A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

Abstract

Background: An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date.

Methods: In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done.

Findings: From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36-66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3-6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6-10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats.

Interpretation: Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions.

Funding: The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and High Level-Hospital Program (Guangdong Health Commission).

Figure 1

Chronology of symptom onset of the Shenzhen family cluster and their contacts in Wuhan Dates filled in red are the dates on which patients 1–6 had close contacts with their relatives (relatives 1–5). Dates filled in yellow are the dates on which patients 3–6 stayed with patient 7. The boxes with an internal red cross are the dates on which patients 1 and 3 or relatives 1, 2, and 3 had stayed overnight (white boxes) at or had visited (blue boxes) the hospital in which relative 1 was admitted for febrile pneumonia. The information of relatives 1–5 was provided by patient 3. No virological data were available.

Figure 2

Representative images of the thoracic CT scans showing multifocal ground-glass changes in the lungs of patient 1 (A), patient 2 (B), patient 3 (C), and patient 5 (D)

Figure 3

Phylogenetic trees of genetic sequences (A) Amplicon fragments of RNA-dependent RNA polymerase of patients 1, 2, 4, 5, and 7. (B) Amplicon fragments of Spike gene of patients 1, 2, 4, 5, and 7. (C) The full genome sequences of strains from patients 2 and 5. Red text indicates the coronavirus (CoV) strains detected in the patients in the present study. 2019-nCoV is 2019 novel coronavirus. HKU-SZ-001 refers to the strain detected in the nasopharyngeal swab of patient 1; HKU-SZ-002a refers to strain detected in the nasopharyngeal swab of patient 2; HKU-SZ-002b refers to strain detected in the serum sample of patient 2; HKU-SZ-004 refers to the strain detected in the nasopharyngeal swab of patient 4; HKU-SZ-005 refers to the strain detected in the throat swab of patient 5; HKU-SZ-005b refers to the strain detected in the sputum sample of patient 5; HKU-SZ-007a refers to the strain detected in the nasopharyngeal swab of patient 7; HKU-SZ-007b refers to the strain detected in the throat swab of patient 7; and HKU-SZ-007c refers to the strain detected in the sputum sample of patient 7 (appendix p 6). The NCBI GenBank accession numbers of the genome sequences are MN938384 (HKU-SZ-002a), MN975262 (HKU-SZ-005b), MG772934 (Bat SL-CoV ZXC21), MG772933 (Bat SL-CoV ZC45), AY274119 (hSARS-CoV Tor2), AY278491 (SARS coronavirus HKU-39849), AY278488 (hSARS-CoV BJ01), AY390556 (hSARS-CoV GZ02), AY515512 (Paguma SARS CoV HC/SZ/61/03), KY417146 (Bat SL-CoV Rs4231), KC881005 (Bat SL-CoV RsSHC014), KC881006 (Bat SL-CoV Rs3367), MK211377 (Bat CoV YN2018C), MK211378 (Bat CoV YN2018D), KY417149 (Bat SL-CoV Rs4255), FJ588686 (Bat SL-CoV Rs672), NC014470 (Bat SARS-related CoV BM48-31), EF065513 (Bat CoV HKU9-1), AY391777 (hCoV OC43), NC006577 (hCoV HKU1), NC019843 (hMERS CoV), NC009020 (Bat CoV HKU5-1), NC009019 (Bat CoV HKU4-1), and NC002645 (hCoV 229E).

Figure 3

Phylogenetic trees of genetic sequences (A) Amplicon fragments of RNA-dependent RNA polymerase of patients 1, 2, 4, 5, and 7. (B) Amplicon fragments of Spike gene of patients 1, 2, 4, 5, and 7. (C) The full genome sequences of strains from patients 2 and 5. Red text indicates the coronavirus (CoV) strains detected in the patients in the present study. 2019-nCoV is 2019 novel coronavirus. HKU-SZ-001 refers to the strain detected in the nasopharyngeal swab of patient 1; HKU-SZ-002a refers to strain detected in the nasopharyngeal swab of patient 2; HKU-SZ-002b refers to strain detected in the serum sample of patient 2; HKU-SZ-004 refers to the strain detected in the nasopharyngeal swab of patient 4; HKU-SZ-005 refers to the strain detected in the throat swab of patient 5; HKU-SZ-005b refers to the strain detected in the sputum sample of patient 5; HKU-SZ-007a refers to the strain detected in the nasopharyngeal swab of patient 7; HKU-SZ-007b refers to the strain detected in the throat swab of patient 7; and HKU-SZ-007c refers to the strain detected in the sputum sample of patient 7 (appendix p 6). The NCBI GenBank accession numbers of the genome sequences are MN938384 (HKU-SZ-002a), MN975262 (HKU-SZ-005b), MG772934 (Bat SL-CoV ZXC21), MG772933 (Bat SL-CoV ZC45), AY274119 (hSARS-CoV Tor2), AY278491 (SARS coronavirus HKU-39849), AY278488 (hSARS-CoV BJ01), AY390556 (hSARS-CoV GZ02), AY515512 (Paguma SARS CoV HC/SZ/61/03), KY417146 (Bat SL-CoV Rs4231), KC881005 (Bat SL-CoV RsSHC014), KC881006 (Bat SL-CoV Rs3367), MK211377 (Bat CoV YN2018C), MK211378 (Bat CoV YN2018D), KY417149 (Bat SL-CoV Rs4255), FJ588686 (Bat SL-CoV Rs672), NC014470 (Bat SARS-related CoV BM48-31), EF065513 (Bat CoV HKU9-1), AY391777 (hCoV OC43), NC006577 (hCoV HKU1), NC019843 (hMERS CoV), NC009020 (Bat CoV HKU5-1), NC009019 (Bat CoV HKU4-1), and NC002645 (hCoV 229E).

Figure 4

Genome organisation of 2019-nCoV and the amino acid identities of different subunits and domains of the Spike between human 2019-nCoV strains (HKU-SZ-002a and HKU-SZ-005b) and bat-SL-CoV-ZC45 2′-O-MT=2′-O-ribose methyltransferase. 3CLpro=3C-like protease. DMV=double-membrane vesicles. E=envelope. EndoU=endoribonuclease. ESD=external subdomain. ExoN=exonuclease. FP=fusion peptide. Hel=helicase. HR1=heptad repeat 1. HR2=heptad repeat 2. M=membrane. N=nucleocapsid. NSP=non-structural protein. NTD=N-terminal domain. ORF=open reading frame. PLpro=papain-like protease. RBD=receptor binding domain. S=spike. S1=subunit 1. S2=subunit 2. SP=signal peptide. TM=transmembrane domain.