China CDC Weekly

Notes from the Field

A Novel Coronavirus Genome Identified in a Cluster of

Pneumonia Cases — Wuhan, China 2019−2020
Wenjie Tan1,2,#;  Xiang Zhao1;  Xuejun Ma1;  Wenling Wang1;  Peihua Niu1;  Wenbo Xu1; 
George F. Gao1;  Guizhen Wu1,2,#

Emerging  and  re-emerging  pathogens  are  great lavage  fluid  (BALF)  from  a  patient  from  Wuhan  by
challenges  to  the  public  health  (1).  A  cluster  of scientists  of  the  National  Institute  of  Viral  Disease
pneumonia  cases  with  an  unknown  cause  occurred  in Control  and  Prevention  (IVDC)  through  a
Wuhan starting on December 21, 2019. As of January combination  of  Sanger  sequencing,  Illumina
20, 2020, a total of 201 cases of pneumonia in China sequencing,  and  nanopore  sequencing.  Three  distinct
have been confirmed. A team of professionals from the strains  have  been  identified,  the  virus  has  been
National  Health  Commission  and  China  CDC designated  as  2019-nCoV,  and  the  disease  has  been
conducted  epidemiological  and  etiological subsequently  named  novel  coronavirus-infected
investigations. On January 3, 2020, the first complete pneumonia (NCIP).
genome of  the  novel   β genus  coronaviruses  (2019- Phylogenetic  analysis  was  conducted  to  determine
nCoVs)  was  identified  in  samples  of  bronchoalveolar the  relationship  between  2019-nCoVs  and  other
 
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FIGURE 1. Phylogenetic  relationships  between  the  genomes  of  the  new  types  of  Betacoronavirus  and  other
Orthocoronavirinae genomes. The viruses in the subfamily Orthocoronavirinae were classified into four genera (prototype or
Refseq  strains  shown):  Alphacoronavirus  (purple),  Betacoronavirus  (orange),  Gammacoronavirus  (green),  and
Deltacoronavirus  (blue).  Classic  subgroup  clusters  for  the  Betacoronavirus  were  labelled  2a–2d.  The  tree  was  based  on
complete  genomes  shown  above  using  the  maximum  likelihood  method  under  the  GTR  +  I  +  Γ  model  of  nucleotide
substitution  as  implemented  in  PhyML.  The  new  types  of  Betacoronavirus,  labelled  with  red  stars,  were  placed  into  the
lineage of Betacoronavirus 2b, which contain the following: avian infectious bronchitis virus (AIBV), Middle East respiratory
syndrome  coronavirus  (MERS-CoV),  mouse  hepatitis  virus  (MHV),  porcine  enteric  diarrhea  virus  (PEDV),  severe  acute
respiratory syndrome coronavirus (SARS-CoV), SARS-related coronavirus (SARSr-CoV), and Human coronavirus (HCoV).

Chinese Center for Disease Control and Prevention CCDC Weekly / Vol. 2 / No. 4 61
 China CDC Weekly
sequences  under  the  Orthocoronavirinae  subfamily
using  MAFFT  v7.455  (Figure 1)  (2),  and  maximum
likelihood inference was calculated using PhyML v3.3
(3), employing the GTR + I + Γ model of nucleotide
substitution,  and  1,000  bootstrap  replicates.  The
2019-nCoVs  have  features  typical  of  the  coronavirus
family  and  were  placed  in  the  Betacoronavirus  2b
lineage.  Alignment  of  these  strains’  full  genomes  and
other available genomes of Betacoronavirus showed the
closest  relationship  with  Bat  SARS-like  coronavirus
isolate  bat-SL-CoVZC45  (Accession  Number:
MG772933.1)  (Identity  87.99%).  The  typical  crown-
like  particles  of  the  2019-nCoVs  can  be  observed
under  transmission  electron  microscope  (TEM)  with
negative  staining  (www.gisaid.org).  The  origin  of  the
2019-nCoVs  is  still  being  investigated.  However,  all
current evidence points to wild animals sold illegally in
the Huanan Seafood Wholesale Market.
Several complete genome sequences of 2019-nCoVs
were  successfully  obtained  and  released  recently  via
www.gisaid.org to provide a first look at the molecular
characteristics  of  this  emerging  pathogen,  and  all
related  information  has  also  been  reported  to  the
World  Health  Organization  (WHO).  Several  rapid
62 CCDC Weekly / Vol. 2 / No. 4
and  sensitive  detection  tests  have  been  developed  by
China CDC and will be applied to the prevention and
control of this 2019-nCoV outbreak.
Data  availability.  The  new  Betacoronavirus  genome
sequence  has  been  deposited  in  GISAID  (www.gisaid.
org)  under  the  accession  number  EPI_ISL_402119,
EPI_ISL_ 402020 and EPI_ISL_402121.
#
  Corresponding  authors:  Wenjie  Tan,  tanwj@ivdc.chinacdc.cn;
Guizhen Wu, wugz@ivdc.chinacdc.cn.
 
1
  MHC  Key  Laboratory  of  Biosafety,  National  Institute  for  Viral
Disease Control and Prevention, China CDC, Beijing, China; 2 Center
for  Biosafety  Mega-Science,  Chinese  Academy  of  Sciences,  Beijing,
China.
Submitted: January 19, 2020; Accepted: January 20, 2020
References
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Chinese Center for Disease Control and Prevention