新冠病毒分析
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https://www.medrxiv.org/content/10.1101/2020.03.30.20048108v3
中国 美国等CDC用的试剂盒对比 -
https://sci-hub.st/10.3390/cimb43020061
Next-Generation Sequencing (NGS) in COVID-19: A Tool for
SARS-CoV-2 Diagnosis, Monitoring New Strains and
Phylodynamic Modeling in Molecular Epidemiology
1.文章提到了两种新冠的检测方法
Molecular-Based Testing Methods 即 RT-PCR
Serological and Immunological-Based Testing Methods
抗体只能检测这个之前有没有得过新冠 而且不是很准确 因为有的人就算被感染过也可能没有抗体
2.NGS检测病原的优势
一个是不用培养 而且不要做针对性的假设 一股脑全给测出来 但是这种方法的成本肯定没有panel低
Using NGS technology for the diagnosis of infectious diseases offers an unbiased approach detecting pathogens that does not rely on culturing or the need for clinical hypotheses.
While standard testing procedures require clinicians to identify possible explanations for a patient’s symptoms and employ tests aimed at those specific pathogens, NGS testing can reveal the presence of all types of microorganisms present in a sample, including bacteria,viruses, fungi, and parasites.
另外一个优势就是病人可能同时 感染了多种病毒 例如新冠 流感病毒 可能同时感染 这对后期的治疗 病因都有影响 这个优势其实就是上面说的第二点 NGS 可以同时测出来多种病原 -
https://gitlab.com/uit-sfb/cbf
https://covid19.sfb.uit.no/
新冠的数据库 包括其源码
他们开发了一个CBF框架 可以管理这些数据 -
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
https://github.com/Psy-Fer/interARTIC/ -
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
https://www.frontiersin.org/articles/10.3389/fgene.2021.711437/full
https://github.com/replikation/poreCov -
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400123/
Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA
Mutation frequency was calculated by taking the ratio of the number of total nucleotide mutations and the number of genome sequences in each week. -
