niman Posted January 28, 2020 Report Share Posted January 28, 2020 (edited) Recently released sequences at GISAID from the cluster in Shenzhen, Guangdong (described in Lancet) and three of the four sequences from the United States (Snohomish County, WA; Cook County,IL : Los Angeles County CA) are in the same lineage defined by C8782T (in orf 1ab) and T28114C (in orf 8), Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/Guangdong/20SF013/2020 Accession ID: EPI_ISL_403933 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-15 Location: Guangdong, China Host: Human Additional location information: Shenzhen City Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/Guangdong/20SF014/2020 Accession ID: EPI_ISL_403934 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-15 Location: Guangdong, China Host: Human Additional location information: Shenzhen City Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/Guangdong/20SF025/2020 Accession ID: EPI_ISL_403935 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-15 Location: Guangdong, China Host: Human Additional location information: Shenzhen City Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/Shenzhen/HKU-SZ-002/2020 Accession ID: EPI_ISL_406030 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01 Location: China / Guangdong / Shenzhen Host: Human Additional location information: Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/Shenzhen/HKU-SZ-005/2020 Accession ID: EPI_ISL_405839 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01 Location: China / Guangdong / Shenzhen Host: Human Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 LOCUS MN938384 29838 bp RNA linear VRL 24-JAN-2020 DEFINITION Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-002a_2020, complete genome. ACCESSION MN938384 VERSION MN938384.1 KEYWORDS . SOURCE Wuhan seafood market pneumonia virus ORGANISM Wuhan seafood market pneumonia virus Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; unclassified Betacoronavirus. REFERENCE 1 (bases 1 to 29838) AUTHORS Chan,J.F.-W., Yuan,S., Kok,K.H., To,K.K.-W., Chu,H., Yang,J., Xing,F., Liu,J., Yip,C.C.-Y., Poon,R.W.-S., Tsai,H.W., Lo,S.K.-F., Chan,K.H., Poon,V.K.-M., Chan,W.M., Ip,J.D., Cai,J.P., Cheng,V.C.-C., Chen,H., Hui,C.K.-M. and Yuen,K.Y. TITLE A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster JOURNAL Lancet (2020) In press REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 29838) AUTHORS Chan,J.F.W. and Yuen,K.-Y. TITLE Direct Submission JOURNAL Submitted (14-JAN-2020) University of Hong Kong-Shenzhen Hospital, 1 Haiyuan 1st Road, Futian District, Shenzhen, Guangdong, P.R.C. COMMENT ##Assembly-Data-START## Assembly Method :: minimap2 v. 14 Jan 2020 Sequencing Technology :: Nanopore ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29838 /organism="Wuhan seafood market pneumonia virus" /mol_type="genomic RNA" /isolate="2019-nCoV_HKU-SZ-002a_2020" /isolation_source="nasopharyngeal swab" /host="Homo sapiens" /db_xref="taxon:2697049" /country="China: Shenzhen" /collection_date="Jan-2020" Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 LOCUS MN975262 29891 bp RNA linear VRL 24-JAN-2020 DEFINITION Wuhan seafood market pneumonia virus isolate 2019-nCoV_HKU-SZ-005b_2020, complete genome. ACCESSION MN975262 VERSION MN975262.1 KEYWORDS . SOURCE Wuhan seafood market pneumonia virus ORGANISM Wuhan seafood market pneumonia virus Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; unclassified Betacoronavirus. REFERENCE 1 (bases 1 to 29891) AUTHORS Chan,J.F.-W., Yuan,S., Kok,K.H., To,K.K.-W., Chu,H., Yang,J., Xing,F., Liu,J., Yip,C.C.-Y., Poon,R.W.-S., Tsai,H.W., Lo,S.K.-F., Chan,K.H., Poon,V.K.-M., Chan,W.M., Ip,J.D., Cai,J.P., Cheng,V.C.-C., Chen,H., Hui,C.K.-M. and Yuen,K.Y. TITLE A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster JOURNAL Lancet (2020) In press REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 29891) AUTHORS Chan,J.F.W. and Yuen,K.-Y. TITLE Direct Submission JOURNAL Submitted (21-JAN-2020) 1 Haiyuan 1st Road, Futian District, The University of Hong Kong- Shenzhen Hospital, Shenzhen, Guangdong, China COMMENT ##Assembly-Data-START## Assembly Method :: minimap2 v. 21 Jan 2020 Sequencing Technology :: Nanopore ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29891 /organism="Wuhan seafood market pneumonia virus" /mol_type="genomic RNA" /isolate="2019-nCoV_HKU-SZ-005b_2020" /isolation_source="sputum" /host="Homo sapiens" /db_xref="taxon:2697049" /country="China" /collection_date="Jan-2020" Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Note: 5' end is primer sequence used Virus detail Virus name: BetaCoV/USA/WA1/2020 Accession ID: EPI_ISL_404895 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-19 Location: USA / Washington / Snohomish County Host: Human Additional location information: Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 LOCUS MN985325 29882 bp RNA linear VRL 24-JAN-2020 DEFINITION Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-WA1/2020, complete genome. ACCESSION MN985325 VERSION MN985325.1 KEYWORDS . SOURCE Wuhan seafood market pneumonia virus ORGANISM Wuhan seafood market pneumonia virus Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; unclassified Betacoronavirus. REFERENCE 1 (bases 1 to 29882) AUTHORS Queen,K., Tao,Y., Li,Y., Paden,C.R., Lu,X., Lynch,B., Zhang,J., Gerber,S.I. and Lindstrom,S. TITLE Full genome sequence of first U.S. case of nCoV-2019 JOURNAL Unpublished REFERENCE 2 (bases 1 to 29882) AUTHORS Queen,K., Tao,Y., Li,Y., Paden,C.R., Lu,X., Zhang,J., Gerber,S.I. and Lindstrom,S. TITLE Direct Submission JOURNAL Submitted (24-JAN-2020) Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30033, USA FEATURES Location/Qualifiers source 1..29882 /organism="Wuhan seafood market pneumonia virus" /mol_type="genomic RNA" /isolate="2019-nCoV/USA-WA1/2020" /isolation_source="oropharyngeal swab" /host="Homo sapiens" /db_xref="taxon:2697049" /country="USA" /collection_date="19-Jan-2020" /note="5' end is primer sequence used" Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/USA/IL1/2020 Accession ID: EPI_ISL_404253 Type: unclassified betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-21 Location: USA / Illinois /Chicago Host: Human Additional location information: Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 LOCUS MN988713 29882 bp RNA linear VRL 25-JAN-2020 DEFINITION Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-IL1/2020, complete genome. ACCESSION MN988713 VERSION MN988713.1 KEYWORDS . SOURCE Wuhan seafood market pneumonia virus ORGANISM Wuhan seafood market pneumonia virus Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; unclassified Betacoronavirus. REFERENCE 1 (bases 1 to 29882) AUTHORS Tao,Y., Queen,K., Paden,C.R., Zhang,J., Li,Y., Uehara,A., Lu,X., Lynch,B., Sakthivel,S.K.K., Whitaker,B.L., Kamili,S., Wang,L., Murray,J.R., Gerber,S.I., Lindstrom,S. and Tong,S. TITLE Novel betacoronavirus, Illinois JOURNAL Unpublished REFERENCE 2 (bases 1 to 29882) AUTHORS Tao,Y., Queen,K., Paden,C.R., Zhang,J., Li,Y., Uehara,A., Lu,X., Lynch,B., Sakthivel,S.K.K., Whitaker,B.L., Kamili,S., Wang,L., Murray,J.R., Gerber,S.I., Lindstrom,S. and Tong,S. TITLE Direct Submission JOURNAL Submitted (25-JAN-2020) Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30033, USA COMMENT ##Assembly-Data-START## Assembly Method :: Minimap v. 2.17 Sequencing Technology :: Nanopore; Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29882 /organism="Wuhan seafood market pneumonia virus" /mol_type="genomic RNA" /isolate="2019-nCoV/USA-IL1/2020" /isolation_source="sputum" /host="Homo sapiens" /db_xref="taxon:2697049" /country="USA: Illinois" /collection_date="21-Jan-2020" /note="5' sequence is the primer sequence used" Link to comment Share on other sites More sharing options...
niman Posted January 28, 2020 Author Report Share Posted January 28, 2020 (edited) Virus detail Virus name: BetaCoV/USA/CA1/2020 Accession ID: EPI_ISL_406034 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-23 Location: USA / California / Los Angeles Host: Human Additional location information: Edited March 6, 2020 by niman Link to comment Share on other sites More sharing options...
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