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sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.
Publication Type: Academic Journal
Source(s): RNA (New York, N.Y.) [RNA] 2022 Mar; Vol. 28 (3), pp. 277-289. Date of Electronic Publication: 2021 Dec 22.
Abstract: Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of...
Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world.
Publication Type: Academic Journal
Source(s): Virus research [Virus Res] 2020 Nov; Vol. 289, pp. 198170. Date of Electronic Publication: 2020 Sep 24.
Abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first identified in Wuhan, China late in 2019. Nine months later (Sept. 23, 2020), the virus has infected > 31.6 million people around the world and caused > 971.000 (3.07 %) fatalities i...
miR-M11 基因编辑对马立克病病毒 体外复制的影响.
Publication Type: Academic Journal
Source(s): Journal of Henan Agricultural Sciences. 2023, Vol. 52 Issue 1, p134-143. 10p.
Abstract: 为探究病毒编码的微小RNA前体基因miR-M11对马立克病病毒 (MDV) 体外复制能力的影响， 以MDV国内分离株HN302为研究对象，利用CRISPR/Cas9系统靶向编辑并敲除位于Mid基因簇的miRM11， 构建1株miR-M11基因编辑缺失毒株HN302ΔM11 (克隆号C58-8-4) 。经过PCR鉴定、测序分析、 间接免疫荧光试验 (IFA) 、实时荧光定量PCR (qPCR) 以及传代稳定性分析，证实HN302编码的miRM11 被精确编辑并从病毒基因组中完全缺失，且未发生回复突变。...
ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids.
Publication Type: Academic Journal
Source(s): GigaScience [Gigascience] 2023 Mar 20; Vol. 12.
Abstract: Background: Genetic recombination is a tremendous source of intrahost diversity in viruses and is critical for their ability to rapidly adapt to new environments or fitness challenges. While viruses are routinely characterized using high-throughput seq...
The genome of the Cauliflower mosaic virus, a plant pararetrovirus, is highly methylated in the nucleus.
Publication Type: Academic Journal
Source(s): FEBS letters [FEBS Lett] 2020 Jun; Vol. 594 (12), pp. 1974-1988.
Abstract: Cytosine methylation is an important defense against invasive DNAs. Here, cytosine methylation profiles of a plant pararetrovirus, Cauliflower mosaic virus (CaMV), were investigated. Nuclear CaMV DNA is highly methylated throughout the genome including...
RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes.
Publication Type: Academic Journal
Source(s): RNA (New York, N.Y.) [RNA] 2020 Dec; Vol. 26 (12), pp. 1905-1918. Date of Electronic Publication: 2020 Sep 14.
Abstract: Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the mole...
Levels of Influenza A Virus Defective Viral Genomes Determine Pathogenesis in the BALB/c Mouse Model.
Publication Type: Academic Journal
Source(s): Journal of virology [J Virol] 2022 Nov 09; Vol. 96 (21), pp. e0117822. Date of Electronic Publication: 2022 Oct 13.
Abstract: Defective viral genomes (DVGs), which are generated by the viral polymerase in error during RNA replication, can trigger innate immunity and are implicated in altering the clinical outcome of infection. Here, we investigated the impact of DVGs on innat...
A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations.
Publication Type: Academic Journal
Source(s): Microbiology and molecular biology reviews : MMBR [Microbiol Mol Biol Rev] 2022 Sep 21; Vol. 86 (3), pp. e0008621. Date of Electronic Publication: 2022 Jun 23.
Abstract: Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of stand...
Intracellular African swine fever virus DNA remains unmethylated in infected Vero cells.
Publication Type: Academic Journal
Source(s): Epigenomics [Epigenomics] 2018 Mar; Vol. 10 (3), pp. 289-299. Date of Electronic Publication: 2018 Jan 12.
Abstract: Aim: Sequence-specific CpG methylation of eukaryotic promoters is an important epigenetic signal for long-term gene silencing. We have now studied the methylation status of African swine fever virus (ASFV) DNA at various times after infection of Vero c...
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.
Publication Type: Academic Journal
Source(s): GigaScience [Gigascience] 2020 Aug 01; Vol. 9 (8).
Abstract: Background: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation o...