We present an updated version of our automated computational pipeline, Infection Pathogen Detector IPD 2.0 with a SARS-CoV-2 module, to perform genomic analysis to understand the pathogenesis and virulence of the virus. Analysing the currently available 208911 SARS-CoV2 genome sequences (as accessed on 28 Dec 2020), we generate an extensive database of sample-wise variants and clade annotation, which forms the core of the SARS-CoV-2 analysis module of the analysis pipeline. A comparative account of lineage specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil along with data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Thus, persistence of pandemic may lead to emergence of newer regional strains with improved fitness. IPD 2.0 also adopts the recent dynamic clade nomenclature and shows improvement in accuracy of clade assignment, processing time and portability, to its predecessor and thus could be a vital tool to help facilitate genomic surveillance in a population to identify variants involved in breakthrough infections.

中文翻译：

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来自20万COVID-19患者的SARS-CoV-2基因组的不断发展的见解

我们提供了带有SARS-CoV-2模块的自动化计算管道Infection Pathogen Detector IPD 2.0的更新版本，以进行基因组分析以了解病毒的发病机理和毒力。分析当前可用的208911 SARS-CoV2基因组序列（于2020年12月28日访问），我们生成了一个广泛的样本方式变体和进化枝注释数据库，该数据库构成了分析管道的SARS-CoV-2分析模块的核心。在英国，南非和巴西出现的新型SARS-CoV-2菌株中，对谱系特异性突变的比较描述以及印度报告的数据确定了重叠和谱系特异性获得性突变，表明其反复趋同和适应性进化。从而，大流行的持续性可能导致出现新的区域性毒株并提高适应性。IPD 2.0还采用了最新的动态进化枝命名法，显示出进化枝进化的准确性，处理时间和可移植性的提高，因此，IPD 2.0可能是帮助促进人群基因组监测以鉴定涉及突破性感染的变异体的重要工具。