The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Abstract

The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

Full text

Consensus statement
https://doi.org/10.1038/s41564-020-0695-z
*A list of authors and their affiliations appears at the end of the paper.
Upon a viral outbreak, it is important to rapidly establish
whether the outbreak is caused by a new or a previously
known virus (Box 1), as this helps decide which approaches
and actions are most appropriate to detect the causative agent, con-
trol its transmission and limit potential consequences of the epi-
demic. The assessment of virus novelty also has implications for
virus naming and, on a different timescale, helps to define research
priorities in virology and public health.
For many human virus infections such as influenza virus1 or
norovirus2 infections, well-established and internationally approved
methods, standards and procedures are in place to identify and
name the causative agents of these infections and report this infor-
mation promptly to public health authorities and the general public.
In outbreaks involving newly emerged viruses, the situation may
be different, and appropriate procedures to deal with these viruses
need to be established or refined with high priority.
Here, we present an assessment of the genetic relatedness of the
newly identified human coronavirus3, provisionally named 2019-
nCoV, to known coronaviruses, and detail the basis for (re)naming
this virus severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2), which will be used hereafter. Given the public interest in nam-
ing newly emerging viruses and the diseases caused by these viruses
in humans, we will give a brief introduction to virus discovery and
classification — specifically the virus species concept — and the roles
of different bodies, such as the World Health Organization (WHO)
and the International Committee on Taxonomy of Viruses (ICTV), in
this process. We hope this will help readers to better understand the
scientific approach we have taken to arrive at this name, and we will
also discuss implications of this analysis and naming decision.
Classifying and naming viruses and virus species
Defining the novelty of viruses is one of the topics that virus
classification deals with. The classification of RNA viruses needs to
consider their inherent genetic variability, which often results in two
or more viruses with non-identical but similar genome sequences
being regarded as variants of the same virus. This immediately
poses the question of how much difference to an existing group is
large enough to recognize the candidate virus as a member of a new,
distinct group. This question is answered in best practice by evalu-
ating the degree of relatedness of the candidate virus to previously
identified viruses infecting the same host or established monophy-
letic groups of viruses, often known as genotypes or clades, which
may or may not include viruses of different hosts. This is formally
addressed in the framework of the official classification of virus tax-
onomy and is overseen and coordinated by the ICTV4. Viruses are
clustered in taxa in a hierarchical scheme of ranks in which the spe-
cies represents the lowest and most populous rank containing the
least diverged groups (taxa) of viruses (Box2). The ICTV maintains
a Study Group for each virus family. The Study Groups are respon-
sible for assigning viruses to virus species and taxa of higher ranks,
such as subgenera, genera and subfamilies. In this context they play
an important role in advancing the virus species concept and high-
lighting its significance5.
Virus nomenclature is a formal system of names used to label
viruses and taxa. The fact that there are names for nearly all viruses
within a species is due to the historical perception of viruses as
causative agents of specific diseases in specific hosts, and to the way
we usually catalogue and classify newly discovered viruses, which
increasingly includes viruses that have not been linked to any known
disease in their respective hosts (Box 1). The WHO, an agency of the
United Nations, coordinates international public health activities
aimed at combating, containing and mitigating the consequences
of communicable diseases—including major virus epidemics—and
is responsible for naming disease(s) caused by newly emerging
human viruses. In doing so, the WHO often takes the traditional
approach of linking names of specific diseases to viruses (Box 1) and
The species Severe acute respiratory syndrome-
related coronavirus: classifying 2019-nCoV and
naming it SARS-CoV-2
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses*
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the
third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic.
The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for develop-
ing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human
pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the
CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome corona-
viruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2.
In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-
CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections
in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the
need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate
significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our
preparedness for future outbreaks.
NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology

Consensus statement NATuRe MICROBIOlOGy
assessing virus novelty by an apparent failure to detect the causative
agent using established diagnostic assays.
Apart from disease, geography and the organism from which a
given virus was isolated also dominate the nomenclature, occasion-
ally engraving connections that may be accidental (rather than typi-
cal) or even stigmatizing, which should be avoided. Establishing a
universal nomenclature for viruses was one of the major tasks of
the ICTV when it was founded more than 50 years ago4. When the
species rank was established in the taxonomy of viruses6, ICTV’s
responsibility for naming viruses was shifted to naming and
establishing species. ICTV Study Groups may also be involved in
virus naming on a case-by-case basis as an extension of their offi-
cial remit, as well as using the special expertise of their members.
As virus species names are often very similar to the name of the
founding member of the respective species, they are frequently con-
fused in the literature with names of individual viruses in this species.
The species name is italicized, starts with a capital letter and should
not be spelled in an abbreviated form7; hence the species name Severe
acute respiratory syndrome-related coronavirus. In contrast, this
convention does not apply to virus names, hence severe acute respi-
ratory syndrome coronavirus, or SARS-CoV, as it is widely known.
Defining the place of SARS-CoV-2 within the Coronaviridae
Researchers studying coronaviruses—a family of enveloped pos-
itive-strand RNA viruses infecting vertebrates8—have been con-
fronted several times with the need to define whether a newly
emerged virus causing a severe or even life-threatening disease in
humans belongs to an existing or a new (yet-to-be-established) spe-
cies. This happened with SARS9–12 and with Middle East respiratory
syndrome (MERS)13,14 a few years later. Each time, the virus was
placed in the taxonomy using information derived from a sequence-
based family classification15,16.
The current classification of coronaviruses recognizes 39 species
in 27 subgenera, five genera and two subfamilies that belong to the
family Coronaviridae, suborder Cornidovirineae, order Nidovirales
and realm Riboviria17–19 (Fig.1). The family classification and tax-
onomy are developed by the Coronaviridae Study Group (CSG), a
working group of the ICTV20. The CSG is responsible for assessing
Box 1 | Virus discovery and naming: from disease-based to phenotype-free
Understanding the cause of a specic disease that spreads among
individuals of the same host species (infectivity) was the major
driving force for the discovery of the rst virus in plants, and
subsequently many others in all forms of life, including humans.
Historically, the range of diseases and hosts that specic viruses
are associated with have been the two key characteristics used
to dene viruses, given that they are invisible to the naked eye46.
Viral phenotypic features include those that, like a disease, are pre-
dominantly shaped by virus–host interactions including transmis-
sion rate or immune correlates of protection, and others that are
largely virus-specic, such as the architecture of virus particles.
ese features are of critical importance to control, and respond
to medically and economically important viruses — especially
during outbreaks of severe disease — and dominate the general
perception of viruses.
However, the host of a given virus may be uncertain, and virus
pathogenicity remains unknown for a major (and fast-growing)
proportion of viruses, including many coronaviruses discovered
in metagenomics studies using next-generation sequencing
technology of environmental samples47,48. ese studies have
identied huge numbers of viruses that circulate in nature and
have never been characterized at the phenotypic level. us, the
genome sequence is the only characteristic that is known for
the vast majority of viruses, and needs to be used in dening
specic viruses. In this framework, a virus is dened by a genome
sequence that is capable of autonomous replication inside cells
and dissemination between cells or organisms under appropriate
conditions. It may or may not be harmful to its natural host.
Experimental studies may be performed for a fraction of known
viruses, while computational comparative genomics is used to
classify (and deduce characteristics of) all viruses. Accordingly,
virus naming is not necessarily connected to disease but rather
informed by other characteristics.
In view of the above advancements and when confronted with
the question of whether the virus name for the newly identied
human virus should be linked to the (incompletely dened) disease
that this virus causes, or rather be established independently from
the virus phenotype, the CSG decided to follow a phylogeny-based
line of reasoning to name this virus whose ontogeny can be traced
in the gure in Box 1.
Virus
Naming authority
Disease
Middle East
respiratory syndrome
(MERS)
Virus
species
Middle East respiratory
syndrome-related
coronavirus
Severe acute respiratory
syndrome-related
coronavirus
MERS-CoV
WHO
ICTV-
CSG
Coronavirus
disease 2019
(COVID-19)
SARS-CoV-2SARS-CoV
Severe acute
respiratory syndrome
(SARS)
Year 2012
First name Name origin
2003 2019
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to
the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
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Consensus statement
NATuRe MICROBIOlOGy
the place of new viruses through their relation to known viruses in
established taxa, including placements relating to the species Severe
acute respiratorysyndrome-related coronavirus. In the classification
of nidoviruses, species are considered biological entities demar-
cated by a genetics-based method21, while generally virus species are
perceived as man-made constructs22. To appreciate the difference
between a nidoviral species and the viruses grouped therein, it may
be instructive to look at their relationship in the context of the full
taxonomy structure of several coronaviruses. Although these viruses
were isolated at different times and locations from different human
and animal hosts (with and without causing clinical disease), they
all belong to the species Severe acute respiratorysyndrome-related
coronavirus, and their relationship parallels that between human
individuals and the species Homo sapiens (Fig.1).
Even without knowing anything about the species concept, every
human recognizes another human as a member of the same species.
However, for assigning individual living organisms to most other
species, specialized knowledge and tools for assessing inter-individ-
ual differences are required. The CSG uses a computational frame-
work of comparative genomics23, which is shared by several ICTV
Study Groups responsible for the classification and nomenclature
of the order Nidovirales and coordinated by the ICTV Nidovirales
Study Group (NSG)24 (Box3). The Study Groups quantify and
partition the variation in the most conserved replicative proteins
encoded in open reading frames 1a and 1b (ORF1a/1b) of the coro-
navirus genome (Fig.2a) to identify thresholds on pair-wise patris-
tic distances (PPDs) that demarcate virus clusters at different ranks.
Consistent with previous reports, SARS-CoV-2 clusters with
SARS-CoVs in trees of the species Severe acute respiratory syn-
drome-related coronavirus (Fig.2b) and the genus Betacoronavirus
(Fig.2c)25–27. Distance estimates between SARS-CoV-2 and the most
closely related coronaviruses vary among different studies depend-
ing on the choice of measure (nucleotide or amino acid) and genome
region. Accordingly, there is no agreement yet on the exact taxo-
nomic position of SARS-CoV-2 within the subgenus Sarbecovirus.
When we included SARS-CoV-2 in the dataset used for the most
recent update (May 2019) of the coronavirus taxonomy currently
being considered by ICTV19, which includes 2,505 coronaviruses,
Box 2 | Identifying viral species
e terms strain and isolate are commonly used to refer to virus
variants, although there are dierent opinions as to which term
should be used in a specic context. If a candidate virus clus-
ters within a known group of isolates, it is a variant of this group
and may be considered as belonging to this known virus group.
In contrast, if the candidate virus is outside of known groups and
its distances to viruses in these groups are comparable to those ob-
served between viruses of dierent groups (intergroup distances),
the candidate virus is distinct and can be considered novel.
is evaluation is usually conducted in silico using
phylogenetic analysis, which may be complicated by uneven
rates of evolution that vary across dierent virus lineages and
genomic sites due to mutation, including the exchange of
genome regions between closely related viruses (homologous
recombination). However, given that the current sampling of
viruses is small and highly biased toward viruses of signicant
medical and economic interest, group composition varies
tremendously among dierent viruses, making decisions on
virus novelty group-specic and dependent on the choice of the
criteria selected for this assessment.
ese challenges are addressed in the framework of virus
taxonomy, which partitions genomic variation above strain or
isolate level and develops a unique taxon nomenclature under
the supervision of the ICTV4,5. To decide on whether a virus
represents a new species—that is, the least diverged (and most
populated) group of viruses—taxonomists use the results of
dierent analyses. Taxonomical classication is hierarchical,
using nested groups (taxa) that populate dierent levels (ranks)
of classication. Taxa of dierent ranks dier in their intra-taxon
pairwise divergence, which increases from the smallest at the
species rank to the largest at the realm rank30. ey may also be
distinguished by taxon-specic markers that characterize natural
groupings. Only the species and genus ranks need to be specied
to classify a new virus; lling other ranks is optional. If a virus
prototypes a new species, it will be regarded as taxonomically
novel. If (within this framework) a virus crosses a host barrier
and acquires novel properties, its classication will not change
(that is, it remains part of the original species) even if the virus
establishes a permanent circulation in the new host, which likely
happened with coronaviruses of the four species that circulate
in humans and display seasonal peaks (reviewed in ref. 50).
Importantly, the criteria used to dene a viral species in one
virus family such as Coronaviridae may not be applicable to
another family such as Retroviridae, and vice versa, since Study
Groups are independent in their approach to virus classication.
Box 3 | Classifying coronaviruses
Initially, the classication of coronaviruses was largely based on
serological (cross-) reactivities to the viral spike protein, but is
now based on comparative sequence analyses of replicative pro-
teins. e choice of proteins and the methods used to analyse
them have gradually evolved since the start of this century20,28,29,51.
e CSG currently analyses 3CLpro, NiRAN, RdRp, ZBD and
HEL1 (ref. 52) (Fig.2a), two domains less than previously used
in the analyses conducted between 2009 and 2015 (refs. 16,18).
According to our current knowledge, these ve essential do-
mains are the only ones conserved in all viruses of the order Ni-
dovirales52. ey are thus used for the classication by all ICTV
nidovirus study groups (coordinated by the NSG).
Since 2011, the classication of coronaviruses and other
nidoviruses has been assisted by the DivErsity pArtitioning
by hieRarchical Clustering (DEmARC) soware, which
denes taxa and ranks23,24. Importantly, the involvement of all
coronavirus genome sequences available at the time of analysis
allows family-wide designations of demarcation criteria for all
ranks, including species, regardless of the taxa sampling size,
be it a single or hundreds of virus(es). DEmARC delineates
monophyletic clusters (taxa) of viruses using weighted linkage
clustering in the PPD space and according to the classication of
ranks dened through clustering cost (CC) minima presented as
PPD thresholds (PPD accounts for multiple substitutions at all
sequence positions and thus may exceed 1.0, which is the limit
for conventional pair-wise distances (PDs)). In the DEmARC
framework, the persistence of thresholds in the face of increasing
virus sampling is interpreted to reect biological forces and
environmental factors21. Homologous recombination, which
is common in coronaviruses53–55, is believed to be restricted in
genome regions encoding the most essential proteins, such as
those used for classication, and to members of the same virus
species. is restriction promotes intra-species diversity and
contributes to inter-species separation. To facilitate the use
of rank thresholds outside of the DEmARC framework, they
are converted into PD and expressed as a percentage, which
researchers commonly use to arrive at a tentative assignment
of a given virus within the coronavirus taxonomy following
conventional phylogenetic analysis of selected viruses.
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Consensus statement NATuRe MICROBIOlOGy
the species composition was not affected and the virus was assigned
to the species Severe acute respiratory syndrome-related coronavirus,
as detailed in Box4.
With respect to novelty, SARS-CoV-2 differs from the two other
zoonotic coronaviruses, SARS-CoV and MERS-CoV, introduced
to humans earlier in the twenty-first century. Previously, the CSG
established that each of these two viruses prototype a new species
in a new informal subgroup of the genus Betacoronavirus15,16. These
two informal subgroups were recently recognized as subgenera
Sarbecovirus and Merbecovirus18,28,29 when the subgenus rank was
established in the virus taxonomy30. Being the first identified repre-
sentatives of a new species, unique names were introduced for the
two viruses and their taxa in line with the common practice and state
of virus taxonomy at the respective times of isolation. The situation
with SARS-CoV-2 is fundamentally different because this virus is
assigned to an existing species that contains hundreds of known
viruses predominantly isolated from humans and diverse bats. All
these viruses have names derived from SARS-CoV, although only
the human isolates collected during the 2002–2003 outbreak have
been confirmed to cause SARS in infected individuals. Thus, the
reference to SARS in all these virus names (combined with the use
of specific prefixes, suffixes and/or genome sequence IDs in pub-
lic databases) acknowledges the phylogenetic (rather than clinical
disease-based) grouping of the respective virus with the prototypic
virus in that species (SARS-CoV). The CSG chose the name SARS-
CoV-2 based on the established practice for naming viruses in this
species and the relatively distant relationship of this virus to the pro-
totype SARS-CoV in a species tree and the distance space (Fig.2b
and the figure in Box4).
The available yet limited epidemiological and clinical data for
SARS-CoV-2 suggest that the disease spectrum and transmission
efficiency of this virus31–35 differ from those reported for SARS-
CoV9. To accommodate the wide spectrum of clinical presentations
and outcomes of infections caused by SARS-CoV-2 (ranging from
asymptomatic to severe or even fatal in some cases)31, the WHO
recently introduced a rather unspecific name (coronavirus disease
19, also known as COVID-19 (ref. 36)) to denote this disease. Also,
the diagnostic methods used to confirm SARS-CoV-2 infections are
not identical to those of SARS-CoV. This is reflected by the specific
recommendations for public health practitioners, healthcare work-
ers and laboratory diagnostic staff for SARS-CoV-2 (for example,
the WHO guidelines for SARS-CoV-2 (ref. 37). By uncoupling the
naming conventions used for coronaviruses and the diseases that
some of them cause in humans and animals, we wish to support the
WHO in its efforts to establish disease names in the most appro-
priate way (for further information, see the WHO’s guidelines for
disease naming38). The further advancement of naming conventions
is also important because the ongoing discovery of new human and
animal viruses by next-generation sequencing technologies can be
expected to produce an increasing number of viruses that do not
(easily) fit the virus–disease model that was widely used in the pre-
genomic era (Box 1). Having now established different names for
the causative virus (SARS-CoV-2) and the disease (COVID-19), the
CSG hopes that this will raise awareness in both the general public
and public health authorities regarding the difference between these
two entities. The CSG promotes this clear distinction because it will
help improve the outbreak management and also reduces the risk of
confusing virus and disease, as has been the case over many years
with SARS-CoV (the virus) and SARS (the disease).
To facilitate good practice and scientific exchange, the CSG rec-
ommends that researchers describing new viruses (that is, isolates)
in this species adopt a standardized format for public databases and
publications that closely resembles the formats used for isolates of
avian coronaviruses39, filoviruses40 and influenza virus1. The pro-
posed naming convention includes a reference to the host organism
that the virus was isolated from, the place of isolation (geographic
location), an isolate or strain number, and the time of isolation (year
or more detailed) in the format virus/host/location/isolate/date; for
Sarbecovirus
Nidovirales Primates
Homo sapiens
CoronavirusesCategory Humans
Order
Family
Subfamily
Subgenus
Genus
Species
Individuum
Suborder
Realm
Coronaviridae
Orthocoronavirinae
Betacoronavirus
Riboviria
Cornidovirineae
Hominidae
Homininae
Homo
Divergence
Dmitri Ivanovsky, Martinus Beijerinck,
Friedrich Loeffler, Barbara McClintock,
Marie Curie, Albert Einstein,
Rosalind Franklin, Hideki Yukawa,
and so on.
SARS-CoVUrbani, SARS-CoVGZ-02,
Bat SARS CoVRf1/2004, Civet SARS
CoVSZ3/2003, SARS-CoVPC4-227,
SARSr-CoVBtKY72, SARS-CoV-2
Wuhan-Hu-1, SARSr-CoVRatG13,
and so on.
Severe acute respiratory
syndrome-related coronavirus
Fig. 1 | Taxonomy of selected coronaviruses. Shown is the full taxonomy of selected coronaviruses in comparison with the taxonomy of humans (the
founders of virology and other eminent scientists represent individual human beings for the sake of this comparison), which is given only for categories
(ranks) that are shared with the virus taxonomy. Note that these two taxonomies were independently developed using completely different criteria.
Although no equivalence is implied, the species of coronaviruses is interpreted sensu stricto as accepted for the species of humans.
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Consensus statement
NATuRe MICROBIOlOGy
0 1,000 nt
5d
nsp4B-TM
nsp5A-3CLpro
nsp5B-3CLpro
nsp6-TM
nsp7
nsp8
nsp9
nsp10-CysHis
nsp12-NiRAN
nsp12-RdRp
nsp13-ZBD
nsp13-1B
nsp13-HEL1core
nsp14A2-ExoN
nsp14B-NMT
nsp15-A1
nsp15B-NendoU
nsp16-OMT
+1
0
−1
SARS-CoV
a
b
SARSr-CoV BtKY72
GU190215.1
MG772933.1
MG772934.1
SARS-CoV-2
SARSr-CoV RaTG13
JX993988.1
DQ412043.1
GQ153547.1
KF294457.1
KY938558.1
DQ412042.1
KJ473813.1
SARS-CoV
AY351680.1
SARS-CoV PC4−227
FJ588686.1 90% ≤ SH
70% ≤ SH < 90%
SH < 70%
0.005
c
HCoV 229E
HCoV NL63
MrufCoV 2JL14
HCoV OC43
ChRCoV HKU24
HCoV HKU1
MHV
EriCoV
MERS-CoV
Ty-BatCoV HKU4
Pi-BatCoV HKU5
Ei-BatCoV C704
Ro-BatCoV HKU9
Ro-BatCoV GCCDC1
Bat Hp-BetaCoV
SARS-CoV
SARS-CoV PC4–227
SARSr-CoV RaTG13
SARS-CoV−2
SARSr-CoV BtKY72
Viruses
0.1
Species
90% ≤ SH
70% ≤ SH < 90%
SH < 70%
Severe acute respiratory
syndrome-related coronavirus
Bat Hp-betacoronavirus Zhejiang2013
Rousettus bat coronavirus GCCDC1
Rousettus bat coronavirus HKU9
Eidolon bat coronavirus C704*
Pipistrellus bat coronavirus HKU5
Tylonycteris bat coronavirus HKU4
Middle East respiratory syndrome-related coronavirus
Hedgehog coronavirus 1
Murine coronavirus
Human coronavirus HKU1
China Rattus coronavirus HKU24
Betacoronavirus 1
Myodes coronavirus 2JL14*
Human coronavirus NL63
Human coronavirus 229E
Fig. 2 | Phylogeny of coronaviruses. a, Concatenated multiple sequence alignments (MSAs) of the protein domain combination44 used for phylogenetic and
DEmARC analyses of the family Coronaviridae. Shown are the locations of the replicative domains conserved in the ordert Nidovirales in relation to several other
ORF1a/b-encoded domains and other major ORFs in the SARS-CoV genome. 5d, 5 domains: nsp5A-3CLpro, two beta-barrel domains of the 3C-like protease;
nsp12-NiRAN, nidovirus RdRp-associated nucleotidyltransferase; nsp12-RdRp, RNA-dependent RNA polymerase; nsp13-HEL1 core, superfamily 1 helicase with
upstream Zn-binding domain (nsp13-ZBD); nt, nucleotide. b, The maximum-likelihood tree of SARS-CoV was reconstructed by IQ-TREE v.1.6.1 (ref. 45) using 83
sequences with the best fitting evolutionary model. Subsequently, the tree was purged from the most similar sequences and midpoint-rooted. Branch support
was estimated using the Shimodaira–Hasegawa (SH)-like approximate likelihood ratio test with 1,000 replicates. GenBank IDs for all viruses except four are
shown; SARS-CoV, AY274119.3; SARS-CoV-2, MN908947.3; SARSr-CoV_BtKY72, KY352407.1; SARS-CoV_PC4-227, AY613950.1. c, Shown is an IQ-TREE
maximum-likelihood tree of single virus representatives of thirteen species and five representatives of the species Severe acute respiratory syndrome-related
coronavirus of the genus Betacoronavirus. The tree is rooted with HCoV-NL63 and HCoV-229E, representing two species of the genus Alphacoronavirus. Purple
text highlights zoonotic viruses with varying pathogenicity in humans; orange text highlights common respiratory viruses that circulate in humans. Asterisks
indicate two coronavirus species whose demarcations and names are pending approval from the ICTV and, thus, these names are not italicized.
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Consensus statement NATuRe MICROBIOlOGy
Box 4 | Classifying SARS-CoV-2
e species demarcation threshold (also known as demarcation
limit) in the family Coronaviridae is dened by viruses whose
PPD(s) may cross the inter-species demarcation PPD threshold
(threshold ‘violators’). Due to their minute share of ~10–4 of the to-
tal number of all intra- and inter-species PPDs, these violators may
not even be visually recognized in a conventional diagonal plot clus-
tering viruses on a species basis (panel a of the gure in Box 4).
Furthermore, they do not involve any virus of the species Severe
acute respiratory syndrome-related coronavirus, as is evident from
the analysis of maximal intraspecies PPDs of 2,505 viruses of all 49
coronavirus species (of which 39 are established and 10 are pending
or tentative) (panel b of the gure in Box 4) and PDs of 256 viruses
of this species (panel c of the gure in Box 4). us, the genomic
variation of the known viruses of the species Severe acute respiratory
syndrome-related coronavirus is smaller compared to that of other
comparably well-sampled species—for example, those prototyped
by MERS-CoV, human coronavirus OC43 (HCoV-OC43) and in-
fectious bronchitis virus (IBV) (panel b of the gure in Box 4)—and
this species is well separated from other known coronavirus species
in the sequence space. Both of these characteristics facilitate the un-
ambiguous assignment of SARS-CoV-2 to this species.
Intra-species PDs of SARS-CoV-2 belong to the top 25% of this
species and also include the largest PD between SARS-CoV-2 and
an African bat virus isolate (SARSr-CoV_BtKY72)56 (panel c of
the gure in Box 4), representing two basal lineages within the
species Severe acute respiratory syndrome-related coronavirus that
constitute very few known viruses (Fig.2b,c). ese relationships
stand in contrast to the shallow branching of the most populous
lineage of this species, which includes all the human SARS-CoV
isolates collected during the 2002–2003 outbreak and the closely
related bat viruses of Asian origin identied in the search for the
potential zoonotic source of that epidemic57. is clade structure
is susceptible to homologous recombination, which is common in
this species44,58,59; to formalize clade denition, it must be revisited
aer the sampling of viruses representing the deep branches has
improved suciently. e current sampling denes a very small
median PD for human SARS-CoVs, which is approximately 15
times smaller than the median PD determined for SARS-CoV-2
(0.16% versus 2.6%; panel c of the gure in Box 4). is small
median PD of human SARS-CoVs also dominates the species-
wide PD distribution (0.25%; panel c of the gure in Box 4).
Pairwise distance demarcation of species in the family Coronaviridae. a,
Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus
species, 39 established and 10 pending or tentative, and ordered from the
most to least populous species, from left to right; green and white, PPDs
smaller and larger than the inter-species threshold, respectively. Areas of the
green squares along the diagonal are proportional to the virus sampling of
the respective species, and virus prototypes of the five most sampled species
are specified to the left; asterisks indicate species that include viruses whose
intra-species PPDs crossed the inter-species threshold (threshold ‘violators’). b,
Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling
(y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated
are the acronyms of virus prototypes of the seven most sampled species.
Green and blue plot sections represent intra-species and intra-subgenera PPD
ranges. The vertical black line indicates the inter-species threshold. c, Shown
are the PDs of non-identical residues (y axis) for four viruses representing
three major phylogenetic lineages (clades) of the species Severe acute
respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256
viruses of this species (‘all pairs’). The PD values were derived from
pairwise distances in the MSA that were calculated using an identity matrix.
Panels a and b were adopted from the DEmARC v.1.4 output.
a
PEDV
MERS-CoV*
IBV*
SARS-CoV
HCoV-OC43*
2,505 coronaviruses
2,505 coronaviruses
0 0.02 0.04 0.06 0.08 0.10
0
0.5
1.0
1.5
2.0
2.5
Maximum intra-species PPD
PEDV MERS-CoV
IBV
SARS-CoV HCoV-OC43
TGEV
PoCoV_HKU15
log10 [sampling size]
b
0
1
2
3
4
5
6
7
Non-identical residues (%)
Inter-species threshold
SARS-CoV-2
SARS-CoV
All pairs
c
SARSr-CoV
BtKY72
SARS-CoV
PC4−227
SARS-CoV-2 versus
SARS-CoV distances
Intra-SARS-CoV
distances
NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology

Consensus statement
NATuRe MICROBIOlOGy
example, SARS-CoV-2/human/Wuhan/X1/2019. This complete
designation along with additional and important characteristics,
such as pathogenic potential in humans or other hosts, should be
included in the submission of each isolate genome sequence to pub-
lic databases such as GenBank. In publications, this name could
be further extended with a sequence database ID—for example,
SARS-CoV-2/human/Wuhan/X1/2019_XYZ12345 (fictional exam-
ple)—when first mentioned in the text. We believe that this format
will provide critical metadata on the major characteristics of each
particular virus isolate (genome sequence) required for subsequent
epidemiological and other studies, as well as for control measures.
Expanding the focus from pathogens to virus species
Historically, public health and fundamental research have been
focused on the detection, containment, treatment and analysis of
viruses that are pathogenic to humans following their discovery
(a reactive approach). Exploring and defining their biological char-
acteristics in the context of the entire natural diversity as a spe-
cies has never been apriority. The emergence of SARS-CoV-2 as a
human pathogen in December 2019 may thus be perceived as com-
pletely independent from the SARS-CoV outbreak in 2002–2003.
Although SARS-CoV-2 is indeed not a descendent of SARS-CoV
(Fig.2b), and the introduction of each of these viruses into humans
was likely facilitated by independent unknown external factors, the
two viruses are genetically so close to each other (Fig.2c, panel c of
the figure in Box 4) that their evolutionary histories and character-
istics are mutually informative.
The currently known viruses of the species Severe acute respi-
ratory syndrome-related coronavirus may be as (poorly) repre-
sentative for this particular species as the few individuals that we
selected to represent H. sapiens in Fig.1. It is thus reasonable to
assume that this biased knowledge of the natural diversity of the
species Severe acute respiratory syndrome-related coronavirus limits
our current understanding of fundamental aspects of the biology
of this species and, as a consequence, our abilities to control zoo-
notic spillovers to humans. Future studies aimed at understanding
the ecology of these viruses and advancing the accuracy and reso-
lution of evolutionary analyses41 would benefit greatly from adjust-
ing our research and sampling strategies. This needs to include an
expansion of our current research focus on human pathogens and
their adaptation to specific hosts to other viruses in this species.
To illustrate the great potential of species-wide studies, it may
again be instructive to draw a parallel to H. sapiens, and specifi-
cally to the impressive advancements in personalized medicine in
recent years. Results of extensive genetic analyses of large num-
bers of individuals representing diverse populations from all con-
tinents have been translated into clinical applications and greatly
contribute to optimizing patient-specific diagnostics and therapy.
They were instrumental in identifying reliable predictive markers
for specific diseases as well as genomic sites that are under selec-
tion. It thus seems reasonable to expect that genome-based analy-
ses with a comparable species coverage will be similarly insightful
for coronaviruses. Also, additional diagnostic tools that target the
entire species should be developed to complement existing tools
optimized to detect individual pathogenic variants (a proactive
approach). Technical solutions to this problem are already avail-
able; for example, in the context of multiplex PCR-based assays42.
The costs for developing and applying (combined or separate) spe-
cies- and virus-specific diagnostic tests in specific clinical and/or
epidemiological settings may help to better appreciate the biologi-
cal diversity and zoonotic potential of specific virus species and
their members. Also, the further reduction of time required to
identify the causative agents of novel virus infections will contrib-
ute to limiting the enormous social and economic consequences of
large outbreaks. To advance such studies, innovative fundraising
approaches may be required.
Although this Consensus Statement focuses on a single virus
species, the issues raised apply to other species in the family and
possibly beyond. A first step towards appreciation of this species
and others would be for researchers, journals, databases and other
relevant bodies to adopt proper referencing to the full taxonomy
of coronaviruses under study, including explicit mentioning of the
relevant virus species and the specific virus(es) within the species
using the ICTV naming rules explained above. This naming con-
vention is, regretfully, rarely observed in common practice, with
mixing of virus and species names being frequently found in the
literature (including by the authors of this Consensus Statement
on several past occasions). The adoption of accurate virus-naming
practices should be facilitated by the major revision of the virus spe-
cies nomenclature that is currently being discussed by the ICTV
and is being planned for implementation in the near future43. With
this change in place, the CSG is resolved to address the existing sig-
nificant overlap between virus and species names that complicates
the appreciation and use of the species concept in its application to
coronaviruses.
Received: 5 February 2020; Accepted: 19 February 2020;
Published: xx xx xxxx
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Acknowledgements
Work on DEmARC advancement and coronavirus and nidovirus taxonomies was
supported by the EU Horizon 2020 EVAg 653316 project and the LUMC MoBiLe
program (to A.E.G.), and on coronavirus and nidovirus taxonomies by a Mercator
Fellowship by the Deutsche Forschungsgemeinschaft (to A.E.G.) in the context of the
SFB1021 (A01 to J.Z.).
We thank all researchers who released SARS-CoV-2 genome sequences through
the GISAID initiative and particularly the authors of the GenBank MN908947 genome
sequence: F. Wu, S. Zhao, B. Yu, Y. M. Chen, W. Wang, Z. G. Song, Y. Hu, Z. W. Tao,
J. H. Tian, Y. Y. Pei, M. L. Yuan, Y. L. Zhang, F. H. Dai, Y. Liu, Q. M. Wang, J. J. Zheng,
L. Xu, E. C. Holmes and Y. Z. Zhang. We thank S. G. Siddell, R. A. M. Fouchier, and
J. H. Kuhn for their comments on a manuscript version posted on 11 February 2020
to bioRxiv. A.E.G. and J.Z. thank W. J. M. Spaan, A. J. Davison and E. J. Lefkowitz for
support. A.E.G. thanks members of the ICTV ExecutiveCommittee for discussions of
classification and nomenclature issues relevant to this paper.
Author contributions
S.C.B., R.S.B., C.D., R.J.D.G., A.E.G., B.L.H., B.W.N., S.P., L.L.M.P., I.S. and J.Z. are
members of the CSG, chaired by J.Z.; R. J.D.G., A.E.G., C.L., B.W.N. and J.Z. are
members of the NSG, chaired by A.E.G.; A.E.G. and J.Z. are members of the ICTV.
A.E.G., A.A.G., C.L., A.M.L., D.P., D.V.S. and I.A.S. are members of the DEmARC team
led by A.E.G. D.V.S. generated the classification of SARS-CoV-2 using a computational
pipeline developed by A.A.G. and using software developed by the DEmARC team; the
CSG considered and approved this classification, and subsequently debated and
decided on the virus name. A.E.G. and J.Z. wrote the manuscript. A.E.G. and D.V.S.
generated the figures. All authors reviewed the manuscript and approved its
submission for publication.
Competing interests
The authors declare no competing interests.
Additional information
Correspondence and requests for materials should be addressed to A.E.G. or J.Z.
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Consensus statement
NATuRe MICROBIOlOGy Consensus statement
NATuRe MICROBIOlOGy
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses
Alexander E. Gorbalenya1,2,3 ✉ , Susan C. Baker4, Ralph S. Baric5, Raoul J. de Groot6, Christian Drosten7,
Anastasia A. Gulyaeva2, Bart L. Haagmans8, Chris Lauber2, Andrey M. Leontovich3,
Benjamin W. Neuman9, Dmitry Penzar3, Stanley Perlman10, Leo L. M. Poon11, Dmitry V. Samborskiy3,
Igor A. Sidorov2, Isabel Sola12 and John Ziebuhr13 ✉
1Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands. 2Department of Medical Microbiology, Leiden
University Medical Center, Leiden, the Netherlands. 3Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology,
Lomonosov Moscow State University, Moscow, Russia. 4Department of Microbiology and Immunology, Loyola University of Chicago, Stritch School
of Medicine, Maywood, IL, USA. 5Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA. 6Division of Virology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands. 7Institute of Virology, Charité –
Universitätsmedizin Berlin, Berlin, Germany. 8Viroscience Lab, Erasmus MC, Rotterdam, the Netherlands. 9Texas A&M University-Texarkana, Texarkana,
TX, USA. 10Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA. 11Centre of Influenza Research & School of Public Health,
The University of Hong Kong, Hong Kong, People’s Republic of China. 12Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-
CSIC), Campus de Cantoblanco, Madrid, Spain. 13Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
✉e-mail: A.E.Gorbalenya@lumc.nl; John.Ziebuhr@viro.med.uni-giessen.de
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