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A Novel Coronavirus from Patients with Pneumonia in China, 2019


Abstract and Figures

In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed another clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.).
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Brief Report
Summ ar y
In December 2019, a cluster of patients with pneumonia of unknown cause was
linked to a seafood wholesale market in Wuhan, China. A previously unknown
betacoronavirus was discovered through the use of unbiased sequencing in samples
from patients with pneumonia. Human airway epithelial cells were used to isolate a
novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus
sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and
SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that
infect humans. Enhanced surveillance and further investigation are ongoing.
(Funded by the National Key Research and Development Program of China and the
National Major Project for Control and Prevention of Infectious Disease in China.)
merging and reemerging pathogens are global challenges for
public health.
Coronaviruses are enveloped RNA viruses that are distributed
broadly among humans, other mammals, and birds and that cause respira-
tory, enteric, hepatic, and neurologic diseases.
Six coronavirus species are known
to cause human disease.
Four viruses — 229E, OC43, NL63, and HKU1 — are
prevalent and typically cause common cold symptoms in immunocompetent indi-
The two other strains — severe acute respiratory syndrome coronavirus
(SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) — are
zoonotic in origin and have been linked to sometimes fatal illness.
SARS-CoV was
the causal agent of the severe acute respiratory syndrome outbreaks in 2002 and
2003 in Guangdong Province, China.
MERS-CoV was the pathogen responsible
for severe respiratory disease outbreaks in 2012 in the Middle East.
Given the high
prevalence and wide distribution of coronaviruses, the large genetic diversity and
frequent recombination of their genomes, and increasing human–animal interface
activities, novel coronaviruses are likely to emerge periodically in humans owing
to frequent cross-species infections and occasional spillover events.
In late December 2019, several local health facilities reported clusters of pa-
tients with pneumonia of unknown cause that were epidemiologically linked to a
seafood and wet animal wholesale market in Wuhan, Hubei Province, China.
December 31, 2019, the Chinese Center for Disease Control and Prevention (China
CDC) dispatched a rapid response team to accompany Hubei provincial and Wuhan
city health authorities and to conduct an epidemiologic and etiologic investigation.
We report the results of this investigation, identifying the source of the pneumonia
From the NHC Key Lab oratory of Biosafe -
ty, National Institute for Viral Disease
Control and Prevention, Chinese Center
for Disease Control and Prevention
(N.Z., W.W., J.S., X.Z., B.H., R.L., P.N.,
X.M., D.W., W.X., G.W., G.F.G., W.T.), and
the Depar tment of Infectious Diseases,
Beijing Ditan Hospital, Capital Medical
University (X.L.) — both in Beijing; Wu-
han Jinyintan Hospital (D.Z.), the Divi-
sion for Viral Disease Detection, Hubei
Provincial Cen ter for Disease Control and
Prevention (B.Y., F.Z.), and the Center for
Biosafety Mega-Science, Chinese Acade-
my of Sciences (W.T.) — all in Wuhan;
and the Shandong First Medical Univer-
sity and Shandong Academy of Medical
Sciences, Jinan, China (W.S.). Address
reprint requests to Dr. Tan at the NHC
Key Laboratory of Biosafety, National In-
stitute for Viral Disease Control and Pre-
vention, China CDC, 155 Changbai Road,
Changping District, Beijing 102206, Chi-
na; or at tanwj@ ivdc . chinacdc . cn, Dr.
Gao at the National Institute for Viral
Disease Control and Prevention, China
CDC, Beijing 102206, China, or at gaof@
im . ac . cn, or Dr. Wu at the NHC Key Labo-
ratory of Biosafety, National Institute for
Viral Disease Control and Prevention,
China CDC, Beijing 102206, China, or at
wugz@ ivdc . chinacdc . cn.
Drs. Zhu, Zhang, W. Wang, Li, and Yang
contributed equally to this article.
This article was published on January 24,
2020, and updated on Januar y 29, 2020,
DOI: 10.1056/NEJMoa 2001017
Copyright © 2020 Massachusetts Medical Society.
A Novel Coronavirus from Patients
with Pneumonia in China, 2019
Na Zhu, Ph.D., Dingyu Zhang, M.D., Wenling Wang, Ph.D., Xingwang Li, M.D.,
Bo Yang, M.S., Jingdong Song, Ph.D., Xiang Zhao, Ph.D., Baoying Huang, Ph.D.,
Weifeng Shi, Ph.D., Roujian Lu, M.D., Peihua Niu, Ph.D., Faxian Zhan, Ph.D.,
Xuejun Ma, Ph.D., Dayan Wang, Ph.D., Wenbo Xu, M.D., Guizhen Wu, M.D.,
George F. Gao, D.Phil., and Wenjie Tan, M.D., Ph.D., for the China Novel
Coronavirus Investigating and Research Team
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clusters, and describe a novel coronavirus de-
tected in patients with pneumonia whose speci-
mens were tested by the China CDC at an early
stage of the outbreak. We also describe clinical
features of the pneumonia in two of these pa-
Viral Diagnostic Methods
Four lower respiratory tract samples, including
bronchoalveolar-lavage fluid, were collected from
patients with pneumonia of unknown cause who
were identified in Wuhan on December 21, 2019,
or later and who had been present at the Huanan
Seafood Market close to the time of their clinical
presentation. Seven bronchoalveolar-lavage fluid
specimens were collected from patients in Beijing
hospitals with pneumonia of known cause to
serve as control samples. Extraction of nucleic
acids from clinical samples (including uninfect-
ed cultures that served as negative controls) was
performed with a High Pure Viral Nucleic Acid
Kit, as described by the manufacturer (Roche).
Extracted nucleic acid samples were tested for
viruses and bacteria by polymerase chain reac-
tion (PCR), using the RespiFinderSmart22kit
(PathoFinder BV) and the LightCycler 480 real-
time PCR system, in accordance with manufac-
turer instructions.
Samples were analyzed for
22 pathogens (18 viruses and 4 bacteria) as de-
tailed in the Supplementary Appendix. In addition,
unbiased, high-throughput sequencing, described
was used to discover microbial se-
quences not identifiable by the means described
above. A real-time reverse transcription PCR (RT-
PCR) assay was used to detect viral RNA by tar-
geting a consensus RdRp region of pan β-CoV, as
described in the Supplementary Appendix.
Isolation of Virus
Bronchoalveolar-lavage fluid samples were col-
lected in sterile cups to which virus transport
medium was added. Samples were then centri-
fuged to remove cellular debris. The supernatant
was inoculated on human airway epithelial cells,
which had been obtained from airway specimens
resected from patients undergoing surgery for
lung cancer and were confirmed to be special-
pathogen-free by NGS.
Human airway epithelial cells were expanded
on plastic substrate to generate passage-1 cells
and were subsequently plated at a density of
cells per well on permeable Transwell-
COL (12-mm diameter) supports. Human airway
epithelial cell cultures were generated in an
air–liquid interface for 4 to 6 weeks to form
well-differentiated, polarized cultures resem-
bling in vivo pseudostratified mucociliary epi-
Prior to infection, apical surfaces of the hu-
man airway epithelial cells were washed three
times with phosphate-buffered saline; 150 μl of
supernatant from bronchoalveolar-lavage fluid
samples was inoculated onto the apical surface
of the cell cultures. After a 2-hour incubation at
37°C, unbound virus was removed by washing with
500 μl of phosphate-buffered saline for 10 min-
utes; human airway epithelial cells were main-
tained in an air–liquid interface incubated at
37°C with 5% carbon dioxide. Every 48 hours,
150 μl of phosphate-buffered saline was applied
to the apical surfaces of the human airway epi-
thelial cells, and after 10 minutes of incubation
at 37°C the samples were harvested. Pseudostrat-
ified mucociliary epithelium cells were main-
tained in this environment; apical samples were
passaged in a 1:3 diluted vial stock to new cells.
The cells were monitored daily with light micros-
copy, for cytopathic effects, and with RT-PCR, for
the presence of viral nucleic acid in the superna-
tant. After three passages, apical samples and
human airway epithelial cells were prepared for
transmission electron microscopy.
Transmission Electron Microscopy
Supernatant from human airway epithelial cell
cultures that showed cytopathic effects was
collected, inactivated with 2% paraformalde-
hyde for at least 2 hours, and ultracentrifuged
to sediment virus particles. The enriched super-
natant was negatively stained on film-coated
grids for examination. Human airway epithelial
cells showing cytopathic effects were collected
and fixed with 2% paraformaldehyde–2.5%
glutaraldehyde and were then f ixed with 1%
osmium tetroxide dehydrated with grade ethanol
embedded with PON812 resin. Sections (80 nm)
were cut from resin block and stained with
uranyl acetate and lead citrate, separately. The
negative stained grids and ultrathin sections
were observed under transmission electron mi-
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Viral Genome Sequencing
RNA extracted from bronchoalveolar-lavage f lu-
id and culture supernatants was used as a tem-
plate to clone and sequence the genome. We
used a combination of Illumina sequencing and
nanopore sequencing to characterize the virus
genome. Sequence reads were assembled into
contig maps (a set of overlapping DNA segments)
with the use of CLC Genomics software, version
4.6.1 (CLC Bio). Specific primers were subse-
quently designed for PCR, and 5′- or 3′-RACE
(rapid amplification of cDNA ends) was used to
fill genome gaps from conventional Sanger se-
quencing. These PCR products were purified
from gels and sequenced with a BigDye Termi-
nator v3.1 Cycle Sequencing Kit and a 3130XL
Genetic Analyzer, in accordance with the manu-
facturers’ instructions.
Multiple-sequence alignment of the 2019-
nCoV and reference sequences was performed
with the use of Muscle. Phylogenetic analysis of
the complete genomes was performed with
RAxML (13) with 1000 bootstrap replicates and
a general time-reversible model used as the nu-
cleotide substitution model.
Resu lts
Three adult patients presented with severe pneu-
monia and were admitted to a hospital in Wu-
han on December 27, 2019. Patient 1 was a
49-year-old woman, Patient 2 was a 61-year-old
man, and Patient 3 was a 32-year-old man.
Clinical profiles were available for Patients 1 and
2. Patient 1 reported having no underlying
chronic medical conditions but reported fever
(temperature, 37°C to 38°C) and cough with
chest discomfort on December 23, 2019. Four
days after the onset of illness, her cough and
chest discomfort worsened, but the fever was
reduced; a diagnosis of pneumonia was based
on computed tomographic (CT) scan. Her occu-
pation was retailer in the seafood wholesale
market. Patient 2 initially reported fever and
cough on December 20, 2019; respiratory dis-
tress developed 7 days after the onset of illness
and worsened over the next 2 days (see chest
radiographs, Fig. 1), at which time mechanical
ventilation was started. He had been a frequent
visitor to the seafood wholesale market. Patients
1 and 3 recovered and were discharged from the
hospital on January 16, 2020. Patient 2 died on
January 9, 2020. No biopsy specimens were ob-
Figure 1. Chest Radiographs.
Shown are chest radiographs from Patient 2 on days 8
and 11 after the onset of illness. The trachea was intu-
bated and mechanical ventilation instituted in the peri-
od between the acquisition of the two images. Bilateral
fluf fy opacities are present in both images but are in-
creased in density, profusion, and conf luence in the
second image; these changes are most marked in the
lower lung fields. Changes consistent with the accu-
mulation of pleural liquid are also visible in the second
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Detection and Isolation of a Novel
Three bronchoalveolar-lavage samples were col-
lected from Wuhan Jinyintan Hospital on De-
cember 30, 2019. No specific pathogens (includ-
ing HCoV-229E, HCoV-NL63, HCoV-OC43, and
HCoV-HKU1) were detected in clinical specimens
from these patients by the RespiFinderSmart-
22kit. RNA extracted from bronchoalveolar-la-
vage fluid from the patients was used as a tem-
plate to clone and sequence a genome using a
combination of Illumina sequencing and nano-
pore sequencing. More than 20,000 viral reads
from individual specimens were obtained, and
most contigs matched to the genome from lin-
eage B of the genus betacoronavirus — showing
more than 85% identity with a bat SARS-like
CoV (bat-SL-CoVZC45, MG772933.1) genome
published previously. Positive results were also
obtained with use of a real-time RT-PCR assay
for RNA targeting to a consensus RdRp region
of pan β-CoV (although the cycle threshold value
was higher than 34 for detected samples). Virus
isolation from the clinical specimens was per-
formed with human airway epithelial cells and
Vero E6 and Huh-7 cell lines. The isolated virus
was named 2019-nCoV.
To determine whether virus particles could be
visualized in 2019-nCoV–infected human airway
epithelial cells, mock-infected and 2019-nCoV–
infected human airway epithelial cultures were
examined with light microscopy daily and with
transmission electron microscopy 6 days after
inoculation. Cytopathic effects were observed 96
hours after inoculation on surface layers of hu-
man airway epithelial cells; a lack of cilium
beating was seen with light microcopy in the
center of the focus (Fig. 2). No specific cyto-
pathic effects were observed in the Vero E6 and
Huh-7 cell lines until 6 days after inoculation.
Electron micrographs of negative-stained
2019-nCoV particles were generally spherical
with some pleomorphism (Fig. 3). Diameter var-
ied from about 60 to 140 nm. Virus particles had
quite distinctive spikes, about 9 to 12 nm, and
gave virions the appearance of a solar corona.
Extracellular free virus particles and inclusion
bodies filled with virus particles in membrane-
bound vesicles in cytoplasm were found in the
human airway epithelial ultrathin sections. This
observed morphology is consistent with the
Coronaviridae family.
To further characterize the virus, de novo se-
quences of 2019-nCoV genome from clinical spec-
imens (bronchoalveolar-lavage fluid) and human
airway epithelial cell virus isolates were obtained
by Illumina and nanopore sequencing. The novel
coronavirus was identified from all three patients.
Two nearly full-length coronavirus sequences
were obtained from bronchoalveolar-lavage fluid
(BetaCoV/Wuhan/IVDC-HB-04/2020, BetaCoV/
Wuhan/IVDC-HB-05/2020|EPI_ISL_402121), and
one full-length sequence was obtained from a
virus isolated from a patient (BetaCoV/Wuhan/
IVDC-HB-01/2020|EPI_ISL_402119). Complete ge-
nome sequences of the three novel coronaviruses
were submitted to GISAID (BetaCoV/Wuhan/
IVDC-HB-01/2019, accession ID: EPI_ISL _402119;
BetaCoV/Wuhan/IVDC-HB-04/2020, accession ID:
EPI_ISL_402120; BetaCoV/Wuhan/IV DC-HB-05/2019,
Figure 2. Cytopathic Effects in Human Airway Epithelial Cell Cultures after Inoculation with 2019-nCoV.
100 µm
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Brie f Rep ort
accession ID: EPI_ISL_402121) and have a 86.9%
nucleotide sequence identity to a previously pub-
lished bat SARS-like CoV (bat-SL-CoVZC45,
MG772933.1) genome. The three 2019-nCoV ge-
nomes clustered together within the sarbecovirus
subgenus, which shows the typical betacorona-
virus organization: a 5′ untranslated region (UTR),
replicase complex (orf1ab), S gene, E gene, M gene,
N gene, 3′ UTR, and several unidentified non-
structural open reading frames.
Although 2019-nCoV is similar to some beta-
coronaviruses detected in bats (Fig. 4), it is dis-
tinct from SARS-CoV and MERS-CoV. The three
2019-nCoV coronaviruses from Wuhan, together
with two bat-derived SARS-like strains, ZC45
and ZXC21, form a distinct clade. SARS-CoV
strains from humans and genetically similar
SARS-like coronaviruses from bats collected
from southwestern China formed another clade
within the subgenus sarbecovirus. Since the se-
quence identity in conserved replicase domains
(ORF 1ab) is less than 90% between 2019-nCoV
and other members of betacoronavirus, the
2019-nCoV — the likely causative agent of the
viral pneumonia in Wuhan — is a novel beta-
coronavirus belonging to the sarbecovirus sub-
genus of Coronaviridae family.
Disc ussion
We report a novel CoV (2019-nCoV) that was
identified in hospitalized patients in Wuhan,
China, in December 2019 and January 2020. Evi-
dence for the presence of this virus includes
identification in bronchoalveolar-lavage fluid in
three patients by whole-genome sequencing, di-
rect PCR, and culture. The illness likely to have
been caused by this CoV was named “novel coro-
navirus-infected pneumonia” (NCIP). Complete
genomes were submitted to GISAID. Phyloge-
netic analysis revealed that 2019-nCoV falls into
the genus betacoronavirus, which includes coro-
naviruses (SARS-CoV, bat SARS-like CoV, and
others) discovered in humans, bats, and other
wild animals.
We report isolation of the virus
and the initial description of its specific cyto-
pathic effects and morphology.
Molecular techniques have been used suc-
cessfully to identify infectious agents for many
years. Unbiased, high-throughput sequencing is
Figure 3. Visualization of 2019-nCoV with Transmission Electron Microscopy.
Negative-stained 2019-nCoV particles are shown in Panel A, and 2019-nCoV particles in the human air way epithelial
cell ultrathin sections are shown in Panel B. Arrowheads indicate extracellular virus particles, arrows indicate inclu-
sion bodies formed by virus components, and triangles indicate cilia.
100 nm 1 µm
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Figure 4. Schematic of 2019-nCoV and Phylogenetic Analysis of 2019-nCoV and Other Betacoronavirus Genomes.
Shown are a schematic of 2019-nCoV (Panel A) and full-leng th phylogenetic analysis of 2019-nCoV and other betacoronavirus genomes
in the Orthocoronavirinae subfamily (Panel B).
KC545386|Betacoronavirus_Erinaceus/VMC/DEU/2012| ErinaceusCoV/2012-216/GER/2012
Nsp2 Nsp3
Nsp9 Nsp12
Nsp13 Nsp14 Nsp15 Nsp16
>BetaCoV/Wuhan/IVDC-HB-01/2019|EPI_ISL_402119 (29892 bp)
Receptor binding
3 E M 78 1314
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Brie f Rep ort
a powerful tool for the discovery of patho-
Next-generation sequencing and bioin-
formatics are changing the way we can respond
to infectious disease outbreaks, improving our
understanding of disease occurrence and trans-
mission, accelerating the identification of patho-
gens, and promoting data sharing. We describe
in this report the use of molecular techniques
and unbiased DNA sequencing to discover a
novel betacoronavirus that is likely to have been
the cause of severe pneumonia in three patients
in Wuhan, China.
Although establishing human airway epithe-
lial cell cultures is labor intensive, they appear
to be a valuable research tool for analysis of hu-
man respiratory pathogens.
Our study showed
that initial propagation of human respiratory se-
cretions onto human airway epithelial cell cul-
tures, followed by transmission electron micros-
copy and whole genome sequencing of culture
supernatant, was successfully used for visualiza-
tion and detection of new human coronavirus
that can possibly elude identification by tradi-
tional approaches.
Further development of accurate and rapid
methods to identify unknown respiratory patho-
gens is still needed. On the basis of analysis of
three complete genomes obtained in this study,
we designed several specific and sensitive assays
targeting ORF1ab, N, and E regions of the 2019-
nCoV genome to detect viral RNA in clinical
specimens. The primer sets and standard oper-
ating procedures have been shared with the
World Health Organization and are intended for
surveillance and detection of 2019-nCoV infec-
tion globally and in China. More recent data
show 2019-nCoV detection in 830 persons in
Although our study does not fulfill Koch’s
postulates, our analyses provide evidence impli-
cating 2019-nCoV in the Wuhan outbreak. Ad-
ditional evidence to confirm the etiologic sig-
nificance of 2019-nCoV in the Wuhan outbreak
include identification of a 2019-nCoV antigen in
the lung tissue of patients by immunohisto-
chemical analysis, detection of IgM and IgG
antiviral antibodies in the serum samples from
a patient at two time points to demonstrate se-
roconversion, and animal (monkey) experiments
to provide evidence of pathogenicity. Of critical
importance are epidemiologic investigations to
characterize transmission modes, reproduction in-
terval, and clinical spectrum resulting from infec-
tion to inform and refine strategies that can pre-
vent, control, and stop the spread of 2019-nCoV.
This work was supported by grants from the National Key
Resea rch and Developmen t Program of Chi na (2016YFD0500301)
and the Nat ional Major Project for Control and Prevention of
Infectious Disease in China (2018ZX10101002).
Disclosure forms provided by the authors are available with
the fu ll text of this article at
We thank Dr. Zhongjie Li, Dr. Guangxue He, Dr. Lance Rode-
wald, Yu Li, Fei Ye, Li Zhao, Weimin Zhou, Jun Liu, Yao Meng,
Huijuan Wang, and many st aff members at t he China CDC for
their contributions and assistance in this preparation and sub-
mission of an earlier version of the manuscript.
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... believed to be induced by an exacerbated inflammatory response; [4][5][6] however, the specific triggers of epithelial/endothelial hyperpermeability and involvement of particular viral factors are not well understood. ...
Full-text available
Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of vascular leak are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to induce barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-β signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-β signaling axis are required for S-mediated barrier dysfunction. Notably, we show that SARS-CoV-2 infection caused leak in vivo, which was reduced by inhibiting integrins. Our findings offer mechanistic insight into SARS-CoV-2-triggered vascular leak, providing a starting point for development of therapies targeting COVID-19. Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction, however, the molecular pathways resulting in endothelial barrier dysfunction and vascular leakage are only sparsely understood. Here, Biering et al. show that SARS-CoV-2 spike protein is sufficient to induce barrier dysfunction and vascular leak. They show a role for integrins, TGF-beta, ECM remodeling enzymes, and glycosaminoglycans in this S-mediated barrier dysfunction.
... It is considered that asymptomatic individuals may carry the virus in the airways and cause transmission, but transmission mainly occurs via contact with infected individuals. The clinical outcomes of COVID-19 can be mild and severe, with varying degrees or even clinical outcomes lead to death (4). To date, it remains unclear why some patients have developed severe symptoms. ...
... A significant proportion of patients with obvious evidence of clinical infection have severe disease. [2] Coronaviruses are a large family of coronaviruses and subtype Coronaviridae that range from the common cold virus to the agent of more severe diseases such as SARS, MERS, and COVID-19. [3][4][5] The new coronavirus 2019 is transmitted through droplets, close contact, aerosols, and possibly fecal-oral transmission, and patients during the incubation period can transmit the virus to other people. ...
Antecedentes: Covid-19 es una enfermedad causada por un nuevo coronavirus conocido como SARS-CoV-2. La proteína viral Spike se une a los receptores corporales ACE2 y determina su infectividad. Este proceso tiene muchos efectos en el huésped, causando daños en el sistema respiratorio y a nivel sistémico en general, evidenciados en la elevación de marcadores de laboratorio como la Interleucina-6, Ferritina y D-Dímero. Objetivo: Analizar los biomarcadores (Interleuquina-6, Ferritina y D-Dímero) como factores de mal pronóstico en Covid-19.Métodos: Se recolectaron los datos de los pacientes con Covid-19 que además tenían resultados de IL-6, D-D y Ferritina obtenidos a través de las bases de datos del hospital IESS Ambato.Resultados: Reportamos 114 pacientes con Covid-19, a quienes analizamos los marcadores serológicos. D-D e IL-6 muestran una OR de 1,34 (C.I.: 1,14 - 1,58) y 1,26 (C.I.: 1,11 - 1,43) respectivamente. La ferritina tuvo una asociación positiva en la población femenina 1,11 OR (C.I.: 0,99 - 1,24), pero en la población masculina, no encontramos una asociación significativa 3,91 OR (C.I.: 0,46 - 32,99). Se encontró que las comorbilidades eran un factor protector con una asociación negativa de OR = 0,88. Las causas secundarias de muerte en los pacientes Covid-19 fueron la parada cardiaca y la neumonía (23,1%).Conclusiones: Los marcadores IL-6, Ferritina y D-D fueron evaluados y demostraron ser herramientas valiosas para predecir el mal pronóstico en pacientes con Covid-19. Estos marcadores procedieron independientemente de otros factores como las comorbilidades. Los hallazgos de este estudio pueden ayudar al manejo y pronóstico.
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a global health crisis after its emergence in 2019. Replication of the virus is initiated by binding of the viral spike (S) protein to human angiotensin-converting enzyme 2 (ACE2) on the target cell surface. Mutations acquired by SARS-CoV-2 S variants likely influence virus-target cell interaction. Here, using single-virus tracking to capture these initial steps, we observe how viruses carrying variant S interact with target cells. Specificity for ACE2 occurs for viruses with the reference sequence or D614G mutation. Analysis of the Alpha, Beta, and Delta SARS-CoV-2 variant S proteins revealed a progressive altered cell interaction with a reduced dependence on ACE2. Notably, the Delta variant S affinity was independent of ACE2. These enhanced interactions may account for the increased transmissibility of variants. Knowledge of how mutations influence cell interaction is essential for vaccine development against emerging variants of SARS-CoV-2.
Tissue-resident memory T (TRM) cells were originally identified as a tissue-sequestered population of memory T cells that show lifelong persistence in non-lymphoid organs. That definition has slowly evolved with the documentation of TRM cells having variable terms of tissue residency combined with a capacity to return to the wider circulation. Nonetheless, reductionist experiments have identified an archetypical population of TRM cells showing intrinsic permanent residency in a wide range of non-lymphoid organs, with one notable exception: the lungs. Despite the fact that memory T cells generated during a respiratory infection are maintained in the circulation, local TRM cell numbers in the lung decline concomitantly with a decay in T cell-mediated protection. This Perspective describes the mechanisms that underpin long-term T cell lodgement in non-lymphoid tissues and explains why residency is transient for select TRM cell subsets. In doing so, it highlights the unusual nature of memory T cell egress from the lungs and speculates on the broader disease implications of this process, especially during infection with SARS-CoV-2. In this Perspective, Francis Carbone considers the unique characteristics of the tissue-resident memory T (TRM) cell populations that develop in the lungs. He discusses how the different properties of lung TRM cells may affect immunity to lung infections, including SARS-CoV-2.
Целью статьи является определение наличия антител (IgG+IgM) к нуклео- капсидному (N) белку вируса SARS CoV-2 у обследованных 89 сотрудников коллектива отдельно взятой организации города Еревана. Вместе с этим отмечается, что соотношение обследованных женщин и мужчин составило 44 (47,7%) и 45 (46,7%) соответственно, а средний возраст составил 44,3 года (наивысший возраст 73 года, наименьший 24 года). Авторы приходят к выводу, что общая серопревалентность (наличие комбинированных антител IgG + IgM) к антигенам SARS CoV-2 у обследованных сотрудников составила 47,2% (95% ДИ 45,6-48,8), в то время как антитела отсутствовали у 47 сотрудников 52,8% (95% ДИ 52,2- 53,4). На основании изучения наличия антител к вирусу SARS CoV-2 в разных возрастных группах установлено, что самые высокие уровни антител обнаружены среди возрастных групп 30-39 лет (23,8%) и 40-49 лет (21,4%), наименьший – в группе лиц старше 70 лет (2,4%). В качестве исследовательской задачи авторами выяснена зависимость инфицированности лиц от группы крови. Известны были группы крови 77 из 89 сотрудников организации (42 женщины и 35 мужчин). В результате исследования выяснено, что по группам крови распределение уровня антител имеет следующее соотношение: 0(I), А(II), В(III), АВ(IV) – 15,7; 44,7; 21,2; 18,4% соответственно. Авторы приходят к выводу, что у лиц с группой крови А(II) инфицированность COVID-19 была выше, более чем в 2 раза, а наименьшая инфицированность отмечена у лиц с 0(I) группой крови, что коррелирует с результатами исследований зарубежных коллег. Հոդվածի նպատակն է պարզել Երևան քաղաքի կազմակերպություններից մեկում հետազոտված 89 աշխատակիցների SARS CoV-2 վիրուսի նուկլեոկապսիդ (N) սպիտակուցի նկատմամբ հակամարմինների (IgG+IgM) առկայությունը։ Հետազոտված տղամարդկանց և կանանց հարաբերակցությունը կազմել է համապատասխանաբար՝ 47,7% (44 տղամարդ ) և 46,7% (45 կին), իսկ միջին տարիքը՝ 44,3 տարեկան (առավելագույնը՝ 73 տարեկան, նվազագույնը՝ 24 տարեկան): Իրականացված ուսումնասիրության արդյունքները վկայում են, որ զննված աշխատակիցների ընդհանուր հակածինների SARS CoV-2 նկատմամբ համակցված IgG + IgM հակամարմիններ առկա են հետազոտվածների 47,2%- ում (95% ՀԳ 45,6-48,8): Ավելին, հակամարմինների ամենաբարձր մակարդակ դիտվել է 30-39 և 40-49 տարիքային խմբերում՝ համապատասխանաբար 23,8% և 21,4%, իսկ ամենացածր մակարդակ՝ 70 տարեկանից բարձր մարդկանց խմբում՝ 2,4%։ Մեր խմբի գիտական հետաքրքրությունների շրջանակում է եղել նաև վերլուծել արյան խմբերի և հակամարմինների մակարդակների միջև առկա կապը արյան խմբերի պատկանելությունը հայտնի 77 (42 կին և 35 տղամարդ) աշխատակիցների դեպքում: Հետազոտության արդյունքում պարզվել է, որ հակամարմինների մա- կարդակի բաշխումը, ըստ արյան խմբերի, ունի հետևյալ հարաբերակ- ցությունը՝ 0(I), A(II), B(III), AB(IV) խմբերում համապատասխանաբար՝ 15,7; 44,7; 21,2; 18,4%: Կատարված վերլուծության արդյունքները փաստում են, որ արյան A(II) խումբ ունեցող մարդկանց COVID-19-ով վարակվածությունը այլ արյան խմբերի համեմատ եղել է ավելի քան 2 անգամ բարձր: Ամենացածր վարակվածություն գրանցվել է 0(I) արյան խումբ ունեցող աշխատակիցների շրջանում, ինչն էլ հարաբերակցվում է միջազգային գիտական գրականության մեջ բերված օտարերկրյա հետազոտողների կողմից իրականացված ուսում- նասիրությունների արդյունքների հետ:
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Emergence of the SARS-CoV-2 Omicron variant of concern (VOC; B.1.1.529) resulted in a new peak of the COVID-19 pandemic, which called for development of effective therapeutics against the Omicron VOC. The receptor binding domain (RBD) of the spike protein, which is responsible for recognition and binding of the human ACE2 receptor protein, is a potential drug target. Mutations in receptor binding domain of the S-protein have been postulated to enhance the binding strength of the Omicron VOC to host proteins. In this study, bioinformatic analyses were performed to screen for potential therapeutic compounds targeting the omicron VOC. A total of 92,699 compounds were screened from different libraries based on receptor binding domain of the S-protein via docking and binding free energy analysis, yielding the top 5 best hits. Dynamic simulation trajectory analysis and binding free energy decomposition were used to determine the inhibitory mechanism of candidate molecules by focusing on their interactions with recognized residues on receptor binding domain. The ADMET prediction and DFT calculations were conducted to determine the pharmacokinetic parameters and precise chemical properties of the identified molecules. The molecular properties of the identified molecules and their ability to interfere with recognition of the human ACE2 receptors by receptor binding domain suggest that they are potential therapeutic agents for SARS-CoV-2 Omicron VOC.
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Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.
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Human coronaviruses (HCoVs) are large RNA viruses that infect the human respiratory tract. The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Various animal models have been established to investigate HCoV infection, including mice and non-human primates. To establish a link between the research conducted in animal models and humans, an organotypic human airway culture system, that recapitulates the human airway epithelium, has been developed. Currently, different cell culture systems are available to recapitulate the human airways, including the Air-Liquid Interface (ALI) human airway epithelium (HAE) model. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. These organotypic human airway cultures represent a universal platform to study respiratory virus-host interaction by offering more detailed insights compared to cell lines. Additionally, the epidemic potential of this virus family highlights the need for both vaccines and antivirals. No commercial vaccine is available but various effective antivirals have been identified, some with potential for human treatment. These morphological airway cultures are also well suited for the identification of antivirals, evaluation of compound toxicity and viral inhibition.
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Super-spreading occurs when a single patient infects a disproportionate number of contacts. The 2015 MERS-CoV, 2003 SARS-CoV, and to a lesser extent 2014-15 Ebola virus outbreaks were driven by super-spreaders. We summarize documented super-spreading in these outbreaks, explore contributing factors, and suggest studies to better understand super-spreading.
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A previously unknown coronavirus was isolated from the sputum of a 60-year-old man who presented with acute pneumonia and subsequent renal failure with a fatal outcome in Saudi Arabia. The virus (called HCoV-EMC) replicated readily in cell culture, producing cytopathic effects of rounding, detachment, and syncytium formation. The virus represents a novel betacoronavirus species. The closest known relatives are bat coronaviruses HKU4 and HKU5. Here, the clinical data, virus isolation, and molecular identification are presented. The clinical picture was remarkably similar to that of the severe acute respiratory syndrome (SARS) outbreak in 2003 and reminds us that animal coronaviruses can cause severe disease in humans.
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In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.
Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.
Objective: This study was conducted to investigate the viral and bacterial etiology and epidemiology of patients with acute febrile respiratory syndrome (AFRS) in Qinghai using a commercial routine multiplex-ligation-nucleic acid amplification test (NAT)-based assay. Methods: A total of 445 nasopharyngeal swabs specimens from patients with AFRS were analyzed using the RespiFinderSmart22kit (PathoFinder BV, Netherlands) and the LightCycler 480 real-time PCR system. Results: Among the 225 (225/445, 51%) positive specimens, 329 positive pathogens were detected, including 298 (90.58%) viruses and 31 (9%) bacteria. The most commonly detected pathogens were influenza virus (IFV; 37.39%; 123/329), adenovirus (AdV; 17.02%; 56/329), human coronaviruses (HCoVs; 10.94%; 36/329), rhinovirus/enterovirus (RV/EV; 10.03%; 33/329), parainfluenza viruses (PIVs; 8.51%; 28/329), and Mycoplasma pneumoniae (M. pneu; 8.51%; 28/329), respectively. Among the co-infected cases (17.53%; 78/445), IFV/AdV and IFV/M. pneu were the most common co-infections. Most of the respiratory viruses were detected in summer and fall. Conclusion: In our study, IFV-A was the most common respiratory pathogen among 22 detected pathogens, followed by AdV, HCoV, RV/EV, PIV, and M. pneu. Bacteria appeared less frequently than viruses, and co-infection was the most common phenomenon among viral pathogens. Pathogens were distributed among different age groups and respiratory viruses were generally active in July, September, and November. Enhanced surveillance and early detection can be useful in the diagnosis, treatment, and prevention of AFRS, as well as for guiding the development of appropriate public health strategies.
100 years after the infamous “Spanish flu” pandemic, the 2017–2018 flu season has been severe, with numerous infections worldwide. In between, there have been continuous, relentless attacks from (re-)emerging viruses. To fully understand viral pathogenesis and develop effective medical countermeasures, we must strengthen current surveillance and basic research efforts. 100 years after the infamous “Spanish flu” pandemic, the 2017–2018 flu season has been severe, with numerous infections worldwide. In between, there have been continuous, relentless attacks from (re-)emerging viruses. To fully understand viral pathogenesis and develop effective medical countermeasures, we must strengthen current surveillance and basic research efforts.
Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.