standOff. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote shown on the same row, so the borrowing can be checked against the thing borrowed from without leaving this page. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
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Abstract. Abstract concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationsSince the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1 – 4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5 – 7 . concept_edgesHere we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. research_questioncontrolscontent_tagsThe sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. contributionconcepts↗claim_relationscontent_tagsNotably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV. Subject terms: Pathogens, Virology, SARS-CoV-2 Characterization of full-length genome sequences from patients infected with a new coronavirus (2019-nCoV) shows that the sequences are nearly identical and indicates that the virus is related to a bat coronavirus. Main concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗Coronaviruses have caused two large-scale pandemics in the past two decades, SARS and Middle East respiratory syndrome (MERS) 8 , 9 . It has generally been thought that SARSr-CoV—which is mainly found in bats—could cause a future disease outbreak 10 , 11 . Here we report on a series of cases caused by an unidentified pneumonia disease outbreak in Wuhan, Hubei province, central China. This disease outbreak—which started from a local seafood market—has grown substantially to infect 2,761 people in China, is associated with 80 deaths and has led to the infection of 33 people in 10 additional countries as of 26 January 2020 12 . Typical clinical symptoms of these patients are fever, dry cough, breathing difficulties (dyspnoea), headache and pneumonia. concept_edgesDisease onset may result in progressive respiratory failure owing to alveolar damage (as observed by transverse chest computerized-tomography images) and even death. phenomenonsensescontent_tagsThe disease was determined to be caused by virus-induced pneumonia by clinicians according to clinical symptoms and other criteria, including a rise in body temperature, decreases in the number of lymphocytes and white blood cells (although levels of the latter were sometimes normal), new pulmonary infiltrates on chest radiography and no obvious improvement after treatment with antibiotics for three days. It appears that most of the early cases had contact history with the original seafood market; however, the disease has now progressed to be transmitted by human-to-human contact. concepts↗concepts↗concepts↗concepts↗unhoused_relationsSamples from seven patients with severe pneumonia (six of whom are sellers or deliverymen from the seafood market), who were admitted to the intensive care unit of Wuhan Jin Yin-Tan Hospital at the beginning of the outbreak, were sent to the laboratory at the Wuhan Institute of Virology (WIV) for the diagnosis of the causative pathogen (Extended Data Table 1 ). As a laboratory investigating CoV, we first used pan-CoV PCR primers to test these samples 13 , given that the outbreak occurred in winter and in a market—the same environment as SARS infections. We found five samples to be PCR-positive for CoVs. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationssensesOne sample (WIV04), collected from the bronchoalveolar lavage fluid (BALF), was analysed by metagenomics analysis using next-generation sequencing to identify potential aetiological agents. claim_typemethod↗mechanismssensescontent_tagscontent_tagsOf the 10,038,758 total reads—of which 1,582 total reads were retained after filtering of reads from the human genome—1,378 (87.1%) sequences matched the sequence of SARSr-CoV (Fig. 1a ). By de novo assembly and targeted PCR, we obtained a 29,891-base-pair CoV genome that shared 79.6% sequence identity to SARS-CoV BJ01 (GenBank accession number AY278488.2 ). High genome coverage was obtained by remapping the total reads to this genome (Extended Data Fig. 1 ). This sequence has been submitted to GISAID ( https://www.gisaid.org/ ) (accession number EPI_ISL_402124). object_of_studylimitationsconcepts↗concepts↗concepts↗concepts↗unhoused_relationscontent_tagsFollowing the name given by the World Health Organization (WHO), we tentatively call it novel coronavirus 2019 (2019-nCoV). Four more full-length genome sequences of 2019-nCoV (WIV02, WIV05, WIV06 and WIV07) (GISAID accession numbers EPI_ISL_402127–402130) that were more than 99.9% identical to each other were subsequently obtained from four additional patients using next-generation sequencing and PCR (Extended Data Table 2 ). Extended Data Table 1 Patient information and diagnosis history Note, some records are missing. All patients are sellers or deliverymen at the seafood market except ICU-01, whose contact history is unclear. All patients were admitted to intensive care unit (ICU) during the first investigation and were now in stable condition. Blood IgM tests have been performed for the following respiratory pathogens for all patients: Legionella pneumophilia , Mycoplasma pneumoniae , Chlamydia pneumoniae , respiratory syncytial virus, adenovirus, Rickettsia , influenza A virus, influenza B virus and parainfluenza virus. *This patient reported fever on 12 December 2019 and then recovered without medical treatment. He came back to the hospital on 27 December 2019 with a fever. His wife was also ill and admitted to the hospital. Both individuals recovered. Fig. 1 Genome characterization of 2019-nCoV. a , Metagenomics analysis of next-generation sequencing of BALF from patient ICU06. b , Genomic organization of 2019-nCoV WIV04. M, membrane. c , Similarity plot based on the full-length genome sequence of 2019-nCoV WIV04. Full-length genome sequences of SARS-CoV BJ01, bat SARSr-CoV WIV1, bat coronavirus RaTG13 and ZC45 were used as reference sequences. d , Phylogenetic tree based on nucleotide sequences of complete genomes of coronaviruses. MHV, murine hepatitis virus; PEDV, porcine epidemic diarrhoea virus; TGEV, porcine transmissible gastroenteritis virus.The scale bars represent 0.1 substitutions per nucleotide position. Descriptions of the settings and software that was used are included in the Methods . Extended Data Fig. 1 NGS raw reads of sample WIV04 mapping to the 2019-nCoV sequence. The x axis indicates the genome nucleotide position and the y axis represents the read depth of the mapping. Extended Data Table 2 Laboratory results Samples from two patients (ICU-01 and ICU-08) were not available during the second investigation. They had been discharged from the hospital. We did a serial test for patient ICU-06 on the following dates: 30 December 2019, 31 December 2019, 1 January 2020 and 10 January 2020, corresponding to 7, 8, 9 and 18 days after disease onset (23 December 2019). Molecular and serological (IgM and IgG) virus-detection results for 2019-nCoV are shown. NA, not available. *Virus isolated. # A full-length genome was obtained. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗The concept_edgesvirus genome consists of six major open-reading frames (ORFs) that are common to coronaviruses and a number of other accessory genes (Fig. 1b ). Further analysis indicates that some of the 2019-nCoV genes shared less than 80% nucleotide sequence identity to SARS-CoV. mechanismslimitationscontrolsconcepts↗sensescontent_tagscontent_tagsHowever, the unhoused_relationsamino acid sequences of the seven conserved replicase domains in ORF1ab that were used for CoV species classification were 94.4% identical between 2019-nCoV and SARS-CoV, suggesting that the two viruses belong to the same species, SARSr-CoV. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗sensesWe then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously detected in Rhinolophus affinis from Yunnan province—showed high sequence identity to 2019-nCoV. We carried out full-length sequencing on this RNA sample (GISAID accession number EPI_ISL_402131). Simplot analysis showed that 2019-nCoV was highly similar throughout the genome to RaTG13 (Fig. 1c ), with an overall genome sequence identity of 96.2%. Using the aligned genome sequences of 2019-nCoV, RaTG13, SARS-CoV and previously reported bat SARSr-CoVs, no evidence for recombination events was detected in the genome of 2019-nCoV. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationsunhoused_relationssensesclaim_relationsconcept_edgescontent_tagsPhylogenetic analysis of the full-length genome and the gene sequences of RdRp and spike ( S ) showed that—for all sequences—RaTG13 is the closest relative of 2019-nCoV and they form a distinct lineage from other SARSr-CoVs (Fig. 1d and Extended Data Fig. 2 ). content_tagsThe receptor-binding spike protein encoded by the S gene was highly divergent from other CoVs (Extended Data Fig. 2 ), with less than 75% nucleotide sequence identity to all previously described SARSr-CoVs, except for a 93.1% nucleotide identity to RaTG13 (Extended Data Table 3 ). The S genes of 2019-nCoV and RaTG13 are longer than other SARSr-CoVs. The major differences in the sequence of the S gene of 2019-nCoV are the three short insertions in the N-terminal domain as well as changes in four out of five of the key residues in the receptor-binding motif compared with the sequence of SARS-CoV (Extended Data Fig. 3 ). limitationsWhether the insertions in the N-terminal domain of the S protein of 2019-nCoV confer sialic-acid-binding activity as it does in MERS-CoV needs to be further studied. The close phylogenetic relationship to RaTG13 provides evidence that 2019-nCoV may have originated in bats. Extended Data Fig. 2 Phylogenetic trees based on the complete S and RdRp gene sequences of coronaviruses. a , b , Phylogenetic trees on the basis of the gene sequences of S ( a ) and RdRp ( b ) are shown. 2019-nCoV and bat CoV RaTG13 are shown in bold and in red. The trees were constructed using the maximum likelihood method using the GTR + G substitution model with bootstrap values determined by 1,000 replicates. Bootstraps values of more than 50% are shown. Extended Data Table 3 Genomic comparison of 2019-nCoV WIV04 with SARS-CoVs and bat SARSr-CoVs Extended Data Fig. 3 Amino acid sequence alignment of the S1 protein of the 2019-nCoV to SARS-CoV and selected bat SARSr-CoVs. The receptor-binding motif of SARS-CoV and the homologous region of other coronaviruses are indicated by the red box. The key amino acid residues involved in the interaction with human ACE2 are numbered at the top of the aligned sequences. The short insertions in the N-terminal domain of the 2019-nCoV are indicated by the blue boxes. Bat CoV RaTG13 was obtained from R. affinis , found in Yunnan province. Bat CoV ZC45 was obtained from R. sinicus , found in Zhejiang province. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationssensesWe rapidly developed a qPCR-based detection method on the basis of the sequence of the receptor-binding domain of the S gene, which was the most variable region of the genome (Fig. 1c ). concept_edgesOur data show that the primers could differentiate 2019-nCoV from all other human coronaviruses including bat SARSr-CoV WIV1, which shares 95% identity with SARS-CoV (Extended Data Fig. 4a, b ). Of the samples obtained from the seven patients, we found that six BALF and five oral swab samples were positive for 2019-nCoV during the first sampling, as assessed by qPCR and conventional PCR. However, we could no longer detect virus-positive samples in oral swabs, anal swabs and blood samples taken from these patients during the second sampling (Fig. 2a ). However, we recommend that other qPCR targets, including the RdRp or envelope ( E ) genes are used for the routine detection of 2019-nCoV. concepts↗concepts↗sensesOn the basis of these findings, we propose that the disease could be transmitted by airborne transmission, although we cannot rule out other possible routes of transmission, as further investigation, including more patients, is required. Extended Data Fig. 4 Molecular detection method used to detect 2019-nCoV. a , Standard curve for qPCR primers. The PCR product of the S gene that was serial diluted in the range of 10 8 to 10 1 (lines from left to right) was used as a template. Primer sequences and experimental conditions are described in the Methods . b , Specificity of the qPCR primers. Nucleotide samples from the indicated pathogens were used. Fig. 2 Molecular and serological investigation of patient samples. a , Molecular detection of 2019-nCoV in seven patients. Patient information can be found in Extended Data Tables 1 , 2 . Detection methods are described in the Methods . AS, anal swab; OS, oral swab. b , Dynamics of 2019-nCoV antibody levels in one patient who showed signs of disease on 23 December 2019 (ICU-06). OD ratio, optical density at 450–630 nm. The right and left y axes indicate ELISA OD ratios for IgM and IgG, respectively. c , Serological test of 2019-nCoV antibodies in five patients (Extended Data Table 2 ). The asterisk indicates data collected from patient ICU-06 on 10 January 2020. b , c , The cut-off was to 0.2 for the IgM analysis and to 0.3 for the IgG analysis, according to the levels of healthy controls. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗sensesFor serological detection of 2019-nCoV, we used a previously developed nucleocapsid (N) protein from bat SARSr-CoV Rp3 as antigen for IgG and IgM enzyme-linked immunosorbent assays (ELISAs), as this protein shared 92% amino acid identity to N protein of 2019-nCoV (Extended Data Fig. 5 ) and showed no cross-reactivity against other human coronaviruses except SARSr-CoV 7 . We were only able to obtain five serum samples from the seven patients with viral infections. We monitored viral antibody levels in one patient (ICU-06) 7, 8, 9 and 18 days after the onset of disease (Extended Data Table 2 ). A clear trend was observed in the IgG and IgM titres, which increased over time, except that the IgM titre was decreased in the last sample (Fig. 2b ). As a second analysis, we tested samples from 5 of the 7 virus-positive patients around 20 days after disease onset for the presence of viral antibodies (Extended Data Tables 1 , 2 ). All patient samples—but not samples from healthy individuals—were strongly positive for viral IgG (Fig. 2b ). There were also three IgM-positive samples, indicating an acute infection. Extended Data Fig. 6 Isolation and antigenic characterization of 2019-nCoV. a , b , Vero E6 cells are shown at 24 h after infection with mock virus ( a ) or 2019-nCoV ( b ). c , d , Mock-virus-infected ( c ) or 2019-nCoV-infected ( d ) samples were stained with rabbit serum raised against recombinant SARSr-CoV Rp3 N protein (red) and DAPI (blue). The experiment was conducted twice independently with similar results. e , The ratio of the number of reads related to 2019-nCoV among the total number of virus-related reads in metagenomics analysis of supernatants from Vero E6 cell cultures. f , Virus growth in Vero E6 cells. g , Viral particles in the ultrathin sections were imaged using electron microscopy at 200 kV. The sample was from virus-infected Vero E6 cells. The inset shows the viral particles in an intra-cytosolic vacuole. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗We next successfully isolated the virus (called 2019-nCoV BetaCoV/Wuhan/WIV04/2019) from both Vero E6 and Huh7 cells using the BALF sample of patient ICU-06. Clear cytopathogenic effects were observed in cells after incubation for three days (Extended Data Fig. 6a, b ). The identity of the strain WIV04 was verified in Vero E6 cells by immunofluorescence microscopy using the cross-reactive viral N antibody (Extended Data Fig. 6c, d ) and by metagenomics sequencing, most of the reads of which mapped to 2019-nCoV, and qPCR analysis showed that the viral load increased from day 1 to day 3 (Extended Data Fig. 6e, f ). Viral particles in ultrathin sections of infected cells displayed a typical coronavirus morphology, as visualized by electron microscopy (Extended Data Fig. 6g ). concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationsTo further confirm the neutralization activity of the viral IgG-positive samples, we conducted serum-neutralization assays in Vero E6 cells using the five patient sera that were IgG-positive. We demonstrate that all samples were able to neutralize 100 TCID 50 (50% tissue-culture-infective dose) of 2019-nCoV at a dilution of 1:40–1:80. We also show that this virus could be cross-neutralized by horse anti-SARS-CoV serum (gift from L.-F. Wang) at dilutions of 1:40; however, the potential for cross-reactivity with SARS-CoV antibodies needs to be confirmed with anti-SARS-CoV serum from humans (Extended Data Table 4 ). Extended Data Table 4 Virus neutralization test of serum samples Each serum sample was tested in triplicate. Serum samples from two healthy individuals from Wuhan and five patients as well as a horse anti-SARS-CoV anti-serum were used. We used 120 TCID 50 viruses per well. Serum samples were used at dilutions of 1:10, 1:20, 1:40 and 1:80. neg, negative; VNT, virus neutralization test. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationsunhoused_relationssensesACE2 is known to be a cell receptor for SARS-CoV 14 . To determine whether 2019-nCoV also uses ACE2 as a cellular entry receptor, we conducted virus infectivity studies using HeLa cells that expressed or did not express ACE2 proteins from humans, Chinese horseshoe bats, civets, pigs and mice. We show that 2019-nCoV is able to use all ACE2 proteins, except for mouse ACE2, as an entry receptor to enter ACE2-expressing cells, but not cells that did not express ACE2, indicating that ACE2 is probably the cell receptor through which 2019-nCoV enters cells (Fig. 3 ). We also show that 2019-nCoV does not use other coronavirus receptors, such as aminopeptidase N (APN) and dipeptidyl peptidase 4 (DPP4) (Extended Data Fig. 7 ). Fig. 3 Analysis of the receptor use of 2019-nCoV. Determination of virus infectivity in HeLa cells that expressed or did not express (untransfected) ACE2. The expression of ACE2 plasmid with S tag was detected using mouse anti-S tag monoclonal antibody. hACE2, human ACE2; bACE2, ACE2 of Rhinolophus sinicus (bat); cACE2, civet ACE2; sACE2, swine ACE2 (pig); mACE2, mouse ACE2. Green, ACE2; red, viral protein (N); blue, DAPI (nuclei). Scale bars, 10 μm. Extended Data Fig. 7 Analysis of 2019-nCoV receptor usage. Determination of virus infectivity in HeLa cells with or without the expression of human APN and DPP4. The expression of ACE2, APN and DPP4 plasmids with S tag were detected using mouse anti-S tag monoclonal antibody. ACE2, APN and DPP4 proteins (green), viral protein (red) and nuclei (blue) are shown. Scale bars, 10 μm. concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗concepts↗unhoused_relationsunhoused_relationsunhoused_relationssensessensesThe study provides a detailed report on 2019-nCoV, the likely aetiological agent responsible for the ongoing epidemic of acute respiratory syndrome in China and other countries. Virus-specific nucleotide-positive and viral-protein seroconversion was observed in all patients tested and provides evidence of an association between the disease and the presence of this virus. However, there are still many urgent questions that remain to be answered. The association between 2019-nCoV and the disease has not been verified by animal experiments to fulfil the Koch’s postulates to establish a causative relationship between a microorganism and a disease. We do not yet know the transmission routine of this virus among hosts. It appears that the virus is becoming more transmissible between humans. We should closely monitor whether the virus continues to evolve to become more virulent. Owing to a shortage of specific treatments and considering the relatedness of 2019-nCoV to SARS-CoV, some drugs and pre-clinical vaccines against SARS-CoV could probably be used to treat this virus. Finally, considering the wide spread of SARSr-CoV in their natural reservoirs, future research should be focused on active surveillance of these viruses for broader geographical regions. In the long term, broad-spectrum antiviral drugs and vaccines should be prepared for emerging infectious diseases that are caused by this cluster of viruses in the future. Most importantly, strict regulations against the domestication and consumption of wildlife should be implemented. limitationsconcepts↗concepts↗sensescontent_tagsNote added in proof: Since this paper was accepted, the ICTV has designated the virus as SARS-CoV-2 15 ; in addition, the WHO has released the official name of the disease caused by this virus, which is COVID-19 16 . Methods Data reporting limitationscontrolsconcepts↗concepts↗concepts↗sensescontent_tagsNo statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. concepts↗concepts↗concepts↗concepts↗Sample collection Human samples, including oral swabs, anal swabs, blood and BALF samples were collected by Jinyintan hospital (Wuhan, China) with the consent of all patients and approved by the ethics committee of the designated hospital for emerging infectious diseases. Patients were sampled without gender or age preference unless indicated. For swabs, 1.5 ml DMEM containing 2% FBS was added to each tube. The supernatant was collected after centrifugation at 2,500 rpm, vortexing for 60 s and a standing period of 15–30 min. The supernatant from swabs or BALF (no pre-treatment) was added to either lysis buffer for RNA extraction or to viral transport medium for isolation of the virus. The viral transport medium was composed of Hank’s balanced salt solution (pH 7.4) containing BSA (1%), amphotericin (15 μg ml −1 ), penicillin G (100 units ml −1 ) and streptomycin (50 μg ml −1 ). Serum was separated by centrifugation at 3,000 g for 15 min within 24 h of collection, followed by inactivation at 56 °C for 1 h, and was then stored at 4 °C until use. concepts↗concepts↗Virus isolation, cell infection, electron microscopy and neutralization assay The following cell lines were used for virus isolation in this study: Vero E6 and Huh7 cells, which were cultured in DMEM containing 10% FBS. All cell lines were tested and free of mycoplasma contamination, submitted for species identification and authenticated by morphological evaluation by microscopy. None of the cell lines was on the list of commonly misidentified cell lines (by ICLAC). Cultured cell monolayers were maintained in their respective medium. The PCR-positive BALF sample from ICU-06 patient was spun at 8,000 g for 15 min, filtered and diluted 1:2 with DMEM supplemented with 16 μg ml −1 trypsin before it was added to the cells. After incubation at 37 °C for 1 h, the inoculum was removed and replaced with fresh culture medium containing antibiotics (see below) and 16 μg ml −1 trypsin. The cells were incubated at 37 °C and observed daily for cytopathogenic effects. The culture supernatant was examined for the presence of virus by qRT–PCR methods developed in this study, and cells were examined by immunofluorescence microscopy using the anti-SARSr-CoV Rp3 N antibody that was generated in-house (1:1,000). Penicillin (100 units ml −1 ) and streptomycin (15 μg ml −1 ) were included in all tissue culture media. Vero E6 cells were infected with the new virus at a multiplicity of infection (MOI) of 0.5 and collected 48 h after infection. Cells were fixed with 2.5% (w/v) glutaraldehyde and 1% osmium tetroxide, dehydrated through a graded series of ethanol concentrations (from 30 to 100%) and embedded with epoxy resin. Ultrathin sections (80 nm) of embedded cells were prepared, deposited onto Formvar-coated copper grids (200 mesh), stained with uranyl acetate and lead citrate, and analysed using a 200-kV Tecnai G2 electron microscope. concepts↗concepts↗concepts↗The virus neutralization test was carried out in a 96-well plate. The patient serum samples were heat-inactivated by incubation at 56 °C for 1 h before use. The serum samples were diluted to 1:10, 1:20, 1:40 or 1:80, and then an equal volume of virus stock was added and incubated at 37 °C for 60 min in a 5% CO 2 incubator. Diluted horse anti-SARS-CoV serum or serum samples from healthy individuals were used as control. After incubation, 100 μl mixtures were inoculated onto a monolayer of Vero E6 cells in a 96-well plate for 1 h. Each serum was assessed in triplicate. After removing the supernatant, the plate was washed twice with DMEM medium. Cells were incubated with DMEM supplemented with 2% FBS for 3 days. Subsequently, the cells were checked for cytopathogenic effects. RNA extraction and PCR Whenever commercial kits were used, the manufacturer’s instructions were followed without modification. RNA was extracted from 200 μl of samples with the High Pure Viral RNA kit (Roche). RNA was eluted in 50 μl of elution buffer and used as the template for RT–PCR. For qPCR analysis, primers based on the S gene of 2019-nCoV were designed: RBD-qF1, 5′-CAATGGTTTAACAGGCACAGG-3′; RBD-qR1, 5′-CTCAAGTGTCTGTGGATCACG-3′. RNA extracted as described above was used for qPCR using the HiScript II One Step qRT–PCR SYBR Green Kit (Vazyme Biotech). Conventional PCRs were also performed using the following primer pairs: ND-CoVs-951F, 5′-TGTKAGRTTYCCTAAYATTAC-3′; ND-CoVs-1805R, 5′-ACATCYTGATANARAACAGC-3′. The 20-μl qPCR reaction mix contained 10 μl 2× One Step SYBR Green mix, 1 μl One Step SYBR Green Enzyme mix, 0.4 μl 50× ROX Reference Dye 1, 0.4 μl of each primer (10 μM) and 2 μl template RNA. Amplification was performed as follows: 50 °C for 3 min, 95 °C for 30 s followed by 40 cycles consisting of 95 °C for 10 s and 60 °C for 30 s, and a default melting curve step in an ABI 7500 Real-time PCR machine. Serological test In-house anti-SARSr-CoV IgG and IgM ELISA kits were developed using SARSr-CoV Rp3 N protein as antigen, which shared more than 90% amino acid identity to all SARSr-CoVs 2 . For IgG analyses, MaxiSorp Nunc-immuno 96-well ELISA plates were coated (100 ng per well) overnight with recombinant N protein. Human sera were used at a dilution of 1:20 for 1 h at 37 °C. An anti-human IgG HRP-conjugated monoclonal antibody (Kyab Biotech) was used at a dilution of 1:40,000. The OD value (450–630 nm) was calculated. For IgM analyses, MaxiSorp Nunc-immuno 96-well ELISA plates were coated (500 ng per well) overnight with anti-human IgM (μ chain). Human sera were used at a 1:100 dilution for 40 min at 37 °C, followed by incubation with an anti-Rp3 N HRP-conjugated antibody (Kyab Biotech) at a dilution of 1:4,000. The OD value (450–630 nm) was calculated. Examination of ACE2 receptor for 2019-nCoV infection HeLa cells transiently expressing ACE2 were prepared using Lipofectamine 3000 (Thermo Fisher Scientific) in a 96-well plate; mock-transfected cells were used as controls. 2019-nCoV grown in Vero E6 cells was used for infection at a MOI of 0.5. APN and DPP4 were analysed in the same way. The inoculum was removed after absorption for 1 h and washed twice with PBS and supplemented with medium. At 24 h after infection, cells were washed with PBS and fixed with 4% formaldehyde in PBS (pH 7.4) for 20 min at room temperature. ACE2 expression was detected using a mouse anti-S tag monoclonal antibody and a FITC-labelled goat anti-mouse IgG H&L (Abcam, ab96879). Viral replication was detected using a rabbit antibody against the Rp3 N protein (generated in-house, 1:1,000) and a Cy3-conjugated goat anti-rabbit IgG (1:200, Abcam, ab6939). Nuclei were stained with DAPI (Beyotime). Staining patterns were examined using confocal microscopy on a FV1200 microscope (Olympus). concepts↗concepts↗High-throughput sequencing, pathogen screening and genome assembly Samples from patient BALF or from the supernatant of virus cultures were used for RNA extraction and next-generation sequencing (NGS) using BGI MGISEQ2000 and Illumina MiSeq 3000 sequencers. Metagenomic analysis was carried out mainly based on the bioinformatics platform MGmapper (PE_2.24 and SE_2.24). The raw NGS reads were first processed by Cutadapt (v.1.18) with minimum read length of 30 base pairs. BWA (v.0.7.12-r1039) was used to align reads to a local database with a filter hits parameter of 0.8 FMM ((match + mismatch)/read length ≥ fraction] value and minimum alignment score of 30. Parameters for post-processing of assigned reads were set to a minimum size normalized abundance of 0.01, minimum read count of 20 and were otherwise set to default parameters. concepts↗concepts↗concepts↗A local nucleic acid database for human and mammals was used to filter reads of host genomes before mapping reads to the virus database. The results of the metagenomic analysis were displayed as pie charts using Microsoft Office 2010. NGS reads were assembled into genomes using Geneious (v.11.0.3) and MEGAHIT (v.1.2.9). PCR and Sanger sequencing was performed to fill gaps in the genome. 5′-rapid amplification of cDNA ends (RACE) was performed to determine the 5′-end of the genomes using a SMARTer RACE 5′/3′ kit (Takara). Genomes were annotated using the Clone Manager Professional Suite 8 (Sci-Ed Software). concepts↗concepts↗concepts↗concepts↗concepts↗Phylogenetic analysis Routine sequence management and analysis was carried out using DNAStar. The sequence alignment of complete genome sequences was performed using MAFFT (v.7.307) with default parameters. The codon alignments of full-length S and RdRp gene sequences were converted from the corresponding protein alignments by PAL2NAL (v.14); the protein alignments were created by Clustal Omega (v.1.2.4) using default parameters. Maximum likelihood phylogenetic trees were generated using RAxML (v.0.9.0) with GTR+G substitution model and 1,000 bootstrap replicates. Reporting summary Further information on research design is available in the Nature Research Reporting Summary linked to this paper. Online content Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41586-020-2012-7. Supplementary information Reporting Summary Acknowledgements We thank P. Zhang and A. Du from the WIV core facility centre for their help with producing transmission electron microscopy micrographs; H.-Z. Liu and P. Yu from WIV for bioinformatics analysis. This work was jointly supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB29010101 to Z.-L.S. and XDB29010104 to P.Z.), China Natural Science Foundation for excellent scholars (81822028 to P.Z., 31770175 to Z.-L.S. and 31800142 to B.H.), Mega-Project for Infectious Disease from Minister of Science and Technology of the People’s Republic of China (2018ZX10305409-004-001 to P.Z.), Youth innovation promotion association of CAS (2019328 to X.-L.Y.). Extended data figures and tables Extended Data Fig. 5 Amino acid sequence alignment of the nucleocapsid protein of 2019-nCoV to bat SARSr-CoV Rp3 and SARS-CoV BJ01. Bat SARSr-CoV Rp3 was obtained from R. sinicus , which is found in Guangxi province. Author contributions Z.-L.S., P.Z., Y.-Y.W. and G.-F.X. conceived the study. X.-G.W., C.-L.H., H.-D.C., F.D., Q.-J.C., F.-X.Z. and L.-L.L. collected patient samples. X.-L.Y., B.Y., W.Z., B.L., J.C., X.-S.Z., Y.L., H.G., R.-D.J., M.-Q.L., Y.C., X.W., X.-R.S. and K.Z. performed qPCR, serology and virus culturing experiments. L.Z., Y.Z., H.-R.S. and B.H. performed genome sequencing and annotations. Data availability Sequence data that support the findings of this study have been deposited in GISAID ( https://www.gisaid.org/ ) with accession numbers EPI_ISL_402124, EPI_ISL_402127–EPI_ISL_402130 and EPI_ISL_402131; GenBank with accession numbers MN996527 – MN996532 ; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences ( https://bigd.big.ac.cn/databases?lang=en ) with accession numbers SAMC133236–SAMC133240 and SAMC133252. Competing interests The authors declare no competing interests. Footnotes Peer review information Nature thanks the anonymous reviewers for their contribution to the peer review of this work. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. These authors contributed equally: Peng Zhou, Xing-Lou Yang, Xian-Guang Wang Change history 9/28/2020 This article was amended to correct the Peer review information. Extended data is available for this paper at 10.1038/s41586-020-2012-7. Supplementary information is available for this paper at 10.1038/s41586-020-2012-7.
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 4 of 5 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | a virus with no name yet - identified, sequenced, classified and provisionally named in one paper, and RENAMED BY A COMMITTEE BEFORE THE PAPER WAS PRINTED | object_of_study | the paper's words | |
| research_question | what the Wuhan pneumonia outbreak was caused by, where it sits taxonomically, and whether it uses the SARS-CoV receptor | research_question | the paper's words | |
| contribution | five full-length genomes from early patients, the 96.2% match to a bat coronavirus, the species assignment, and the confirmation that the virus enters cells through ACE2 | contribution | the paper's words | |
| claim_type | existence | claim_type | the paper's words | |
| phenomenon | an outbreak whose cause was defined CLINICALLY before anything was sequenced - by symptoms, blood counts, radiography, and a failure to improve on antibiotics | phenomenon | the paper's words | |
| method | omics-profiling also in: omics-profiling | method | the paper's words | |
| mechanisms | THE IDENTIFICATION SURVIVES A FILTER THAT REMOVES 99.98% OF THE DATA: `of the 10,038,758 total reads - of which 1,582 total reads were retained after filtering of reads from the human genome - 1,378 (87.1%) sequences matched`. THE 87.1% IS A PERCENTAGE OF THE SURVIVORS, and the finding rests on 1,378 reads out of ten million | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | and the taxonomic placement is a threshold on a CHOSEN SUBSTRING: whole-genome identity to SARS-CoV is 79.6%, but `the seven conserved replicase domains in ORF1ab that were used for CoV species classification were 94.4% identical`. Same species by one measure and twenty per cent apart by another | mechanisms[1] | 0.95 | the tagger's words |
| limitations | THE NAME IN THE BODY IS ALREADY OBSOLETE AND THE PAPER SAYS SO IN A NOTE: `Note added in proof: since this paper was accepted, the ICTV has designated the virus as SARS-CoV-2; in addition, the WHO has released the official name of the disease ... COVID-19`. The record carries both names AND the moment of the change | limitations[0] | 0.95 | the tagger's words |
| limitations | and the name it does use was provisional and institutional from the start: `Following the name given by the World Health Organization (WHO), we tentatively call it novel coronavirus 2019`. Neither name in this paper is the authors' own | limitations[1] | 0.95 | the tagger's words |
| limitations | THE SPECIES BOUNDARY IS A CONVENTION ABOUT WHICH SEQUENCE TO COMPARE, and the paper states the convention in the same clause it applies it - `that were used for CoV species classification`. A different choice of region gives a different answer, and 79.6% is in the same abstract as 94.4% | limitations[2] | 0.95 | the tagger's words |
| limitations | the design is declared to have no statistical structure at all: `No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded`. Five genomes from five patients in an unfolding outbreak | limitations[3] | 0.95 | the tagger's words |
| limitations | and the sequence difference that matters most functionally is left open: whether the three N-terminal insertions in the S protein `confer sialic-acid-binding activity as it does in MERS-CoV needs to be further studied` | limitations[4] | 0.95 | the tagger's words |
| controls | five independent full-length genomes from five different patients eliminates: a single-sample artefact - the four later sequences were 'more than 99.9% identical to each other', and the identification does not rest on one library · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | the species assignment was made on the region conventionally used for it, not on the whole genome eliminates: nothing about the boundary itself - it applies a convention rather than testing one, and the paper reports both figures (79.6% whole-genome, 94.4% replicase) in the same abstract · outcome: partial | controls[1] | 0.95 | the tagger's words |
| controls | the design's statistical structure eliminates: nothing, declared: 'No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded' · outcome: failed | controls[2] | 0.95 | the tagger's words |
| concepts | 2019-nCoV also in: 2019-nCoV | concepts[0] | 0.95 | the paper's words |
| concepts | SARS-CoV-2 also in: SARS-CoV-2 | concepts[1] | 0.95 | the paper's words |
| concepts | COVID-19 also in: COVID-19 | concepts[2] | 0.95 | the paper's words |
| concepts | SARSr-CoV also in: SARSr-CoV | concepts[3] | 0.95 | the paper's words |
| concepts | SARSr-CoVs also in: SARSr-CoVs | concepts[4] | 0.95 | the paper's words |
| concepts | RaTG13 also in: RaTG13 | concepts[5] | 0.95 | the paper's words |
| concepts | ACE2 also in: ACE2 | concepts[6] | 0.95 | the paper's words |
| concepts | natural reservoir host also in: natural reservoir host | concepts[7] | 0.95 | the paper's words |
| concepts | bats also in: bats | concepts[8] | 0.95 | the paper's words |
| concepts | potential to infect humans also in: potential to infect humans | concepts[9] | 0.95 | the paper's words |
| concepts | epidemic of acute respiratory syndrome | concepts[10] | 0.95 | the paper's words |
| concepts | laboratory-confirmed infections also in: laboratory-confirmed infections | concepts[11] | 0.95 | the paper's words |
| concepts | full-length genome sequences also in: full-length genome sequences | concepts[12] | 0.95 | the paper's words |
| concepts | 79.6% sequence identity also in: 79.6% sequence identity | concepts[13] | 0.95 | the paper's words |
| concepts | 96% identical at the whole-genome level | concepts[14] | 0.95 | the paper's words |
| concepts | bronchoalveolar lavage fluid also in: bronchoalveolar lavage fluid | concepts[15] | 0.95 | the paper's words |
| concepts | neutralized by sera also in: neutralized by sera | concepts[16] | 0.95 | the paper's words |
| concepts | cell entry receptor also in: cell entry receptor | concepts[17] | 0.95 | the paper's words |
| concepts | unidentified pneumonia disease outbreak | concepts[18] | 0.95 | the paper's words |
| concepts | local seafood market also in: local seafood market | concepts[19] | 0.95 | the paper's words |
| concepts | fever also in: fever | concepts[20] | 0.95 | the paper's words |
| concepts | dry cough also in: dry cough | concepts[21] | 0.95 | the paper's words |
| concepts | breathing difficulties (dyspnoea) also in: breathing difficulties (dyspnoea) | concepts[22] | 0.95 | the paper's words |
| concepts | progressive respiratory failure also in: progressive respiratory failure | concepts[23] | 0.95 | the paper's words |
| concepts | alveolar damage also in: alveolar damage | concepts[24] | 0.95 | the paper's words |
| concepts | virus-induced pneumonia also in: virus-induced pneumonia | concepts[25] | 0.95 | the paper's words |
| concepts | new pulmonary infiltrates also in: new pulmonary infiltrates | concepts[26] | 0.95 | the paper's words |
| concepts | treatment with antibiotics for three days | concepts[27] | 0.95 | the paper's words |
| concepts | human-to-human contact also in: human-to-human contact | concepts[28] | 0.95 | the paper's words |
| concepts | pan-CoV PCR primers also in: pan-CoV PCR primers | concepts[29] | 0.95 | the paper's words |
| concepts | causative pathogen also in: causative pathogen | concepts[30] | 0.95 | the paper's words |
| concepts | PCR-positive for CoVs also in: PCR-positive for CoVs | concepts[31] | 0.95 | the paper's words |
| concepts | metagenomics analysis also in: metagenomics analysis | concepts[32] | 0.95 | the paper's words |
| concepts | next-generation sequencing also in: next-generation sequencing | concepts[33] | 0.95 | the paper's words |
| concepts | potential aetiological agents also in: potential aetiological agents | concepts[34] | 0.95 | the paper's words |
| concepts | human genome also in: human genome | concepts[35] | 0.95 | the paper's words |
| concepts | de novo assembly also in: de novo assembly | concepts[36] | 0.95 | the paper's words |
| concepts | 29,891-base-pair CoV genome also in: 29,891-base-pair CoV genome | concepts[37] | 0.95 | the paper's words |
| concepts | GISAID also in: GISAID | concepts[38] | 0.95 | the paper's words |
| concepts | novel coronavirus 2019 also in: novel coronavirus 2019 | concepts[39] | 0.95 | the paper's words |
| concepts | more than 99.9% identical to each other | concepts[40] | 0.95 | the paper's words |
| concepts | virus genome also in: virus genome | concepts[41] | 0.95 | the paper's words |
| concepts | six major open-reading frames (ORFs) also in: six major open-reading frames (ORFs) | concepts[42] | 0.95 | the paper's words |
| concepts | accessory genes also in: accessory genes | concepts[43] | 0.95 | the paper's words |
| concepts | seven conserved replicase domains also in: seven conserved replicase domains | concepts[44] | 0.95 | the paper's words |
| concepts | CoV species classification also in: CoV species classification | concepts[45] | 0.95 | the paper's words |
| concepts | 94.4% identical also in: 94.4% identical | concepts[46] | 0.95 | the paper's words |
| concepts | same species, SARSr-CoV also in: same species, SARSr-CoV | concepts[47] | 0.95 | the paper's words |
| concepts | RNA-dependent RNA polymerase (RdRp) also in: RNA-dependent RNA polymerase (RdRp) | concepts[48] | 0.95 | the paper's words |
| concepts | Rhinolophus affinis also in: Rhinolophus affinis | concepts[49] | 0.95 | the paper's words |
| concepts | full-length sequencing also in: full-length sequencing | concepts[50] | 0.95 | the paper's words |
| concepts | Simplot analysis also in: Simplot analysis | concepts[51] | 0.95 | the paper's words |
| concepts | overall genome sequence identity of 96.2% | concepts[52] | 0.95 | the paper's words |
| concepts | recombination events also in: recombination events | concepts[53] | 0.95 | the paper's words |
| concepts | Phylogenetic analysis also in: Phylogenetic analysis | concepts[54] | 0.95 | the paper's words |
| concepts | closest relative also in: closest relative | concepts[55] | 0.95 | the paper's words |
| concepts | distinct lineage also in: distinct lineage | concepts[56] | 0.95 | the paper's words |
| concepts | receptor-binding spike protein also in: receptor-binding spike protein | concepts[57] | 0.95 | the paper's words |
| concepts | receptor-binding motif also in: receptor-binding motif | concepts[58] | 0.95 | the paper's words |
| concepts | three short insertions also in: three short insertions | concepts[59] | 0.95 | the paper's words |
| concepts | N-terminal domain also in: N-terminal domain | concepts[60] | 0.95 | the paper's words |
| concepts | sialic-acid-binding activity also in: sialic-acid-binding activity | concepts[61] | 0.95 | the paper's words |
| concepts | qPCR-based detection method also in: qPCR-based detection method | concepts[62] | 0.95 | the paper's words |
| concepts | receptor-binding domain of the S gene | concepts[63] | 0.95 | the paper's words |
| concepts | all other human coronaviruses also in: all other human coronaviruses | concepts[64] | 0.95 | the paper's words |
| concepts | oral swab samples also in: oral swab samples | concepts[65] | 0.95 | the paper's words |
| concepts | routine detection also in: routine detection | concepts[66] | 0.95 | the paper's words |
| concepts | airborne transmission also in: airborne transmission | concepts[67] | 0.95 | the paper's words |
| concepts | other possible routes of transmission | concepts[68] | 0.95 | the paper's words |
| concepts | nucleocapsid (N) protein also in: nucleocapsid (N) protein | concepts[69] | 0.95 | the paper's words |
| concepts | enzyme-linked immunosorbent assays (ELISAs) | concepts[70] | 0.95 | the paper's words |
| concepts | cross-reactivity also in: cross-reactivity | concepts[71] | 0.95 | the paper's words |
| concepts | viral antibody levels also in: viral antibody levels | concepts[72] | 0.95 | the paper's words |
| concepts | IgG and IgM titres also in: IgG and IgM titres | concepts[73] | 0.95 | the paper's words |
| concepts | acute infection also in: acute infection | concepts[74] | 0.95 | the paper's words |
| concepts | Vero E6 also in: Vero E6 | concepts[75] | 0.95 | the paper's words |
| concepts | Huh7 cells also in: Huh7 cells | concepts[76] | 0.95 | the paper's words |
| concepts | cytopathogenic effects also in: cytopathogenic effects | concepts[77] | 0.95 | the paper's words |
| concepts | immunofluorescence microscopy also in: immunofluorescence microscopy | concepts[78] | 0.95 | the paper's words |
| concepts | viral load also in: viral load | concepts[79] | 0.95 | the paper's words |
| concepts | typical coronavirus morphology also in: typical coronavirus morphology | concepts[80] | 0.95 | the paper's words |
| concepts | electron microscopy also in: electron microscopy | concepts[81] | 0.95 | the paper's words |
| concepts | serum-neutralization assays also in: serum-neutralization assays | concepts[82] | 0.95 | the paper's words |
| concepts | viral IgG-positive samples also in: viral IgG-positive samples | concepts[83] | 0.95 | the paper's words |
| concepts | 50% tissue-culture-infective dose also in: 50% tissue-culture-infective dose | concepts[84] | 0.95 | the paper's words |
| concepts | horse anti-SARS-CoV serum also in: horse anti-SARS-CoV serum | concepts[85] | 0.95 | the paper's words |
| concepts | virus infectivity studies also in: virus infectivity studies | concepts[86] | 0.95 | the paper's words |
| concepts | HeLa cells also in: HeLa cells | concepts[87] | 0.95 | the paper's words |
| concepts | mouse ACE2 also in: mouse ACE2 | concepts[88] | 0.95 | the paper's words |
| concepts | entry receptor also in: entry receptor | concepts[89] | 0.95 | the paper's words |
| concepts | other coronavirus receptors also in: other coronavirus receptors | concepts[90] | 0.95 | the paper's words |
| concepts | aminopeptidase N (APN) also in: aminopeptidase N (APN) | concepts[91] | 0.95 | the paper's words |
| concepts | dipeptidyl peptidase 4 (DPP4) also in: dipeptidyl peptidase 4 (DPP4) | concepts[92] | 0.95 | the paper's words |
| concepts | likely aetiological agent also in: likely aetiological agent | concepts[93] | 0.95 | the paper's words |
| concepts | viral-protein seroconversion also in: viral-protein seroconversion | concepts[94] | 0.95 | the paper's words |
| concepts | Koch’s postulates also in: Koch’s postulates | concepts[95] | 0.95 | the paper's words |
| concepts | causative relationship also in: causative relationship | concepts[96] | 0.95 | the paper's words |
| concepts | transmission routine also in: transmission routine | concepts[97] | 0.95 | the paper's words |
| concepts | more transmissible between humans also in: more transmissible between humans | concepts[98] | 0.95 | the paper's words |
| concepts | specific treatments also in: specific treatments | concepts[99] | 0.95 | the paper's words |
| concepts | active surveillance also in: active surveillance | concepts[100] | 0.95 | the paper's words |
| concepts | broad-spectrum antiviral drugs and vaccines | concepts[101] | 0.95 | the paper's words |
| concepts | strict regulations also in: strict regulations | concepts[102] | 0.95 | the paper's words |
| concepts | sample size also in: sample size | concepts[103] | 0.95 | the paper's words |
| concepts | randomized also in: randomized | concepts[104] | 0.95 | the paper's words |
| concepts | blinded to allocation also in: blinded to allocation | concepts[105] | 0.95 | the paper's words |
| concepts | oral swabs also in: oral swabs | concepts[106] | 0.95 | the paper's words |
| concepts | anal swabs also in: anal swabs | concepts[107] | 0.95 | the paper's words |
| concepts | blood also in: blood | concepts[108] | 0.95 | the paper's words |
| concepts | viral transport medium also in: viral transport medium | concepts[109] | 0.95 | the paper's words |
| concepts | multiplicity of infection (MOI) of 0.5 | concepts[110] | 0.95 | the paper's words |
| concepts | ultrathin sections also in: ultrathin sections | concepts[111] | 0.95 | the paper's words |
| concepts | virus neutralization test also in: virus neutralization test | concepts[112] | 0.95 | the paper's words |
| concepts | healthy individuals also in: healthy individuals | concepts[113] | 0.95 | the paper's words |
| concepts | triplicate also in: triplicate | concepts[114] | 0.95 | the paper's words |
| concepts | High-throughput sequencing also in: High-throughput sequencing | concepts[115] | 0.95 | the paper's words |
| concepts | Cutadapt also in: Cutadapt | concepts[116] | 0.95 | the paper's words |
| concepts | host genomes also in: host genomes | concepts[117] | 0.95 | the paper's words |
| concepts | MEGAHIT also in: MEGAHIT | concepts[118] | 0.95 | the paper's words |
| concepts | Sanger sequencing also in: Sanger sequencing | concepts[119] | 0.95 | the paper's words |
| concepts | MAFFT also in: MAFFT | concepts[120] | 0.95 | the paper's words |
| concepts | PAL2NAL also in: PAL2NAL | concepts[121] | 0.95 | the paper's words |
| concepts | maximum likelihood phylogenetic trees | concepts[122] | 0.95 | the paper's words |
| concepts | GTR+G substitution model also in: GTR+G substitution model | concepts[123] | 0.95 | the paper's words |
| concepts | 1,000 bootstrap replicates also in: 1,000 bootstrap replicates | concepts[124] | 0.95 | the paper's words |
| concepts | cell receptor for SARS-CoV also in: cell receptor for SARS-CoV | concepts[125] | 0.95 | the paper's words |
| concepts | SARS-related coronaviruses (SARSr-CoVs) | concepts[126] | 0.95 | the paper's words |
| concepts | these samples also in: these samples | concepts[127] | 0.95 | the paper's words |
| concepts | full-length genome sequences of 2019-nCoV | concepts[128] | 0.95 | the paper's words |
| concepts | closest relative of 2019-nCoV also in: closest relative of 2019-nCoV | concepts[129] | 0.95 | the paper's words |
| concepts | close phylogenetic relationship to RaTG13 | concepts[130] | 0.95 | the paper's words |
| concepts | originated in bats also in: originated in bats | concepts[131] | 0.95 | the paper's words |
| concepts | sequence of the receptor-binding domain of the S gene | concepts[132] | 0.95 | the paper's words |
| concepts | five patient sera also in: five patient sera | concepts[133] | 0.95 | the paper's words |
| concepts | ACE2 proteins also in: ACE2 proteins | concepts[134] | 0.95 | the paper's words |
| concepts | association between the disease and the presence of this virus | concepts[135] | 0.95 | the paper's words |
| concepts | association between 2019-nCoV and the disease | concepts[136] | 0.95 | the paper's words |
| concepts | animal experiments also in: animal experiments | concepts[137] | 0.95 | the paper's words |
| concepts | future research also in: future research | concepts[138] | 0.95 | the paper's words |
| unhoused_relations | 2019-nCoV → same species, SARSr-CoV The conserved-domain comparison suggests that 2019-nCoV belongs to the same species, SARSr-CoV; the gate does not admit 'belongs to' as an is-a cue. | unhoused_relations[0] | 0.95 | the tagger's words |
| unhoused_relations | ACE2 → cell receptor for SARS-CoV ACE2 is known to be a cell receptor for SARS-CoV; the intervening 'known to be' wording is outside the gate's is-a cue vocabulary. | unhoused_relations[1] | 0.95 | the tagger's words |
| unhoused_relations | SARS-related coronaviruses (SARSr-CoVs) → bats Bats are identified as the natural reservoir host of SARS-related coronaviruses; reservoir-host-of is absent from the eight types. — the relation stated: Abstract. Abstract Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1 – 4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5 – 7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV | unhoused_relations[2] | 0.95 | the tagger's words |
| unhoused_relations | pan-CoV PCR primers → these samples The broad coronavirus primers were used to test the seven severe-pneumonia samples; used-to-test is absent from the governed types. | unhoused_relations[3] | 0.95 | the tagger's words |
| unhoused_relations | metagenomics analysis → potential aetiological agents Metagenomic next-generation sequencing was used to identify candidate aetiological agents; used-for is absent from the governed types. | unhoused_relations[4] | 0.95 | the tagger's words |
| unhoused_relations | full-length genome sequences of 2019-nCoV → more than 99.9% identical to each other Four additional patient genomes were more than 99.9% identical to one another; similarity-at is absent from the governed types. | unhoused_relations[5] | 0.95 | the tagger's words |
| unhoused_relations | RaTG13 → closest relative of 2019-nCoV Every reported phylogeny places RaTG13 as the closest sampled relative of 2019-nCoV; closest-relative-of is absent from the eight types. | unhoused_relations[6] | 0.95 | the tagger's words |
| unhoused_relations | close phylogenetic relationship to RaTG13 → originated in bats The close phylogenetic relationship is presented as evidence for a possible bat origin; supports-origin-inference is absent and the conclusion is hedged. | unhoused_relations[7] | 0.95 | the tagger's words |
| unhoused_relations | qPCR-based detection method → sequence of the receptor-binding domain of the S gene The qPCR detection method is based on the S-gene receptor-binding-domain sequence; based-on is absent from the governed types. | unhoused_relations[8] | 0.95 | the tagger's words |
| unhoused_relations | five patient sera → 2019-nCoV All five IgG-positive patient sera neutralized the virus in the cell assay; neutralizes is absent from the governed types. | unhoused_relations[9] | 0.95 | the tagger's words |
| unhoused_relations | 2019-nCoV → ACE2 proteins The virus used the tested ACE2 proteins except mouse ACE2 as entry receptors; uses-receptor is absent from the governed types. | unhoused_relations[10] | 0.95 | the tagger's words |
| unhoused_relations | viral-protein seroconversion → association between the disease and the presence of this virus Seroconversion and virus-specific nucleotide positivity support an association between disease and virus presence; supports-association is absent. | unhoused_relations[11] | 0.95 | the tagger's words |
| unhoused_relations | association between 2019-nCoV and the disease → animal experiments The association had not been verified by animal experiments to fulfil Koch's postulates; verification-by is absent and the paper states the limitation explicitly. | unhoused_relations[12] | 0.95 | the tagger's words |
| unhoused_relations | future research → active surveillance The authors recommend that future research focus on active surveillance over broader regions; recommended-focus-on is absent from the governed types. | unhoused_relations[13] | 0.95 | the tagger's words |
| senses | `2019-nCoV` - THE NAME THIS PAPER USES THROUGHOUT, AND IT WAS DEAD BEFORE PUBLICATION. `Following the name given by the WHO, we TENTATIVELY call it ...`, and then the note in proof: `the ICTV has designated the virus as SARS-CoV-2`. The record's own subject terms say SARS-CoV-2 while its text says 2019-nCoV | senses[0] | 0.95 | the tagger's words |
| senses | `the same species` - AS OPERATIONALISED HERE, 94.4% amino-acid identity across SEVEN CONSERVED REPLICASE DOMAINS, `that were used for CoV species classification`. The whole-genome figure in the same abstract is 79.6%. THE SPECIES IS A PROPERTY OF THE REGION YOU ALIGN | senses[1] | 0.95 | the tagger's words |
| senses | `87.1%` - a percentage of 1,582 reads, which are what remained of 10,038,758 after human sequence was filtered out. The denominator of the headline proportion is the SURVIVORS OF A FILTER, not the sample | senses[2] | 0.95 | the tagger's words |
| senses | the disease, BEFORE ANY VIRUS: defined by `clinical symptoms and other criteria, including a rise in body temperature, decreases in the number of lymphocytes and white blood cells ..., new pulmonary infiltrates on chest radiography and no obvious improvement after treatment with antibiotics for three days`. A definition partly by failure of a treatment | senses[3] | 0.95 | the tagger's words |
| senses | Pathogen identification - the study combines pan-coronavirus PCR, metagenomic reads, assembly and full-length patient genomes to identify the outbreak virus | senses[4] | 0.95 | the tagger's words |
| senses | Species versus nearest relative - conserved replicase domains support SARSr-CoV species membership, while whole-genome phylogeny identifies RaTG13 as the closest sampled relative | senses[5] | 0.95 | the tagger's words |
| senses | Bat-origin inference - the paper treats the close RaTG13 phylogenetic relationship as evidence for, not proof of, origin in bats | senses[6] | 0.95 | the tagger's words |
| senses | Diagnostic aperture - an S-gene RBD qPCR assay separates the virus from tested human coronaviruses, but the authors recommend additional RdRp or envelope targets for routine detection | senses[7] | 0.95 | the tagger's words |
| senses | Transmission uncertainty - airborne transmission is proposed while other routes remain possible and more patients are required | senses[8] | 0.95 | the tagger's words |
| senses | Serological trajectory - IgG and IgM generally rise over serial samples, with a late IgM decrease and incomplete serum availability | senses[9] | 0.95 | the tagger's words |
| senses | Receptor specificity - 2019-nCoV enters cells expressing several ACE2 orthologues except mouse ACE2, and does not use APN or DPP4 in this assay | senses[10] | 0.95 | the tagger's words |
| senses | Causal boundary - patient nucleotide and seroconversion evidence establishes association, but no animal experiment had fulfilled Koch's postulates | senses[11] | 0.95 | the tagger's words |
| senses | Design boundary - sample size was not statistically predetermined and experiments were neither randomized nor allocation-blinded | senses[12] | 0.95 | the tagger's words |
| senses | Response horizon - the paper moves from immediate surveillance and possible SARS-directed treatments to broad-spectrum countermeasures and wildlife regulation | senses[13] | 0.95 | the tagger's words |
| claim_relations | supports → the standing expectation that a SARS-related coronavirus from bats could cause a future outbreak - stated in the paper's own opening as what 'has generally been thought' | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | extends → the SARS-CoV literature, by showing the new virus uses the same cell entry receptor | claim_relations[1] | 0.95 | the tagger's words |
| concept_edges | 2019-nCoV —distinct-from→ SARSr-CoVs also in: 2019-nCoV · SARSr-CoVs | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | 2019-nCoV —causes→ epidemic of acute respiratory syndrome direction on the measure: increases · the relation itself is separately evidenced · strength of the relation: 1 · note: The abstract directly says the newly characterized coronavirus caused the human epidemic. also in: 2019-nCoV · epidemic of acute respiratory syndrome | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | alveolar damage —causes→ progressive respiratory failure direction on the measure: increases · the relation itself is separately evidenced · strength of the relation: 0.6 — the record marks this weak · note: Weight preserves the paper's 'may result' qualification. also in: alveolar damage · progressive respiratory failure | concept_edges[2] | 0.95 | the tagger's words |
| concept_edges | six major open-reading frames (ORFs) —part-of→ virus genome the relation itself is separately evidenced · strength of the relation: 1 · note: The genome is explicitly said to consist of these ORFs and accessory genes. also in: six major open-reading frames (ORFs) · virus genome | concept_edges[3] | 0.95 | the tagger's words |
| concept_edges | 2019-nCoV —distinct-from→ all other human coronaviruses differs in: amplification by the study's S-gene qPCR primers · the relation itself is separately evidenced · strength of the relation: 1 · differs in (stated by the tagger, no quotation): amplification by the study's S-gene qPCR primers · note: The primer test is reported to differentiate 2019-nCoV from the other human coronaviruses tested. also in: 2019-nCoV · all other human coronaviruses | concept_edges[4] | 0.95 | the tagger's words |
| content_tags | THE VIRUS WAS RENAMED BETWEEN ACCEPTANCE AND PUBLICATION, AND THE PAPER RECORDS IT: `Note added in proof: Since this paper was accepted, the ICTV has designated the virus as SARS-CoV-2; ... the WHO has released the official name of the disease ... COVID-19` | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | and the name used in the body was itself provisional and borrowed: `FOLLOWING THE NAME GIVEN BY THE WHO, WE TENTATIVELY CALL IT novel coronavirus 2019` | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | THE SPECIES ASSIGNMENT IS A THRESHOLD ON A CHOSEN REGION: 94.4% identity across the seven replicase domains `that were used for CoV species classification`, against 79.6% whole-genome identity to SARS-CoV in the same abstract | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | the identification rests on 1,378 reads: `of the 10,038,758 total reads - of which 1,582 total reads were retained after filtering of reads from the human genome - 1,378 (87.1%) sequences matched`. THE 87.1% IS OF THE SURVIVORS | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | 96.2% whole-genome identity to the bat coronavirus RaTG13, which is the closest relative in every tree, the two forming a lineage distinct from other SARSr-CoVs | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | the spike protein is the divergent part - under 75% nucleotide identity to all previously described SARSr-CoVs, except 93.1% to RaTG13 | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | THE VIRUS USES THE SAME CELL ENTRY RECEPTOR AS SARS-CoV - ACE2 - which is the finding that made the paper immediately actionable | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | the disease was defined CLINICALLY before any virus was named, partly by A FAILURE OF TREATMENT: `no obvious improvement after treatment with antibiotics for three days` | content_tags.findings[7] | 0.95 | the tagger's words |
| content_tags | and the design is declared to have no statistical structure: no predetermined sample size, no randomisation, no blinding | content_tags.findings[8] | 0.95 | the tagger's words |
| content_tags | percent whole-genome sequence identity to SARS-CoV - the figure that does NOT decide the species | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | percent identity across the seven replicase domains - the figure that DOES | content_tags.quantities[1] | 0.95 | the tagger's words |
| content_tags | reads retained from 10,038,758 after human sequence was filtered out | content_tags.quantities[2] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.