COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest.
COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest.
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DOI：
10.7554/elife.63409
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发表时间：
2021-02-23
期刊：
影响因子：
7.7
通讯作者：
Deverman BE
中科院分区：
文献类型：
--
作者：
Chen AT;Altschuler K;Zhan SH;Chan YA;Deverman BE
COVID-19 CG (covidcg.org) 是一个开放资源，用于使用 GISAID 数据库上的病毒基因组跟踪 SARS-CoV-2 单核苷酸变异 (SNV)、谱系和进化枝，同时按位置、日期、基因和感兴趣的突变进行过滤。 COVID-19 CG 为 SARS-CoV-2 传播、进化、诊断、治疗、疫苗和干预跟踪项目提供了大量的时间、劳动力和成本节省。在这里，我们描述了案例研究，其中用户可以询问（1）不同地理区域的 SARS-CoV-2 刺突受体结合域（RBD）中的 SNV，为治疗方法的设计和测试提供信息；（2）可能影响常用诊断引物敏感性的 SNV；以及（3）2020 年澳大利亚出现的含有 S477N RBD 突变的显性谱系。 为了加速 COVID-19 的工作，COVID-19 CG 将通过新功能进行升级，以便用户随着病毒在整个大流行期间的演变以及对治疗和公共卫生干预措施的响应而快速查明突变。导致 2019 年冠状病毒病 (COVID-19) 的病毒传播速度更快的变种的发现引起了人们的警惕。这些新变体是病毒遗传密码发生变化（称为突变）的结果。病毒每次繁殖时都可能发生随机突变。尽管大多数突变不会带来任何有意义的变化，但有些突变可以改变病毒的特征，例如帮助病毒更容易传播、重新感染以前感染过 COVID-19 的人，或降低对治疗或疫苗的敏感性。科学家需要尽快了解病毒中导致治疗或疫苗效果降低的突变，以便他们能够调整大流行应对措施。因此，追踪这些基因变化至关重要。但个别科学家或公共卫生机构可能没有人员、时间或计算机资源来从不断增加的可用遗传数据中提取可用信息。由 Chen 等人创建的免费在线工具。可能有助于科学家和公共卫生官员更轻松地追踪病毒的变化。 COVID-19 CoV 遗传学工具 (COVID-19 CG) 可以快速提供特定时期内某个地区存在哪些病毒突变的信息。它通过处理从全球数十万 COVID-19 患者收集的病毒遗传物质中发现的突变数据来实现这一点，这些数据托管在现有的在线数据库中。 COVID-19 CG 工具提供可定制的交互式数据可视化。 100 多个国家/地区的数千名科学家、公共卫生机构以及 COVID-19 疫苗和治疗开发商已经在使用 COVID-19 CG 工具来查找其所在地区最常见的突变并将其用于研究。他们可以利用这些信息来开发更有效的疫苗或治疗方法。陈等人。随着更多信息的出现，计划更新和改进该工具，以帮助推进全球努力结束 COVID-19 大流行。
COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to projects on SARS-CoV-2 transmission, evolution, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. To accelerate COVID-19 efforts, COVID-19 CG will be upgraded with new features for users to rapidly pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions. The discovery of faster spreading variants of the virus that causes coronavirus disease 2019 (COVID-19) has raised alarm. These new variants are the result of changes (called mutations) in the virus’ genetic code. Random mutations can occur each time a virus multiplies. Although most mutations do not introduce any meaningful changes, some can alter the characteristics of the virus, for instance, helping the virus to spread more easily, reinfecting people who have had COVID-19 before, or reducing the sensitivity to treatments or vaccines. Scientists need to know about mutations in the virus that make treatments or vaccines less effective as soon as possible, so they can adjust their pandemic response. As a result, tracking these genetic changes is essential. But individual scientists or public health agencies may not have the staff, time or computer resources to extract usable information from the growing amount of genetic data available. A free online tool created by Chen et al. may help scientists and public health officials to track changes to the virus more easily. The COVID-19 CoV Genetics tool (COVID-19 CG) can quickly provide information on which virus mutations are present in an area during a specific period. It does this by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in an existing online database. The COVID-19 CG tool presents customizable, interactive visualizations of the data. Thousands of scientists, public health agencies, and COVID-19 vaccine and treatment developers in over 100 countries are already using the COVID-19 CG tool to find the most common mutations in their area and use it for research. They can use this information to develop more effective vaccines or treatments. Chen et al. plan to update and improve the tool as more information becomes available to help advance global efforts to end the COVID-19 pandemic.