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G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication
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#Coronavirus on TikTok: User engagement with misinformation as a potential threat to public health behavior
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Coronavirus prevalence in Brazilian Amazon and Sao Paulo city
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Profiling of linear B-cell epitopes against human coronaviruses in pooled sera sampled early in the COVID-19 pandemic
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PhIP-Seq/VirScan Coronavirus phage display assay in maternal-infant dyads
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F I G U R E 1 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 1 Structural diagrams of spike glycoproteins of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2. All spike proteins of coronaviruses contain S1 subunit and S2 subunit, which were divided by the S cleavage sites. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor‐binding domain, contains core binding motif in the external subdomain; SP, signal peptide
F I G U R E 2 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 2 Phylogenetic analysis of sequences of coronavirus spike glycoproteins. The sequences of spike glycoproteins of SARS‐CoV‐2, bat SARS‐like CoV, pangolin SARS‐like CoV, and SARS‐CoV were analyzed. The red stars indicate pangolin SARS‐like CoV and bat SARS‐like CoV. Host flags are marked after the clusters. SARS‐CoV‐2, severe respiratory syndrome coronavirus‐2
Figure 2 in Bat Coronaviruses in China
Figure 2. Genetic diversity of bat CoV in China. Sequences of 440 bp conserved the viral polymerase (RdRp) region for each CoV species were compared to related reference sequences. Reference genomes used: BtCoV-HKU10, NC_018871.1; BtRfCoV-HuB13, NC_028814.1; BtMiCoV-1, EU420138.1; BtMiCoV-HKU8, NC_010438.1; BtRhCoV-HKU2, MF094682.1; BtHpCoV-ZJ13, NC_025217.1; MERSr-CoV, NC_038294.1; BtPiCoV-HKU5, NC_009020.1; BtTyCoV-HKU4, NC_009019.1; BtRoCoV-GCCDC1, MG762606.1; BtRoCoV-HKU9, NC_009021.1; and SARSr-CoV, NC_004718.3. Notably, samples that were positive for BtMy-Sax11, BtNy-Sc13, and BtScCoV-512 were also identified in China. These were not taken into account here as too few sequences were available.
Figure 1 in Bat Coronaviruses in China
Figure 1. Geographical distribution of bat coronaviruses (CoVs) and their corresponding bat hosts in China. Each red box represents one CoV positive sample found in that particular bat species. One dot matrix was drawn for each province where a CoV positive sample had been reported. Guangdong Province, where SARS and SADS began, is circled in red. Abbreviations of bat species and virus species are indicated.
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Box 4 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Box 4 | Classifying SARS-CoV-2 The species demarcation threshold (also known as demarcation limit) in the family Coronaviridae is defined by viruses whose PPD(s) may cross the inter-species demarcation PPD threshold (threshold 'violators'). Due to their minute share of ~10–4 of the to- tal number of all intra- and inter-species PPDs, these violators may not even be visually recognized in a conventional diagonal plot clus- tering viruses on a species basis (panel a of the figure in Box 4). Furthermore, they do not involve any virus of the species Severe acute respiratory syndrome-related coronavirus, as is evident from the analysis of maximal intraspecies PPDs of 2,505 viruses of all 49 coronavirus species (of which 39 are established and 10 are pending or tentative) (panel b of the figure in Box 4) and PDs of 256 viruses of this species (panel c of the figure in Box 4). Thus, the genomic variation of the known viruses of the species Severe acute respiratory syndrome-related coronavirus is smaller compared to that of other comparably well-sampled species—for example, those prototyped by MERS-CoV, human coronavirus OC43 (HCoV-OC43) and in- fectious bronchitis virus (IBV) (panel b of the figure in Box 4)—and this species is well separated from other known coronavirus species in the sequence space. Both of these characteristics facilitate the un- ambiguous assignment of SARS-CoV-2 to this species. Intra-species PDs of SARS-CoV-2 belong to the top 25% of this species and also include the largest PD between SARS-CoV-2 and an African bat virus isolate (SARSr-CoV_BtKY72)56 (panel c of the figure in Box 4), representing two basal lineages within the species Severe acute respiratory syndrome-related coronavirus that constitute very few known viruses (Fig. 2b,c). These relationships stand in contrast to the shallow branching of the most populous lineage of this species, which includes all the human SARS-CoV isolates collected during the 2002–2003 outbreak and the closely related bat viruses of Asian origin identified in the search for the potential zoonotic source of that epidemic57. This clade structure is susceptible to homologous recombination, which is common in this species44,58,59; to formalize clade definition, it must be revisited after the sampling of viruses representing the deep branches has improved sufficiently. The current sampling defines a very small median PD for human SARS-CoVs, which is approximately 15 times smaller than the median PD determined for SARS-CoV-2 (0.16% versus 2.6%; panel c of the figure in Box 4). This small median PD of human SARS-CoVs also dominates the species- wide PD distribution (0.25%; panel c of the figure in Box 4). Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
Fig. 2 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Fig. 2 | Phylogeny of coronaviruses. a, Concatenated multiple sequence alignments (MSAs) of the protein domain combination44 used for phylogenetic and DEmARC analyses of the family Coronaviridae. Shown are the locations of the replicative domains conserved in the ordert Nidovirales in relation to several other ORF1a/b-encoded domains and other major ORFs in the SARS-CoV genome. 5d, 5 domains: nsp5A-3CLpro, two beta-barrel domains of the 3C-like protease; nsp12-NiRAN, nidovirus RdRp-associated nucleotidyltransferase; nsp12-RdRp, RNA-dependent RNA polymerase; nsp13-HEL1 core, superfamily 1 helicase with upstream Zn-binding domain (nsp13-ZBD); nt, nucleotide. b, The maximum-likelihood tree of SARS-CoV was reconstructed by IQ-TREE v.1.6.1 (ref. 45) using 83 sequences with the best fitting evolutionary model. Subsequently, the tree was purged from the most similar sequences and midpoint-rooted. Branch support was estimated using the Shimodaira–Hasegawa (SH)-like approximate likelihood ratio test with 1,000 replicates. GenBank IDs for all viruses except four are shown; SARS-CoV, AY274119.3; SARS-CoV-2, MN908947.3; SARSr-CoV_BtKY72, KY352407.1; SARS-CoV_PC4-227, AY613950.1. c, Shown is an IQ-TREE maximum-likelihood tree of single virus representatives of thirteen species and five representatives of the species Severe acute respiratory syndrome-related coronavirus of the genus Betacoronavirus. The tree is rooted with HCoV-NL63 and HCoV-229E, representing two species of the genus Alphacoronavirus. Purple text highlights zoonotic viruses with varying pathogenicity in humans; orange text highlights common respiratory viruses that circulate in humans. Asterisks indicate two coronavirus species whose demarcations and names are pending approval from the ICTV and, thus, these names are not italicized.
FIG 3 in Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat
FIG 3 Bayesian phylogenies of clade c betacoronaviruses, including NeoCoV. (A) Phylogenies of ORF1a, ORF1b, and ORFs coding for structural proteins. (B) Phylogenies of the S1 and S2 subunits, corresponding to amino acid positions 1 to 747 and 748 to 1353, respectively, of MERS-CoV strain EMC/2012. NeoCoV is shown in red, camel MERS-CoV is shown in blue, and human MERS-CoV is shown in cyan. HCoV-OC43 was used as an outgroup. (C) Phylogeny of MERS-CoV full genomes. MERS-CoVs obtained from humans are shown in black, and MERS-CoVs from camels are shown in blue. NeoCoV was used for rooting the tree. For all trees, statistical support of grouping from Bayesian posterior probabilities is shown at deep nodes. Only values above 0.7 are shown. The bar represents genetic distance. GenBank accession numbers are KJ477102 for NRCE-HKU205, KJ156881 for Wadi-Ad-Dawasir 1 2013, JX869059 for EMC/2012, KJ650296 for KFU-HKU19D, KC776174 for Jordan- N3/2012, KJ650297 for KFU-HKU1, KJ156910 for Hafr-Al-Batin2 2013, KF600613 for Riyadh 3 2013, KF186567 for Al-Hasa 1 2013, KC164505 for England1, KF961221 for Qatar3, KJ713299 for KSA-CAMEL-376, KJ156949 for Taif1 2013, KJ556336 for Jeddah1 2013, KJ713297 for KSA-CAMEL-503, KJ713295 for KSA-CAMEL-505, KF192507 for Munich 2013, KJ650098 for Qatar 2 2014, KF745068 for FRA/UAE, KF600630 for Buraidah1 2013, KJ650295 for KFU-HKU13, KF600628 for Hafr-Al-Batin1 2013, KJ713298 for KSA-CAMEL-363, KJ713296 for KSA-CAMEL-378, KF600620 for Bisha1 2012, KC869678 for NeoCoV, NC_005147 for HCoV-OC43, EF065512 for HKU5-5, NC_009020 for HKU5-1, NC_008315 for BtCoV/133, NC_009019 for HKU4-1, KC545386 for EriCoV/2012-216, KC545383 for EriCoV/2012- 174, and KM027259 for Jeddah 2014 C9055.
Fig 4 in Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus
Fig 4. Alignment of nucleotide sequences of ORF8 or ORF8a/8b. The start codons and stop codons of ORF8, 8a and 8b are marked with black boxes and the forward and reverse arrows, respectively. The deletion responsible for the split ORF8a and 8b in human SARS-CoV BJ01, Tor2 and bat SARSr-CoV Rs4084 is marked with red boxes. See the legend for Fig 3 for the origin of various sequences used in this alignment. https://doi.org/10.1371/journal.ppat.1006698.g004
Fig 3 in Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus
Fig 3. Amino acid sequence comparison of the S1 subunit (corresponding to aa 1–660 of the spike protein of SARS-CoV). The receptor-binding domain (aa 318–510) of SARS-CoV and the homologous region of bat SARSr-CoVs are indicated by the red box. The key aa residues involved in the interaction with human ACE2 are numbered on top of the aligned sequences. SARS-CoV GZ02, BJ01 and Tor2 were isolated from patients in the early, middle and late phase, respectively, of the SARS outbreak in 2003. SARS-CoV SZ3 was identified from civets in 2003. SARSr-CoV Rs 672 and YN2013 were identified from R. sinicus collected in Guizhou and Yunnan Province, respectively. SARSr-CoV Rf1 and JL2012 were identified from R. ferrumequinum collected in Hubei and Jilin Province, respectively. WIV1, WIV16, RsSHC014, Rs4081, Rs4084, Rs4231, Rs4237, Rs4247, Rs7327 and Rs4874 were identified from R.sinicus, and Rf4092 from R. ferrumequinum in the cave surveyed in this study. https://doi.org/10.1371/journal.ppat.1006698.g003
Fig 5 in Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus
Fig 5. Detection of potential recombination events by similarity plot and boot scan analysis. (A) Fulllength genome sequence of SARSr-CoV WIV16 was used as query sequence and WIV1, Rs4231 and Rs4081 as reference sequences. (B) Full-length genome sequence of SARS-CoV SZ3 was used as query sequence and SARSr-CoV WIV16, Rf4092 and Rs4081 as reference sequences. All analyses were performed with a Kimura model, a window size of 1500 base pairs, and a step size of 150 base pairs. The gene map of query genome sequences are used to position breakpoints. https://doi.org/10.1371/journal.ppat.1006698.g005
Fig. 1 in Identifying SARS-CoV-2related coronaviruses in Malayan pangolins
Fig. 1 | Evolutionary relationships among human SARS-CoV-2,the pangolin coronavirus sequences obtained in this study,and the other reference coronaviruses.(A) Genome organization of coronaviruses including the pangolin coronaviruses,with the predicted ORFs shown in different colors (ORF1a is omitted for clarity).(B) Phylogeny of the subgenus Sarbecovirus (genus Betacoronavirus; n=53) estimated from the concatenated ORF1ab-S-E- M-N genes.Red circles indicate the pangolin coronavirus sequences generated in this study (Extended Data Table 1). Note that GD/P1L is the consensus sequence re-assembled from the raw data previously published7. Phylogenies were estimated using a maximum likelihood approach employing the GTRGAMMA nucleotide substitution model and 1,000 bootstrap replicates.
Coronavirus tweets TEST
<p><strong>limit</strong>: without deleting dublicates and retweets, during parsing were several disconnections (April 7-8)</p> <p><strong>request 1</strong>: coronavirus', 'فايروس كورونا', '新冠', 'коронавирус', 'corona vírus', 'ویروس کرونا', 'kορονοϊός', 'korona vírus'</p> <p><strong>request 2</strong>: cov19', 'covid19', 'covid-19', 'SARS-CoV-2', 'كوفيد-19' ,'سارس', '病毒', '抗疫', '病例', '流行病', 'ков19', 'ковид19','ковид-19', 'کووید۱۹', 'کووید-۱۹'</p>
Network-based Drug Repurposing for Human Coronavirus
<p>Datasets from a study in which network-based methodologies were used to identify potential repurposable drugs and drug combinations for successfully targeting the 2019 novel coronavirus.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.