Direct RNA sequencing and early evolution of SARS-CoV-2

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

Опубликована: Март 7, 2020

Abstract Fundamental aspects of SARS-CoV-2 biology remain to be described, having the potential provide insight response effort for this high-priority pathogen. Here we describe first native RNA sequence SARS-CoV-2, detailing coronaviral transcriptome and epitranscriptome, share these data publicly. A data-driven inference viral genetic features evolutionary rate is also made. The rapid sharing information throughout pandemic represents an inflection point public health genomic epidemiology, providing early insights into evolution emerging

Язык: Английский

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The SARS-CoV-2 subgenome landscape and its novel regulatory features

Molecular Cell, Год журнала: 2021, Номер 81(10), С. 2135 - 2147.e5

Опубликована: Март 6, 2021

Язык: Английский

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V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

Bioinformatics, Год журнала: 2021, Номер 37(12), С. 1673 - 1680

Опубликована: Янв. 8, 2021

High-throughput sequencing technologies are used increasingly not only in viral genomics research but also clinical surveillance and diagnostics. These facilitate the assessment of genetic diversity intra-host virus populations, which affects transmission, virulence pathogenesis infections. However, there two major challenges analysing diversity. First, amplification errors confound identification true biological variants, second, large data volumes represent computational limitations.To support high-throughput studies, we developed V-pipe, a bioinformatics pipeline combining various state-of-the-art statistical models tools for automated end-to-end analyses raw reads. V-pipe supports quality control, read mapping alignment, low-frequency mutation calling, inference haplotypes. For generating high-quality alignments, novel method, called ngshmmalign, based on profile hidden Markov tailored to small highly diverse genomes. includes benchmarking functionality providing standardized environment comparative evaluations different configurations. We demonstrate this capability by assessing impact three aligners (Bowtie 2, BWA MEM, ngshmmalign) variant callers (LoFreq, ShoRAH) performance calling single-nucleotide variants populations. configurations is implemented modular fashion adaptations continuously changing technology landscape.V-pipe freely available at https://github.com/cbg-ethz/V-pipe.Supplementary Bioinformatics online.

Язык: Английский

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The epigenetic implication in coronavirus infection and therapy

Clinical Epigenetics, Год журнала: 2020, Номер 12(1)

Опубликована: Окт. 21, 2020

Abstract Epigenetics is a relatively new field of science that studies the genetic and non-genetic aspects related to heritable phenotypic changes, frequently caused by environmental metabolic factors. In host, epigenetic machinery can regulate gene expression through series reversible modifications, such as histone methylation acetylation, DNA/RNA methylation, chromatin remodeling, non-coding RNAs. The coronavirus disease 19 (COVID-19) highly transmittable pathogenic viral infection. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China, spread worldwide, causes it. COVID-19 severity consequences largely depend on patient age health status. this review, we will summarize comparatively analyze how viruses host epigenome. Mainly, be focusing respiratory RNA virus infections coronaviruses. context, alterations might play an essential role onset complications. Although many therapeutic approaches are under study, more research urgently needed identify effective vaccine or safer chemotherapeutic drugs, including cope with outbreak develop pre- post-exposure prophylaxis against COVID-19.

Язык: Английский

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tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

RNA, Год журнала: 2019, Номер 25(10), С. 1229 - 1241

Опубликована: Июль 2, 2019

Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length known to affect nuclear export, stability, translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) assessment. These methods identify genes connected tail measurements indirectly by short-read alignment genetic 3′-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific sequencing containing entire tail. However, assessing through base-calling has so far not been possible due inability resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr , an R package estimate on long-read data. operates unaligned, base-called It measures from both native DNA sequencing, which makes studies cDNA approaches first time. We assess ’s performance across different lengths, demonstrating versatile tool providing estimates wide range conditions.

Язык: Английский

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