niman

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Tonight at 11 PM ET Dr. Henry Niman, PhDChina Confirms First Death From SARS Like Virus, 6 In Critical This Is Far Worse Than The Beginning Of The SARS OutbreakWuhan Department of Health Reports 1st Confirmed Death From CoronavirusWuhon Coronavirus Sequence At Genbank WH-Human_1|China|2019-Dec

Tonight at 11 PM ET Dr. Henry Niman, PhDChina Confirms First Death From SARS Like Virus, 6 In Critical This Is Far Worse Than The Beginning Of The SARS OutbreakWuhan Department of Health Reports 1st Confirmed Death From CoronavirusWuhon Coronavirus Sequence At Genbank WH-Human_1|China|2019-Dec

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.

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"

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"

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##

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##

Distance tree of results Sequences producing significant alignments: Select for downloading or viewing reports Description Max Score Total Score Query Cover E value Per. Ident Accession Select seq MG772933.1 Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome 26936 35297 93% 0.0 89.12% MG772933.1 Select seq MG772934.1 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome 22223 35237 92% 0.0 88.65% MG772934.1 Select seq AY395003.1 SARS coronavirus ZS-C, complete genome 15213 22494 86% 0.0 82.34% AY395003.1 Select seq AY394996.1 SARS coronavirus ZS-B, complete genome 15213 22529 86% 0.0 82.34% AY394996.1 Select seq AY304488.1 SARS coronavirus SZ16, complete genome 15202 22524 86% 0.0 82.33% AY304488.1 Select seq AY304486.1 SARS coronavirus SZ3, complete genome 15202 22509 87% 0.0 82.33% AY304486.1 Select seq AY390556.1 SARS coronavirus GZ02, complete genome 15191 22507 86% 0.0 82.32% AY390556.1 Select seq EU371564.1 SARS coronavirus BJ182-12, complete genome 15186 22443 86% 0.0 82.32% EU371564.1 Select seq AY394985.1 SARS coronavirus HSZ-Bb, complete genome 15186 22206 86% 0.0 82.31% AY394985.1 Select seq AY278554.2 SARS coronavirus CUHK-W1, complete genome 15186 22507 86% 0.0 82.32% AY278554.2 Select seq EU371559.1 SARS coronavirus ZJ02, complete genome 15180 22507 86% 0.0 82.31% EU371559.1 Select seq AY559093.1 SARS coronavirus Sin845, complete genome 15180 22480 86% 0.0 82.31% AY559093.1 Select seq AY394994.1 SARS coronavirus HSZ-Bc, complete genome 15180 22496 86% 0.0 82.31% AY394994.1 Select seq AY394986.1 SARS coronavirus HSZ-Cb, complete genome 15180 22456 86% 0.0 82.31% AY394986.1 Select seq MK211376.1 Coronavirus BtRs-BetaCoV/YN2018B, complete genome 15176 22605 89% 0.0 82.32% MK211376.1 Select seq KY417146.1 Bat SARS-like coronavirus isolate Rs4231, complete genome 15176 22473 89% 0.0 82.30% KY417146.1 Select seq JX163927.1 SARS coronavirus isolate Tor2/FP1-10851, complete genome 15175 22411 86% 0.0 82.30% JX163927.1 Select seq JX163926.1 SARS coronavirus isolate Tor2/FP1-10912, complete genome 15175 22419 86% 0.0 82.30% JX163926.1 Select seq JX163923.1 SARS coronavirus isolate Tor2/FP1-10912, complete genome 15175 22411 86% 0.0 82.30% JX163923.1 Select seq JQ316196.1 SARS coronavirus HKU-39849 isolate UOB, complete genome 15175 22496 86% 0.0 82.30% JQ316196.1 Select seq FJ882963.1 SARS coronavirus P2, complete genome 15175 22444 86% 0.0 82.30% FJ882963.1 Select seq DQ898174.1 SARS coronavirus strain CV7, complete genome 15175 22496 86% 0.0 82.30% DQ898174.1 Select seq AY864806.1 SARS coronavirus BJ202, complete genome 15175 22502 86% 0.0 82.30% AY864806.1 Select seq AY714217.1 SARS Coronavirus CDC#200301157, complete genome 15175 22496 86% 0.0 82.30% AY714217.1 Select seq AY559096.1 SARS coronavirus Sin850, complete genome 15175 22489 86% 0.0 82.30% AY559096.1 Select seq AY559095.1 SARS coronavirus Sin847, complete genome 15175 22474 86% 0.0 82.30% AY559095.1 Select seq AY559086.1 SARS coronavirus Sin849, complete genome 15175 22478 86% 0.0 82.30% AY559086.1 Select seq AY559085.1 SARS coronavirus Sin848, complete genome 15175 22474 86% 0.0 82.30% AY559085.1 Select seq AY559084.1 SARS coronavirus Sin3765V, complete genome 15175 22480 86% 0.0 82.30% AY559084.1 Select seq AY559083.1 SARS coronavirus Sin3408, complete genome 15175 22476 86% 0.0 82.30% AY559083.1 Select seq AY559082.1 SARS coronavirus Sin852, complete genome 15175 22474 86% 0.0 82.30% AY559082.1 Select seq AY274119.3 Severe acute respiratory syndrome-related coronavirus isolate Tor2, complete genome 15175 22491 86% 0.0 82.30% AY274119.3 Select seq AY323977.2 SARS coronavirus HSR 1, complete genome 15175 22502 86% 0.0 82.30% AY323977.2 Select seq AY291451.1 SARS coronavirus TW1, complete genome 15175 22502 86% 0.0 82.30% AY291451.1 Select seq AY502928.1 SARS coronavirus TW5, complete genome 15175 22496 86% 0.0 82.30% AY502928.1 Select seq AY502926.1 SARS coronavirus TW3, complete genome 15175 22489 86% 0.0 82.30% AY502926.1 Select seq AY502923.1 SARS coronavirus TW10, complete genome 15175 22502 86% 0.0 82.30% AY502923.1 Select seq AY394999.1 SARS coronavirus LC2, complete genome 15175 22441 86% 0.0 82.30% AY394999.1 Select seq AY394998.1 SARS coronavirus LC1, complete genome 15175 22491 86% 0.0 82.30% AY394998.1 Select seq AY394995.1 SARS coronavirus HSZ-Cc, complete genome 15175 22485 86% 0.0 82.30% AY394995.1 Select seq AY394993.1 SARS coronavirus HGZ8L2, complete genome 15175 22491 86% 0.0 82.31% AY394993.1 Select seq AY394992.1 SARS coronavirus HZS2-C, complete genome 15175 22496 86% 0.0 82.31% AY394992.1 Select seq AY394991.1 SARS coronavirus HZS2-Fc, complete genome 15175 22496 86% 0.0 82.30% AY394991.1 Select seq AY394987.1 SARS coronavirus HZS2-Fb, complete genome 15175 22478 86% 0.0 82.30% AY394987.1 Select seq AY394983.1 SARS coronavirus HSZ2-A, complete genome 15175 22465 86% 0.0 82.30% AY394983.1 Select seq AY394978.1 SARS coronavirus GZ-B, complete genome 15175 22391 86% 0.0 82.30% AY394978.1 Select seq AY357075.1 SARS coronavirus PUMC02, complete genome 15175 22487 86% 0.0 82.30% AY357075.1 Select seq AY282752.2 SARS coronavirus CUHK-Su10, complete genome 15175 22491 86% 0.0 82.30% AY282752.2 Select seq AY427439.1 SARS coronavirus AS, complete genome 15175 22496 86% 0.0 82.30% AY427439.1 Select seq AY283796.1 SARS coronavirus Sin2679, complete genome 15175 22502 86% 0.0 82.30% AY283796.1 Select seq AP006561.1 SARS coronavirus TWY genomic RNA, complete genome 15175 22502 86% 0.0 82.30% AP006561.1 Select seq JX163925.1 SARS coronavirus isolate Tor2/FP1-10895, complete genome 15173 22409 86% 0.0 82.30% JX163925.1 Select seq JX163928.1 SARS coronavirus isolate Tor2/FP1-10895, complete genome 15171 22419 86% 0.0 82.30% JX163928.1 Select seq JX163924.1 SARS coronavirus isolate Tor2/FP1-10851, complete genome 15169 22415 86% 0.0 82.30% JX163924.1 Select seq GU553363.1 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00001, complete genome 15169 22409 86% 0.0 82.30% GU553363.1 Select seq EU371563.1 SARS coronavirus BJ182-8, complete genome 15169 22463 86% 0.0 82.30% EU371563.1 Select seq EU371561.1 SARS coronavirus BJ182b, complete genome 15169 22468 86% 0.0 82.30% EU371561.1 Select seq EU371560.1 SARS coronavirus BJ182a, complete genome 15169 22468 86% 0.0 82.30% EU371560.1 Select seq AY864805.1 SARS coronavirus BJ162, complete genome 15169 22496 86% 0.0 82.30% AY864805.1 Select seq AY278741.1 SARS coronavirus Urbani, complete genome 15169 22502 86% 0.0 82.30% AY278741.1 Select seq AY559087.1 SARS coronavirus Sin3725V, complete genome 15169 22483 86% 0.0 82.29% AY559087.1 Select seq AY394989.1 SARS coronavirus HZS2-D, complete genome 15169 22491 86% 0.0 82.30% AY394989.1 Select seq AY485278.1 SARS coronavirus Sino3-11, complete genome 15169 22485 86% 0.0 82.30% AY485278.1 Select seq AY502927.1 SARS coronavirus TW4, complete genome 15167 22489 86% 0.0 82.29% AY502927.1 Select seq GU553365.1 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00003, complete genome 15165 22400 86% 0.0 82.29% GU553365.1 Select seq KJ473816.1 BtRs-BetaCoV/YN2013, complete genome 15163 21667 83% 0.0 82.29% KJ473816.1 Select seq EU371562.1 SARS coronavirus BJ182-4, complete genome 15158 22457 86% 0.0 82.29% EU371562.1 Select seq MK211377.1 Coronavirus BtRs-BetaCoV/YN2018C, complete genome 15149 22390 87% 0.0 82.29% MK211377.1 Select seq KY417145.1 Bat SARS-like coronavirus isolate Rf4092, complete genome 15134 22310 85% 0.0 82.26% KY417145.1 Select seq MK211375.1 Coronavirus BtRs-BetaCoV/YN2018A, complete genome 15117 22358 87% 0.0 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% 0.0 82.35% KF294455.1 Select seq JX993988.1 Bat coronavirus Cp/Yunnan2011, complete genome 15043 21828 85% 0.0 82.18% JX993988.1 Select seq KJ473814.1 BtRs-BetaCoV/HuB2013, complete genome 14970 22299 85% 0.0 82.20% KJ473814.1 Select seq DQ648857.1 Bat coronavirus (BtCoV/279/2005), complete genome 14916 22120 85% 0.0 82.16% DQ648857.1 Select seq JX993987.1 Bat coronavirus Rp/Shaanxi2011, complete genome 14892 21814 86% 0.0 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% 0.0 81.89% KF294457.1 Select seq MK211374.1 Coronavirus BtRl-BetaCoV/SC2018, complete genome 14731 21823 85% 0.0 82.02% MK211374.1 Select seq KJ473813.1 BtRf-BetaCoV/SX2013, complete genome 14722 21320 85% 0.0 81.82% KJ473813.1 Select seq KJ473812.1 BtRf-BetaCoV/HeB2013, complete genome 14683 21222 85% 0.0 81.79% KJ473812.1 Select seq KJ473811.1 BtRf-BetaCoV/JL2012, complete genome 14683 21061 85% 0.0 81.79% KJ473811.1 Select seq GQ153542.1 Bat SARS coronavirus HKU3-7, complete genome 14683 21924 87% 0.0 81.82% GQ153542.1 Select seq GQ153543.1 Bat SARS coronavirus HKU3-8, complete genome 14678 21962 86% 0.0 81.82% GQ153543.1 Select seq KY770860.1 Bat coronavirus isolate Jiyuan-84, complete genome 14628 21379 85% 0.0 81.74% KY770860.1 Select seq DQ648856.1 Bat coronavirus (BtCoV/273/2005), complete genome 14556 21331 86% 0.0 81.66% DQ648856.1 Select seq DQ412042.1 Bat SARS coronavirus Rf1, complete genome 14556 21327 86% 0.0 81.66% DQ412042.1 Select seq GQ153547.1 Bat SARS coronavirus HKU3-12, complete genome 14550 21797 87% 0.0 81.68% GQ153547.1 Select seq KF294456.1 SARS-related bat coronavirus isolate Jiyuan-331 orf1ab polyprotein gene, complete cds 14539 15829 64% 0.0 81.66% KF294456.1 Select seq FJ211859.1 Recombinant coronavirus clone Bat SARS-CoV, complete sequence 14517 21803 87% 0.0 81.65% FJ211859.1 Select seq DQ084199.1 bat SARS coronavirus HKU3-2, complete genome 14512 21784 87% 0.0 81.64% DQ084199.1 Select seq GQ153540.1 Bat SARS coronavirus HKU3-5, complete genome 14506 21758 87% 0.0 81.63% GQ153540.1 Select seq GQ153539.1 Bat SARS coronavirus HKU3-4, complete genome 14506 21764 87% 0.0 81.63% GQ153539.1 Select seq GQ153546.1 Bat SARS coronavirus HKU3-11, complete genome 14501 21747 87% 0.0 81.63% GQ153546.1 Select seq DQ022305.2 Bat SARS coronavirus HKU3-1, complete genome 14501 21786 87% 0.0 81.63% DQ022305.2 Select seq DQ084200.1 bat SARS coronavirus HKU3-3, complete genome 14501 21779 87% 0.0 81.63% DQ084200.1 Select seq GQ153548.1 Bat SARS coronavirus HKU3-13, complete genome 14495 21736 87% 0.0 81.63% GQ153548.1 Select seq GQ153541.1 Bat SARS coronavirus HKU3-6, complete genome 14495 21764 87% 0.0 81.62% GQ153541.1 Select seq GQ153545.1 Bat SARS coronavirus HKU3-10, complete genome 14484 21725 87% 0.0 81.61% GQ153545.1 Select seq GQ153544.1 Bat SARS coronavirus HKU3-9, complete genome 14484 21725 87% 0.0 81.61% GQ153544.1 Select seq KU182964.1 Bat coronavirus isolate JTMC15, complete genome 13501 20234 77% 0.0 82.94% KU182964.1 Select seq KY938558.1 Bat coronavirus strain 16BO133, complete genome 13452 20134 77% 0.0 82.88% KY938558.1

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 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]

Wuhan Municipal Health and Health Commission's Report on Unexplained Viral Pneumonia Issuing authority: Wuhan City health committee | Published: 2020-01-11 07:04:11 | Hits: 4410 After the pathogen of "unknown cause of viral pneumonia" was initially determined to be a new type of coronavirus, the national, provincial and municipal expert groups immediately revised and improved plans for diagnosis, treatment, and monitoring of unexplained viral pneumonia. The Wuhan Municipal Health and Health Committee has organized tests on existing patient specimens. As of 14:00 on January 10, 2020, pathogenic nucleic acid testing has been completed. The national, provincial and municipal expert groups comprehensively judged the clinical manifestations, epidemiological history, and laboratory test results of patients admitted to the hospital for treatment, and 41 cases of pneumonia with a new coronavirus infection were initially diagnosed, of which 2 were discharged, Seven cases were severe and one died. The remaining patients were in stable condition. All 739 close contacts, including 419 medical staff, have undergone medical observation and no related cases have been found. Since the outbreak, with the support of the state and Hubei Province, Wuhan has cooperated with relevant departments to carry out the prevention and treatment in an orderly manner. First, we have tried our best to treat patients. Develop a diagnosis and treatment work plan, and effectively achieve early detection, early diagnosis, early isolation, and early treatment, and focus on experts and resources to give full treatment. The second is to carry out in-depth epidemiological investigations. The investigation found that the patients were mainly operating and purchasing staff of the South China Seafood Wholesale Market in Wuhan. On January 1, 2020, the South China Seafood Wholesale Market has been closed and measures have been taken to strengthen the prevention of disease and environmental hygiene in public places in the city, especially the farmers' market. management. The third is to widely publicize disease prevention knowledge and enhance public self-protection awareness. The fourth is to cooperate with the state and province to carry out pathogenic research. The fifth is to cooperate with the National Health and Health Commission to report the epidemic situation information to the World Health Organization in a timely manner. No new cases have been detected since January 3, 2020. At present, no medical staff infections have been found, and no clear evidence of human-to-human transmission has been found. Our city will continue to strengthen patient treatment, epidemiological investigations, carry out in-depth patriotic health campaigns, do a good job in spreading knowledge of disease prevention, and safeguard the health of the people. At present, it is in the season of high incidence of infectious diseases in winter and spring. The public must maintain indoor air circulation, try to avoid closed public places and crowded places, and wear masks if necessary. If you have fever, respiratory infection symptoms, especially persistent fever, go to a medical institution in time. January 11, 2020

As of 14:00 on January 10, 2020, pathogenic nucleic acid testing has been completed. The national, provincial and municipal expert groups comprehensively judged the clinical manifestations, epidemiological history, and laboratory test results of patients admitted to the hospital for treatment, and 41 cases of pneumonia with a new coronavirus infection were initially diagnosed, of which 2 were discharged, Seven cases were severe and one died. http://wjw.wuhan.gov.cn/front/web/showDetail/2020011109035

This thread will tally confirmed Wuhan fatalities linked to the novel coronavirus.

“Plenty of people are working on the outbreak,” says Xu Jianguo, head of an evaluation committee advising the Chinese government. XU JIANGUO Mystery virus found in Wuhan resembles bat viruses but not SARS, Chinese scientist says By Dennis NormileJan. 10, 2020 , 12:30 PM SHANGHAI—A new coronavirus identified by Chinese scientists is the putative cause of an outbreak of unusual pneumonia in the central city of Wuhan, according to Chinese news reports yesterday. In an interview today with Science, Xu Jianguo, head of an evaluation committee advising the Chinese government, confirmed that scientists have a complete sequence of the novel virus’s genome. The World Health Organization on 9 January requested sequence data, a spokesperson in Geneva says, and many scientists urge the country to make the sequence public quickly, but the decision is up to the top leadership of the Chinese Center for Disease Control and Prevention, says Xu, who is director of the Beijing-based State Key Laboratory for Infectious Disease Prevention and Control, part of China CDC. (The center’s head, George Gao, did not respond to emails from Science seeking comment.) Xu says the investigation is being led by China CDC but numerous groups in other government agencies are involved. “Plenty of people are working on the outbreak,” he says. The role of the evaluation committee Xu leads is to review all the findings and make recommendations to the National Health Commission. Xu also said the novel coronavirus resembles known bat viruses, but not the coronaviruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The following transcript has been edited for clarity and brevity. Q: The virus has been isolated from one patient, is that correct? A: Correct. Two groups isolated the virus from samples from one patient. The viruses are nearly identical in morphology under electron microscopy. Researchers did laboratory investigations of 34 patients. A total of 15 were positive for the novel virus, [based on] sequencing samples of [fluid injected into the lung and collected for examination]. The teams got complete genome sequence data from about 10 patients. They are now attempting to isolate the virus from those samples as well. There are 19 cases with no evidence of the virus. There is no information available for the results of the remaining 25 cases. Q: How close is this new virus to the SARS coronavirus? A: The virus is similar to some of the published viruses collected from bats. But it is not close to SARS and not close to MERS. Q: Are close contacts of patients and market workers being tested for antibodies to the new virus? A: [Investigators] have just gotten the virus, they now need the chance to prepare reagents for antibody tests, but there are no data yet. Q: The 5 January report from the Wuhan Municipal Health Commission, the latest available, says a total of 59 pneumonia patients have been identified as possibly carrying the virus. Have more patients been found? A: It should be mentioned that the 59 reported pneumonia patients in Wuhan were clinically diagnosed; of those, 15 were confirmed to be infected by the new coronavirus. No new patients have appeared, as far as I understand. It’s good news. People fear something like SARS in 2003, but this is a different case. The outbreak is limited, but we should test patients one by one [to identify] pneumonia caused by other pathogens. Q: Are researchers trying to replicate the disease in lab animals to prove that it is really the cause of the outbreak? A: People have recommended that [investigators] do tests to see if the virus can cause the infection in animals, but they need time. Q: Is there any progress in tracing the original source of the virus? A: I have no information. Personally, I’m interested, too. The virus looks like viruses isolated from bats, but how it was transmitted from bats to people is still a question. Several groups in China have been working on bat coronaviruses for years. I imagine they’re working on this but so far there is no information. Q: Are other live animal markets being checked? A: The Wuhan market has been closed. I have no information about other [markets]. Wild animals carry the risk of exposing people to new viruses. I think we should have more strict regulations and inspections of markets that sell wild animals, especially since the source of the new coronavirus has not been identified and eliminated. With reporting by Jon Cohen. Posted in: Asia/Pacific Health People & Events doi:10.1126/science.aba8542 Dennis Normile https://www.sciencemag.org/news/2020/01/mystery-virus-found-wuhan-resembles-bat-viruses-not-sars-chinese-scientist-says

There have been at least 1 or 2 clusters of cases within families that have raised suspicions of limited person-to-person spread, a source familiar with the outbreak told STAT. https://www.statnews.com/2020/01/09/chinese-scientists-obtain-genetic-sequence-of-mysterious-virus-a-key-step-in-containment-efforts/

Disease information Vaccines Other travel health risks General precautions Mode of travel considerations WHO advice for international travel and trade in relation to the outbreak of pneumonia caused by a new coronavirus in China 10 January 2020 On 31 December 2019, a cluster of pneumonia of unknown etiology was reported in Wuhan City, Hubei Province of China. On 9 January Chinese authorities reported in the media that the cause of this viral pneumonia was initially identified as a new type of coronavirus, which is different from any other human coronaviruses discovered so far . Coronaviruses are a large family of respiratory viruses that can cause diseases ranging from the common cold to the Middle-East Respiratory Syndrome and the Severe Acute Respiratory Syndrome (SARS). The clinical signs and symptoms of the patients reported in this cluster are mainly fever, with a few patients having difficulty in breathing, and chest radiographs showing bilateral lung infiltrates. Some cases were operating dealers or vendors in Huanan Seafood Market. From the currently available information, preliminary investigation suggests that there is no significant human-to-human transmission, and no infections among health care workers have occurred. More information is required to better understand the mode of transmission and clinical manifestation of this new virus. The source of this new virus is not yet known. International travellers: practice usual precautions While the cause of the pneumonia seems to be a novel coronavirus, transmission potential and modes of transmission remain unclear. Therefore, it would be prudent to reduce the general risk of acute respiratory infections while travelling in or from affected areas (currently Wuhan City) by: avoiding close contact with people suffering from acute respiratory infections; frequent hand-washing, especially after direct contact with ill people or their environment; avoiding close contact with live or dead farm or wild animals; travellers with symptoms of acute respiratory infection should practice cough etiquette (maintain distance, cover coughs and sneezes with disposable tissues or clothing, and wash hands). Health practitioners and public health authorities should provide to travellers information to reduce the general risk of acute respiratory infections, via travel health clinics, travel agencies, conveyance operators and at points of entry. If a traveller on board of an aircraft/a ship has signs and symptoms indicative of acute respiratory infections, the model of Maritime declaration of health (Annex 8 of IHR) or the health part of the aircraft general declaration (Annex 9 of IHR) can be used to register the health information onboard and submit to POE health authorities when required by a State Party. A passenger locator form can be used in the event of a sick traveller detected on board a plane. This form is useful for collecting contact information for passengers and can be used for follow-up if necessary. Travellers should also be encouraged to self-report if they feel ill. The cabin crew should follow the operational procedures recommended by International Air Transport Association (IATA) with regard to managing suspected communicable disease on board an aircraft. International traffic: no restrictions recommended Wuhan city is a major domestic and international transport hub. Currently, there are no reports of cases outside of Wuhan City. Given the heavy population movements, expected to significantly increase during the Chinese New Year in the last week of January, the risk of cases being reported form elsewhere is increased. WHO does not recommend any specific health measures for travellers. It is generally considered that entry screening offers little benefit, while requiring considerable resources. In case of symptoms suggestive to respiratory illness before, during or after travel, the travellers are encouraged to seek medical attention and share travel history with their health care provider. WHO advises against the application of any travel or trade restrictions on China based on the information currently available on this event. As provided by the International Health Regulations (2005) (IHR), countries should ensure that: routine measures, trained staff, appropriate space and stockpile of adequate equipment in place at points of entry for assessing and managing ill travellers detected before travel, on board conveyances (such as planes and ships) and on arrival at points of entry; procedures and means are in place for communicating information on ill travellers between conveyances and points of entry as well as between points of entry and national health authorities; safe transportation of symptomatic travellers to hospitals or designated facilities for clinical assessment and treatment is organized; a functional public health emergency contingency plan at points of entry in place to respond to public health events. https://www.who.int/ith/2020-0901_outbreak_of_Pneumonia_caused_by_a_new_coronavirus_in_C/en/?fbclid=IwAR0um9rSJ8DWBHv446phYalVIPR3M2zfdwJycoyoy5IdEWLx-hFIaoErvNE

Published Date: 2020-01-10 11:37:53 Subject: PRO/AH/EDR> Undiagnosed pneumonia - China (HU) (08): novel coronavirus, WHO Archive Number: 20200110.6881082 UNDIAGNOSED PNEUMONIA - CHINA (HUBEI) (08): NOVEL CORONAVIRUS, WHO ****************************************************************** A ProMED-mail post http://www.promedmail.org ProMED-mail is a program of the International Society for Infectious Diseases http://www.isid.org In this update: [1] WHO statement [2] Sina Tech News: Evolution of pathogen identification [3] Stat News: Overview ****** [1] WHO statement Date: Thu 9 Jan 2020 Source: WHO press release [edited] https://www.who.int/china/news/detail/09-01-2020-who-statement-regarding-cluster-of-pneumonia-cases-in-wuhan-china WHO statement regarding cluster of pneumonia cases in Wuhan, China [9 Jan 2020] statement -------------------------------------------------------------------------------- Chinese authorities have made a preliminary determination of a novel (or new) coronavirus, identified in a hospitalized person with pneumonia in Wuhan. Chinese investigators conducted gene sequencing of the virus, using an isolate from one positive patient sample. Preliminary identification of a novel virus in a short period of time is a notable achievement and demonstrates China's increased capacity to manage new outbreaks. Initial information about the cases of pneumonia in Wuhan provided by Chinese authorities last week [week of 1 Jan 2020] -- including the occupation, location, and symptom profile of the people affected -- pointed to a coronavirus (CoV) as a possible pathogen causing this cluster. Chinese authorities subsequently reported that laboratory tests ruled out SARS-CoV, MERS-CoV, influenza, avian influenza, adenovirus, and other common respiratory pathogens. Coronaviruses are a large family of viruses with some causing less-severe disease, such as the common cold, and others more severe disease such as MERS and SARS. Some transmit easily from person to person, while others do not. According to Chinese authorities, the virus in question can cause severe illness in some patients and does not transmit readily between people. Globally, novel coronaviruses emerge periodically in different areas, including SARS in 2002 and MERS in 2012. Several known coronaviruses are circulating in animals that have not yet infected humans. As surveillance improves more coronaviruses are likely to be identified. China has strong public health capacities and resources to respond and manage respiratory disease outbreaks. In addition to treating the patients in care and isolating new cases as they may be identified, public health officials remain focused on continued contact tracing, conducting environmental assessments at the seafood market, and investigations to identify the pathogen causing the outbreak. In the coming weeks, more comprehensive information is required to understand the current status and epidemiology of the outbreak, and the clinical picture. Further investigations are also required to determine the source, modes of transmission, extent of infection, and countermeasures implemented. WHO continues to monitor the situation closely and, together with its partners, is ready to provide technical support to China to investigate and respond to this outbreak. The preliminary determination of a novel virus will assist authorities in other countries to conduct disease detection and response. Over the past week, people with symptoms of pneumonia and reported travel history to Wuhan have been identified at international airports. WHO does not recommend any specific measures for travellers. WHO advises against the application of any travel or trade restrictions on China based on the information currently available. Media Contacts Paige Snider External Relations and Communication World Health Organization <[email protected]> -- Communicated by: ProMED-mail Rapporteur Kunihiko Iizuka ****** [2] Sina Tech News: Evolution of pathogen identification Date: Thu 9 Jan 2020 19:37:00 CST Source: Sina Technology, Caijing Magazine report [in Chinese, trans., edited] http://tech.sina.com.cn/roll/2020-01-09/doc-iihnzahk3089851.shtml When a virus strikes, identifying the pathogen quickly and accurately is the key to success. This depends on the development of scientific research, the improvement of the disease surveillance system and the continuous openness and transparency of information. The "new coronavirus" has caused several cases of unexplained pneumonia in Wuhan [Hubei] to be initially "identified." According to Xinhua News Agency, on [9 Jan 2020], Xu Jianguo, the leader of the preliminary assessment of pathogenic test results and an academician of the Chinese Academy of Engineering, said that the expert group believes that the pathogen of this unexplained viral pneumonia case was initially determined to be a new type of coronavirus. At 21:00 [9 PM] on [7 Jan 2020], the expert group detected a new coronavirus in the laboratory and obtained its entire genome sequence. A scholar close to the expert group told the reporter of Caijing that the wild animals sold in the South China Seafood Market are currently under inspection to track down the source of the virus. The Wuhan Municipal Health and Health Commission reported that as of [5 Jan 2020], there were 59 cases of viral pneumonia, of which 7 were critically ill patients, and the remaining patients had overall stable vital signs and no deaths. On [8 Jan 2020], 8 patients were cured and discharged. In previous reports, viruses such as SARS and avian influenza have been excluded. A person in charge of the pathogenic laboratory of a disease control center in a northwestern province told the Caijing reporter that after getting the specimens, the laboratory could screen for a known or common virus within a day. These include influenza, avian influenza, adenovirus, SARS, etc. However, it takes longer to detect and identify unknown viruses. The SARS epidemic that broke out in 2003 took scientists more than 5 months to finally determine the new coronavirus; the H7N9 avian influenza epidemic in 2013 took more than one month from the 1st case to the diagnosis of the virus. The Wuhan epidemic was first notified on [31 Dec 2019], and was initially identified as "new coronavirus" by research experts at an interval of 9 days. Relying on the progress of scientific research and the prevention and control system of infectious diseases, the detection time of pathogens has been greatly shortened. Coronavirus disorder -------------------- The virus that causes unexplained pneumonia in Wuhan, like SARS, is a coronavirus. Under the microscope, the virus had obvious stick-shaped particle protrusions on the outer mold, so it looked like the crown of medieval European emperors and was named "Coronavirus". The virus was first isolated from chickens more than 80 years ago. In 1965, scientists isolated the 1st human coronavirus. [A] virus is a simple microorganism composed of nucleic acid and protein shell, including DNA and RNA viruses. Coronaviruses are RNA viruses. Its variability is high because its recombination rate between RNA and RNA is very high. In other words, the genetic material that determines its viral characteristics is constantly changing. The current research progress is that the coronavirus family contains nearly 20 viruses of the genus [alpha, beta, gamma, delta] among which there are 6 types of coronavirus known to infect humans. Among them, the 4 coronaviruses are more common in the population, and they are less pathogenic, and generally cause only minor respiratory symptoms similar to the common cold. The other 2, SARS and Middle East respiratory syndrome coronavirus, can cause severe respiratory diseases. The former (SARS) has obvious interpersonal transmission, causing the disease to spread rapidly. Classical coronavirus infection, which mainly occurs in winter and spring, is an important cause of acute exacerbation of chronic bronchitis in adults. Due to the high variability of the coronavirus, the original vaccine will fail and immunity will fail. Li Gang, director of the Wuhan Municipal Center for Disease Control and Prevention, said in a media interview that the clinical manifestations of patients in Wuhan were viral pneumonia. More stringent preventive public health measures such as patient isolation and close contact tracing are needed. According to the Wuhan Health Commission, the clinical manifestations of unexplained pneumonia in Wuhan were mainly fever, a few patients had difficulty breathing, and chest radiographs showed invasive lesions of both lungs. The main difference from SARS symptoms is that no clear evidence of human-to-human transmission has been found. "No clear evidence of human-to-human transmission or medical staff infection was found." In 3 circulars issued by the Wuhan Health Commission, this sentence repeated. An influenza control expert told a Caijing reporter that whether human-to-human transmission occurs after infection with the virus depends on the characteristics of the virus, especially its binding to the receptor. This characteristic is also related to whether the virus is likely to infect humans. In 2003, H5N1 human bird flu cases continued to appear, causing a high lethality. The flu control experts explained that the tissue structure of the avian influenza virus receptors is different compared to human influenza viruses. The human upper respiratory tract does not have avian influenza virus receptors, so it is difficult to infect humans. But people in the lower respiratory tract have receptors for avian influenza virus in the lungs. Once avian influenza virus affects human lungs, it can cause human infection and the symptoms are severe. Despite a long history of confrontation with viruses, to this day, humans still cannot fully understand such a small, simple structure of acellular microorganisms. 9 days from initial notification -------------------------------- In the face of virus invasion, rapid and accurate identification of the pathogen is the key to success. "The pathogen of unexplained viral pneumonia cases was initially identified as a new type of coronavirus", which is the latest news of unexplained pneumonia in Wuhan. 9 days from the 1st notification. At 1 pm on [31 Dec 2019], a staff member of the Wuhan Centers for Disease Control and Prevention told a reporter from Caijing that the Wuhan Centers for Disease Control and Prevention had tested the specimens, and the Hubei Province Centers for Disease Control and Prevention was organizing experts to review the case specimens. Only by knowing the pathogen can we target medicine. In this race against time, "every second counts" is not an exaggeration. This depends on the development of scientific research, the improvement of the disease surveillance system and the continuous openness and transparency of information. In April 2003, the World Health Organization (WHO) announced in Geneva that the pathogen of SARS is a new coronavirus known as SARS coronavirus. This time, more than 5 months away from the 1st case notification. On the afternoon of [29 Mar 2013], the Chinese Center for Disease Control and Prevention isolated 3 strains of H7N9 avian influenza virus from the specimens submitted for examination and confirmed the diagnosis. At this time, the 1st case had been onset for more than a month. During the "unknown pneumonia" incident in Wuhan, the pathogen identification time was significantly reduced. The latest bulletin on [9 Jan 2020] showed that the laboratory used methods such as genome sequencing, nucleic acid detection, and virus isolation to etiologically detect samples from patients with alveolar lavage fluid, throat swabs, and blood. To confirm the cause of an epidemic disease, 3 points need to be met: 1st, the suspected pathogen must be found in the patient, and the pathogenic nucleic acid can be detected in the patient's clinical sample. 2nd, pathogens can be successfully isolated from clinical samples of patients. In addition, isolated pathogens can cause the same disease symptoms when infecting a host animal. The patient's serum antibody titer during the recovery period increased 4-fold, which can help identify the pathogen. Scientific research, such as pathogen isolation and pathogenicity identification, typically takes weeks. A director of the Respiratory Department of Beijing Top Three Hospital analyzed the reporter of Caijing that whether the cultured virus can grow depends on the amount and viability of the virus in clinical specimens. Immunological methods are able to detect viral antigens from respiratory secretions, but the final results also depend on a relatively high viral load. The person in charge of one of the aforementioned pathogen laboratories added that the virus lives in the cell and must find the specific cell it grows in, and mutation may occur during isolation. Even if the virus is isolated, animal experiments need to be performed to verify compliance with the clinical manifestations of existing patients and determine the virus in question. After that, the virus must be cultivated, which is also a time-consuming task, sometimes it takes at least 20 days. The emergence of molecular biology technology has enabled experimenters to find the pathogen's nucleic acid, genome and other evidence in a short period of time, and identify whether it is a known virus or a type of virus. One of the achievements of the "National Major Project for Infectious Diseases" released by the Ministry of Science and Technology in 2017 is to establish a detection technology system that identifies 300 known pathogens within 72 hours. The genetic information of the virus is stored in the nucleic acid, which at the same time indicates the characteristics of the virus and also acts as an "identity card", which can help researchers distinguish the specific virus type. The main principle is to design another nucleic acid sequence that can match the virus identity information. In the vast ocean of nucleic acids, like a probe, paired with a specific "identity" virus. The director of the Beijing Respiratory Department told the Caijing reporter that using the above principles, the existing technology can detect 12-15 viruses at the same time, which has become the standard method for respiratory virus detection. 1st, such technologies will be used to screen for known or common pneumonia viruses. The person in charge of the above-mentioned pathogen laboratory said, "In less than a day, it is possible to determine whether there are a dozen known pneumonia viruses." These include influenza, avian influenza, adenovirus, SARS, etc. If the specific virus type has not been identified, the laboratory director will commission a testing company to compare the specimen with the genetic information in the pathogen database to determine the virus type. The above method requires predicting the pathogen sequence, and is powerless against unknown pathogens and pathogens with large sequence variation. "If these methods are still uncertain, we will consider whether it is a new pathogen. The virus needs to be isolated and cultured, and then identified by various methods." The person in charge of the said pathogen laboratory said. In the end, the expert group believed that the pathogen of unexplained viral pneumonia cases in Wuhan was initially determined as a new type of coronavirus. Track down the root cause of the virus -------------------------------------- Only by knowing where the virus came from can we control its outbreak from the source. At present, the etiology of unexplained pneumonia in Wuhan is still ongoing. A scholar close to the expert group told Caijing that at present, wild animals appearing in the South China seafood market are being inspected to track down the source of the virus. Taking the SARS coronavirus as an example, the traceability of the virus from civet to bat is not easy. It took more than 2 years. In 2003, researchers isolated 3 SARS-like viruses from 6 civet specimens, confirming that civet sold on the market is the direct cause of SARS infection. But it was not until 2 years later that the original host of SARS was discovered. An article published by Shi Zhengli's team at the Wuhan Institute of Virology of the Chinese Academy of Sciences in the journal Science revealed that bats are "natural hosts of SARS-like coronavirus." Although many domestic markets for wildlife trading have been restricted or facing closures since the outbreak of SARS and bird flu, the phenomenon of buying, selling, and eating wildlife is still very common. In the South China Seafood Market in Wuhan, "wild meat" was never completely banned at the outbreak of viral pneumonia of unknown cause. According to previous reports by Red Star News, there are a lot of abandoned rabbit heads and animal offal in the corner of Sixth Street in the western part of the market. The owner of the stall said that there are several shops selling wild game in the market, including pheasant and snake. The multiple unexplained pneumonia cases in Wuhan this time reminded the danger of wildlife trading again. Yuan Guoyong, a microbiologist at the University of Hong Kong who is involved in the SARS virus research, mentioned in an article in the famous scientific journal "Nature" that wildlife habitats should not be disturbed, and wildlife should not be brought into the market for circulation and trading. In Yuan Guoyong's view, learning to respect nature and respect it is "very important to prevent the occurrence of new infectious diseases." This article is the exclusive cooperation content between Caijing and Tencent News. [Byline: Wen, Zhu He, and editor Wang Xiao] -- Communicated by: ProMED-mail Rapporteur Kunihiko Iizuka [A very good review of the process involved in the identification of viral etiologies for respiratory diseases. The ending conclusion on the need to respect the wildlife and the danger in wildlife trading leads one to remember that in the past 25 or more years, 75 percent of new human diseases involved species jumps from "domestic" animals (which include livestock and camels); and 70 percent of new disease in domestic animals involved species jumps from wildlife to domestic animals. With respect to the SARS-CoV, the jump was from bats, to civets, to humans via the wet markets and then human-to-human, and with the MERS-CoV, while the full transmission isn't completely defined yet, there was the jump from bats, to camels, to humans, and in selected settings, human-to-human transmission. - Mod.MPP] ****** [3] Stat News: Overview Date: Thu 9 Jan 2020 Source: Stat News [edited] https://www.statnews.com/2020/01/09/chinese-scientists-obtain-genetic-sequence-of-mysterious-virus-a-key-step-in-containment-efforts/ Chinese scientists have recovered a previously unknown virus from an infected individual and generated a full genetic sequence of it, a key step in efforts to learn more about the cause of an outbreak of unusual pneumonia in the city of Wuhan, state-run media reported [Thu 9 Jan 2020]. Fragments of the same virus were picked up in testing of 15 patients among the 59 who have been identified as infected with the mysterious pneumonia. The speed of the findings is impressive; the 1st case in this outbreak became ill less than a month ago. "Preliminary identification of a novel virus in a short period of time is a notable achievement and demonstrates China's increased capacity to manage new outbreaks," the World Health Organization's representative in China, Dr Gauden Galea, said in a statement. But more work is needed to confirm whether the virus is the cause of the outbreak and, if it is, to identify what animal species transmitted the virus to people and whether there are other cases elsewhere, Galea said. The report on CCTV appears to be the 1st official confirmation from Chinese authorities that they believe a new virus is responsible for this outbreak -- specifically a coronavirus, a type of virus in the family that includes SARS and MERS. When viewed under an electron microscope, it exhibits the crown-like halo that gives coronaviruses their name, said Xu Jianguo, identified by CCTV as the leader of the preliminary assessment of the test results and a member of the Chinese Academy of Engineering. The outbreak is occurring in Wuhan, about 700 miles [about 1127 km] south of Beijing. Wuhan is a leading center for virology research in China, and infectious diseases experts watching this outbreak have predicted scientists there would quickly find the cause. Still, they cautioned that this discovery does not mean the outbreak is over or the threat has passed. "Everybody's assuming ... that this coronavirus is the cause. We don't know that. They're assuming that market was the origin. We don't know that. And we don't know how many other cases are walking around right now," said Peter Daszak, president of EcoHealth Alliance, a non-profit organization that works in this sphere. The 1st known case in the Wuhan outbreak became noticeably ill on [12 Dec 2019], according to a statement released [Sun 5 Jan 2020] by the Wuhan Municipal Health Commission. The discovery of an outbreak and identification of a new virus in a period of less than one month is exceptional, experts said. "I am stunned by the timeline and speed of this isolation and characterization, if it's all true," said Matthew Frieman, a coronavirus expert at the University of Maryland School of Medicine. The community of scientists who research emerging infectious diseases has been speculating for days that the source of the outbreak was a new coronavirus, a class of viruses that has shown itself adept at making the leap from animals to people. Coronaviruses originate in bats but are able to infect a number of mammals. Confirmation that scientists have the genetic sequence of the virus will increase pressure on China to release at least part of that sequence, so that health facilities around the world know what to look for as they try to detect possible cases from this outbreak and prevent spread elsewhere. During the 2003 SARS outbreak, infected travelers spread the virus from China to Hong Kong and from there to Viet Nam, Singapore, Taiwan, and Toronto, Canada. In the United States, the Centers for Disease Control and Prevention on [Wed 8 Jan 2020] instructed doctors to ask patients with severe respiratory infections whether they have been to Wuhan. Hong Kong and other countries in Southeast Asia are isolating any such cases until they can be tested for influenza, rhinoviruses, and other viruses that cause colds and flu. This type of very broad net will draw in many people who were in or near Wuhan and who have a respiratory tract infection but who have nothing to do with this outbreak -- especially in the middle of flu season. That will eat up resources and the time of doctors, laboratories, and sick people who don't need to be isolated. "If the Chinese truly have sequenced the virus and they've demonstrated that it's present in other patients, that's means there's a PCR diagnostic test available. And the Chinese need to make that available to the rest of the world immediately," said Ralph Baric, a coronavirus expert at the University of North Carolina. "And the longer they wait, the more likely the scientific community will go from a positive response to a negative response, in terms of how China is handling this outbreak," he said. The CCTV report did not provide details on the type of coronavirus that has been discovered -- for instance if it is one of several SARS-like viruses that have been found in bats in China, and if so, how genetically different it is from SARS. A number of these SARS-like viruses are able to infect human tissue cells in the laboratory, suggesting they might be able to spill over into people if given the right circumstances. Xu said more research on the new virus is needed. There has been limited information about the nature of the illness in people who have been infected. Chinese authorities have said no one has died from this infection; 7, however, were in critical condition as of [Sun 5 Jan 2020]. In a statement that same day, the WHO said that the main symptom was fever; some patients had difficulty breathing. The CCTV report also did not indicate whether scientists investigating the outbreak had identified the source of the virus -- which will be key to any effort to determine if the virus is spreading in other locations as well. [Baric] said coronaviruses could jump to people directly from bats, which are eaten in China. But this virus could have used what is known as an intermediate host -- an animal species that becomes infected with a bat virus that then transmits it to people. Daszak said he believes efforts to look for the virus in animals have not started. "There are probably a dozen to 2 dozen target species that you would go after to do a wildlife investigation. I don't know if they're doing that," he said, adding that EcoHealth Alliance hopes to partner with Chinese researchers on the work "once the politics have died down." China was roundly criticized for its early bungling of the SARS outbreak and it is widely believed authorities there have no wish to be embarrassed like that again. The capacity of the country to respond to infectious diseases outbreaks increased markedly in the aftermath of SARS. During that outbreak, it was determined that palm civets, a wild animal eaten as a delicacy in southern China, were transmitting the virus. Chinese authorities ordered a widespread culling of civets to help stop the outbreak. The Wuhan outbreak has been linked to a large seafood market that also sells the meat of exotic animals for consumption. The market was closed and decontaminated on [1 Jan 2020]. But it is important to know if other markets are selling infected animals, said Malik Peiris, a microbiologist at the University of Hong Kong. "If it can jump once, then it will jump again," Peiris said of the virus. He was one of the scientists who first identified the coronavirus that caused the 2003 SARS outbreak, which infected more than 8000 people and killed nearly 800. The WHO said [Wed 8 Jan 2020] that Chinese authorities believe the virus "does not transmit readily between people." Earlier statements from the Wuhan Municipal Health Authority said there has been no person-to-person spread, but disease experts challenged that claim, saying it is impossible to rule out at this stage in the exploration of a new disease. "I don't know how you know that at all," Frieman said of China's claim there is no person-to-person transmission. He noted the number of cases reported makes it seem unlikely that animal-to-human transmission is the only way this virus spreads. There have been at least 1 or 2 clusters of cases within families that have raised suspicions of limited person-to-person spread, a source familiar with the outbreak told STAT. News of the pneumonia cases first emerged on [30 Dec 2019], when the local health authority told hospitals to be on the lookout for cases. The next day Chinese authorities informed the WHO that they were dealing with what looked like an outbreak caused by an unknown virus. [Byline: Helen Branswell] -- Communicated by: ProMED-mail <[email protected]> [A very good overview of the status of the investigation and the many questions that remain to be answered. One piece of new information in the report above is the mention that "there have been at least 1 or 2 clusters of cases within families that have raised suspicions of limited person-to-person spread...". Now that the virus has been identified, further work is needed on the epidemiology of the transmission, including how much community wide transmission may have occurred. It is important to mention that more and more countries are announcing "suspected cases, with media reports on respiratory illnesses in individuals who had been in Wuhan. Countries include South Korea, Thailand, Viet Nam, and Taiwan. In addition, neighboring Hong Kong has now identified 48 individuals who have a febrile respiratory illness with a history of travel to Wuhan. The Hong Kong Center for Health Protection maintains a line listing that is updated daily and includes the viral etiologies from specimens of these suspected cases. Etiologies include influenza viruses, human metapneumovirus, adenovirus, and coronavirus HKU1, to name a few (see https://www.chp.gov.hk/files/pdf/enhanced_sur_pneumonia_wuhan_eng.pdf). There are patients who have not had any known viral pathogens isolated among these 48 cases, so it will be interesting to know results if and when testing for the novel coronavirus becomes available outside of Wuhan. A map showing locations of major cities in China can be found at https://www.chinadiscovery.com/china-maps/city-maps.html. HealthMap/ProMED-mail map of China: http://healthmap.org/promed/p/5294. - Mod.MPP] See Also Undiagnosed pneumonia - China (HU) (07): official confirmation of novel coronavirus 20200108.6878869 Undiagnosed pneumonia - China (06): (HU) Hong Kong surveillance, USA CDC alert 20200108.6876648 Undiagnosed pneumonia - China (05): (HU) novel coronavirus identified 20200108.6877694 Undiagnosed pneumonia - China (04): (HU) Hong Kong surveillance 20200106.6874277 Undiagnosed pneumonia - China (03): (HU) updates, SARS, MERS ruled out, WHO, RFI 20200105.6872267 Undiagnosed pneumonia - China (02): (HU) updates, other country responses, RFI 20200103.6869668 Undiagnosed pneumonia - China (01): (HU) wildlife sales, market closed, RFI 20200102.6866757 2019 ---- Undiagnosed pneumonia - China: (HU) RFI 20191230.6864153 .................................................mpp/ml/mj/ml

Pneumonia cases possibly associated with a novel coronavirus in Wuhan, China Risk assessment 9 Jan 2020 Cite: Citation Link TwitterFacebookLinked InMail On 31 December 2019, the Wuhan Municipal Health Commission reported a cluster of 27 pneumonia cases, including seven severe cases, with a common reported link to Wuhan’s South China Seafood City market. Executive summary Between 31 December 2019 and 5 January 2020, 59 pneumonia cases possibly associated with a novel coronavirus have been reported in Wuhan, China with a common exposure link to Wuhan’s South China Seafood City market. The cases showed symptoms such as fever, dyspnoea, and radiological tests compatible with bilateral lung infiltrative lesions. Seven severe cases have been reported, but no deaths. No cases have been reported outside of Wuhan. According to Chinese authorities, no human to human transmission could be documented. Epidemiological investigations including contact tracing activities are ongoing and hygiene- and environmental sanitation activities in the affected market have been carried out in Wuhan. Three EU airports have direct flight connections to Wuhan and there are indirect flight connections to other EU hubs. Considering there is no indication of human-to-human transmission and no cases detected outside of China, the likelihood of introduction to the EU is considered to be low, but cannot be excluded. However, more epidemiological and laboratory information is needed in order to elaborate a comprehensive assessment of this event and the possible risk for the international spread. ECDC is monitoring this event through epidemic intelligence activities. For options for response and safety precautions, see ECDC’s threat assessment. ECDC risk assessment for the EU/EEA Chinese authorities have ruled out SARS-CoV, MERS-CoV, seasonal influenza virus, avian influenza virus, adenovirus and other common respiratory pathogens. Reports indicate that a new coronavirus has been identified as the etiological agent for viral pneumonia in hospitalised cases belonging to the pneumonia cluster in Wuhan. Media reports cite Xu Jianguo, who confirms identification of a new coronavirus, however, no sequence data have been made publicly available yet. To date, no cases belonging to the cluster in Wuhan have been identified outside of Wuhan and no suspected or possible cases with unknown pneumonia and travel to Wuhan have been reported from EU/EEA countries or globally. To date, only local people living and working in Wuhan seem to be affected. The seafood market in Wuhan is mentioned as a suspected place of exposure, which could indicate an exposure link to animals. Although the seafood market has now been closed and disinfected, the source of infection has not been identified. Information on case characteristics, aetiology, epidemiological data, exposure and applied case definition to identify cases belonging to the cluster in Wuhan is limited. There are still many unknowns about this outbreak, introducing a high level of uncertainty to the assessment below. Risk for travellers, introduction and further spread in the EU: three EU airports have direct flight connections to Wuhan and there are indirect flight connections to other EU hubs. The upcoming Chinese New Year celebrations at the end of January will cause an increased volume of travel to/from China and within China, thus increasing the likelihood of possible cases arriving. However, given that there is no indication of human-to-human transmission, the risk to travellers is considered to be low. For the same reason, and since no cases have been detected outside of Wuhan, the likelihood of introduction to the EU is considered to be low, but cannot be excluded. Consequently, the risk of further spread within the EU should a case be identified is considered low to very low. Risk of nosocomial transmission, infection prevention and control: So far, no human-to-human transmission or spread to healthcare workers or medical personal has been reported in China. Therefore, the likelihood of nosocomial transmission is low. https://www.ecdc.europa.eu/sites/default/files/documents/Threat-assessment-Pneumonia-cases-possibly-associated-to-a-novel-coronavirus-in-Wuhan-China.pdf

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Dr. Henry Niman, PhDMore On The Dangerous, New, Coronavirus In ChinaBats Were Sold at Wuhan Wet Market Where Vendors Were Infected By Novel CoronavirusThe Rich gene pool of bat SARS-related coronaviruses

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Wuhan ‘pneumonia’: Hong Kong takes tougher precautions with more powers to investigate suspected cases Passengers arriving in city from mainland will be screened by health officials before they get off the train City leader says intervention is part of government’s rapid response to mystery outbreak Natalie Wong andElizabeth Cheung Published: 12:41pm, 7 Jan, 2020 189 Extra checks have been put in place for passengers arriving in Hong Kong by high-speed rail from Wuhan. Photo: May Tse Hong Kong is taking tougher precautions against a mysterious, pneumonia-like virus in central China, laying the legal groundwork to put patients under quarantine if necessary and making it mandatory for doctors to notify the authorities of any suspected cases in the city. Nine more travellers who returned from Wuhan with symptoms of either fever and respiratory infection or pneumonia were placed in hospital isolation wards on Tuesday, taking the total to 30 – 13 of whom have already been discharged after treatment – since December 31, 2019. Hong Kong’s leader, Chief Executive Carrie Lam Cheng Yuet-ngor, said that travellers entering the city from Wuhan had been put through extra temperature screenings since Monday night. This came soon after the Food and Health Bureau said it expected to list the unidentified virus as a notifiable disease by the end of the week, empowering the authorities to enforce quarantine measures. The Department of Health then announced on Tuesday afternoon that it would gazette a bill to amend the Prevention and Control of Disease Ordinance on Wednesday, including “severe respiratory disease associated with a novel infectious agent” as a statutory notifiable infectious disease with immediate effect. Mystery pneumonia infects at least 59 people in Wuhan, China “Recently some patients have been leaving hospitals before completing medical check-ups,” Secretary for Food and Health Sophia Chan Siu-chee said. “The amendment of the law this time would be important for Hong Kong in preventing the spread of a new disease.” But Dr Henry Yeung Chiu-fat, president of the Hong Kong Doctors Union, warned of difficulties in meeting the notification requirement stipulated in the amended ordinance. “The definition is wide and vague. I don’t think we have the right to detain a patient at our clinic for too long just because they may have been to Wuhan and come down with a slight cold,” Yeung said. https://www.scmp.com/news/hong-kong/health-environment/article/3044957/wuhan-pneumonia-hong-kong-officials-board-trains

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Supporting information S1 Fig.pptx figshare 1 / 12 download Two clades of the SARSr-CoVs identified from bats in the studied cave are indicated with vertical lines on the left. (PPTX) S1 Fig. Alignment of amino acid sequences of the receptor-binding motif (corresponding to aa 424–495 of SARS-CoV S protein). Two clades of the SARSr-CoVs identified from bats in the studied cave are indicated with vertical lines on the left. https://doi.org/10.1371/journal.ppat.1006698.s001 (PPTX) S2 Fig. Alignment of nucleotide sequences of a genomic region covering ORF6 to ORF7a. ORFX is located between ORF6 and ORF7a in the genomes of WIV1, WIV16, Rs7327 and Rs4874. The start codon and stop codon of ORFX are marked with red boxes. The deletion responsible for the long ORFX in Rs7327 and Rs4874 is marked with the blue box. https://doi.org/10.1371/journal.ppat.1006698.s002 (PPTX) S3 Fig. Phylogenetic analyses based on nucleotide sequences of the S gene (A), ORF3a (B) and ORF8 (C). The trees were constructed by the maximum likelihood method using the LG model with bootstrap values determined by 1000 replicates. Only bootstraps > 50% are shown. Rs, Rhinolophus sinicus; Rf, Rhinolophus ferremequinum; Rm, Rhinolophus macrotis; Ra, Rhinolophus affinis; Rp, Rhinolophus pusillus; As, Aselliscus stoliczkanus; Cp, Chaerephon plicata. SARSr-CoVs detected in bats from the single cave surveyed in this study are in bold. https://doi.org/10.1371/journal.ppat.1006698.s003 (PPTX) S4 Fig. Alignment of amino acid sequences of ORF3b protein. https://doi.org/10.1371/journal.ppat.1006698.s004 (PPTX) S5 Fig. Detection of potential recombination events by similarity plot and boot scan analysis. (A) Full-length genome sequence of SARSr-CoV Rs4084 was used as query sequence and RsSHC014, Rf4092 and Rs4081 as reference sequences. (B) Full-length genome sequence of SARSr-CoV Rs4237 was used as query sequence and SARSr-CoV Rs4247, Rs4081 and Rs3367 as reference sequences. All analyses were performed with a Kimura model, a window size of 1500 base pairs, and a step size of 150 base pairs. https://doi.org/10.1371/journal.ppat.1006698.s005 (PPTX) S6 Fig. Chinese provinces where bat SARSr-CoVs have been detected. https://doi.org/10.1371/journal.ppat.1006698.s006 (PPTX) S7 Fig. The successful or failed rescue of the chimeric SARSr-CoVs. (A) Cytopathic effects in Vero E6 cells transfected with the infectious BAC clones constructed with the backbone of WIV1 and various S genes of different bat SARSr-CoV strains. Microphotographs were taken 24 hours post transfection. (B) The culture media supernatant collected from the cells transfected with the infectious BAC clones was used to infect Vero E6 cells. Immunofluorescent assay (IFA) was performed to detect infection and viral replication. Cells were fixed 24 hours post infection, and stained using rabbit antibody against the SARSr-CoV Rp3 nucleocapsid protein and a Cy3-conjugated anti-rabbit IgG. https://doi.org/10.1371/journal.ppat.1006698.s007 (PPTX) S8 Fig. Quantification of SARSr-CoV in individual bat fecal samples. The number of genome copies of SARSr-CoV per gram of bat feces was determined by quantitative real-time PCR targeting the RdRp gene. Samples from which the SARSr-CoV RBD sequences were successfully amplified are indicated in red. https://doi.org/10.1371/journal.ppat.1006698.s008 (PPTX) S9 Fig. Spike substitution strategy. The original fragments E and F were shortened to leave spike gene as an independent fragment. The new fragments were designated as Es and Fs. BsaI or BsmBI sites were introduced into the junctions of Es/Spike and Spike/Fs. Then any spike could be substituted into the genome of SARSr-CoV WIV1 through this strategy. https://doi.org/10.1371/journal.ppat.1006698.s009 (TIF) S1 Table. Comparison of the novel bat SARSr-CoVs identified in this study with human/civet SARS-CoVs and previously described bat SARSr-CoVs. https://doi.org/10.1371/journal.ppat.1006698.s010 (DOCX) S2 Table. Distribution of SARSr-CoVs highly similar to SARS-CoV in the variable S, ORF3 and ORF8 genes in the single cave. https://doi.org/10.1371/journal.ppat.1006698.s011 (DOCX) S1 Dataset. Full-length genome sequences of bat SARSr-CoVs newly identified in this study. https://doi.org/10.1371/journal.ppat.1006698.s012 (FAS) Acknowledgments We thank Ji-Hua Zhou and Wei-Hong Yang from Yunnan Institute of Endemic Diseases Control and Prevention for the assistance in sample collection. We thank the Center for Instrumental Analysis and Metrology of Wuhan Institute of Virology, CAS, for the assistance in taking confocal microscope pictures (Dr. Ding Gao) and flow cytometry (Ms. Juan Min).