niman

il 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

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 Additional location information: Institute information Originating lab: The University of Hong Kong - Shenzhen Hospital Address: 1 Haiyuan 1st Road, Futian District, Shenzhen 518053, Guangdong, China Sample ID given by the sample provider: HKU-SZ-005_2020 Submitting lab: Li Ka Shing Faculty of Medicine, The University of Hong Kong Address: 21 Sassoon Road, Pokfulam, Hong Kong, Hong Kong (SAR) Sample ID given by the submitting laboratory: 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. Submitter information Submitter: Jasper Fuk Woo Chan Submission Date: 2020-01-24 Address: Li Ka Shing Faculty of Medicine, The University of Hong Kong 21 Sassoon Road, Pokfulam, Hong Kong, Hong Kong (SAR) FASTA >BetaCoV/Shenzhen/HKU-SZ-005/2020|EPI_ISL_405839

s 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:

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:

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:

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

Ministry of Health confirms three more coronavirus cases in Bavaria They are apparently related to the first case: the coronavirus has been detected in three other people in Bavaria. 40 more colleagues are to be tested on Wednesday. In Bavaria , three other people have been infected with the novel corona virus. They were related to the first confirmed case of the new lung disease in Germany, said a spokesman for the Ministry of Health in Munich. The three newly infected patients are also employees of the Webasto company from the district of Starnberg, where the first person affected is employed. "It was decided that the three new patients should also be admitted to the Munich Klinik Schwabing and medically monitored and isolated there," the ministry said. "A few other contact persons are currently testing whether they are also infected with the corona virus." The Bavarian Ministry of Health and the State Office for Health and Food Safety want to report on details in a press release on Wednesday. A spokesman initially did not provide any further information in the evening. Infection during training The man , who was first infected in Germany, had been infected on January 21 during a training event with a Chinese colleague. The woman reportedly flew back to China on January 23. On January 27, the company informed the health department of the Chinese woman's illness. Bavaria's Minister of Health Melanie Huml ( CSU ) said according to the message: "A total of around 40 employees of the company were identified who could be considered as close contacts. Those affected should be tested on Wednesday as a precaution." The novel coronavirus 2019-nCoV can trigger a lung disease from which more than 100 people have already died in the main spreading country China - most of them were elderly patients with serious previous illnesses. The total number of diseases known worldwide has now risen to more than 4,500; in China at least 106 people died of the lung disease. The first coronavirus patient had tested positive for the virus on Monday - by then he had gone back to work. "He is doing very well, yesterday morning he was still working," said LGL President Andreas Zapf. "He is fever-free and currently has no respiratory symptoms," added the treating chief physician Clemens Wendtner from the Schwabing Clinic. The man is in an isolation room, there is no danger for other patients. Nurseries are also under surveillance According to LGL, the people who had contact with the Chinese and the first sick German Webasto employee are under surveillance and are called upon not to leave their homes. The 33-year-old patient is a father, his child goes to a crèche in the Landsberg am Lech district, according to the Ministry of Health. This is now also under observation, said LGL President Zapf. At first nothing was known about the marital status of the three other patients. The head of the Infectiology Task Force, Martin Hoch, emphasized: "The number can still increase." https://www.spiegel.de/wissenschaft/medizin/coronavirus-drei-weitere-faelle-in-bayern-bestaetigt-a-99fbe5d4-0e47-464e-a75e-362481fad33a

No.This is a lineage with a couple of changes that create a significant evolutionary advantage in humans.

Virus detail Virus name: BetaCoV/USA/AZ1/2020 Accession ID: EPI_ISL_406223 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-22 Location: USA / Arizona / Phoenix Host: Human Additional location information:

Full sequences for all five confirmed cases in the United States have been released and all except for Orange Co in California have the orf 8 mutation present in Shenzhen cluster described in Lancet. The orf 8 gene acquired in 29 nt deletion and was present in the physician at the Metropole Hotel who was the index case for the international expansion of SARS in 2003.

Virus detail Virus name: BetaCoV/USA/AZ1/2020 Accession ID: EPI_ISL_406223 Type: betacoronavirus Passage details/history: Original Sample information Collection date: 2020-01-22 Location: USA / Arizona / Phoenix Host: Human

Sequence from Maricopa County, Arizona released at GISAID. It also matches recently released sequences 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),

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:

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"

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:

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"

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:

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"

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"

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

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:

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

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

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

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),