Wuhan Coronavirus 2019-nCoV Sequences

niman · January 11, 2020

The first novel coronavirus has been released (WH-Human_1`|China|2019-Dec). This thread will analyze additional sequences.

Initial genome release of novel coronavirus

Novel 2019 coronavirus

arambautARTIC Network

2

2h

10th January 2020
This posting is communicated by Edward C. Holmes, University of Sydney on behalf of the consortium led by Professor Yong-Zhen Zhang, Fudan University, Shanghai

The Shanghai Public Health Clinical Center & School of Public Health, in collaboration with the Central Hospital of Wuhan, Huazhong University of Science and Technology, the Wuhan Center for Disease Control and Prevention, the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control, and the University of Sydney, Sydney, Australia is releasing a coronavirus genome from a case of a respiratory disease from the Wuhan outbreak. The sequence has also been deposited on GenBank (accession MN908947) and will be released as soon as possible.

The sequence can be downloaded here:

WH-Human_1.fasta.gz (8.9 KB – this is a fasta file compressed using gzip. Uncompress using gzip -d WH-Human_1.fasta.gz)

Disclaimer:
Please feel free to download, share, use, and analyze this data. We ask that you communicate with us if you wish to publish results that use these data in a journal. If you have any other questions –then please also contact us directly.

Professor Yong-Zhen Zhang,
Shanghai Public Health Clinical Center & School of Public Health,
Fudan University,
Shanghai, China.

email: [email protected]

Edited January 11, 2020 by niman

niman · January 11, 2020

Distance tree of results

Sequences producing significant alignments:
Select for downloading or viewing reports	Description	Max Score	Total Score	Query Cover	Per. Ident	Accession
Select seq MG772933.1	Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome	26936	35297	93%	89.12%	MG772933.1
Select seq MG772934.1	Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome	22223	35237	92%	88.65%	MG772934.1
Select seq AY395003.1	SARS coronavirus ZS-C, complete genome	15213	22494	86%	82.34%	AY395003.1
Select seq AY394996.1	SARS coronavirus ZS-B, complete genome	15213	22529	86%	82.34%	AY394996.1
Select seq AY304488.1	SARS coronavirus SZ16, complete genome	15202	22524	86%	82.33%	AY304488.1
Select seq AY304486.1	SARS coronavirus SZ3, complete genome	15202	22509	87%	82.33%	AY304486.1
Select seq AY390556.1	SARS coronavirus GZ02, complete genome	15191	22507	86%	82.32%	AY390556.1
Select seq EU371564.1	SARS coronavirus BJ182-12, complete genome	15186	22443	86%	82.32%	EU371564.1
Select seq AY394985.1	SARS coronavirus HSZ-Bb, complete genome	15186	22206	86%	82.31%	AY394985.1
Select seq AY278554.2	SARS coronavirus CUHK-W1, complete genome	15186	22507	86%	82.32%	AY278554.2
Select seq EU371559.1	SARS coronavirus ZJ02, complete genome	15180	22507	86%	82.31%	EU371559.1
Select seq AY559093.1	SARS coronavirus Sin845, complete genome	15180	22480	86%	82.31%	AY559093.1
Select seq AY394994.1	SARS coronavirus HSZ-Bc, complete genome	15180	22496	86%	82.31%	AY394994.1
Select seq AY394986.1	SARS coronavirus HSZ-Cb, complete genome	15180	22456	86%	82.31%	AY394986.1
Select seq MK211376.1	Coronavirus BtRs-BetaCoV/YN2018B, complete genome	15176	22605	89%	82.32%	MK211376.1
Select seq KY417146.1	Bat SARS-like coronavirus isolate Rs4231, complete genome	15176	22473	89%	82.30%	KY417146.1
Select seq JX163927.1	SARS coronavirus isolate Tor2/FP1-10851, complete genome	15175	22411	86%	82.30%	JX163927.1
Select seq JX163926.1	SARS coronavirus isolate Tor2/FP1-10912, complete genome	15175	22419	86%	82.30%	JX163926.1
Select seq JX163923.1	SARS coronavirus isolate Tor2/FP1-10912, complete genome	15175	22411	86%	82.30%	JX163923.1
Select seq JQ316196.1	SARS coronavirus HKU-39849 isolate UOB, complete genome	15175	22496	86%	82.30%	JQ316196.1
Select seq FJ882963.1	SARS coronavirus P2, complete genome	15175	22444	86%	82.30%	FJ882963.1
Select seq DQ898174.1	SARS coronavirus strain CV7, complete genome	15175	22496	86%	82.30%	DQ898174.1
Select seq AY864806.1	SARS coronavirus BJ202, complete genome	15175	22502	86%	82.30%	AY864806.1
Select seq AY714217.1	SARS Coronavirus CDC#200301157, complete genome	15175	22496	86%	82.30%	AY714217.1
Select seq AY559096.1	SARS coronavirus Sin850, complete genome	15175	22489	86%	82.30%	AY559096.1
Select seq AY559095.1	SARS coronavirus Sin847, complete genome	15175	22474	86%	82.30%	AY559095.1
Select seq AY559086.1	SARS coronavirus Sin849, complete genome	15175	22478	86%	82.30%	AY559086.1
Select seq AY559085.1	SARS coronavirus Sin848, complete genome	15175	22474	86%	82.30%	AY559085.1
Select seq AY559084.1	SARS coronavirus Sin3765V, complete genome	15175	22480	86%	82.30%	AY559084.1
Select seq AY559083.1	SARS coronavirus Sin3408, complete genome	15175	22476	86%	82.30%	AY559083.1
Select seq AY559082.1	SARS coronavirus Sin852, complete genome	15175	22474	86%	82.30%	AY559082.1
Select seq AY274119.3	Severe acute respiratory syndrome-related coronavirus isolate Tor2, complete genome	15175	22491	86%	82.30%	AY274119.3
Select seq AY323977.2	SARS coronavirus HSR 1, complete genome	15175	22502	86%	82.30%	AY323977.2
Select seq AY291451.1	SARS coronavirus TW1, complete genome	15175	22502	86%	82.30%	AY291451.1
Select seq AY502928.1	SARS coronavirus TW5, complete genome	15175	22496	86%	82.30%	AY502928.1
Select seq AY502926.1	SARS coronavirus TW3, complete genome	15175	22489	86%	82.30%	AY502926.1
Select seq AY502923.1	SARS coronavirus TW10, complete genome	15175	22502	86%	82.30%	AY502923.1
Select seq AY394999.1	SARS coronavirus LC2, complete genome	15175	22441	86%	82.30%	AY394999.1
Select seq AY394998.1	SARS coronavirus LC1, complete genome	15175	22491	86%	82.30%	AY394998.1
Select seq AY394995.1	SARS coronavirus HSZ-Cc, complete genome	15175	22485	86%	82.30%	AY394995.1
Select seq AY394993.1	SARS coronavirus HGZ8L2, complete genome	15175	22491	86%	82.31%	AY394993.1
Select seq AY394992.1	SARS coronavirus HZS2-C, complete genome	15175	22496	86%	82.31%	AY394992.1
Select seq AY394991.1	SARS coronavirus HZS2-Fc, complete genome	15175	22496	86%	82.30%	AY394991.1
Select seq AY394987.1	SARS coronavirus HZS2-Fb, complete genome	15175	22478	86%	82.30%	AY394987.1
Select seq AY394983.1	SARS coronavirus HSZ2-A, complete genome	15175	22465	86%	82.30%	AY394983.1
Select seq AY394978.1	SARS coronavirus GZ-B, complete genome	15175	22391	86%	82.30%	AY394978.1
Select seq AY357075.1	SARS coronavirus PUMC02, complete genome	15175	22487	86%	82.30%	AY357075.1
Select seq AY282752.2	SARS coronavirus CUHK-Su10, complete genome	15175	22491	86%	82.30%	AY282752.2
Select seq AY427439.1	SARS coronavirus AS, complete genome	15175	22496	86%	82.30%	AY427439.1
Select seq AY283796.1	SARS coronavirus Sin2679, complete genome	15175	22502	86%	82.30%	AY283796.1
Select seq AP006561.1	SARS coronavirus TWY genomic RNA, complete genome	15175	22502	86%	82.30%	AP006561.1
Select seq JX163925.1	SARS coronavirus isolate Tor2/FP1-10895, complete genome	15173	22409	86%	82.30%	JX163925.1
Select seq JX163928.1	SARS coronavirus isolate Tor2/FP1-10895, complete genome	15171	22419	86%	82.30%	JX163928.1
Select seq JX163924.1	SARS coronavirus isolate Tor2/FP1-10851, complete genome	15169	22415	86%	82.30%	JX163924.1
Select seq GU553363.1	SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00001, complete genome	15169	22409	86%	82.30%	GU553363.1
Select seq EU371563.1	SARS coronavirus BJ182-8, complete genome	15169	22463	86%	82.30%	EU371563.1
Select seq EU371561.1	SARS coronavirus BJ182b, complete genome	15169	22468	86%	82.30%	EU371561.1
Select seq EU371560.1	SARS coronavirus BJ182a, complete genome	15169	22468	86%	82.30%	EU371560.1
Select seq AY864805.1	SARS coronavirus BJ162, complete genome	15169	22496	86%	82.30%	AY864805.1
Select seq AY278741.1	SARS coronavirus Urbani, complete genome	15169	22502	86%	82.30%	AY278741.1
Select seq AY559087.1	SARS coronavirus Sin3725V, complete genome	15169	22483	86%	82.29%	AY559087.1
Select seq AY394989.1	SARS coronavirus HZS2-D, complete genome	15169	22491	86%	82.30%	AY394989.1
Select seq AY485278.1	SARS coronavirus Sino3-11, complete genome	15169	22485	86%	82.30%	AY485278.1
Select seq AY502927.1	SARS coronavirus TW4, complete genome	15167	22489	86%	82.29%	AY502927.1
Select seq GU553365.1	SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00003, complete genome	15165	22400	86%	82.29%	GU553365.1
Select seq KJ473816.1	BtRs-BetaCoV/YN2013, complete genome	15163	21667	83%	82.29%	KJ473816.1
Select seq EU371562.1	SARS coronavirus BJ182-4, complete genome	15158	22457	86%	82.29%	EU371562.1
Select seq MK211377.1	Coronavirus BtRs-BetaCoV/YN2018C, complete genome	15149	22390	87%	82.29%	MK211377.1
Select seq KY417145.1	Bat SARS-like coronavirus isolate Rf4092, complete genome	15134	22310	85%	82.26%	KY417145.1
Select seq MK211375.1	Coronavirus BtRs-BetaCoV/YN2018A, complete genome	15117	22358	87%	82.26%	MK211375.1
Select seq KF294455.1	SARS-related bat coronavirus isolate Anlong-111 orf1ab polyprotein and orf1a polyprotein genes, complete cds	15084	16324	63%	82.35%	KF294455.1
Select seq JX993988.1	Bat coronavirus Cp/Yunnan2011, complete genome	15043	21828	85%	82.18%	JX993988.1
Select seq KJ473814.1	BtRs-BetaCoV/HuB2013, complete genome	14970	22299	85%	82.20%	KJ473814.1
Select seq DQ648857.1	Bat coronavirus (BtCoV/279/2005), complete genome	14916	22120	85%	82.16%	DQ648857.1
Select seq JX993987.1	Bat coronavirus Rp/Shaanxi2011, complete genome	14892	21814	86%	82.00%	JX993987.1
Select seq KF294457.1	SARS-related bat coronavirus isolate Longquan-140 orf1ab polyprotein, spike glycoprotein, envelope protein, membrane protein, and nucleocapsid protein genes, complete cds	14759	23734	90%	81.89%	KF294457.1
Select seq MK211374.1	Coronavirus BtRl-BetaCoV/SC2018, complete genome	14731	21823	85%	82.02%	MK211374.1
Select seq KJ473813.1	BtRf-BetaCoV/SX2013, complete genome	14722	21320	85%	81.82%	KJ473813.1
Select seq KJ473812.1	BtRf-BetaCoV/HeB2013, complete genome	14683	21222	85%	81.79%	KJ473812.1
Select seq KJ473811.1	BtRf-BetaCoV/JL2012, complete genome	14683	21061	85%	81.79%	KJ473811.1
Select seq GQ153542.1	Bat SARS coronavirus HKU3-7, complete genome	14683	21924	87%	81.82%	GQ153542.1
Select seq GQ153543.1	Bat SARS coronavirus HKU3-8, complete genome	14678	21962	86%	81.82%	GQ153543.1
Select seq KY770860.1	Bat coronavirus isolate Jiyuan-84, complete genome	14628	21379	85%	81.74%	KY770860.1
Select seq DQ648856.1	Bat coronavirus (BtCoV/273/2005), complete genome	14556	21331	86%	81.66%	DQ648856.1
Select seq DQ412042.1	Bat SARS coronavirus Rf1, complete genome	14556	21327	86%	81.66%	DQ412042.1
Select seq GQ153547.1	Bat SARS coronavirus HKU3-12, complete genome	14550	21797	87%	81.68%	GQ153547.1
Select seq KF294456.1	SARS-related bat coronavirus isolate Jiyuan-331 orf1ab polyprotein gene, complete cds	14539	15829	64%	81.66%	KF294456.1
Select seq FJ211859.1	Recombinant coronavirus clone Bat SARS-CoV, complete sequence	14517	21803	87%	81.65%	FJ211859.1
Select seq DQ084199.1	bat SARS coronavirus HKU3-2, complete genome	14512	21784	87%	81.64%	DQ084199.1
Select seq GQ153540.1	Bat SARS coronavirus HKU3-5, complete genome	14506	21758	87%	81.63%	GQ153540.1
Select seq GQ153539.1	Bat SARS coronavirus HKU3-4, complete genome	14506	21764	87%	81.63%	GQ153539.1
Select seq GQ153546.1	Bat SARS coronavirus HKU3-11, complete genome	14501	21747	87%	81.63%	GQ153546.1
Select seq DQ022305.2	Bat SARS coronavirus HKU3-1, complete genome	14501	21786	87%	81.63%	DQ022305.2
Select seq DQ084200.1	bat SARS coronavirus HKU3-3, complete genome	14501	21779	87%	81.63%	DQ084200.1
Select seq GQ153548.1	Bat SARS coronavirus HKU3-13, complete genome	14495	21736	87%	81.63%	GQ153548.1
Select seq GQ153541.1	Bat SARS coronavirus HKU3-6, complete genome	14495	21764	87%	81.62%	GQ153541.1
Select seq GQ153545.1	Bat SARS coronavirus HKU3-10, complete genome	14484	21725	87%	81.61%	GQ153545.1
Select seq GQ153544.1	Bat SARS coronavirus HKU3-9, complete genome	14484	21725	87%	81.61%	GQ153544.1
Select seq KU182964.1	Bat coronavirus isolate JTMC15, complete genome	13501	20234	77%	82.94%	KU182964.1
Select seq KY938558.1	Bat coronavirus strain 16BO133, complete genome	13452	20134	77%	82.88%	KY938558.1

niman · January 11, 2020

Top match at Genbank

Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome

GenBank: MG772933.1

FASTA Graphics

Go to:

LOCUS       MG772933               29802 bp    RNA     linear   VRL 28-MAR-2018
DEFINITION  Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome.
ACCESSION   MG772933
VERSION     MG772933.1
KEYWORDS    .
SOURCE      Bat SARS-like coronavirus
  ORGANISM  Bat SARS-like coronavirus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Nidovirales; Coronaviridae; Coronavirinae; Betacoronavirus.
REFERENCE   1  (bases 1 to 29802)
  AUTHORS   Hu,D.
  TITLE     Genomic Characterization and Infectivity of A Novel SARS-like
            coronavirus in Chinese Bats
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 29802)
  AUTHORS   Hu,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2018) Institute of Military Medicine Nanjing
            Command, Nanjing, Institute of Military Medicine Nanjing Command,
            Nanjing, NO. 293 East Zhongshan Road, Nanjing, JangSu 210002, China
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##

niman · January 11, 2020

Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome

GenBank: MG772934.1

FASTA Graphics

Go to:

LOCUS       MG772934               29732 bp    RNA     linear   VRL 28-MAR-2018
DEFINITION  Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome.
ACCESSION   MG772934
VERSION     MG772934.1
KEYWORDS    .
SOURCE      Bat SARS-like coronavirus
  ORGANISM  Bat SARS-like coronavirus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Nidovirales; Coronaviridae; Coronavirinae; Betacoronavirus.
REFERENCE   1  (bases 1 to 29732)
  AUTHORS   Hu,D.
  TITLE     Genomic Characterization and Infectivity of A Novel SARS-like
            coronavirus in Chinese Bats
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 29732)
  AUTHORS   Hu,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2018) Institute of Military Medicine Nanjing
            Command, Nanjing, Institute of Military Medicine Nanjing Command,
            Nanjing, NO. 293 East Zhongshan Road, Nanjing, JangSu 210002, China
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##

niman · January 11, 2020

SARS coronavirus ZS-C, complete genome

GenBank: AY395003.1

FASTA Graphics

Go to:

LOCUS       AY395003               29647 bp    RNA     linear   VRL 29-JAN-2004
DEFINITION  SARS coronavirus ZS-C, complete genome.
ACCESSION   AY395003
VERSION     AY395003.1
KEYWORDS    .
SOURCE      SARS coronavirus ZS-C
  ORGANISM  SARS coronavirus ZS-C
            Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae;
            Orthocoronavirinae; Betacoronavirus; Sarbecovirus.
REFERENCE   1  (bases 1 to 29647)
  CONSRTM   The SARS epidemiology consortium of Guangdong
  TITLE     From independent foci of epidemic outbreak to large genomic
            alteration in late phase viruses: evolution of the SARS-coronavirus
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 29647)
  CONSRTM   The SARS epidemiology consortium of Guangdong
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-2003) Guangdong, China
FEATURES             Location/Qualifiers
     source          1..29647
                     /organism="SARS coronavirus ZS-C"
                     /mol_type="genomic RNA"
                     /isolate="ZS-C"
                     /db_xref="taxon:249088"

niman · January 11, 2020

LOCUS       AY304488               29731 bp    RNA     linear   VRL 05-NOV-2003
DEFINITION  SARS coronavirus SZ16, complete genome.
ACCESSION   AY304488
VERSION     AY304488.1
KEYWORDS    .
SOURCE      Civet SARS CoV SZ16/2003
  ORGANISM  Civet SARS CoV SZ16/2003
            Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae;
            Orthocoronavirinae; Betacoronavirus; Sarbecovirus.
REFERENCE   1  (bases 1 to 29731)
  AUTHORS   Guan,Y., Zheng,B.J., He,Y.Q., Liu,X.L., Zhuang,Z.X., Cheung,C.L.,
            Luo,S.W., Li,P.H., Zhang,L.J., Guan,Y.J., Butt,K.M., Wong,K.L.,
            Chan,K.W., Lim,W., Shortridge,K.F., Yuen,K.Y., Peiris,J.S. and
            Poon,L.L.
  TITLE     Isolation and characterization of viruses related to the SARS
            coronavirus from animals in southern China
  JOURNAL   Science 302 (5643), 276-278 (2003)
   PUBMED   12958366
REFERENCE   2  (bases 1 to 29731)
  AUTHORS   Guan,Y. and Zheng,B.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAY-2003) Microbiology, The University of Hong Kong,
            University Pathology Building, Queen Mary Hospital, Pokfulam Road,
            Hong Kong, China
FEATURES             Location/Qualifiers
     source          1..29731
                     /organism="Civet SARS CoV SZ16/2003"
                     /mol_type="genomic RNA"
                     /isolate="SZ16"
                     /db_xref="taxon:231515"
                     /country="Hong Kong"

niman · January 11, 2020

LOCUS       AY278554               29736 bp    RNA     linear   VRL 31-JUL-2003
DEFINITION  SARS coronavirus CUHK-W1, complete genome.
ACCESSION   AY278554
VERSION     AY278554.2
KEYWORDS    .
SOURCE      SARS coronavirus CUHK-W1
  ORGANISM  SARS coronavirus CUHK-W1
            Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae;
            Orthocoronavirinae; Betacoronavirus; Sarbecovirus.
REFERENCE   1  (bases 1 to 29736)
  AUTHORS   Tsui,S.K., Chim,S.S. and Lo,Y.M.
  CONSRTM   Chinese University of Hong Kong Molecular SARS Research Group
  TITLE     Coronavirus genomic-sequence variations and the epidemiology of the
            severe acute respiratory syndrome
  JOURNAL   N. Engl. J. Med. 349 (2), 187-188 (2003)
   PUBMED   12853594
REFERENCE   2  (bases 1 to 29736)
  AUTHORS   Tsui,S.K.W., Lo,Y.M.D., Tam,J.S., Fung,K.P., Chim,S.S.C., Au,C.C.,
            Chan,A.H., Wan,A.W.K., Au,K.W., Chan,C.W., Kou,C.Y.C., Lam,H.M.,
            Lam,W.Y., Lau,S.K., Lau,Y.L., Lau,Y.M., Law,S.L., Law,T.W.,
            Li,M.L.Y., Tse,C.H., Wong,C.H., Yiu,W.H., Lee,C.Y., Chan,A.K.C.,
            Chiu,R.W.K., Ng,E.K.O., Tong,Y.K., Chan,P.K.S., Au-Yeung,C.,
            Cheung,J.K.L., Chu,I., Hung,E.C.W. and Waye,M.M.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-2003) Department of Biochemistry, Chinese
            University of Hong Kong, MMW Bldg. Rm 608, Shatin, NT SAR, China
COMMENT     On Apr 21, 2003 this sequence version replaced AY278554.1.

niman · January 11, 2020

Tonight at 11 PM ET

Dr. Henry Niman, PhD

China Confirms First Death
From SARS Like Virus,
6 In Critical
This Is Far Worse Than
The Beginning Of The SARS Outbreak

Wuhan Department of Health Reports 1st
Confirmed Death From Coronavirus

Wuhon Coronavirus Sequence At Genbank
WH-Human_1|China|2019-Dec

niman · January 11, 2020

3 minutes ago, niman said:

Tonight at 11 PM ET

Dr. Henry Niman, PhD

China Confirms First Death
From SARS Like Virus,
6 In Critical
This Is Far Worse Than
The Beginning Of The SARS Outbreak

Wuhan Department of Health Reports 1st
Confirmed Death From Coronavirus

Wuhon Coronavirus Sequence At Genbank
WH-Human_1|China|2019-Dec

https://www.renseradio.com/listenlive.php

niman · January 11, 2020

2 hours ago, niman said:

Tonight at 11 PM ET

Dr. Henry Niman, PhD

China Confirms First Death
From SARS Like Virus,
6 In Critical
This Is Far Worse Than
The Beginning Of The SARS Outbreak

Wuhan Department of Health Reports 1st
Confirmed Death From Coronavirus

Wuhon Coronavirus Sequence At Genbank
WH-Human_1|China|2019-Dec

http://mediaarchives.gsradio.net/rense/special/rense_011020_hr3.mp3

niman · January 11, 2020

Wuhan pneumonia: new strain ‘bears close similarity to Sars’ as Hong Kong health minister assures public city is prepared

Secretary for Food and Health Sophia Chan says Hong Kong has plenty of beds and protective gear, but appeals to retailers not to jack up prices of masks

Victor Ting

Published: 2:21pm, 11 Jan, 2020

Sophia Chan, secretary for food and health in Hong Kong. Photo: May Tse

A new strain of pneumonia that claimed its first fatality in mainland China on Saturday has been revealed as a Sars-like coronavirus, with close to 80 per cent similarity to the widespread global epidemic that broke out in 2003, according to an unofficial international analysis.

Hong Kong officials confirmed the findings meant all people tested for infection locally so far did not carry the virus.

A group of international experts from institutions including the Shanghai Public Health Clinical Centre and Centre of Public Health, Central Hospital of Wuhan, and the University of Sydney analysed the coronavirus genome from a respiratory disease case from the Wuhan outbreak and released the results on Friday.

They showed a group-2B coronavirus, with close to 80 per cent similarity to the severe acute respiratory syndrome genome. Its primary source was likely to be bats, like Sars, and it attacked humans through a cell receptor known as ACE2.

Patients at the accident and emergency unit of Queen Elizabeth Hospital in Yau Ma Tei. Photo: Edmond So

In a joint press conference with health officials, University of Hong Kong professor and microbiologist Yuen Kwok-yung said diagnosis tests of suspected cases in the city had covered the new coronavirus genome and no patients had tested positive for the disease.

He said more clinical research by mainland medical professionals was needed to determine the coronavirus’s potency, as the genome sequence could change rapidly after transmission.

Dr Wong Ka-hing, controller at the government’s Centre for Health Protection, said: “The prevention strategy of the past 10 days is in the right direction. It will continue ... medical professionals and residents should stay vigilant and we will monitor the situation.”

https://www.scmp.com/news/hong-kong/health-environment/article/3045659/wuhan-pneumonia-hong-kong-health-minister-assures

niman · January 12, 2020

Five human Wuhan sequences have been released at GISAID

Newly discovered betacoronavirus, Wuhan 2019-2020

A previously unknown betacoronavirus was detected in patients during an outbreak of respiratory illnesses, including atypical pneumonia, that started mid-December 2019 in the city of Wuhan, the capital of Central China’s Hubei Province.

The newly discovered coronavirus is similar to some of the betacoronaviruses detected in bats, but it is distinct from SARS-CoV and MERS-CoV.

The genome of the newly discovered CoV consists of a single, positive-stranded RNA that is approximately 30k nucleotides long. The overall genome organization of the newly discovered CoV is similar to that of other coronaviruses. The newly sequenced virus genome encodes the open reading frames (ORFs) common to all betacoronaviruses, including ORF1ab that encodes many enzymatic proteins, the spike-surface glycoprotein (S), the small envelope protein (E), the matrix protein (M), and the nucleocapsid protein (N), as well as several nonstructural proteins.

Virus name	Accession ID	Passage details/history	Collection date	Host	Originating lab	Submitting lab

Virus name	Accession ID	Passage details/history	Collection date	Host	Originating lab	Submitting lab
BetaCoV/Wuhan/IVDC-HB-01/2019	EPI_ISL_402119	Virus Isolate, Passage 1	2019-12-30	Human	National Institute for Viral Disease Control and Prevention, China CDC	National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-04/2020	EPI_ISL_402120	Original	2020-01-01	Human	National Institute for Viral Disease Control and Prevention, China CDC	National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-05/2019	EPI_ISL_402121	Original	2019-12-30	Human	National Institute for Viral Disease Control and Prevention, China CDC	National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IPBCAMS-WH-01/2019	EPI_ISL_402123	Original	2019-12-24	Human	Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College	Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
BetaCoV/Wuhan/WIV04/2019	EPI_ISL_402124	Original	2019-12-30	Human	Wuhan Jinyintan Hospital	Wuhan

niman · January 12, 2020

Virus name	BetaCoV/Wuhan/WIV04/2019
Accession ID	EPI_ISL_402124
Passage details/history	Original
Collection date	2019-12-30
Host	Human