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== 2019-nCov == * https://www.gisaid.org/ * https://db.cngb.org/datamart/disease/DATAdis19/ * https://www.ncbi.nlm.nih.gov/sars-cov-2/ * [https://www.jax.org/mgi-coronavirus-info Mouse Models for Coronavirus Research] * [https://www.chictr.org.cn/searchproj.aspx 中国临床试验注册中心] Find all other Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences at: https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ <br> === 参考序列 === 第一个参考序列为 NC_045512.2,2020年1月18日公布出来的第一株序列,来自武汉采集样本,原始 GenBank accession number 为:MN908947,refseq 库 accession number 为 NC_045512.2,长度 29903bp,原始数据为 SRR10971381。 参考序列网址:https://www.ncbi.nlm.nih.gov/nuccore/NC_045512 文章:https://www.nature.com/articles/s41586-020-2008-3.pdf SARS 参考基因组 accession number 为 NC_004718.3,物种分类 ID 为 694009。https://www.ncbi.nlm.nih.gov/nuccore/NC_004718.3 蝙蝠分离株参考基因组,命名为 batSARS,参考序列株为MG772933 https://www.ncbi.nlm.nih.gov/nuccore/MG772933 <source lang=bash> $ wget https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz # 2019-nCov $ efetch -db nuccore -format fasta -id NC_045512 > 2019nCov.fa # SARS-nCov $ efetch -db nuccore -format fasta -id NC004718 > SARS.fa # SARS-like $ efetch -db nuccore -format fasta -id KT444582 > SARS-like-WIV16.fa # batSARS $ efetch -db nuccore -format fasta -id MG772933 > batSARS.fa $ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets' $ chmod +x datasets $ curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/dataformat' $ curl -o datasets.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/datasets.exe" </source> efetch guide: https://dataguide.nlm.nih.gov/edirect/efetch.html [https://dataguide.nlm.nih.gov/eutilities/utilities.html#efetch cmd parameters] <br> === 命名和分型 === WHO 新冠病毒变种株命名规则: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ 目前使用较多的 Pangolin 分型法:https://cov-lineages.org/pangolin.html “Phylogenetic Assignment of Named Global Outbreak Lineages(以系统发育归类命名全球暴发分支)”。研究基于GISAID 数据库中 SARS⁃CoV⁃2 基因组序列的系统发育提出了一个合理和动态的命名,即使用一个系统发育框架来识别当下活跃的病毒分支。 以A,B为主分支,最近比较火的,英国发现的变异病毒“B1.1.7”,就是基于这种分型方法。可以在线分析数据 https://pangolin.cog-uk.io/ 把 fasta 文件拖拽上去即可。 '''Examples:''' <source lang=bash> >>> B.1.617.2 Predominantly India lineage with several spike mutations (WHO: Delta) B.1.1.529 South Africa and Botswana lineage (WHO: Omicron) ------ BA.1 Alias of B.1.1.529.1, named at 2021/12/07, BJCDC@2022-01-07 BA.1.1 Alias of, BJCDC@2022-01-01 ~ 2022-03 BA.1.1.1 Alias of, BJCDC@2022-01-07 BA.2 Alias of, BJCDC@2022-01-12 ~ 04-09 BA.2.2 Alias of, BJCDC@2022-08-29 BA.2.2.1 Alias of B.1.1.529.2.2.1, China lineage, named at 2022/06/13, BJCDC@2022-05 BA.2.3.7 BA.2.76 Alias of B.1.1.529.2.76, mainly found in India and USA, named at 2022/07/02 ------ BA.2.75 Alias of B.1.1.529.2.75, mainly found in India, named at 2022/06/24 CH.1.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1, defined by S:L452R, named at 2022/10/13 BA.5.2 Alias of B.1.1.529.5.2, mainly found in South Africa, England and USA, named at 2022/05/25 XBB Alias of B.1.1.529.2.75 (BA.2.75 or BJ.1) with breakpoint in S1, found in USA and Singapore, named at 2022/09/17 XBB.1 Alias of B.1.1.529.2.75.1 (XBB with S:G252V), named at 2022/10/03 XBB.1.1 Alias of B.1.1.529.2.75.1.1, (ORF1a:P309L), named at 2022/10/15 XBB.1.2 Alias of B.1.1.529.2.75.1.2, (S:S640F), named at 2022/10/17 XBB.1.3 Alias of B.1.1.529.2.75.1.3, (S:A484T), named at 2022/10/23 XBB.1.4 Alias of B.1.1.529.2.75.1.4, (S:T883I), named at 2022/11/06 XBB.1.5 Alias of B.1.1.529.2.75.1.5, (S:F486P), found in USA, named at 2022/11/08 XBB.1.6 Alias of B.1.1.529.2.75.1.6, (S:L216F, S:H146K), named at 2022/12/16 XBB.1.7 Alias of B.1.1.529.2.75.1.7, (S:V608I), named at 2022/12/22 XBF Alias of B.1.1.529.5.2.3 (BA.5.2.3 or CJ.1), mainly found in Australia, , named at 2022/11/03 BF.7 Alias of B.1.1.529.5.2.1.7, mainly found in Belgium, England and Denmark, named at 2022/05/25, named at 2022/07/16 BF.7.13 Alias of B.1.1.529.5.2.1.7.13, Belgium, ORF1a:H388Y, ORF1a:H1160Y, named at 2022/11/03 BF.7.13.1 Alias of B.1.1.529.5.2.1.7.13.1, Europe, S:T430I, S:P681S, named at 2022/11/03 BQ.1 Alias of B.1.1.529.5.3.1.1.1.1.1, Nigeria lineage, named at 2022/09/02 BQ.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1, found globally, defining mutations ORF1b:N1191S and S:R346T, named at 2022/09/09 BQ.1.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.1, Europe, ORF1b:V1639A, named at 2022/10/15 BQ.1.1.17 Alias of B.1.1.529.5.3.1.1.1.1.1.1.17, France, ORF1a:S2273F, named at 2022/10/31 BQ.1.1.19 Alias of B.1.1.529.5.3.1.1.1.1.1.1.19, England, N:Q380H, named at 2022/10/31 </source> 按照 WHO 最新命名规则: * Alpha (B.1.1.7),2020/9 月发现于英国,https://www.ncbi.nlm.nih.gov/nuccore/MZ310552 * Beta (B.1.351),2020/5 月发现于南非, https://www.ncbi.nlm.nih.gov/nuccore/MZ202314 * Delta (B.1.617.2),2020/10 发现于印度,https://www.ncbi.nlm.nih.gov/nuccore/MZ318159 * Gamma (P.1),2020/11 月发现于巴西,https://www.ncbi.nlm.nih.gov/nuccore/MZ169911 * Zeta (P.2),2020/11 月发现于巴西,https://www.ncbi.nlm.nih.gov/nuccore/MZ169912 * Kappa (B.1.617.1),2020/10 发现于印度,https://www.ncbi.nlm.nih.gov/nuccore/MZ310580 * Omicron,'''B.1.1.529''' (BA.1),2021/11/24 南非报告,https://www.ncbi.nlm.nih.gov/nuccore/ [https://www.who.int/zh/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern WHO 提醒] 第一例已知 B.1.1.529 确诊感染来自2021年11月9日采集的一份样本 * BQ.1.1 (BA.5.3.1.1.1.1.1.1),2022/9 尼日尼亚发现, * CH.1.1 (B.1.1.529.2.75.3.4.1.1.1.1),2022/11 香港 <br> === VOC === 监测:https://ngdc.cncb.ac.cn/ncov/ * BA.2.75 与 BA.5 未来的进化趋势 * BA.5 ** BA.5.2 ** BA.5.2.1.7 (BF.7) ** BA.5.3.1.1.1.1.1.1 (BQ.1.1) * XBB (BJ.1/BA.2.75) ** XBB.1.5, 2022/11 CovSpectrum queries to track both lineages already: BA.5: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=12160A%2C9866.%2C27259A&pangoLineage=BA.2*&nucMutations1=22792T%2C22916A%2C23767G&pangoLineage1=BA.2*& BA.4: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=12160A%2C9866.%2C27788T&pangoLineage=BA.2*&nucMutations1=22792T%2C22916A%2C23767G&pangoLineage1=BA.2*& * https://cov-lineages.org/lineage_list.html * https://github.com/cov-lineages/pango-designation/issues * [https://www.ncbi.nlm.nih.gov/books/NBK570580/ Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19)] <br> === Reference === * [http://wiki.jackslab.org/FV7 Fields Virology 7th Edtion Vol 3 RNA Virus] <br>
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