diagnosis, animal plant breeding. Despite initial concerns about high error rates, continuous innovation platforms algorithm analysis effectively addressed accuracy. During coronavirus (COVID‐19) pandemic, critical detecting severe acute respiratory syndrome coronavirus‐2 virus genome containing pandemic. However, lack understanding this may limit popularization application. Nanopore poised to become mainstream choice for preventing controlling COVID‐19 future epidemics while creating value other such as oncology botany. This work introduces contributions during pandemic promote public use emerging outbreaks worldwide. We discuss application microbial detection, cancer genomes, genomes summarize strategies improve

Язык: Английский

Процитировано

36

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure DOI Creative Commons
Hugh K. Haddox,

Georg Angehrn,

Luca Sesta

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Abstract RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the type (e.g., A → C , G etc.) and can vary between sites in viral genome. Understanding this variation shed light mutational processes at play, is crucial for quantitative modeling Using millions available full-genome sequences, we estimate rates synonymous all 12 possible nucleotide types examine how much these sites. We find surprisingly level variability several striking patterns: four suddenly increase one two gene boundaries; most strongly depend site’s local sequence context, with up 56-fold differences contexts; consistent previous study, some are lower engaged secondary structure. simple log-linear model features explains ∼15-60% fold-variation sites, depending type; more complex models only modestly improve predictive power out sample. fitness effect each based number times it actually occurs versus expected occur model. identify small regions genome where or noncoding less often than expected, indicative strong purifying selection that independent protein sequence. Overall, work expands our basic understanding SARS-CoV-2’s evolution by characterizing virus’s process individual uncovering patterns arise from unknown mechanisms.

Язык: Английский

Процитировано

2

In vivo structure and dynamics of the SARS-CoV-2 RNA genome DOI Creative Commons
Yan Zhang, Kun Huang, Dejian Xie

и другие.

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Сен. 28, 2021

Abstract The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay comprehensively map the in vivo RNA-RNA interactome genome across viral life cycle. We report canonical alternative structures including 5′-UTR 3′-UTR, frameshifting element (FSE) pseudoknot cyclization both cells virions. provide direct evidence interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, reveal short long distance arches around FSE. More importantly, find that within virions, while undergoes intensive compaction, domains remain stable but with strengthened demarcation local weakened global cyclization. Taken together, our analysis reveals structural basis for regulation replication, transcription translational frameshifting, conformations maintenance organization during whole cycle SARS-CoV-2, anticipate will help better antiviral strategies.

Язык: Английский

Процитировано

53