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Summary
Background An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Published Online
Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No January 24, 2020
https://doi.org/10.1016/
data on person-to-person or nosocomial transmission have been published to date. S0140-6736(20)30154-9
See Online/Comment
Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of https://doi.org/10.1016/
five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong S0140-6736(20)30184-7, and
province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic https://doi.org/10.1016/
S0140-6736(20)30185-9
analysis of genetic sequences from these patients were done.
*Contributed equally
Findings From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between State Key Laboratory of
Emerging Infectious Diseases,
Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with Carol Yu Centre for Infection,
the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the Department of Microbiology,
virus after several days of contact with four of the family members. None of the family members had contacts with Li Ka Shing Faculty of Medicine,
Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36–66 years) The University of Hong Kong,
Pokfulam, Hong Kong Special
presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days Administrative Region, China
after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) (J F-W Chan MD, S Yuan PhD,
6–10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung K-H Kok PhD, K K-W To MD,
H Chu PhD, C C-Y Yip PhD,
opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung
R W-S Poon PhD, H-W Tsoi MPhil,
changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The K-H Chan PhD,
nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care V K-M Poon MPhil,
multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal W-M Chan PhD, J D Ip MSc,
J-P Cai BSc, V C-C Cheng MD,
RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by
Prof H Chen PhD); and
Sanger sequencing. Phylogenetic analysis of these five patients’ RT-PCR amplicons and two full genomes by next- Department of Clinical
generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory Microbiology and Infection
syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. Control (J F-W Chan, K K-W To,
J Yang MD, F Xing MD,
J Liu BNurs, S K-F Lo MPhil,
Interpretation Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital Prof H Chen, Prof K-Y Yuen MD)
and family settings, and the reports of infected travellers in other geographical regions. and Department of Medicine
(C K-M Hui, MD), The University
of Hong Kong-Shenzhen
Funding The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited,
Hospital, Shenzhen,
Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Guangdong Province, China
Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and Correspondence to:
High Level-Hospital Program (Guangdong Health Commission). Prof Kwok-Yung Yuen,
Department of Clinical
Microbiology and Infection
Copyright © 2020 Elsevier Ltd. All rights reserved.
Control, The University of
Hong Kong-Shenzhen
Introduction geographically linked to the Huanan seafood wholesale Hospital, Shenzhen,
The Health Commission of Hubei province, China, first market, which was subsequently reported by journalists Guangdong Province 518009,
China
announced a cluster of unexplained cases of pneumonia to be selling freshly slaughtered game animals.3 To
kyyuen@hku.hk
on Dec 31, 2019.1 27 patients were initially reported, date, no evidence of person-to-person transmission or
which was subsequently revised to 41 on Jan 11, 2020, affected health-care workers has been published in the
with seven severe cases and one death.2 Some patients scientific literature. The Chinese health authority said
were reported to have radiographic ground-glass lung that the patients initially tested negatively for common
changes; normal or lower than average white blood respiratory viruses and bacteria, but later tested positive
cell lymphocyte, and platelet counts; hypoxaemia; and for a novel coronavirus.2 The virus was soon isolated
deranged liver and renal function. Most were said to be and its genome sequenced by a number of Chinese
Research in context
Evidence before this study confirmed the presence of a novel coronavirus in five of
We searched PubMed on Jan 13, 2020, with no starting date six patients with radiological changes of viral pneumonia.
limitations, using the terms “family”, “pneumonia”, “Wuhan”, The phylogenetic analysis of this novel coronavirus suggested
“coronavirus”, and “novel” for articles in English. Our search its linkage to a possible animal source.
did not reveal any reports of novel coronavirus pneumonia in
Implications of all the available evidence
Wuhan before 2020. We only noted family clusters of
Although this novel coronavirus might have first originated
pneumonia due to the novel severe acute respiratory syndrome
from animals and now jumped into humans, the possibility of
(SARS) coronavirus in 2003, and Middle East respiratory
person-to-person transmission could not be excluded, as seen
syndrome coronavirus in 2012.
in this family cluster with no known history of exposure to
Added value of this study markets or animals, and rapid intercity spread might be
The epidemiological, clinical, laboratory, radiological, and possible by air travel. Vigilant epidemiological control in the
microbiological findings of unexplained pneumonia in a community and health-care facilities is important to prevent
Shenzhen family cluster connected to a Wuhan hospital were another SARS-like epidemic.
presented. The diagnostic tests from relevant clinical samples
scientists.4 The virus was tentatively named by WHO as HCoV-Oc43, HCoV-HKU1, and MERS-CoV], human
the 2019 novel coronavirus (2019-nCoV). Here, we report metapneumovirus, respiratory syncytial virus, human
the epidemiological, clinical, radiological, laboratory, and rhinovirus or entero virus, influenza A viruses [H1,
genomic findings of a family cluster of five patients in H1-2009 and H3], influenza B virus, parainfluenza viruses
Shenzhen who had a history of travel to Wuhan, and one [types 1–4], Bordetella pertussis, Bordetella parapertussis,
other family member who has not travelled to Wuhan. Chlamydophila pneumoniae, and Mycoplasma pneumoniae),
samples were tested using BioFire FilmArray Respiratory
Methods Panel 2 plus (bioMérieux, Marcy l’Etoile, France) according
Cases to the manufacturer’s instructions.7 The two faecal sam
On Jan 10, 2020, we initially enrolled two patients who ples were taken from the patients who had diarrhoea as
initially presented to The University of Hong Kong- part of their symptoms, and the samples were tested by
Shenzhen Hospital (Shenzhen, Guangdong province, BioFire FilmArray Gastrointestinal panel (bioMérieux) for
China) with fever, respiratory symptoms, and pulmonary 22 diarrhoeal pathogens.
infiltrates on chest radiographs. Subsequently, between
Jan 11, and Jan 15, 2020, five other members of this family Reverse transcription, in-house conventional RT-PCR
also presented to our hospital for the assessment of their and sequencing
health conditions. Reverse transcription was done using the SuperScript IV
We recorded and analysed the history, physical reverse transcriptase (Invitrogen, Carlsbad, USA) as prev
findings, and haematological, biochemical, radiological, iously described.8 The reaction mixture (10 μL) contained
and microbiological investigation results. All laboratory 5·5 μL of RNA, 2 μL of 5 × SuperScript IV buffer, 0·5 μL of
procedures for clinical samples have been previously 100 mM dithiothreitol, 0·5 μL of 10 mM deoxynucleotide
reported.5 Briefly, nasopharyngeal and throat swabs and triphosphate (dNTP) mixture, 0·5 μL of 50 μM random
stool and urine samples were taken and put into viral hexamers, 0·5 μL of SuperScript IV reverse transcriptase
transport media. Plasma was separated from EDTA (200 U/μL), and 0·5 μl of RNase-free water. The mixtures
bottles and serum were separated from clotted blood were incubated at 23°C for 10 min, followed by 50°C for
bottles. 10 min and 80°C for 10 min. The PCR mixture (25 μL)
This study was approved by the Institutional Review contained 1 μL of cDNA, 2·5 μL of 10X PCR buffer II, 2 μL
Board of The University of Hong Kong-Shenzhen of 25 mM MgCl₂, 0·5 μL of 10 mM dNTP mix, 2·5 μL of
Hospital (number [2015]90). We obtained written consent each 10 μM forward and reverse primer, 0·125 μL of
from the patients. AmpliTaq Gold Polymerase (Applied Biosystems, Foster
City, USA; 5 U/μL), and nuclease-free water.
Respiratory and diarrhoeal pathogen detection The first set of primers was the forward pri m
Respiratory samples of the patients were tested for er (5ʹ-CAAGTGGGGTAAGGCTAGACTTT-3ʹ) and the
influenza A and B viruses and respiratory syncytial virus reverse primer (5ʹ-ACTTAGGATAATCCCAACCCAT-3ʹ)
using the Xpert Xpress Flu/RSV assay (GeneXpert targeting 344 bp of RNA-dependent RNA poly
System, Cepheid, Sunnyvale, CA, USA) according to the merase (RdRp) gene of all severe acute respiratory
manufacturer’s instructions.6 To detect the presence of syndrome (SARS)-related coronaviruses. The second set
18 respiratory virus targets and four bacteria (including of primers was designed after our first 2019-nCoV
adenovirus, coronaviruses [HCoV-229E, HCoV-Nl63, genome sequence by Nanopore sequencing from
Fever, cough, and Attended Attended Attended HKU-SZH for persistent symptoms
generalised weakness clinic 1 clinic 2
(RT-PCR and CT positive)
Patient 2 (father) 26 27 28 29 30 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Fever and Cough and Attended Attended HKU-SZH for persistent symptoms
generalised weakness attended clinic 1 clinic 2
(CT positive)
26 27 28 29 30 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Patient 3 (daugther)
Fever and diarrhoea Pleuritic chest pain Attended HKU-SZH for investigation
(RT-PCR and CT positive)
26 27 28 29 30 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Patient 4 (son-in-law)
Fever and diarrhoea Cough and runny nose Attended HKU-SZH for investigation
(RT-PCR and CT positive)
26 27 28 29 30 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Patient 5 (grandson)
B Wuhan
December, 2019 January, 2020
Relative 1
26 27 28 29 30 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
(son of relative 2)
Table 1: Summary of clinical features and laboratory results of the family cluster infected with 2019 novel coronavirus, at presentation
the positive clinical samples: the forward primer (pp 1–2). The consensus sequence of HKU-SZ-002a
(5ʹ-CCTACTAAATTAAATGATCTCTGCTTTACT-3ʹ) and (accession number MN938384) and HKU-SZ-005b
the reverse primer (5ʹ-CAAGCTATAACGCAGCCTGTA-3ʹ) (accession number MN975262) have been deposited
targeting the 158 bp of Spike (S) gene of this novel into GenBank. Raw reads, after excluding human reads,
coronavirus. These sets were used for PCR using an have been deposited into BioProject (accession number For BioProject see https://www.
automated thermocycler (Applied Biosystems) with a PRJNA601630). ncbi.nlm.nih.gov/bioproject/
changes, or any concomitant radiological changes of had radiological changes of viral pneumonia, among
dense consolidation, pleural effusion, lymphadenopathy, whom five (patients 1, 2, 4, 5, and 7) tested positive for
or pneumomediastinum were seen. 2019-nCoV by RT-PCR. Five patients (patients 1, 2, 3, 4,
All respiratory samples were negative on two point-of-
care multiplex PCR systems for 18 respiratory viral and
four bacterial targets. The two faecal samples from A
patients 3 and 4 who had preceding diarrhoea were nega 0·1 97 Bat SL-CoV ZC45 2018
Bat SL-CoV ZXC21 2018
tive on a multiplex PCR assay for common diarrhoeal 2019-nCoV HKU-SZ-001 2020
viruses, bacteria, and parasites (table 2). The respiratory 2019-nCoV HKU-SZ-002a 2020
samples of patients 1, 2, 4, 5, and 7 were positive for both 100
2019-nCoV HKU-SZ-004 2020
2019-nCoV HKU-SZ-005b 2020 2019-nCoV
RdRp and S genes by conventional RT-PCR, and for the 98
2019-nCoV HKU-SZ-007a 2020
S gene by real-time RT-PCR, which were confirmed by 2019-nCoV HKU-SZ-007b 2020
Sanger sequencing of all amplicons (appendix pp 3–5). 2019-nCoV HKU-SZ-007c 2020
Although the respiratory samples of patient 3 were Human SARS-CoV GZ02 2003
Human SARS-CoV BJ01 2003
negative for both RdRp and S gene (collected 9 days after
Human SARS-CoV Tor2 2003
symptom onset), she was still regarded as an infected Human SARS-CoV HKU-39849 2003
lineage B
case because she was strongly epidemiologically linked 98 Paguma SARS CoV HC/SZ/61/03 2003
to the Wuhan hospital exposure and radiologically Bat SL-CoV RsSHC014 2013
Bat SL-CoV Rs4255 2016
showing multifocal ground-glass lung opacities. Only the Bat SL-CoV Rs3367 2013
serum sample of patient 2 was positive and all other Bat SL-CoV Rs4231 2016
97
patients' serum, urine, and faecal samples were negative Bat CoV YN2018D 2018
for this novel coronavirus. Phylogenetic analysis of the 72 Bat CoV YN2018C 2018
Bat SL-CoV Rs672 2006
PCR products showed that the amplicon sequences of
Bat SARS-related CoV BM48-31 2009
both RdRp and S genes from these five patients were Bat CoV HKU9-1 2006 lineage D
novel (figure 3) and different from other known human Bat CoV HKU4-1 2006
or animal coronaviruses, including the SARS and bat Bat CoV HKU5-1 2006 lineage C
99 Human MERS-CoV 2012
SARS-related coronaviruses.
Human CoV HKU1 2004
Two complete virus genomes (HKU-SZ-002a and HKU- 99 Human CoV OC43 2003
lineage A
SZ-005b) were sequenced using Nanopore technology and Human CoV 229E 2000
showed a novel coronavirus that is most closely related to
B
those of the bat SARS-like coronavirus bat-SL-CoVZXC21 2019-nCoV HKU-SZ-007a 2020
0·2
(NCBI accession number MG772934) and bat-SL-CoVZC45 2019-nCoV HKU-SZ-007b 2020
(NCBI accession number MG772933). Their genome 2019-nCoV HKU-SZ-005b 2020
2019-nCoV HKU-SZ-005 2020
organisation is typical of a lineage B betacoronavirus. The 91
2019-nCoV HKU-SZ-004 2020
size of the virus genomes from patient 2 (HKU-SZ-002a) 2019-nCoV HKU-SZ-002b 2020 2019-nCoV
and patient 5 (HKU-SZ-005b) are around 29·8 kilobases 2019-nCoV HKU-SZ-002a 2020
2019-nCoV HKU-SZ-001 2020
with GC content of 38% (appendix p 6). HKU-SZ-002a and
2019-nCoV HKU-SZ-007c 2020
HKU-SZ-005b differ from each other by only two bases. Bat SL-CoV ZXC21 2018
One of them is a non-synonymous mutation at amino acid Bat SL-CoV ZC45 2018
position 336 of non-structural protein 4 (Ser336 for HKU- 99 Bat CoV YN2018C 2018
lineage B
SZ-002a; Leu336 for HKU-SZ-005b; figure 4). Although Bat SL-CoV Rs4255 2016
97 Bat SL-CoV Rs672 2006
amino acid sequence of the N-terminal domain of Spike 87 Bat CoV YN2018D 2018
subunit 1 of this novel coronavirus is approximately 66% Human SARS-CoV GZ02 2003
identical to those of the SARS-related coronaviruses, and Human SARS-CoV Tor2 2003
the core domain of the receptor binding domain of this Human SARS-CoV HKU-39849 2003
97 Human SARS-CoV BJ01 2003
novel coronavirus has about 68% amino acid identity with Paguma SARS CoV HC/SZ/61/03 2003
100
those of the SARS-related coronavirus, the protein sequence Bat SL-CoV Rs3367 2013
of the external subdomain region of receptor binding Bat SL-CoV RsSHC014 2013
domain of Spike subunit 1 has only 39% identity, which 99 Bat SL-CoV Rs4231 2016
might affect the choice of human receptor and therefore the Bat SARS-related CoV BM48-31 2009
Bat CoV HKU5-1 2006
biological behaviour of this virus (figure 4). Human MERS-CoV 2012 lineage C
All six patients were admitted to hospital under isolation, Bat CoV HKU4-1 2006
supportive care, and remained stable as of Jan 20, 2020. Human CoV HKU1 2004
lineage A
Human CoV OC43 2003
Bat CoV HKU9-1 2006
Discussion Human CoV 229E 2000
lineage D
threshold value indicating a higher viral load. Patient 2 had SP NTD ESD FP HR1 HR2 TM
shown in this study, it is still crucial to isolate patients 8 Peiris JS, Lai ST, Poon LL, et al. Coronavirus as a possible cause of
and trace and quarantine contacts as early as possible severe acute respiratory syndrome. Lancet 2003; 361: 1319–25.
9 Chan JF, Zhang AJ, Chan CC, et al. Zika virus infection in
because asymptomatic infection appears possible (as dexamethasone-immunosuppressed mice demonstrating
shown in one of our patients), educate the public on both disseminated infection with multi-organ involvement including
food and personal hygiene, and alert health-care workers orchitis effectively treated by recombinant type I interferons.
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on compliance to infection control to prevent super- 10 To KKW, Chan WM, Li KSM, et al. High prevalence of four novel
spreading events. Unlike the 2003 SARS outbreak, the astrovirus genotype species identified from rodents in China.
improved surveillance network and laboratory capability J Gen Virol 2017; 98: 1004–15.
11 Woo PC, Lau SK, Teng JL, et al. Metagenomic analysis of viromes of
of China was able to recognise this outbreak within a few dromedary camel fecal samples reveals large number and high
weeks and announced the virus genome sequences that diversity of circoviruses and picobirnaviruses. Virology 2014;
would allow the development of rapid diagnostic tests 471–73: 117–25.
and efficient epidemiological control. Our study showed 12 Tse H, Tsang AK, Tsoi HW, et al. Identification of a novel bat
papillomavirus by metagenomics. PLoS One 2012; 7: e43986.
that person-to-person transmission in family homes or 13 Lewandowski K, Xu Y, Pullan ST, et al. Metagenomic nanopore
hospital, and intercity spread of this novel coronavirus sequencing of influenza virus direct from clinical respiratory
are possible, and therefore vigilant control measures are samples. J Clin Microbiol 2019; 58: e00963–19.
14 Lau SK, Feng Y, Chen H, et al. Severe acute respiratory syndrome
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Contributors coronavirus from greater horseshoe bats through recombination.
JF-WC and K-YY had roles in the study design, clinical management, J Virol 2015; 89: 10532–47.
patient recruitment, data collection, data analysis, data interpretation, 15 Peiris JS, Chu CM, Cheng VC, et al. Clinical progression and viral
literature search, and writing of the manuscript. SY, K-HK, KK-WT, load in a community outbreak of coronavirus-associated SARS
HChu, CC-YY, RW-SP, H-WT, SK-FL, K-HC, VK-MP, W-MC, JDI, J-PC, pneumonia: a prospective study. Lancet 2003; 361: 1767–72.
VC-CC, and HChe had roles in the experiments, data collection, data 16 Cheng VC, Lau SK, Woo PC, Yuen KY. Severe acute respiratory
analysis, and data interpretation. JY, CK-MH, FX, and JL had roles in syndrome coronavirus as an agent of emerging and reemerging
infection. Clin Microbiol Rev 2007; 20: 660–94.
recruitment, data collection, and clinical management. All authors
reviewed and approved the final version of the manuscript. 17 Che XY, Di B, Zhao GP, et al. A patient with asymptomatic severe
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Declaration of interests 2003–2004 community outbreak of SARS in Guangzhou, China.
We declare no competing interests. Clin Infect Dis 2006; 43: e1–5.
18 Cheng VC, Hung IF, Tang BS, et al. Viral replication in the
Acknowledgments nasopharynx is associated with diarrhea in patients with severe
This study was partly supported by the Shaw Foundation Hong Kong; acute respiratory syndrome. Clin Infect Dis 2004; 38: 467–75.
Michael Seak-Kan Tong; Respiratory Viral Research Foundation; 19 Chan JF, Lau SK, To KK, Cheng VC, Woo PC, Yuen KY. Middle East
Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited; respiratory syndrome coronavirus: another zoonotic betacoronavirus
Marina Man-Wai Lee; the Hong Kong Hainan Commercial Association causing SARS-like disease. Clin Microbiol Rev 2015; 28: 465–522.
South China Microbiology Research Fund; Sanming Project of Medicine 20 Zhou J, Li C, Zhao G, et al. Human intestinal tract serves as an
in Shenzhen, China (SZSM201911014 and SZSM201612096); and the alternative infection route for Middle East respiratory syndrome
High Level-Hospital Program, Health Commission of Guangdong coronavirus. Sci Adv 2017; 3: eaao4966.
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