niman Posted February 17, 2020 Report Share Posted February 17, 2020 Beijing has released four full sequences from 2017 Guangxi Pangolins. Closest matches at Genbank are COVID-2019 sequences from human cases in Wuhan, China and United States Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 BetaCoV/pangolin/Guangxi/P5E/2017 Original EPI_ISL_410541 2017 2020-02-17 29806 Manis javanica Asia / China / Guangxi Beijing Institute of Microbiology and Epidemiology Beijing Institute of Microbiology and Epidemiology BetaCoV/pangolin/Guangxi/P5L/2017 Original EPI_ISL_410540 2017 2020-02-17 29806 Manis javanica Asia / China / Guangxi Beijing Institute of Microbiology and Epidemiology Beijing Institute of BetaCoV/pangolin/Guangxi/P1E/2017 Original EPI_ISL_410539 2017 2020-02-17 29801 Manis javanica Asia / China / Guangxi Beijing Institute of Microbiology and Epidemiology Beijing Institute of Microbiology and Epidemiology BetaCoV/pangolin/Guangxi/P4L/2017 Original EPI_ISL_410538 2017 2020-02-17 29806 Manis javanica Asia / China / Guangxi Beijing Institute of Microbiology and Epidemiology Beijing Institute of Microbiology and Epidemiology Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 BetaCoV/pangolin/Guangxi/P4L/2017|EPI_ISL_410538 Select for downloading or viewing reports Description Max Score Total Score Query Cover E value Per. Ident Accession Select seq MN997409.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-AZ1/2020, complete genome 34188 34188 99% 0.0 85.47% MN997409.1 Select seq MN975262.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV_HKU-SZ-005b_2020, complete genome 34188 34188 99% 0.0 85.47% MN975262.1 Select seq MN985325.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-WA1/2020, complete genome 34184 34184 99% 0.0 85.47% MN985325.1 Select seq MN988669.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV WHU02, complete genome 34170 34170 99% 0.0 85.46% MN988669.1 Select seq MN988668.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV WHU01, complete genome 34170 34170 99% 0.0 85.46% MN988668.1 Select seq NC_045512.2 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome 34170 34170 99% 0.0 85.46% NC_045512.2 Select seq MN938384.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV_HKU-SZ-002a_2020, complete genome 34167 34167 99% 0.0 85.46% MN938384.1 Select seq MN994468.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-CA2/2020, complete genome 34161 34161 99% 0.0 85.45% MN994468.1 Select seq MN994467.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-CA1/2020, complete genome 34161 34161 99% 0.0 85.45% MN994467.1 Select seq MN988713.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-IL1/2020, complete genome 34160 34160 99% 0.0 85.44% MN988713.1 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 Virus detail updated 2020-02-17 Virus name: BetaCoV/pangolin/Guangxi/P4L/2017 Accession ID: EPI_ISL_410538 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2017 Location: Asia / China / Guangxi Host: Manis javanica Additional location information: Gender: Unknown Patient age: Unknown Patient status: Specimen source: Lung tissue Additional host information: Outbreak: Last vaccinated: Treatment: Sequencing technology: Assembly method: Coverage: Comment: Institute information Originating lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the sample provider: Submitting lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the submitting laboratory: Authors: Wu-Chun Cao; Tommy Tsan-Yuk Lam; Na Jia; Ya-Wei Zhang; Jia-Fu Jiang; Bao-Gui Jiang Submitter information Submitter: Tsan Yuk Lam Submission Date: 2020-02-17 Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China FASTA >BetaCoV/pangolin/Guangxi/P4L/2017|EPI_ISL_410538 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 Virus detail Virus name: BetaCoV/pangolin/Guangxi/P1E/2017 Accession ID: EPI_ISL_410539 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2017 Location: Asia / China / Guangxi Host: Manis javanica Additional location information: Gender: Unknown Patient age: Unknown Patient status: Specimen source: Intestine tissue Additional host information: Outbreak: Last vaccinated: Treatment: Sequencing technology: Assembly method: Coverage: Comment: Institute information Originating lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the sample provider: Submitting lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the submitting laboratory: Authors: Wu-Chun Cao; Tommy Tsan-Yuk Lam; Na Jia; Ya-Wei Zhang; Jia-Fu Jiang; Bao-Gui Jiang Submitter information Submitter: Tsan Yuk Lam Submission Date: 2020-02-17 Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China FASTA >BetaCoV/pangolin/Guangxi/P1E/2017|EPI_ISL_410539 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 BetaCoV/pangolin/Guangxi/P1E/2017|EPI_ISL_410539 top 10 matches at Genbank AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments Sequences producing significant alignments: Select for downloading or viewing reports Description Max Score Total Score Query Cover E value Per. Ident Accession Select seq MN997409.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-AZ1/2020, complete genome 34165 34241 99% 0.0 85.45% MN997409.1 Select seq MN975262.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-005b_2020, complete genome 34165 34241 99% 0.0 85.45% MN975262.1 Select seq MN985325.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-WA1/2020, complete genome 34160 34237 99% 0.0 85.45% MN985325.1 Select seq MN988669.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV WHU02, complete genome 34147 34223 99% 0.0 85.44% MN988669.1 Select seq MN988668.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV WHU01, complete genome 34147 34223 99% 0.0 85.44% MN988668.1 Select seq NC_045512.2 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome 34147 34223 99% 0.0 85.44% NC_045512.2 Select seq MN938384.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-002a_2020, complete genome 34144 34220 99% 0.0 85.44% MN938384.1 Select seq MN994468.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-CA2/2020, complete genome 34138 34214 99% 0.0 85.43% MN994468.1 Select seq MN994467.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-CA1/2020, complete genome 34138 34214 99% 0.0 85.43% MN994467.1 Select seq MN988713.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-IL1/2020, complete genome 34137 34213 99% 0.0 85.42% MN988713.1 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 Virus detail Virus name: BetaCoV/pangolin/Guangxi/P5E/2017 Accession ID: EPI_ISL_410541 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2017 Location: Asia / China / Guangxi Host: Manis javanica Additional location information: Gender: Unknown Patient age: Unknown Patient status: Specimen source: Intestine tissue Additional host information: Outbreak: Last vaccinated: Treatment: Sequencing technology: Assembly method: Coverage: Comment: Institute information Originating lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the sample provider: Submitting lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the submitting laboratory: Authors: Wu-Chun Cao; Tommy Tsan-Yuk Lam; Na Jia; Ya-Wei Zhang; Jia-Fu Jiang; Bao-Gui Jiang Submitter information Submitter: Tsan Yuk Lam Submission Date: 2020-02-17 Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China FASTA >BetaCoV/pangolin/Guangxi/P5E/2017|EPI_ISL_410541 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 BetaCoV/pangolin/Guangxi/P5E/2017|EPI_ISL_410541 top 10 matches at Genbank AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments Sequences producing significant alignments: Select for downloading or viewing reports Description Max Score Total Score Query Cover E value Per. Ident Accession Select seq MN997409.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-AZ1/2020, complete genome 34150 34227 99% 0.0 85.44% MN997409.1 Select seq MN975262.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-005b_2020, complete genome 34150 34227 99% 0.0 85.44% MN975262.1 Select seq MN985325.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-WA1/2020, complete genome 34146 34222 99% 0.0 85.44% MN985325.1 Select seq MN988669.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV WHU02, complete genome 34132 34209 99% 0.0 85.42% MN988669.1 Select seq MN988668.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV WHU01, complete genome 34132 34209 99% 0.0 85.42% MN988668.1 Select seq NC_045512.2 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome 34132 34209 99% 0.0 85.42% NC_045512.2 Select seq MN938384.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-002a_2020, complete genome 34130 34206 99% 0.0 85.43% MN938384.1 Select seq MN994468.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-CA2/2020, complete genome 34123 34200 99% 0.0 85.42% MN994468.1 Select seq MN994467.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-CA1/2020, complete genome 34123 34200 99% 0.0 85.42% MN994467.1 Select seq MN988713.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-IL1/2020, complete genome 34122 34199 99% 0.0 85.41% MN988713.1 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 Virus detail Virus name: BetaCoV/pangolin/Guangxi/P5L/2017 Accession ID: EPI_ISL_410540 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2017 Location: Asia / China / Guangxi Host: Manis javanica Additional location information: Gender: Unknown Patient age: Unknown Patient status: Specimen source: Lung tissue Additional host information: Outbreak: Last vaccinated: Treatment: Sequencing technology: Assembly method: Coverage: Comment: Institute information Originating lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the sample provider: Submitting lab: Beijing Institute of Microbiology and Epidemiology Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China Sample ID given by the submitting laboratory: Authors: Wu-Chun Cao; Tommy Tsan-Yuk Lam; Na Jia; Ya-Wei Zhang; Jia-Fu Jiang; Bao-Gui Jiang Submitter information Submitter: Tsan Yuk Lam Submission Date: 2020-02-17 Address: 20 Dongda Street, Fengtai District, 100071 Beijing, China FASTA >BetaCoV/pangolin/Guangxi/P5L/2017|EPI_ISL_410540 Link to comment Share on other sites More sharing options...
niman Posted February 17, 2020 Author Report Share Posted February 17, 2020 BetaCoV/pangolin/Guangxi/P5L/2017|EPI_ISL_410540 Top 5 matches at Genbank AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments Sequences producing significant alignments: Select for downloading or viewing reports Description Max Score Total Score Query Cover E value Per. Ident Accession Select seq MN997409.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-AZ1/2020, complete genome 34196 34273 99% 0.0 85.48% MN997409.1 Select seq MN975262.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV_HKU-SZ-005b_2020, complete genome 34196 34273 99% 0.0 85.48% MN975262.1 Select seq MN985325.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-WA1/2020, complete genome 34192 34268 99% 0.0 85.47% MN985325.1 Select seq MN938384.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV_HKU-SZ-002a_2020, complete genome 34176 34252 99% 0.0 85.47% MN938384.1 Select seq MN994467.1 Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-CA1/2020, complete genome 34169 34246 99% 0.0 85.46% MN994467.1 Link to comment Share on other sites More sharing options...
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