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Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus

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A large number of SARS-related coronaviruses (SARSr-CoV) have been detected in horseshoe bats since 2005 in different areas of China. However, these bat SARSr-CoVs show sequence differences from SARS coronavirus (SARS-CoV) in different genes (S, ORF8, ORF3, etc) and are considered unlikely to represent the direct progenitor of SARS-CoV. Herein, we report the findings of our 5-year surveillance of SARSr-CoVs in a cave inhabited by multiple species of horseshoe bats in Yunnan Province, China. The full-length genomes of 11 newly discovered SARSr-CoV strains, together with our previous findings, reveals that the SARSr-CoVs circulating in this single location are highly diverse in the S gene, ORF3 and ORF8. Importantly, strains with high genetic similarity to SARS-CoV in the hypervariable N-terminal domain (NTD) and receptor-binding domain (RBD) of the S1 gene, the ORF3 and ORF8 region, respectively, were all discovered in this cave. In addition, we report the first discovery of bat SARSr-CoVs highly similar to human SARS-CoV in ORF3b and in the split ORF8a and 8b. Moreover, SARSr-CoV strains from this cave were more closely related to SARS-CoV in the non-structural protein genes ORF1a and 1b compared with those detected elsewhere. Recombination analysis shows evidence of frequent recombination events within the S gene and around the ORF8 between these SARSr-CoVs. We hypothesize that the direct progenitor of SARS-CoV may have originated after sequential recombination events between the precursors of these SARSr-CoVs. Cell entry studies demonstrated that three newly identified SARSr-CoVs with different S protein sequences are all able to use human ACE2 as the receptor, further exhibiting the close relationship between strains in this cave and SARS-CoV. This work provides new insights into the origin and evolution of SARS-CoV and highlights the necessity of preparedness for future emergence of SARS-like diseases.
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RESEARCH ARTICLE
Discovery of a rich gene pool of bat SARS-
related coronaviruses provides new insights
into the origin of SARS coronavirus
Ben Hu
1
, Lei-Ping Zeng
1
, Xing-Lou Yang
1
, Xing-Yi Ge
1
, Wei Zhang
1
, Bei Li
1
, Jia-
Zheng Xie
1
, Xu-Rui Shen
1
, Yun-Zhi Zhang
2,3
, Ning Wang
1
, Dong-Sheng Luo
1
, Xiao-
Shuang Zheng
1
, Mei-Niang Wang
1
, Peter Daszak
4
, Lin-Fa Wang
5
, Jie Cui
1
*, Zheng-
Li Shi
1
*
1CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases of
Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 2Yunnan Institute of Endemic
Diseases Control and Prevention, Dali, China, 3Dali University, Dali, China, 4EcoHealth Alliance, New
York, New York, United States of America, 5Programme in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore
These authors contributed equally to this work.
*jiecui@wh.iov.cn (JC); zlshi@wh.iov.cn (Z-LS)
Abstract
A large number of SARS-related coronaviruses (SARSr-CoV) have been detected in horse-
shoe bats since 2005 in different areas of China. However, these bat SARSr-CoVs show
sequence differences from SARS coronavirus (SARS-CoV) in different genes (S, ORF8,
ORF3, etc) and are considered unlikely to represent the direct progenitor of SARS-CoV.
Herein, we report the findings of our 5-year surveillance of SARSr-CoVs in a cave inhabited
by multiple species of horseshoe bats in Yunnan Province, China. The full-length genomes
of 11 newly discovered SARSr-CoV strains, together with our previous findings, reveals that
the SARSr-CoVs circulating in this single location are highly diverse in the S gene, ORF3
and ORF8. Importantly, strains with high genetic similarity to SARS-CoV in the hypervari-
able N-terminal domain (NTD) and receptor-binding domain (RBD) of the S1 gene, the
ORF3 and ORF8 region, respectively, were all discovered in this cave. In addition, we report
the first discovery of bat SARSr-CoVs highly similar to human SARS-CoV in ORF3b and in
the split ORF8a and 8b. Moreover, SARSr-CoV strains from this cave were more closely
related to SARS-CoV in the non-structural protein genes ORF1a and 1b compared with
those detected elsewhere. Recombination analysis shows evidence of frequent recombina-
tion events within the S gene and around the ORF8 between these SARSr-CoVs. We
hypothesize that the direct progenitor of SARS-CoV may have originated after sequential
recombination events between the precursors of these SARSr-CoVs. Cell entry studies
demonstrated that three newly identified SARSr-CoVs with different S protein sequences
are all able to use human ACE2 as the receptor, further exhibiting the close relationship
between strains in this cave and SARS-CoV. This work provides new insights into the origin
and evolution of SARS-CoV and highlights the necessity of preparedness for future emer-
gence of SARS-like diseases.
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 1 / 27
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OPEN ACCESS
Citation: Hu B, Zeng L-P, Yang X-L, Ge X-Y, Zhang
W, Li B, et al. (2017) Discovery of a rich gene pool
of bat SARS-related coronaviruses provides new
insights into the origin of SARS coronavirus. PLoS
Pathog 13(11): e1006698. https://doi.org/10.1371/
journal.ppat.1006698
Editor: Christian Drosten, Charite
Universitatsmedizin Berlin, GERMANY
Received: February 10, 2017
Accepted: October 17, 2017
Published: November 30, 2017
Copyright: ©2017 Hu et al. This is an open access
article distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in
any medium, provided the original author and
source are credited.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information
files. The complete genome sequences of the 11
bat SARS-related coronaviruses newly identified in
this study have been deposited in the GenBank
database and assigned accession numbers
KY417142 to KY417152, respectively.
Funding: This work was jointly funded by National
Natural Science Foundation of China (81290341,
31621061) to ZLS, China Mega-Project for
Infectious Disease (2014ZX10004001-003) to ZLS,
Author summary
Increasing evidence has been gathered to support the bat origin of SARS coronavirus
(SARS-CoV) in the past decade. However, none of the currently known bat SARSr-CoVs
is thought to be the direct ancestor of SARS-CoV. Herein, we report the identification of a
diverse group of bat SARSr-CoVs in a single cave in Yunnan, China. Importantly, all of
the building blocks of SARS-CoV genome, including the highly variable S gene, ORF8
and ORF3, could be found in the genomes of different SARSr-CoV strains from this single
location. Based on the analysis of full-length genome sequences of the newly identified bat
SARSr-CoVs, we speculate that the direct ancestor of SARS-CoV may have arisen from
sequential recombination events between the precursors of these bat SARSr-CoVs prior to
spillover to an intermediate host. In addition, we found bat SARSr-CoV strains with dif-
ferent S proteins that can all use the receptor of SARS-CoV in humans (ACE2) for cell
entry, suggesting diverse SARSr-CoVs capable of direct transmission to humans are circu-
lating in bats in this cave. Our current study therefore offers a clearer picture on the evolu-
tionary origin of SARS-CoV and highlights the risk of future emergence of SARS-like
diseases.
Introduction
Severe Acute Respiratory Syndrome (SARS) is a severe emerging viral disease with high fatality
characterized by fever, headache and severe respiratory symptoms including cough, dyspnea
and pneumonia [1]. Due to its high transmissibility among humans, after its first emergence in
southern China in late 2002, it rapidly led to a global pandemic in 2003 and was marked as one
of the most significant public health threats in the 21
st
century [2,3]. The causative agent,
SARS coronavirus (SARS-CoV), has been previously assigned to group 2b CoV and is now a
member of the lineage B of genus Betacoronavirus in the family Coronaviridae [4]. It shares
similar genome organization with other coronaviruses, but exhibits a unique genomic struc-
ture which includes a number of specific accessory genes, including ORF3a, 3b, ORF6, ORF7a,
7b, ORF8a, 8b and 9b [5,6].
Masked palm civets (Paguma larvata) were initially hypothesized to be the animal origin of
SARS-CoV [7,8]. However, since a large number of genetically diverse SARS-related coronavi-
ruses (SARSr-CoV) have been detected in multiple species of horseshoe bats (genus Rhinolo-
phus) from different areas of China and Europe in the aftermath of SARS, it is prevailingly
considered that SARS-CoV originated in horseshoe bats with civets acting as the intermediate
amplifying and transmitting host [916]. Recently we have reported four novel SARSr-CoVs
from Chinese horseshoe bats that shared much higher genomic sequence similarity to the epi-
demic strains, particularly in their S gene, of which two strains (termed WIV1 and WIV16)
have been successfully cultured in vitro [17,18]. These newly identified SARSr-CoVs have been
demonstrated to use the same cellular receptor (angiotensin converting enzyme-2 [ACE-2]) as
SARS-CoV does and replicate efficiently in primary human airway cells [1719].
Despite the cumulative evidence for the emergence of SARS-CoV from bats, all bat SARSr-
CoVs described so far are clearly distinct from SARS-CoV in the S gene and/or one or more
accessory genes such as ORF3 and ORF8, suggesting they are likely not the direct ancestor of
SARS-CoV. Thus a critical gap remains in our understanding of how and where SARS-CoV
originated from bat reservoirs. Previously, we reported a number of bat SARSr-CoVs with
diverse S protein sequences from a single cave in Yunnan Province, including the four strains
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 2 / 27
Scientific and technological basis special project
(2013FY113500) to YZZ and ZLS from the Ministry
of Science and Technology of China, the Strategic
Priority Research Program of the Chinese
Academy of Sciences (XDPB0301) to ZLS, the
National Institutes of Health (NIAID R01AI110964),
the USAID Emerging Pandemic Threats (EPT)
PREDICT program to PD and ZLS, CAS Pioneer
Hundred Talents Program to JC, NRF-CRP grant
(NRF-CRP10-2012-05) to LFW and WIV “One-
Three-Five” Strategic Program (WIV-135-TP1) to
JC and ZLS. The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing interests: The authors have declared
that no competing interests exist.
mentioned above most closely related to SARS-CoV [17,18]. Here we report the latest results
of our 5-year longitudinal surveillance of bat SARSr-CoVs in this single location and system-
atic evolutionary analysis using full-length genome sequences of 15 SARSr-CoV strains (11
novel ones and 4 from previous studies). Efficiency of human ACE2 usage and the functions of
accessory genes ORF8 and 8a were also evaluated for some of the newly identified strains.
Results
Continued circulation of diverse SARSr-CoVs in bats from a single
location
We have carried out a five-year longitudinal surveillance (April 2011 to October 2015) on
SARSr-CoVs in bats from a single habitat in proximity to Kunming city, Yunnan province,
China, which was mainly inhabited by horseshoe bats. A total of 602 alimentary specimens
(anal swabs or feces) were collected and tested for the presence of CoVs by a Pan-CoV
RT-PCR targeting the 440-nt RdRp fragment that is conserved among all known α- and β-
CoVs [20]. In total, 84 samples tested positive for CoVs. Sequencing of the PCR amplicons
revealed the presence of SARSr-CoVs in the majority (64/84) of the CoV-positive samples
(Table 1). Host species identification by amplification of either Cytb or ND1 gene suggested
that most (57/64) of the SARSr-CoV positive samples were from Rhinolophus sinicus, while the
remaining 7 samples were from Rhinolophus ferrumequinum,Rhinolophus affinis and from
Aselliscus stoliczkanus which belongs to the family Hipposideridae.
Based on the preliminary analysis of the partial RdRp sequences, all of the 64 bat SARSr-
CoV sequences showed high similarity among themselves and with other reported bat SARSr-
CoVs and SARS-CoVs from humans and civets. To understand the genetic diversity of these
bat SARSr-CoVs, the most variable region of the SARSr-CoV S gene, corresponding to the
receptor-binding domain (RBD) of SARS-CoV, were amplified and sequenced. Due to low viral
load in some samples, RBD sequences were successfully amplified only from 49 samples. These
RBD sequences displayed high genetic diversity and could be divided into two large clades, both
of which included multiple genotypes. Clade 1 strains shared an identical size and higher amino
acid (aa) sequence identity with SARS-CoV RBD, while clade 2 had a shorter size than SARS-
CoV S due to two deletions (5 and 12–13 aa, respectively) (S1 Fig). Co-infections by two strains
of different clades were detected in two samples, Rs3262 and Rs4087 (S1 Fig).
Table 1. Summary of SARSr-CoV detection in bats from a single habitat in Kunming, Yunnan.
Sampling time Sample type Sample Numbers SARSr-CoV + bat species (No.)
Total CoV + SARSr-CoV +
April, 2011 anal swab 14 1 1 R.sinicus (1)
October, 2011 anal swab 8 3 3 R.sinicus (3)
May, 2012 anal swab & feces 54 9 4 R.sinicus (4)
September, 2012 feces 39 20 19 R.sinicus (16)
R.ferrumequinum (3)
April, 2013 feces 52 21 16 R.sinicus (16)
July, 2013 anal swab & feces 115 9 8 R.sinicus (8)
May, 2014 feces 131 8 4 A.stoliczkamus (3)
R.affinis (1)
October, 2014 anal swab 19 4 4 R.sinicus (4)
May, 2015 feces 145 3 0
October, 2015 anal swab 25 6 5 R.sinicus (5)
Total 602 84 64 R (61) A (3)
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Genomic characterization of the novel SARSr-CoVs
Based on the diversity of RBD sequences, 11 novel SARSr-CoV strains named by abbreviation
of bat species and sample ID (Rs4081, Rs4084, Rs4231, Rs4237, Rs4247, Rs4255, Rs4874,
Rs7327, Rs9401, Rf4092 and As6526) were selected for full-length genomic sequencing based
on sample abundance, genotype of RBD as well as sampling time. For each RBD genotype and
each time of sampling, at least one representative strain was selected. The genome size of these
novel SARSr-CoVs ranged from 29694 to 30291 nucleotides (nt). This gave a total of 15 full-
length genomes of bat SARSr-CoVs from this single location (13 from R.sinicus, and one each
from R.ferrumequinum and A.stoliczkanus), including our previously reported strains,
Rs3367, RsSHC014, WIV1 and WIV16 [17,18]. The genomes of all 15 SARSr-CoVs circulating
in this single cave shared 92.0% to 99.9% nt sequence identity. The overall nt sequence identity
between these SARSr-CoVs and human and civet SARS-CoVs is 93.2% to 96%, significantly
higher than that observed for bat SARSr-CoVs reported from other locations in China (88–
93%) [9,10,12,14,21,22]. The genome sequence similarity among the 15 SARSr-CoVs and
SARS-CoV SZ3 strain was examined by Simplot analysis (Fig 1). The 15 SARSr-CoVs are
Fig 1. Similarity plot based on the full-length genome sequence of civet SARS CoV SZ3. Full-length genome sequences of all SARSr-
CoV detected in bats from the cave investigated in this study were used as reference sequences. The analysis was performed with the
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.g001
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highly conserved and share a uniformly high sequence similarity to SARS-CoV in the non-
structural gene ORF1a (96.6% to 97.1% nt sequence identity, 98.0% to 98.3% aa sequence iden-
tity) and ORF1b (96.1% to 96.6% nt sequence identity, 99.0% to 99.4% aa sequence identity).
In contrast, a considerable genetic diversity is shown in the S gene (corresponding to SZ3
genome position 21477 to 25244) and ORF8 (corresponding to SZ3 genome position 27764 to
28132) (Fig 1).
The 11 novel SARSr-CoVs identified from this single location generally shared similar
genome organization with SARS-CoV and other bat SARSr-CoVs. In our previous study, we
identified an additional ORF termed ORFx present between ORF6 and ORF7 in strain WIV1
and WIV16 [18,23]. In this study, ORFx was also found in the genomes of Rs7327 and Rs4874.
Compared with that of WIV1 and WIV16, the length of ORFx in Rs7327 and Rs4874 was
extended to 510 nt due to a deletion of 2 nt in a poly-T sequence that resulted in a shift of read-
ing frame (Fig 2 and S2 Fig).
Co-circulation of different bat SARSr-CoVs with S, ORF8 and ORF3
sequences similar to those in SARS-CoV at a single location
The primary difference between SARS-CoV and most bat SARSr-CoVs is located in S gene.
The S protein is functionally divided into two subunits, denoted S1 and S2, which is responsi-
ble for receptor binding and cellular membrane fusion, respectively. S1 consists of two
domains, the N-terminal domain (NTD) and C-terminal domain (CTD) which is also known
as the RBD in SARS-CoV [24]. SARS-CoV and bat SARSr-CoVs share high sequence identity
in the S2 region in contrast to the S1 region. Among the 15 SARSr-CoVs identified from bats
in the surveyed cave, six strains with deletions in their RBD regions (Rs4081, Rs4237, Rs4247,
Rs4255, Rf4092 and As6526) showed 78.2% to 80.2% aa sequence identity to SARS-CoV in the
S protein, while the other nine strains without deletions were much more closely related to
SARS-CoV, with 90.0% (Rs4084) to 97.2% (Rs4874) aa sequence identity. These nine SARSr-
CoVs can be further divided into four genotypes according to their S1 sequences (Fig 2):
RsSHC014/Rs4084 showed more genetic differences from SARS-CoV in both NTD and RBD
regions; The RBD sequences of SARSr-CoV Rs7327, Rs9401 and previously reported WIV1/
Rs3367 closely resembled that of SARS-CoV. However, they were distinct from SARS-CoV but
similar to RsSHC014 in NTD. In contrast, we found a novel SARSr-CoV, termed Rs4231,
which shared highly similar NTD, but not RBD sequence with SARS-CoV (Figs 2and 3). Its S
protein showed 94.6% to 95% aa sequence identity to those of human and civet SARS-CoVs
(S1 Table). Strains with both NTD and RBD highly homologous to those of SARS-CoV were
also present in this cave. In addition to WIV16 which we described previously [18], Rs4874
was also found to have the S protein closest to SARS-CoV S (>97% aa sequence identity) of all
the bat SARSr-CoVs reported to date (Figs 2and 3). In addition to the SARSr-CoVs subjected
to full-length genome sequencing, we also obtained the RBD and NTD sequences from other
samples collected in this cave. The sequences with high identity to SARS-CoV RBD were
amplified from 10 more R.sinicus samples. SARSr-CoVs with this genotype of RBD were
detected in different seasons throughout the five years. Strains containing the NTD similar to
SARS-CoV were only found in 2013 (S2 Table).
ORF8 is another highly variable gene among different SARS-CoV and SARSr-CoV strains
[25,26]. We aligned the ORF8 nt sequences of the representative SARSr-CoVs discovered in
this surveillance with those of other SARSr-CoVs and SARS-CoVs (Fig 4). Though WIV16,
WIV1, Rs4231 and RsSHC014 were genetically closer to SARS-CoV in S gene, they contained
a single 366-nt ORF8 without the 29-nt deletion present in most human SARS-CoVs and
showed only 47.1% to 51.0% nt sequence identity to human and civet SARS-CoVs. However,
A gene pool of bat SARS-related coronaviruses
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Fig 2. Schematic diagram illustrating the genomic regions or ORFs with most variation between
different SARS-CoV and SARSr-CoV isolates. Coding regions of the N-terminal domain (NTD) and
receptor-binding domain (RBD) of the spike protein, ORF3a/b and ORF8 (8a/b) in bat SARSr-CoV genomes
highly similar to those in SARS CoV genome are indicated with black boxes or arrows while the hollow boxes
or arrows represent corresponding regions with less sequence similarity to those of SARS-CoV. The deletions
in the RBD of some SARSr-CoVs are indicated by two vertical lines.
https://doi.org/10.1371/journal.ppat.1006698.g002
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Fig 3. Amino acid sequence comparison of the S1 subunit (correspondingto aa 1–660 of the spike protein of SARS-CoV). The
receptor-binding domain (aa 318–510) of SARS-CoV and the homologous region of bat SARSr-CoVs are indicated by the red box. The key aa
A gene pool of bat SARS-related coronaviruses
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the ORF8 of strain Rf4092 from R.ferrumequinum exhibited high similarity to that of civet
SARS-CoV. It possessed a single long ORF8 of the same length (369 nt) as that of civet SARS--
CoV strain SZ3, with only 10 nt mutations and 3 aa mutations detected (Fig 4). Similar ORF8
sequences were also amplified from other 7 samples collected in the cave during 2011 to 2013,
from both R.ferrumequinum and R.sinicus (S2 Table). The ORF8 of Rs4084 was highly similar
to Rf4092’s but was split into two overlapping ORFs, ORF8a and ORF8b, due to a short 5-nt
deletion (Figs 2and 4). The position of start codons and stop codons of the two ORFs were
consistent with those in most human SARS-CoV strains. Excluding the 8-aa insertion, Rs4084
and SARS-CoV strain BJ01 displayed identical aa sequence of ORF8a, and only three different
residues involved in the interaction with human ACE2 are numbered on top of the aligned sequences. SARS-CoV GZ02, BJ01 and Tor2 were
isolated from patients in the early, middle and late phase, respectively, of the SARS outbreak in 2003. SARS-CoV SZ3 was identified from civets
in 2003. SARSr-CoV Rs 672 and YN2013 were identified from R.sinicus collected in Guizhou and Yunnan Province, respectively. SARSr-CoV
Rf1 and JL2012 were identified from R.ferrumequinum collected in Hubei and Jilin Province, respectively. WIV1, WIV16, RsSHC014, Rs4081,
Rs4084, Rs4231, Rs4237, Rs4247, Rs7327 and Rs4874 were identified from R.sinicus, and Rf4092 from R.ferrumequinum in the cave
surveyed in this study.
https://doi.org/10.1371/journal.ppat.1006698.g003
Fig 4. Alignment of nucleotide sequences of ORF8 or ORF8a/8b. The start codons and stopcodons of ORF8, 8a and 8b
are marked with black boxes and the forward and reverse arrows, respectively. The deletion responsible for the split ORF8a
and 8b in human SARS-CoV BJ01, Tor2 and bat SARSr-CoV Rs4084 is marked with red boxes. See the legend for Fig 3 for
the origin of various sequences used in this alignment.
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aa residues were observed between their ORF8b (Fig 4). To our knowledge, Rs4084 was the
first bat SARSr-CoV reported that resembled the late human SARS-CoVs in both ORF8 gene
organization and sequence.
Another key difference between SARS-CoV and bat SARSr-CoV genomes is the ORF3
coding region [10,17,21]. We analyzed the ORF3a sequences amplified from 42 samples and
found that most of the SARSr-CoVs closely related to SARS-CoV in the S gene shared
higher ORF3a sequence similarity (96.4% to 98.9% aa identity) with SARS-CoV (S3 Fig and
S2 Table). The ORF3b of SARS CoV, sharing a large part of its coding sequence with the
ORF3a, encodes a 154-aa protein [27], but it is truncated to different extents at the C-termi-
nal in previously described bat SARSr-CoVs including WIV1 and WIV16 (S4 Fig). In the
current study, we identified a non-truncated ORF3b for the first time (Rs7327), which
maintained the nuclear localization signal at its C-terminal. Moreover, it shared 98.1% aa
sequence identity with SARS-CoV strain Tor2 with only three aa substitutions (S4 Fig).
Thus, Rs7327 is the bat SARSr-CoV most similar to SARS-CoV in the ORF3 region known
to date.
Recombination analysis
The full-length genome sequences of all 15 SARSr-CoVs from the surveyed cave were screened
for evidence of potential recombination events. Both similarity plot and bootscan analyses
revealed frequent recombination events among these SARSr-CoV strains. It was suggested that
WIV16, the closest progenitor of human SARS-CoV known to date [18], was likely to be a
recombinant strain from three SARSr-CoVs harbored by bats in the same cave, namely WIV1,
Rs4231 and Rs4081, with strong Pvalue (<10
30
). Breakpoints were identified at genome posi-
tions nt 18391, 22615 and 28160 (Fig 5A). In the genomic region between nt 22615 and 28160,
which contained the region encoding the RBD and the S2 subunit of the S protein, WIV16 was
highly similar to WIV1, sharing 99% sequence identity. In contrast, in the region between nt
18391 and 22615, which covered a part of ORF1b and the region encoding the NTD of the S
gene, WIV16 showed substantially closer relationship to Rs4231. Meanwhile, the ORF1ab
sequences upstream from nt 18391 of WIV16 displayed the highest genetic similarity (99.8%
nt sequence identity) to that of Rs4081.
Evidence of recombination event was also detected in the genome of the novel SARSr-CoV
Rs4084, which had a unique genome organization with split ORF8a and 8b. The previously
reported strain RsSHC014 and the newly identified strain Rf4092 were suggested to be the
major and minor parent of Rs4084, respectively (Pvalue <10
80
). The breakpoint was located
at nt 26796 (S5 Fig). In the region downstream of the breakpoint including ORF8, Rs4084
showed closet genetic relationship with Rf4092, sharing 98.9% nt sequence identity, while it
shared the highest nt sequence identity (99.4%) with RsSHC014 in the majority of its genome
upstream from the breakpoint.
When civet SARS-CoV SZ3 was used as the query sequence in similarity plot and bootscan
analysis, evidence for recombination events was also detected (Fig 5B). In the region between
the two breakpoints at the genome positions nt 21161 and nt 27766, including the S gene,
closer genetic relationship between SZ3 and WIV16 was observed. However, from position nt
27766 towards the 3’ end of its genome, a notably close genetic relationship was observed
between SZ3 and Rf4092 instead. Throughout the non-structural gene, moreover, SZ3 shared
a similarly high sequence identity with WIV16 and Rf4092. It indicates that civet SARS-CoV
was likely to be the descendent from a recombinant of the precursors of WIV16 and Rf4092,
or that the SARSr-CoVs found in this cave, like WIV16 or Rf4092, may have been the descen-
dants of the SARS-CoV lineage.
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A gene pool of bat SARS-related coronaviruses
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Phylogenetic analysis
Phylogenetic trees were constructed using the nt sequences of nonstructural protein gene
ORF1a and ORF1b. Unlike the high genetic diversity in the S gene, nearly all SARSr-CoVs
from the bat cave we surveyed were closely clustered, and showed closer phylogenetic relation-
ship to SARS-CoV than the majority of currently known bat SARSr-CoVs discovered from
other locations, except YNLF_31C and 34C which were recently reported in greater horseshoe
bats from another location in Yunnan [22] (Fig 6). The phylogeny of SARSr-CoVs in ORF1a
and ORF1b appeared to be associated with their geographical distribution rather than with
host species. Regardless of different host bat species, SARS-CoV and SARSr-CoVs detected in
bats from southwestern China (Yunnan, Guizhou and Guangxi province) formed one clade, in
which SARSr-CoV strains showing closer relationship to SARS-CoV were all from Yunnan.
SARSr-CoVs detected in southeastern, central and northern provinces, such as Hong Kong,
Hubei and Shaanxi, formed the other clade which was phylogenetically distant to human and
civet SARS-CoVs (Fig 6 and S6 Fig).
Rescue of bat SARSr-CoVs and virus infectivity experiments
In the current study, we successfully cultured an additional novel SARSr-CoV Rs4874 from a
single fecal sample using an optimized protocol and Vero E6 cells [17]. Its S protein shared
99.9% aa sequence identity with that of previously isolated WIV16 and it was identical to
WIV16 in RBD. Using the reverse genetics technique we previously developed for WIV1 [23],
we constructed a group of infectious bacterial artificial chromosome (BAC) clones with the
backbone of WIV1 and variants of S genes from 8 different bat SARSr-CoVs. Only the infec-
tious clones for Rs4231 and Rs7327 led to cytopathic effects in Vero E6 cells after transfection
(S7 Fig). The other six strains with deletions in the RBD region, Rf4075, Rs4081, Rs4085,
Rs4235, As6526 and Rp3 (S1 Fig) failed to be rescued, as no cytopathic effects was observed
and viral replication cannot be detected by immunofluorescence assay in Vero E6 cells (S7
Fig). In contrast, when Vero E6 cells were respectively infected with the two successfully res-
cued chimeric SARSr-CoVs, WIV1-Rs4231S and WIV1-Rs7327S, and the newly isolated
Rs4874, efficient virus replication was detected in all infections (Fig 7). To assess whether the
three novel SARSr-CoVs can use human ACE2 as a cellular entry receptor, we conducted virus
infectivity studies using HeLa cells with or without the expression of human ACE2. All viruses
replicated efficiently in the human ACE2-expressing cells. The results were further confirmed
by quantification of viral RNA using real-time RT-PCR (Fig 8).
Activation of activating transcription factor 6 (ATF6) by the ORF8
proteins of different bat SARSr-CoVs
The induction of the ATF6-dependent transcription by the ORF8s of SARS-CoV and bat
SARSr-CoVs were investigated using a luciferase reporter, 5×ATF6-GL3. In HeLa cells tran-
siently transfected with the expression plasmids of the ORF8s of bat SARSr-CoV Rf1, Rf4092
and WIV1, the relative luciferase activities of the 5×ATF6-GL3 reporter was enhanced by 5.56
to 9.26 folds compared with cells transfected with the pCAGGS empty vector, while it was
Fig 5. Detection of potential recombination events by similarity plot and boot scan analysis. (A) Full-
length genome sequence of SARSr-CoV WIV16 was used as query sequence and WIV1, Rs4231 and
Rs4081 as reference sequences. (B) Full-length genome sequence of SARS-CoV SZ3 was used as query
sequence and SARSr-CoV WIV16, Rf4092 and Rs4081 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. The
gene map of query genome sequences are used to position breakpoints.
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A gene pool of bat SARS-related coronaviruses
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Fig 6. Phylogenetic trees based on nucleotide sequences of ORF1a (A) and ORF1b (B). 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. The scale bars represent 0.03 (A) and 0.02 (B) substitutions per
A gene pool of bat SARS-related coronaviruses
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increased by 4.42 fold by the SARS-CoV GZ02 ORF8. As a control, the treatment with tunica-
myxin (TM) stimulated the transcription by about 11 folds (Fig 9A). The results suggests that
various ORF8 proteins of bat SARSr-CoVs can activate ATF6, and those of some strains have a
stronger effect than the SARS-CoV ORF8.
Induction of apoptosis by the ORF8a of the newly identified bat SARSr-
CoV
We conducted transient transfection to examine whether the ORF8a of SARSr-CoV Rs4084
triggered apoptosis. As shown in Fig 9B, 11.76% and 9.40% of the 293T cells transfected with
the SARSr-CoV Rs4084-ORF8a and SARS-CoV Tor2-ORF8a expression plasmid underwent
apoptosis, respectively. In contrast, transfection with the empty vector resulted in apoptosis in
only 2.79% of the cells. The results indicate that Rs4084 ORF8a has an apoptosis induction
activity similar to that of SARS-CoV [28].
Discussion
Genetically diverse SARSr-CoVs have been detected in various horseshoe bat species across a
wide geographic range in China in the past decade [912,14,29]. However, most bat SARSr-
CoVs show considerable genetic distance to SARS-CoV, particularly in the highly variable S1,
ORF8 and ORF3 regions [10,25]. Recently, several novel SARSr-CoVs have been described to
be more closely related to SARS-CoV, either in the S gene or in ORF8. The S proteins of
RsSHC014, Rs3367, WIV1 and WIV16, which were reported in our previous studies, shared
90% to 97% aa sequence identities to those of human/civet SARS-CoVs [17,18]. Another strain
from Rhinolophus affinis in Yunnan termed LYRa11 showed 90% aa sequence identity to
SARS-CoV in the S gene [13]. In addition, two studies have described 4 novel SARSr-CoVs
(YNLF_31C/34C and GX2013/YN2013) which possessed a full-length ORF8 with substantially
higher similarity to that of SARS-CoV [22,30]. These findings provide strong genetic evidence
for the bat origin of SARS-CoV with regard to the S gene or ORF8. However, all of these
SARSr-CoVs were distinct from SARS-CoV in at least one other gene, suggesting that none of
them was the immediate progenitor of SARS-CoV. Moreover, these SARSr-CoVs were discov-
ered in bat populations from physically distinct locations. The site of origin of the true progen-
itor of SARS-CoV and the evolutionary origin of SARS-CoV have until now remained elusive.
In the current study, we have identified a bat habitat potentially important for SARSr-CoV
evolution where a series of recombination events have likely occurred among different SARSr-
CoV strains, which provides new insights into the origin of SARS-CoV.
SARS first emerged in Guangdong province in late 2002 [7]. However, SARSr-CoVs discov-
ered in bats from neighboring areas of Guangdong to date have shown phylogenetic disparity
from SARS-CoV especially in the S gene [9,10,14], suggesting SARS-CoV may have originated
from another region. Our analysis of the phylogeny of SARS-CoVs and all known bat SARSr-
CoVs using the nt sequence of their non-structural ORF1a and ORF1b genes, which constitute
the majority of the genome, shows that SARSr-CoV evolution is strongly correlated with their
geographical origin, but not host species. It is noteworthy that SARSr-CoVs detected in Yun-
nan are more closely related to SARS-CoV than strains from other regions in China. This find-
ing implies that Yunnan, or southwestern China, is more likely to be the geographical source
nucleotide position. 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. Sequences detected in
southwestern China are indicated in red.
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Fig 7. Infection of Vero E6 cells by bat SARSr-CoV WIV1, Rs4874, WIV1-Rs4231S and WIV1-Rs7327S.
(A) The successful infection was confirmed by immunofluorescent antibody staining using rabbit antibody
against the SARSr-CoV Rp3 nucleocapsid protein. The columns (from left to right) show staining of nuclei
(blue), virus replication (red), and both nuclei and virus replication (merged double-stain images). (B) The
growth curves in Vero E6 cells with a MOI of 1.0 and 0.01.
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Fig 8. Analysis of receptor usage by immunofluorescence assay (A) and real-time PCR (B). Virus
infectivity of Rs4874, WIV1-Rs4231S and WIV1-Rs7327S was determined in HeLa cells with and without the
expression of human ACE2. ACE2 expression was detected with goat anti-human ACE2 antibody followed by
fluorescein isothiocyanate (FITC)-conjugated donkey anti-goat IgG. Virus replication was detected with rabbit
antibody against the SARSr-CoV Rp3 nucleocapsid protein followed by cyanine 3 (Cy3)-conjugated mouse
anti-rabbit IgG. Nuclei were stained with DAPI (49,6-diamidino-2-phenylindole).The columns (from left to
right) show staining of nuclei (blue), ACE2 expression (green), virus replication (red) and the merged triple-
stained images, respectively.
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of SARS-CoV than other regions in China, but data from more extensive surveillance are yet
needed to support this inference.
In our longitudinal surveillance of SARSr-CoVs in a single cave in Yunnan where we dis-
covered Rs3367, RsSHC014, WIV1 and WIV16, the CoV prevalence in fecal samples varied
among different sampling time. Generally, a higher prevalence was observed in autumn (Sep-
tember and October) than in spring and early summer (April and May). This may be due to
Fig 9. Functional characterization of diverse ORF8 and ORF8a proteins of bat SARSr-CoVs. (A) The
ORF8 proteins of SARS-CoV and bat SARSr-CoVs induces the ATF6-dependent transcriptional activity.
HeLa cells were transiently transfected with the pcAGGS expression plasmids of the ORF8 of SARS-CoV
GZ02, bat SARSr-CoV Rf1, WIV1 and Rf4092 and the reporter plasmid 5×ATF6-GL3 for 40h. Control cells
were co-transfected with the reporter plasmid and the empty pCAGGS vector for 24h, and treated with or
without TM (2μg/ml) for an additional 16h. The cell lysates were harvested for dual luciferase assay and data
are shown as the average values from triplicate wells. (B) The ORF8a proteins of SARS-CoV and bat SARSr-
CoV triggered apoptosis. 293T cells were transfected with the expression plasmids of the ORF8a of
SARS-CoV Tor2 and bat SARSr-CoV Rs4084 and a pcAGGS vector control for 24h. Apoptosis was analyzed
by flow cytometry after annexin V staining and the percentage of apoptotic cells were calculated. Data are
shown as the average values from triplicate cells. Error bars indicate SDs. *P<0.05.
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the establishment of a susceptible subpopulation of newborn bats which had not developed
their own immunity after the parturition period [31]. Another factor may be the changes in
the composition of bat species in the cave at different sampling dates. For example, in Septem-
ber 2012 when the CoV prevalence reached 51.3%, the majority of samples were from R.sini-
cus, but in May 2015 when only 3 out of the 145 samples tested positive, Aselliscus stoliczkanus
was the predominant bat species in the cave. We failed to amplify the RBD sequences from 15
of the 64 SARSr-CoV positive samples. Most of these samples had comparatively low viral con-
centration (<10
7
copies/g) (S8 Fig), as revealed by our previous quantitative studies [32]. The
unsuccessful amplification of RBD in some samples with high viral concentration was proba-
bly because of the more divergent sequences in this region of these SARSr-CoV genomes.
In this cave, we have now obtained full-length genome sequences of additional 11 novel
SARSr-CoVs from bats. Our findings suggest the co-circulation of different bat SARSr-CoVs
highly similar to SARS-CoV in the most variable S1 (NTD and RBD), ORF8 and ORF3
regions, respectively, in this single location. In the ORF1a, ORF1b, E, M and N genes, the
SARSr-CoVs circulating in this cave also shared >98% aa sequence identities with human/
civet SARS-CoVs. Thus, all of the building blocks of the SARS-CoV genome were present in
SARSr-CoVs from this single location in Yunnan during our sampling period. Furthermore,
strains closely related to different representative bat SARSr-CoVs from other provinces (e.g.
Rs672, HKU3 and Rf1) in the RBD region were also detected there. Therefore, this cave could
be regarded as a rich gene pool of bat SARSr-CoVs, wherein concurrent circulation of a high
diversity of SARSr-CoV strains has led to an unusually diverse assemblage of SARSr-CoVs.
During our 5-year surveillance in this single cave, we first reported Rs3367 and WIV1 in 2013,
with RBD sequence closely resembling that of SARS-CoV [17]. More recently, we discovered
WIV16 which had an RBD almost identical to WIV1’s but shared much higher similarity with
SARS-CoV than WIV1 in the NTD region of S1, making it the closest SARSr-CoV to the epi-
demic strains identified to date [18]. In this study, we found a novel strain Rs4231 from the same
location sharing almost identical NTD sequence with WIV16 but distinct from it in the RBD,
with evidence of a recombination event. Our recombination analysis indicated that a recombina-
tion event may have taken place at the junction between the coding region of NTD and RBD in
the Rs4231 and WIV1 genomes and resulted in WIV16. Recombination at this genomic position
also happened among other SARSr-CoVs relatively distant to SARS-CoV found in this location
(e.g. Rs4081 and Rs4247, S5 Fig). The frequent recombination at this hotspot in the S gene
increased the genetic diversity of SARSr-CoVs harbored in these bat populations and might have
been responsible for the generation of the S gene of the direct progenitor strain of SARS-CoV.
The genomes of SARS-CoVs from patients during the early epidemic phase and civet SARS--
CoVs all contained a single full-length ORF8 [3,7]. We have found that a number of bat SARSr-
CoVs from this cave possessed a complete ORF8 highly similar to that of early human/civet
SARS-CoV (>97% nt sequence identity), represented by strain Rf4092 (S3C Fig). This provided
further evidence for the source of human SARS-CoV ORF8 in bats [22,30]. In contrast, the
ORF8 was split into overlapping ORF8a and ORF8b in most human SARS-CoV strains from
later-phase patients due to the acquisition of a 29-nt deletion [8,26]. In this study, we have dis-
covered for the first time a bat SARSr-CoV with ORF8a and ORF8b highly similar to the later-
phase human SARS-CoVs, though the split of ORF8 in the bat SARSr-CoV and that in human
SARS-CoV were two independent events. Our recombination analysis suggests that this strain,
Rs4084, likely acquired its ORF8 from Rf4092 through recombination, followed by the develop-
ment of the 5-nt deletion which led to the splitting. It suggests that ORF8 region in bat SARSr-
CoV genomes is prone to deletions as in human SARS-CoV [3,25]. Finally, the recombination
analysis suggests that an ancestral strain of SARS-CoV SZ3 would have been generated if the
recombination around ORF8 had occurred between the lineages that led to WIV16 and Rf4092.
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Taken together, the evidence of recombination events among SARSr-CoVs harbored by bats in
this single location suggests that the direct progenitor of SARS-CoV may have originated as a
result of a series of recombination within the S gene and around ORF8. This could have been
followed by the spillover from bats to civets and people either in the region, or during move-
ment of infected animals through the wildlife trade. However, given the paucity of data on ani-
mal trade prior to the SARS outbreak, the likely high geographical sampling bias in bat
surveillance for SARSr-CoVs in southern China, and the possibility that other caves harbor sim-
ilar bat species assemblages and a rich diversity of SARSr-CoVs, a definite conclusion about the
geographical origin of SARS-CoV cannot be drawn at this point.
R.sinicus are regarded as the primary natural host of SARS-CoV, as all SARSr-CoVs highly
homologous to SARS-CoV in the S gene were predominantly found in this species. However,
it is noted that two SARSr-CoVs previously reported from R.ferrumequinum showed the clos-
est phylogenetic position to SARS-CoV in the ORF1a/1b trees. These strains were discovered
in another location in Yunnan 80 km from the cave surveyed in the current study [22]. This
information also supports the speculation that SARS-CoV may have originated from this
region. Nonetheless, since the correlation between the host species and the phylogeny of
SARSr-CoV ORF1ab seems limited, more SARSr-CoV sequences need to be obtained from
different Rhinolophus bat species in both locations in Yunnan, and from other locations in
southern China. In particular, it will be important to assess whether R.ferrumequinum played
a more important role in the evolution of SARS-CoV ORF1ab.
The cave we studied is located approximately 60 km from the city of Kunming. Beside a
number of rhinolophid and hipposiderid species from which SARSr-CoVs have been detected,
other bats like myotis were also present there. The temperature in the cave is around 22–25˚C
and the humidity around 85%-90%. The physical nature of the cave is not unique, but it does
appear to host a particularly dense population of bats in the reproductive season. Similar caves
co-inhabited by bat populations of different species are not rare in other areas in Yunnan. We
propose that efforts to study the ecology, host species diversity, and viral strain populations of
these caves may provide critical information on what drives SARSr-CoV evolution.
Our previous studies demonstrated the capacity of both WIV1 and WIV16 to use ACE2
orthologs for cell entry and to efficiently replicate in human cells [17,18]. In this study, we con-
firmed the use of human ACE2 as receptor of two novel SARSr-CoVs by using chimeric
viruses with the WIV1 backbone replaced with the S gene of the newly identified SARSr-
CoVs. Rs7327’s S protein varied from that of WIV1 and WIV16 at three aa residues in the
receptor-binding motif, including one contact residue (aa 484) with human ACE2. This differ-
ence did not seem to affect its entry and replication efficiency in human ACE2-expressing
cells. A previous study using the SARS-CoV infectious clone showed that the RsSHC014 S pro-
tein could efficiently utilize human ACE2 [33], despite being distinct from SARS-CoV and
WIV1 in the RBD (S1 Fig). We examined the infectivity of Rs4231, which shared similar RBD
sequence with RsSHC014 but had a distinct NTD sequence, and found the chimeric virus
WIV1-Rs4231S also readily replicated in HeLa cells expressing human ACE2 molecule. The
novel live SARSr-CoV we isolated in the current study (Rs4874) has an S gene almost identical
to that of WIV16. As expected, it is also capable of utilizing human ACE2. These results indicate
that diverse variants of SARSr-CoV S protein without deletions in their RBD are able to use
human ACE2. In contrast, our previous study revealed that the S protein of a R.sinicus SARSr-
CoV with deletions (Rp3) failed to use human, civet and bat ACE2 for cell entry [34]. In this
study, in addition to Rs4231 and Rs7327, we also constructed infectious clones with the S gene
of Rs4081, Rf4075, Rs4085, Rs4235 and As6526, which all contained the deletions in their RBD.
These 7 strains, plus Rs4874 and the previously studied WIV1 and RsSHC014, could represent
all types of S variants of SARSr-CoVs in this location (S3A Fig). However, none of the strains
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with deletions in the RBD could be rescued from Vero E6 cells. Therefore, the two distinct
clades of SARSr-CoV S gene may represent the usage of different receptors in their bat hosts.
The full-length ORF8 protein of SARS-CoV is a luminal endoplasmic reticulum (ER) mem-
brane-associated protein that induces the activation of ATF6, an ER stress-regulated transcrip-
tion factor that activates the transcription of ER chaperones involved in protein folding [35].
We amplified the ORF8 genes of Rf1, Rf4092 and WIV1, which represent three different geno-
types of bat SARSr-CoV ORF8 (S3C Fig), and constructed the expression plasmids. All of the
three ORF8 proteins transiently expressed in HeLa cells can stimulate the ATF6-dependent
transcription. Among them, the WIV1 ORF8, which is highly divergent from the SARS-CoV
ORF8, exhibited the strongest activation. The results indicate that the variants of bat SARSr-
CoV ORF8 proteins may play a role in modulating ER stress by activating the ATF6 pathway.
In addition, the ORF8a protein of SARS-CoV from the later phase has been demonstrated to
induce apoptosis [28]. In this study, we have found that the ORF8a protein of the newly identi-
fied SARSr-CoV Rs4084, which contained an 8-aa insertion compared with the SARS-CoV
ORF8a, significantly triggered apoptosis in 293T cells as well.
Compared with the 154-aa ORF3b of SARS-CoV, the ORF3b proteins of all previously
identified bat SARSr-CoVs were smaller in size due to the early translation termination. How-
ever, for the first time, we discovered an ORF3b without the C-terminal truncation in a bat
SARSr-CoV, Rs7327, which differed from the ORF 3b of SARS-CoV GZ02 strain at only one
aa residue. The SARS-CoV ORF3b antagonizes interferon function by modulating the activity
of IFN regulatory factor 3 (IRF3) [27]. As previous studies suggested, the nuclear localization
signal-containing C-terminal may not be required for the IFN antagonist activity of ORF3b
[36]. Our previous studies also demonstrated that the ORF3b protein of a bat SARSr-CoV,
termed Rm1, which was C-terminally truncated to 56 aa and shared 62% aa sequence identity
with SARS-CoV, still displayed the IFN antagonist activity [37]. It is very interesting to investi-
gate in further studies whether Rs7327’s ORF3b and other versions of truncated ORF3b such
as WIV1 and WIV16 also show IFN antagonism profiles.
As a whole, our findings from a 5-year longitudinal study conclusively demonstrate that all
building blocks of the pandemic SARS-CoV genome are present in bat SARSr-CoVs from a sin-
gle location in Yunnan. The data show that frequent recombination events have happened
among those SARSr-CoVs in the same cave. While we cannot rule out the possibility that similar
gene pools of SARSr-CoVs exist elsewhere, we have provided sufficient evidence to conclude
that SARS-CoV most likely originated from horseshoe bats via recombination events among
existing SARSr-CoVs. In addition, we have also revealed that various SARSr-CoVs capable of
using human ACE2 are still circulating among bats in this region. Thus, the risk of spillover into
people and emergence of a disease similar to SARS is possible. This is particularly important
given that the nearest village to the bat cave we surveyed is only 1.1 km away, which indicates a
potential risk of exposure to bats for the local residents. Thus, we propose that monitoring of
SARSr-CoV evolution at this and other sites should continue, as well as examination of human
behavioral risk for infection and serological surveys of people, to determine if spillover is already
occurring at these sites and to design intervention strategies to avoid future disease emergence.
Materials and methods
Ethics statement
All sampling procedures were performed by veterinarians with approval from Animal Ethics
Committee of the Wuhan Institute of Virology (WIVH05210201). The study was conducted in
accordance with the Guide for the Care and Use of Wild Mammals in Research of the People’s
Republic of China.
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Sampling
Bat samplings were conducted ten times from April 2011 to October 2015 at different seasons
in their natural habitat at a single location (cave) in Kunming, Yunnan Province, China. All
members of field teams wore appropriate personal protective equipment, including N95
masks, tear-resistant gloves, disposable outerwear, and safety glasses. Bats were trapped and
fecal swab samples were collected as described previously [9]. Clean plastic sheets measuring
2.0 by 2.0 m were placed under known bat roosting sites at about 18:00 h each evening for col-
lection of fecal samples. Fresh fecal pellets were collected from sheets early in the next morn-
ing. Each sample (approximately 1 gram of fecal pellet) was collected in 1ml of viral transport
medium composed of Hank’s balanced salt solution at pH7.4 containing BSA (1%), amphoter-
icin (15 μg/ml), penicillin G (100 units/ml), and streptomycin (50 μg/ml), and were stored at
-80˚C until processing. Bats trapped for this study were released back into their habitat.
RNA extraction, PCR screening and sequencing
Fecal swab or pellet samples were vortexed for 1 min, and 140 μl of supernatant was collected
from each sample after centrifuge at 3000 rpm under 4˚C for 1min. Viral RNA was extracted
with Viral RNA Mini Kit (Qiagen) following the manufacturer’s instructions. RNA was eluted
in 60 μl of buffer AVE (RNase-free water with 0.04% sodium azide, Qiagen), aliquoted, and
stored at -80˚C. One-step hemi-nested RT-PCR (Invitrogen) was employed to detect the pres-
ence of coronavirus sequences as described previously using a set of primers that target a
440-nt fragment in the RNA-dependent RNA polymerase gene (RdRp) of all known alpha-
and betacoronaviruses [20]. For the first round PCR, the 25 μl reaction mix contained 12.5 μl
PCR 2 ×reaction mix buffer, 10 pmol of each primer, 2.5 mM MgSO
4
, 20 U RNase inhibitor,
1μl SuperScript III/Platinum Taq Enzyme Mix and 5 μl RNA template. The amplification was
performed as follows: 50˚C for 30 min, 94˚C for 2 min, followed by 40 cycles consisting of
94˚C for 15 sec, 52˚C for 30 sec, 68˚C for 40 sec, and a final extension of 68˚C for 5 min. For
the second round PCR, the 25 μl reaction mix contained 2.5 μl PCR reaction buffer, 5 pmol of
each primer, 50 mM MgCl
2
, 0.5mM dNTP, 0.1 μl Platinum Taq Enzyme (Invitrogen) and 1 μl
product of the first round PCR. The amplification was performed as follows: 94˚C for 3 min
followed by 35 cycles consisting of 94˚C for 30 sec, 52˚C for 30 sec, 72˚C for 40 sec, and a final
extension of 72˚C for 7 min. The RBD region was amplified using the one-step nested
RT-PCR method previously described [17].
PCR products were gel purified and sequenced with an ABI Prism 3730 DNA analyzer
(Applied Biosystems, USA). PCR products with low concentration or generating heterogeneity
in the sequencing chromatograms were cloned into pGEM-T Easy Vector (Promega) for
sequencing. The positive samples in this study were termed using the abbreviated name of bat
species plus the sample ID number (e.g. Rs4081). To confirm the bat species of individual sam-
ple, PCR amplification of cytochrome b (Cytob) or NADH dehydrogenase subunit 1 (ND1)
gene was performed using DNA extracted from the feces or swabs [38,39].
Sequencing of full-length genomes
Full genomic sequences of 11 SARSr-CoVs were determined by One-step PCR (Invitrogen)
amplification of overlapping genomic fragments with degenerate primers designed by multiple
alignment of available SARS-CoV and bat SARSr- CoV sequences deposited in GenBank, and
additional specific primers designed from the results of previous rounds of sequencing in this
study. Primer sequences are available upon request. Sequences of the 5’ and 3’ genomic ends
were obtained by 5’ and 3’ RACE (Roche), respectively. PCR products with expected size were
gel-purified and subjected directly to sequencing. Each fragment was sequenced at least twice.
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The sequencing chromatogram of each product was thoroughly examined and sequence het-
erogeneity was not observed. For some fragments with low concentration of amplicons, the
PCR products were cloned into pGEM-T Easy Vector (Promega) for sequencing. At least five
independent clones were sequenced to obtain a consensus sequence. Co-presence of sequences
of distinct SARSr-CoVs was not found in any of the amplicons. The sequences of overlapping
genomic fragments were assembled to obtain the full-length genome sequences, with each
overlapping sequence longer than 100 bp.
Evolution analysis
Full-length genome sequences of the 15 SARSr-CoVs detected from bats in the cave surveyed
in this study were aligned with those of selected SARS-CoVs using MUSCLE [40]. The aligned
sequences were scanned for recombination events by Recombination Detection Program
(RDP) [41]. The potential recombination events suggested by strong Pvalues (<10
20
) were
further confirmed using similarity plot and bootscan analyses implemented in Simplot 3.5.1
[42]. Phylogenetic trees based on nucleotide sequences were constructed using the Maximum
Likelihood algorithm under the LG model with bootstrap values determined by 1000 replicates
in the PhyML (version 3.0) software package [43].
Virus isolation
The Vero E6 cell line was kindly provided by Australian Animal Health Laboratory, CSIRO
(Geelong, Australia). Vero E6 monolayer was maintained in DMEM medium supplemented
with 10% fetal calf serum (FCS). Fecal samples (in 200 μl buffer) were gradient centrifuged at
3,000–12,000 g, and the supernatant was diluted 1:10 in DMEM before being added to Vero
E6 cells. After incubation at 37˚C for 1 h, the inoculum was removed and replaced with fresh
DMEM medium with 2% FCS. The cells were incubated at 37˚C and checked daily for cyto-
pathic effect. All tissue culture media were supplemented with triple antibiotics penicillin/
streptomycin/amphotericin (Gibco) (penicillin 200 IU/ml, streptomycin 0.2 mg/ml, ampho-
tericin 0.5 μg/ml). Three blind passages were carried out for each sample. After each passage,
both the culture supernatant and cell pellet were examined for presence of SARSr-CoV by
RT-PCR using specific primers targeting the RdRp or S gene. The viruses which caused obvi-
ous cytopathic effect and could be detected in three blind passages by RT-PCR were further
confirmed by electron microscopy.
Construction of recombinant viruses
Recombinant viruses with the S gene of the novel bat SARSr-CoVs and the backbone of the
infectious clone of SARSr-CoV WIV1 were constructed using the reverse genetic system
described previously [23] (S9 Fig). The fragments E and F were re-amplified with primer pairs
(FE, 5’-AGGGCCCACCTGGCACTGGTAAGAGTCATTTTGC-3’, R-EsBsaI, 5’-ACTGGT
CTCTTCGTTTAGTTATTAACTAAAATATCACTAGACACC-3’) and (F-FsBsaI, 5’-TGA
GGTCTCCGAACTTATGGATTTGTTTATGAG-3’, RF, 5’-AGGTAGGCCTCTAGGGCA
GCTAAC-3’), respectively. The products were named as fragment Es and Fs, which leave the
spike gene coding region as an independent fragment. BsaI sites (5’-GGTCTCN|NNNN-3’)
were introduced into the 3’ terminal of the Es fragment and the 5’ terminal of the Fs fragment,
respectively. The spike sequence of Rs4231 was amplified with the primer pair (F-Rs4231-
BsmBI, 5’-AGTCGTCTCAACGAACATGTTTATTTTCTTATTCTTTCTCACTCTCAC-3’
and R-Rs4231-BsmBI, 5’-TCACGTCTCAGTTCGTTTATGTGTAATGTAATTTGACAC
CCTTG-3’). The S gene sequence of Rs7327 was amplified with primer pair (F-Rs7327-BsaI,
5’-AGTGGTCTCAACGAACATGAAATTGTTAGTTTTAGTTTTTGCTAC-3’ and R-
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 21 / 27
Rs7327-BsaI, 5’- TCAGGTCTCAGTTCGTTTATGTGTAATGTAATTTAACACCCTTG-3’).
The fragment Es and Fs were both digested with BglI (NEB) and BsaI (NEB). The Rs4231 S
gene was digested with BsmBI. The Rs7327 S gene was digested with BsaI. The other fragments
and bacterial artificial chromosome (BAC) were prepared as described previously. Then the
two prepared spike DNA fragments were separately inserted into BAC with Es, Fs and other
fragments. The correct infectious BAC clones were screened. The chimeric viruses were res-
cued as described previously [23].
Determination of virus infectivity by immunofluorescence assay
The HeLa cell line was kindly provided by Australian Animal Health Laboratory, CSIRO (Gee-
long, Australia). HeLa cells expressing human ACE2 were constructed as described previously
[17]. HeLa cells expressing human ACE2 and Vero E6 cells were cultured on coverslips in
24-well plates (Corning) incubated with the newly isolated or recombinant bat SARSr-CoVs at
a multiplicity of infection (MOI) = 1.0 for 1h. The inoculum was removed and the cells were
washed twice with PBS and supplemented with medium. Vero E6 cells without virus inocula-
tion and HeLa cells without ACE2 were used as negative control. Twenty-four hours after
infection, cells were rinsed with PBS and fixed with 4% formaldehyde in PBS (pH7.4) at 4˚C
for 20 min. ACE2 expression was detected by using goat anti-human ACE2 immunoglobulin
followed by FITC-labelled donkey anti-goat immunoglobulin (PTGLab). Virus replication was
detected by using rabbit antibody against the nucleocapsid protein of bat SARSr-CoV Rp3 fol-
lowed by Cy3-conjugated mouse anti-rabbit IgG. Nuclei were stained with DAPI. Staining pat-
terns were observed under an FV1200 confocal microscope (Olympus).
Determination of virus replication in Vero E6 cells by plaque assay
Vero E6 cells were infected with WIV1, Rs4874, WIV1-Rs4231S, and WIV1-Rs7327S at an
MOI of 1.0 and 0.01. After incubation for an hour, the cells were washed with DHanks for
three times and supplied with DMEM containing 2% FCS. Samples were collected at 0, 10, 27,
and 48 h post infection. The viral titers were determined by plaque assay.
Determination of virus replication in HeLa cells expressing human ACE2
by quantitative RT-PCR
HeLa cells expressing human ACE2 were inoculated with WIV1, Rs4874, WIV1-Rs4231S, and
WIV1-Rs7327S at an MOI of 1.0, and were incubated for 1h at 37˚C. After the inoculum was
removed, the cells were supplemented with medium containing 1% FBS. Supernatants were
collected at 0, 12, 24 and 48h. Virus titers were determined using quantitative RT-PCR target-
ing the partial N gene with a standard curve which expresses the correlation between Ct value
and virus titer (shown as TCID50/ml). The standard curve was made using RNA dilutions
from the purified Rs4874 virus stock (with a titer of 2.15 ×10
6
TCID50/ml). For qPCR, RNA
was extracted from 140 μl of each supernatant with Viral RNA Mini Kit (Qiagen) following
manufacturer’s instructions and eluted in 60 μl AVE buffer. The PCR was performed with the
TaqMan AgPath-ID One-Step RT–PCR Kit (Applied Biosystems) in a 25 μl reaction mix con-
taining 4 μl RNA, 1 ×RT–PCR enzyme mix, 1 ×RT–PCR buffer, 40 pmol forward primer (5’-
GTGGTGGTGACGGCA AAATG-3’), 40 pmol reverse primer (5’-AAGTGAAGCTTCTGG
GCCAG-3’) and 12 pmol probe (5’-FAM-AAAGAGCTCAGCCCCAGATG-BHQ1-3’). The
amplification was performed as follows: 50˚C for 10 min, 95˚C for 10 min followed by 50
cycles consisting of 95˚C for 15 sec and 60˚C for 20 sec.
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 22 / 27
Plasmids
The ORF8 genes of bat SARSr-CoV WIV1 and Rf4092 and the ORF8a gene of bat SARSr-CoV
Rs4084 were amplified by PCR from the viral RNA extracted from the isolated virus or fecal sam-
ples. The ORF8 gene of SARS-CoV GZ02 and bat SARSr-CoV Rf1, and the ORF8a gene of
SARS-CoV Tor2 were synthesized by Tsingke Biological Technology Co., Ltd (Wuhan, China).
All genes were cloned into the pCAGGS vector constructed with a C-terminal HA tag. Expression
of the proteins was confirmed by Western blotting using a mAb against the HA tag. Five tandem
copies of the ATF6 consensus binding sites were synthesized and inserted into the pGL3-Basic
vector to construct the luciferase reporter plasmid 5×ATF6-GL3, in which the luciferase gene is
under the control of the c-fos minimal promoter and the ATF6 consensus binding sites.
Luciferase reporter assay
HeLa cells in 24-well plates were transfected using Lipofectamine 3000 reagent (Life Technolo-
gies) following the manufacturer’s instruction. Cells per well were co-transfected with 600ng
of the 5×ATF6-GL3 reporter plasmid, with 300ng of each expression plasmid of SARS-CoV
and SARSr-CoV ORF8 or empty vector and 20ng of pRL-TK (Promega) which served as an
internal control. The cells were incubated for 24h, and were treated with or without 2μg/ml
tunicamycin for 16h. Cells were harvested and lysed. Luciferase activity was determined using
a dual-luciferase assay system (Promega). The experiment was performed in triplicate wells.
Quantification of apoptotic cells
293T cells in 12-well plates were transfected using Lipofectamine 3000 reagent (Life Technolo-
gies) following the manufacturer’s instruction. Cells per well were transfected with 3μg of the
expression plasmid of SARS-CoV Tor2 or SARSr-CoV Rs4084 ORF8a, or the empty vector.
24h post transfection, apoptotic cells were quantified by using the Annexin V-fluorescein iso-
thiocyanate (FITC)/PI Apoptosis Detection Kit (Yeasen Biotech, Shanghai) in accordance
with the manufacturer’s instruction. Apoptosis was analyzed by flow cytometry. The experi-
ment was performed in triplicate wells.
Accession numbers
The complete genome sequences of bat SARS-related coronavirus strains As6526, Rs4081,
Rs4084, Rf4092, Rs4231, Rs4237, Rs4247, Rs4255, Rs4874, Rs7327 and Rs9401 have been
deposited in the GenBank database with the accession numbers from KY417142 to KY417152,
respectively.
Supporting information
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.
(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.
(PPTX)
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 23 / 27
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.
(PPTX)
S4 Fig. Alignment of amino acid sequences of ORF3b protein.
(PPTX)
S5 Fig. Detection of potential recombination events by similarity plot and boot scan analy-
sis. (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.
(PPTX)
S6 Fig. Chinese provinces where bat SARSr-CoVs have been detected.
(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 trans-
fected 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.
(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 suc-
cessfully amplified are indicated in red.
(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.
(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.
(DOCX)
S2 Table. Distribution of SARSr-CoVs highly similar to SARS-CoV in the variable S,
ORF3 and ORF8 genes in the single cave.
(DOCX)
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 24 / 27
S1 Dataset. Full-length genome sequences of bat SARSr-CoVs newly identified in this
study.
(FAS)
Acknowledgments
We thank Ji-Hua Zhou and Wei-Hong Yang from Yunnan Institute of Endemic Diseases Con-
trol and Prevention for the assistance in sample collection. We thank the Center for Instru-
mental 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).
Author Contributions
Conceptualization: Lin-Fa Wang, Jie Cui, Zheng-Li Shi.
Data curation: Ben Hu.
Formal analysis: Ben Hu, Xing-Yi Ge, Jie Cui.
Funding acquisition: Peter Daszak, Lin-Fa Wang, Jie Cui, Zheng-Li Shi.
Investigation: Ben Hu, Lei-Ping Zeng, Xing-Lou Yang, Wei Zhang, Bei Li, Jia-Zheng Xie, Xu-
Rui Shen, Ning Wang, Dong-Sheng Luo, Xiao-Shuang Zheng.
Methodology: Lei-Ping Zeng, Zheng-Li Shi.
Project administration: Zheng-Li Shi.
Resources: Xing-Lou Yang, Xing-Yi Ge, Yun-Zhi Zhang, Dong-Sheng Luo, Mei-Niang Wang.
Software: Jie Cui.
Supervision: Zheng-Li Shi.
Validation: Ben Hu.
Visualization: Ben Hu, Zheng-Li Shi.
Writing – original draft: Ben Hu.
Writing – review & editing: Peter Daszak, Lin-Fa Wang, Jie Cui, Zheng-Li Shi.
References
1. Peiris JS, Guan Y, Yuen KY. Severe acute respiratory syndrome. Nat Med. 2004; 10: S88–97. https://
doi.org/10.1038/nm1143 PMID: 15577937
2. Zhong NS, Zheng BJ, Li YM, Poon, Xie ZH, Chan KH, et al. Epidemiology and cause of severe acute
respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. Lancet.
2003; 362: 1353–1358. PMID: 14585636
3. Chinese SMEC. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic
in China. Science. 2004; 303: 1666–1669. https://doi.org/10.1126/science.1092002 PMID: 14752165
4. Drexler JF, Corman VM, Drosten C. Ecology, evolution and classification of bat coronaviruses in the
aftermath of SARS. Antiviral Res. 2014; 101: 45–56. https://doi.org/10.1016/j.antiviral.2013.10.013
PMID: 24184128
5. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, et al. The Genome sequence
of the SARS-associated coronavirus. Science. 2003; 300: 1399–1404. https://doi.org/10.1126/science.
1085953 PMID: 12730501
6. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al. Unique and conserved fea-
tures of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2
lineage. J Mol Biol. 2003; 331: 991–1004. PMID: 12927536
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 25 / 27
7. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of
viruses related to the SARS coronavirus from animals in southern China. Science. 2003; 302: 276–
278. https://doi.org/10.1126/science.1087139 PMID: 12958366
8. Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, et al. Cross-host evolution of severe acute
respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A. 2005; 102:
2430–2435. https://doi.org/10.1073/pnas.0409608102 PMID: 15695582
9. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, et al. Bats are natural reservoirs of SARS-like coronavi-
ruses. Science. 2005; 310: 676–679. https://doi.org/10.1126/science.1118391 PMID: 16195424
10. Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, et al. Severe acute respiratory syndrome coro-
navirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A. 2005; 102: 14040–14045.
https://doi.org/10.1073/pnas.0506735102 PMID: 16169905
11. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, et al. Prevalence and genetic diversity of coro-
naviruses in bats from China. J Virol. 2006; 80: 7481–7490. https://doi.org/10.1128/JVI.00697-06
PMID: 16840328
12. Yuan J, Hon CC, Li Y, Wang D, Xu G, Zhang H, et al. Intraspecies diversity of SARS-like coronaviruses
in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol.
2010; 91: 1058–1062. https://doi.org/10.1099/vir.0.016378-0 PMID: 20016037
13. He B, Zhang Y, Xu L, Yang W, Yang F, Feng Y, et al. Identification of diverse alphacoronaviruses and
genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in
China. J Virol. 2014; 88: 7070–7082. https://doi.org/10.1128/JVI.00631-14 PMID: 24719429
14. Wu Z, Yang L, Ren X, He G, Zhang J, Yang J, et al. Deciphering the bat virome catalog to better under-
stand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J.
2016; 10: 609–620. https://doi.org/10.1038/ismej.2015.138 PMID: 26262818
15. Drexler JF, Gloza-Rausch F, Glende J, Corman VM, Muth D, Goettsche M, et al. Genomic characteriza-
tion of severe acute respiratory syndrome-related coronavirus in European bats and classification of
coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. J Virol. 2010; 84:
11336–11349. https://doi.org/10.1128/JVI.00650-10 PMID: 20686038
16. Tong S, Conrardy C, Ruone S, Kuzmin IV, Guo X, Tao Y, et al. Detection of novel SARS-like and other
coronaviruses in bats from Kenya. Emerg Infect Dis. 2009; 15: 482–485. https://doi.org/10.3201/
eid1503.081013 PMID: 19239771
17. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, et al. Isolation and characterization of a bat
SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013; 503: 535–538. https://doi.org/10.
1038/nature12711 PMID: 24172901
18. Yang XL, Hu B, Wang B, Wang MN, Zhang Q, Zhang W, et al. Isolation and Characterization of a Novel
Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coro-
navirus. J Virol. 2016; 90: 3253–3256.
19. Menachery VD, Yount BL Jr., Sims AC, Debbink K, Agnihothram SS, Gralinski LE, et al. SARS-like
WIV1-CoV poised for human emergence. Proc Natl Acad Sci U S A. 2016; 113: 3048–3053. https://doi.
org/10.1073/pnas.1517719113 PMID: 26976607
20. de Souza Luna LK, Heiser V, Regamey N, Panning M, Drexler JF, Mulangu S, et al. Generic detection
of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and non-
fluorescent low-density microarray. J Clin Microbiol. 2007; 45: 1049–1052. https://doi.org/10.1128/
JCM.02426-06 PMID: 17229859
21. Ren W, Li W, Yu M, Hao P, Zhang Y, Zhou P, et al. Full-length genome sequences of two SARS-like
coronaviruses in horseshoe bats and genetic variation analysis. J Gen Virol. 2006; 87: 3355–3359.
https://doi.org/10.1099/vir.0.82220-0 PMID: 17030870
22. Lau SK, Feng Y, Chen H, Luk HK, Yang WH, Li KS, et al. Severe Acute Respiratory Syndrome (SARS)
Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats
through Recombination. J Virol. 2015; 89: 10532–10547. https://doi.org/10.1128/JVI.01048-15 PMID:
26269185
23. Zeng LP, Gao YT, Ge XY, Zhang Q, Peng C, Yang XL, et al. Bat Severe Acute Respiratory Syndrome-
Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host
Immune Response. J Virol. 2016; 90: 6573–6582. https://doi.org/10.1128/JVI.03079-15 PMID:
27170748
24. Li F. Evidence for a common evolutionary origin of coronavirus spike protein receptor-binding subunits.
J Virol. 2012; 86: 2856–2858. https://doi.org/10.1128/JVI.06882-11 PMID: 22205743
25. Lau SK, Li KS, Huang Y, Shek CT, Tse H, Wang M, et al. Ecoepidemiology and complete genome com-
parison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in
China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events. J
Virol. 2010; 84: 2808–2819. https://doi.org/10.1128/JVI.02219-09 PMID: 20071579
A gene pool of bat SARS-related coronaviruses
PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1006698 November 30, 2017 26 / 27
26. Oostra M, de Haan CA, Rottier PJ. The 29-nucleotide deletion present in human but not in animal
severe acute respiratory syndrome coronaviruses disrupts the functional expression of open reading
frame 8. J Virol. 2007; 81: 13876–13888. https://doi.org/10.1128/JVI.01631-07 PMID: 17928347
27. Kopecky-Bromberg SA, Martinez-Sobrido L, Frieman M, Baric RA, Palese P. Severe acute respiratory
syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as
interferon antagonists. J Virol. 2007; 81: 548–557. https://doi.org/10.1128/JVI.01782-06 PMID:
17108024
28. Chen CY, Ping YH, Lee HC, Chen KH, Lee YM, Chen YJ, et al. Open reading frame 8a of the human
severe acute respiratory syndrome coronavirus not only promotes viral replication but also induces apo-
ptosis. J Infect Dis. 2007; 196: 405–415. https://doi.org/10.1086/519166 PMID: 17597455
29. Yang L, Wu Z, Ren X, Yang F, He G, Zhang J, et al. Novel SARS-like betacoronaviruses in bats, China,
2011. Emerg Infect Dis. 2013; 19: 989–991. https://doi.org/10.3201/eid1906.121648 PMID: 23739658
30. Wu Z, Yang L, Ren X, Zhang J, Yang F, Zhang S, et al. ORF8-Related Genetic Evidence for Chinese
Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus. J Infect
Dis. 2016; 213: 579–583. https://doi.org/10.1093/infdis/jiv476 PMID: 26433221
31. Drexler JF, Corman VM, Wegner T, Tateno AF, Zerbinati RM, Gloza-Rausch F, et al. Amplification of
emerging viruses in a bat colony. Emerg Infect Dis. 2011; 17: 449–456. https://doi.org/10.3201/
eid1703.100526 PMID: 21392436
32. Wang MN, Zhang W, Gao YT, Hu B, Ge XY, Yang XL, et al. Longitudinal surveillance of SARS-like coro-
naviruses in bats by quantitative real-time PCR. Virol Sin. 2016; 31: 78–80. https://doi.org/10.1007/
s12250-015-3703-3 PMID: 26920711
33. Menachery VD, Yount BL Jr., Debbink K, Agnihothram S, Gralinski LE, Plante JA, et al. A SARS-like
cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med. 2015; 21:
1508–1513. https://doi.org/10.1038/nm.3985 PMID: 26552008
34. Ren W, Qu X, Li W, Han Z, Yu M, Zhou P, et al. Difference in receptor usage between severe acute
respiratory syndrome (SARS) coronavirus and SARS-like coronavirus of bat origin. J Virol. 2008; 82:
1899–1907. https://doi.org/10.1128/JVI.01085-07 PMID: 18077725
35. Sung SC, Chao CY, Jeng KS, Yang JY, Lai MM. The 8ab protein of SARS-CoV is a luminal ER mem-
brane-associated protein and induces the activation of ATF6. Virology. 2009; 387: 402–413. https://doi.
org/10.1016/j.virol.2009.02.021 PMID: 19304306
36. Freundt EC, Yu L, Park E, Lenardo MJ, Xu XN. Molecular determinants for subcellular localization of
the severe acute respiratory syndrome coronavirus open reading frame 3b protein. J Virol. 2009; 83:
6631–6640. https://doi.org/10.1128/JVI.00367-09 PMID: 19403678
37. Zhou P, Li H, Wang H, Wang LF, Shi Z. Bat severe acute respiratory syndrome-like coronavirus ORF3b
homologues display different interferon antagonist activities. J Gen Virol. 2012; 93: 275–281. https://
doi.org/10.1099/vir.0.033589-0 PMID: 22012463
38. Irwin DM, Kocher TD, Wilson AC. Evolution of the cytochrome b gene of mammals. J Mol Evol. 1991;
32: 128–144. PMID: 1901092
39. Mayer F, von Helversen O. Cryptic diversity in European bats. Proc Biol Sci. 2001; 268: 1825–1832.
https://doi.org/10.1098/rspb.2001.1744 PMID: 11522202
40. Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013; 30: 1229–
1235. https://doi.org/10.1093/molbev/mst012 PMID: 23486614
41. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. RDP3: a flexible and fast computer pro-
gram for analyzing recombination. Bioinformatics. 2010; 26: 2462–2463. https://doi.org/10.1093/
bioinformatics/btq467 PMID: 20798170
42. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, et al. Full-length human
immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence
of intersubtype recombination. J Virol. 1999; 73: 152–160. PMID: 9847317
43. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to
estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;
59: 307–321. https://doi.org/10.1093/sysbio/syq010 PMID: 20525638
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... SARS-CoV is responsible for the first pandemic of the 21 st century, which broke out at the end of February 2003, though no outbreak or transmission has been reported since May 2004 (40). This virus causes SARS, which is characterized by severe pneumonia and diffuse alveolar damage (41)(42)(43). ...
... SARS-CoV originated in horseshoe bats by recombination events in SARS related CoVs (41). A study proposed that after its origin, SARS-CoV was transmitted to farmed civet (or another mammal), which got transmitted to other civets (intermediary host) by oral-fecal mode of transmission. ...
... A high diversity of SARS and MERS related coronaviruses exists in primary and intermediate hosts (41,99), as a result of which evolution and emergence of new coronaviruses are very much possible in the near future. One study (6) showed that there existed a high probability of emergence of a SARS-and MERS-CoV like coronavirus in China itself, and in less than a year, it became true. ...
Article
Full-text available
Viruses are the most abundant biological entities on our planet. On the basis of parameters like capsid structure, morphology, genetic material, etc., they are classified into different families. The Coronaviridae family of viruses includes a diverse group of positive strand RNA viruses and a subset of these viruses infects humans. Though some of these human-infecting coronaviruses cause minor respiratory ailments in healthy adults but three of them are responsible for major pandemics of the 21st century. These pandemics claimed thousands to several hundred thousands of human lives and have plunged the regional economies and even the global economy into an abyss. This work highlights the current research on human coronaviruses involving their diversity, evolution, clinical, and zoonotic attributes. An economic impact analysis of major coronaviruses is also presented to point out how these pathogens have claimed billions of dollars.
... A small region within the spike proteins of sarbecoviruses, known as the receptor binding domain (RBD), contains all of the structural information necessary to engage with the host receptor. We and others have experimentally classified the majority of published sarbecovirus RBDs into different clades based on sequence and functional data: clade 1, identified in Asian bats, contains no deletions and binds to host receptor, Angiotensin-Converting Enzyme 2 (ACE2), whereas clade 2, also identified in Asian bats, contains 2 deletions and does not use ACE2 and clade 3 viruses, found more widely in African and European bats, contain 1 deletion and have recently been shown can infect using primarily bat ACE2 [1][2][3][4][5][6][7][8][9][10]. In 2021, several viruses were identified in China that comprise a fourth clade that also interact with ACE2 [11]. ...
... Phylogenetic analysis of the spike RBD further reflected the close relatedness between Khosta -1 and -2 with BM48-31 and other clade 3 RBD viruses we have previously tested from Uganda and Rwanda [1,13] (Fig 1A). Clade 3 RBDs, including the Khosta viruses, contain a truncated surface-exposed loop, as compared to the ACE2-dependent, clade 1 viruses such as SARS-CoV, and additionally vary in many of the residues known for clade 1 viruses to interact with human ACE2 [1,2,13,14]. ...
... Bat sarbecoviruses resist immune response to SARS-CoV-2 among closely related viruses may even represent an evolutionary strategy for viral persistence within the reservoir host population [2]. ...
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Spillover of sarbecoviruses from animals to humans has resulted in outbreaks of severe acute respiratory syndrome SARS-CoVs and the ongoing COVID-19 pandemic. Efforts to identify the origins of SARS-CoV-1 and -2 has resulted in the discovery of numerous animal sarbecoviruses–the majority of which are only distantly related to known human pathogens and do not infect human cells. The receptor binding domain (RBD) on sarbecoviruses engages receptor molecules on the host cell and mediates cell invasion. Here, we tested the receptor tropism and serological cross reactivity for RBDs from two sarbecoviruses found in Russian horseshoe bats. While these two viruses are in a viral lineage distinct from SARS-CoV-1 and -2, the RBD from one virus, Khosta 2, was capable of using human ACE2 to facilitate cell entry. Viral pseudotypes with a recombinant, SARS-CoV-2 spike encoding for the Khosta 2 RBD were resistant to both SARS-CoV-2 monoclonal antibodies and serum from individuals vaccinated for SARS-CoV-2. Our findings further demonstrate that sarbecoviruses circulating in wildlife outside of Asia also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2
... Bats are reservoirs for SARS-related coronaviruses 3,4 . Multiple sarbecoviruses have been detected in bats [5][6][7][8] and, more recently, in pangolins 9 . SARS-CoV-2 variants of concern (VOC) have emerged since late 2020, probably in response to immune responses in the human population 10 . ...
... Biotinylated RBDs from SARS-CoV-2 Delta plus, Mu, Lambda and Omicron BA.2, bat CoVs BANAL-52, BANAL-236, WIV1, Rs2018B, LYRa11 and RsSHC014, and pangolin CoV GD-1 were produced in-house. Briefly, the RBD coding sequences were cloned into pcDNA3.1 vector with SARS-CoV-2 signal peptide (amino acid [1][2][3][4][5][6][7][8][9][10][11][12][13][14] at the N terminus and 10x his-tag, followed by AviTag at the C terminus. After transfection of expression plasmid into HEK293T cells using Fugene6 in Opti-MEM media, expressed proteins were collected at day 3 or day 6 post transfection. ...
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The SARS-CoV-2 Omicron variant (B.1.1.529 lineage) escapes antibodies that neutralize the ancestral virus. We tested human serum panels from participants with differing infection and vaccination status using a multiplex surrogate virus neutralization assay targeting 20 sarbecoviruses. We found that bat and pangolin sarbecoviruses showed significantly less neutralization escape than the Omicron variant. We propose that SARS-CoV-2 variants have emerged under immune selection pressure and are evolving differently from animal sarbecoviruses.
... Although the direct progenitor of SARS-CoV-2 remains unknown, its closest relative (RaTG13) has been detected in a horseshoe bat (Rhinolophus sinicus), indicating horseshoe bats as its potential reservoir hosts. Moreover, horseshoe bats were also found to harbor other groups of coronaviruses including the SARS-CoV (Ge et al. 2013;Hu et al. 2017;Li et al. 2005), indicating their critical role in the maintenance of human sensitive coronaviruses. Since the outbreak of COVID-19, multiple animal species have been infected and diseased by coronavirus, including pangolins, cats, tigers, etc. (Lam et al. 2020;Liu et al. 2019;McAloose et al. 2020;Newman et al. 2020;Zhang et al. 2020). ...
Article
Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.
... Although the evidence presented is circumstantial, it outlines the potential of salmon lice as a vector for PMCV and could explain the unusual spread pattern of CMS observed at Atlantic salmon farms, although . In addition to SARS-COV2, a number of other human diseases have originated in animals such as ebola (Pourrut et al., 2005), Midde East respiratory syndrome (MERS) (Mohd et al., 2016), rabies (Badrane and Tordo, 2001), smallpox (Gubser et al., 2004), severe acute respiratory syndrome (SARS) (Hu et al., 2017), measles (Weiss, 2001) and human immunodeficiency virus (HIV) (Gao et al., 1999), as well as recurring bacterial diseases such as anthrax, brucellosis, tetanus, salmonellosis, Escherichia coli and tuberculosis (Murphree et al., 2011;Dudley et al., 2016;Muturi et al., 2018;Murphy et al., 2021) and various parasites (Aloo, 2002;Mackenstedt, 2015). ...
... SARSr-CoV) have been found in bats located across Asia [17]. More recently, SARSr-CoV sequences, containing all the genetic elements required to form SARS-CoV, were isolated from bats found in a single cave in Yunnan province, China [18]. Identifying one location containing extensive SARS-CoV genetic diversity, combined with the ability of CoV to undergo recombination [19,20], suggests hotspots exist that are poised for generating future zoonotic CoV [16]. ...
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Monoclonal antibodies (MAbs) that retain neutralizing activity against distinct coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV) and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743-749, which interact with the C-terminal end of the SH helix in the S postfusion conformation. The crystal structure shows that BNMAb 1249A8 disrupts SH secondary structure and packing rearrangements required for CoV S to adopt its prefusion conformation that mediates membrane fusion and ultimately infection. The mechanisms regulating BNMAb 1249A8 CoV S specificity are also defined. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.
Research
Special issue on the new coronavirus causing the COVID-19 outbreak
Article
Predicting the evolution of virus host range has proven to be extremely difficult, in part because of the sheer diversity of viruses, each with unique biology and ecological interactions. We have not solved this problem, but to make the problem more tractable, we narrowed our focus to three traits intrinsic to all viruses that may play a role in host-range evolvability: mutation rate, recombination rate, and phenotypic heterogeneity. Although each trait should increase evolvability, they cannot do so unbounded because fitness trade-offs limit the ability of all three traits to maximize evolvability. By examining these constraints, we can begin to identify groups of viruses with suites of traits that make them especially concerning, as well as ecological and environmental conditions that might push evolution toward accelerating host-range expansion.
Chapter
The COVID-19 pandemic is widely seen as a failure of global health and pandemic preparedness. But where precisely does that failure lie? This chapter argues that many aspects of the pandemic preparedness regime worked as designed, suggesting a broader failure in the overall vision of global health security, including its focus on virus discovery and ‘early warning’ of outbreaks. Contrasting global health and planetary health as two distinct morphologies of health surveillance and intervention—each taking up the problem of emerging disease according to different spatial and formal logics—the chapter points toward new approaches to pandemic preparedness built on the management of social, ecological, and planetary drivers of disease emergence.KeywordsGlobal healthPlanetary healthSurveillancePreparednessGlobal virome
Article
Increasing evidence supports inter‐species transmission of SARS‐CoV‐2 variants from human to domestic or wild animals during the ongoing COVID‐19 pandemic, which is posing great challenges to epidemic control. Clarifying the host range of emerging SARS‐CoV‐2 variants will provide instructive information for the containment of viral spillover. The spike protein (S) of SARS‐CoV‐2 is the key determinant of receptor utilization, and therefore amino acid mutations on S will probably alter viral host range. Here, in order to evaluate the impact of S mutations, we constructed 20 Hela cell lines stably expressing ACE2 orthologs from different animals, and prepared 27 pseudotyped SARS‐CoV‐2 carrying different spike mutants, among which 20 bear single mutation and the other 7 were cloned from emerging SARS‐CoV‐2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Lambda (B.1.429) and Mu (B.1.621). Using pseudoviral reporter assay, we identified that the substitutions of T478I and N501Y enabled the pseudovirus to utilize chicken ACE2, indicating potential infectivity to avian species. Furthermore, the S mutants of real SARS‐CoV‐2 variants comprising N501Y showed significantly acquired abilities to infect cells expressing mouse ACE2, indicating a critical role of N501Y in expanding SARS‐CoV‐2 host range. In addition, A262S and T478I significantly enhanced the utilization of various mammals ACE2. In summary, our results indicated that T478I and N501Y substitutions were two S mutations important for receptor adaption of SARS‐CoV‐2, potentially contributing to the spillover of the virus to many other animal hosts. Therefore, more attention should be paid to SARS‐CoV‐2 variants with these two mutations. This article is protected by copyright. All rights reserved.
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Outbreaks from zoonotic sources represent a threat to both human disease as well as the global economy. Despite a wealth of metagenomics studies, methods to leverage these datasets to identify future threats are underdeveloped. In this study, we describe an approach that combines existing metagenomics data with reverse genetics to engineer reagents to evaluate emergence and pathogenic potential of circulating zoonotic viruses. Focusing on the severe acute respiratory syndrome (SARS)-like viruses, the results indicate that the WIV1-coronavirus (CoV) cluster has the ability to directly infect and may undergo limited transmission in human populations. However, in vivo attenuation suggests additional adaptation is required for epidemic disease. Importantly, available SARS monoclonal antibodies offered success in limiting viral infection absent from available vaccine approaches. Together, the data highlight the utility of a platform to identify and prioritize prepandemic strains harbored in animal reservoirs and document the threat posed by WIV1-CoV for emergence in human populations.
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Wereport the isolation and characterization of a novel bat coronavirus which is much closer to the severe acute respiratory syndrome coronavirus (SARS-CoV) in genomic sequence than others previously reported, particularly in its S gene. Cell entry and susceptibility studies indicated that this virus can use ACE2 as a receptor and infect animal and human cell lines. Our results provide further evidence of the bat origin of the SARS-CoV and highlight the likelihood of future bat coronavirus emergence in humans.
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The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV underscores the threat of cross-species transmission events leading to outbreaks in humans. Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations. Using the SARS-CoV reverse genetics system, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis. Evaluation of available SARS-based immune-therapeutic and prophylactic modalities revealed poor efficacy; both monoclonal antibody and vaccine approaches failed to neutralize and protect from infection with CoVs using the novel spike protein. On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations.
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Several lineage B betacoronaviruses termed Severe Acute Respiratory Syndrome (SARS) - like CoVs (SL-CoVs) were identified from Rhinolophus bats in China. These viruses are characterized by a set of Unique Accessory ORFs (UA-ORFs) that are located between the M and N genes. Among UA-ORFs, ORF8 is most hyper-variable. In this study, we classified the ORF8s of all SL-CoVs into three types and found for the first time that very few SL-CoVs from R. sinicus have ORF8s that are identical to that of human SARS-CoV. This finding provides new genetic evidence for Chinese horseshoe bats as the source of human SARS-CoV.
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Importance: Although horseshoe bats are the primary reservoir of SARS-related-coronaviruses (SARSr-CoVs), it is still unclear how these bat viruses have evolved to cross the species barrier to infect civet/human. Most human SARS-CoV epidemic strains contained a signature 29-nt deletion in ORF8 compared to civet SARSr-CoVs, suggesting that ORF8 may be important for interspecies transmission. However, the origin of SARS-CoV ORF8 remains obscure. In particular, SARSr-Rs-BatCoVs from Chinese horseshoe bats exhibited <40% aa identities to human/civet SARS-CoV in ORF8. We detected diverse alphacoronaviruses and betacoronaviruses among various bat species in Yunnan, including two SARSr-Rf-BatCoVs from greater horseshoe bats that possessed an ORF8 with exceptionally high aa identities to that of human/civet SARSr-CoVs. We demonstrated recombination events around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. Our findings offer insight into the evolutionary origin of SARS-CoV ORF8 which was likely acquired from SARSr-CoVs of greater horseshoe bats through recombination.
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Studies have demonstrated that ~ 60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.
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Unlabelled: Although many severe acute respiratory syndrome-like coronaviruses (SARS-like CoVs) have been identified in bats in China, Europe, and Africa, most have a genetic organization significantly distinct from human/civet SARS CoVs in the receptor-binding domain (RBD), which mediates receptor binding and determines the host spectrum, resulting in their failure to cause human infections and making them unlikely progenitors of human/civet SARS CoVs. Here, a viral metagenomic analysis of 268 bat rectal swabs collected from four counties in Yunnan Province has identified hundreds of sequences relating to alpha- and betacoronaviruses. Phylogenetic analysis based on a conserved region of the RNA-dependent RNA polymerase gene revealed that alphacoronaviruses had diversities with some obvious differences from those reported previously. Full genomic analysis of a new SARS-like CoV from Baoshan (LYRa11) showed that it was 29,805 nucleotides (nt) in length with 13 open reading frames (ORFs), sharing 91% nucleotide identity with human/civet SARS CoVs and the most recently reported SARS-like CoV Rs3367, while sharing 89% with other bat SARS-like CoVs. Notably, it showed the highest sequence identity with the S gene of SARS CoVs and Rs3367, especially in the RBD region. Antigenic analysis showed that the S1 domain of LYRa11 could be efficiently recognized by SARS-convalescent human serum, indicating that LYRa11 is a novel virus antigenically close to SARS CoV. Recombination analyses indicate that LYRa11 is likely a recombinant descended from parental lineages that had evolved into a number of bat SARS-like CoVs. Importance: Although many severe acute respiratory syndrome-like coronaviruses (SARS-like CoVs) have been discovered in bats worldwide, there are significant different genic structures, particularly in the S1 domain, which are responsible for host tropism determination, between bat SARS-like CoVs and human SARS CoVs, indicating that most reported bat SARS-like CoVs are not the progenitors of human SARS CoV. We have identified diverse alphacoronaviruses and a close relative (LYRa11) to SARS CoV in bats collected in Yunnan, China. Further analysis showed that alpha- and betacoronaviruses have different circulation and transmission dynamics in bat populations. Notably, full genomic sequencing and antigenic study demonstrated that LYRa11 is phylogenetically and antigenically closely related to SARS CoV. Recombination analyses indicate that LYRa11 is a recombinant from certain bat SARS-like CoVs circulating in Yunnan Province.
Article
Importance: Bats harbor genetically diverse SARS-like coronaviruses (SL-CoVs) and some of them have the potential of interspecies transmission. A unique open reading frame (ORFX) was identified in the genome of two recently isolated bat SL-CoV strains (WIV1 & 16). It will therefore be critical to clarify whether and how this protein would contribute to virulence during viral infection. Here we revealed that the unique ORFX is a functional gene involving in the modulation of host immune response, but not essential for in vitro viral replication. Our results provide important information for further exploration of the ORFX function in the future. Moreover, the reverse genetics system we constructed will be helpful for pathogenesis study of this group of viruses and develop therapeutics for future control of emerging SARS-like infections.
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[Figure not available: see fulltext.] © 2016, Wuhan Institute of Virology, CAS and Springer Science+Business Media Singapore.