niman Posted February 17, 2020 Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
niman Posted February 17, 2020 Author Report 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
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