human coronavirus strain 229e  (ATCC)

Journal: bioRxiv

Article Title: Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

doi: 10.64898/2026.04.17.719293

Figure Lengend Snippet: A) Experimental protocol with sample collection at 24 and 48 hours post infection (hpi) for two duplicate experiments (A and B). For scRNA-seq, this resulted in transcriptomes from 13,913 cells across all samples, including 4,192 mock-infected and 2,724 virus-infected cells at 24 hpi and 3,593 mock-infected and 3,404 virus-infected cells at 48 hpi. B) The viral load across samples after quality control. The median log1p(viral reads) detected in 24 hpi sample A is 7.0 (SD 1.0), in 24 hpi sample B is 7.1 (SD 0.9), and across samples A and B is 7.1 (SD 1.0). The median log1p(viral reads) detected in 48 hpi sample A is 6.6 (SD 1.0), in 48 hpi sample B is 6.4 (SD 1.0), and across samples A and B is 6.5 (SD 1.0). C) Venn diagram representing the number of differentially expressed genes in a cell-level, time-matched 229E-infected versus mock-control differential expression test at a threshold of adjusted p-value < 0.001 and |log ₂ FC| > 2.

Article Snippet: Human coronavirus strain 229E (HCoV-229E) from ATCC ((#VR-740, Lot #70053995) was used for in-house virus batch propagation.

Techniques: Infection, Virus, Control, Quantitative Proteomics

Journal: bioRxiv

Article Title: Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

doi: 10.64898/2026.04.17.719293

Figure Lengend Snippet: A) The median aggregated accessibility profiles centered on the transcription start sites (TSS; ±3kb) for mock and 229E-infected samples at 24 and 48 hpi. The bold lines show median and mean profiles computed over mean profiles across all samples, while lower opacity profiles show variability across replicates. B) The mean aggregated accessibility profiles centered on the transcription start sites (TSS; ±3kb) for mock and 229E-infected samples at 24 and 48 hpi. The bold lines show median and mean profiles computed over mean profiles across all samples, while lower opacity profiles show variability across replicates. C) Principal component analysis (PCA) of accessibility profiles separates mock-control and 229E infected samples at 24 and 48 hpi. Axes indicate the variance explained by each principal component, marker shapes indicate time point, and marker colors indicate infection status. D) Volcano plots of differential accessibility (infected versus mock-control) at 24 (left) and 48 (right) hpi. Each point is an open chromatin region, and blue points indicate significantly increased accessibility, while orange points indicate significantly decreased accessibility. Gray points are not significant. At 24 hpi, 6% of open chromatin regions (OCRs) show increased chromatin accessibility (blue) and 5% show decreased chromatin accessibility (orange). At 48 hpi, 20% of OCRs show increased chromatin accessibility (blue), and 13% show decreased chromatin accessibility (orange).

Article Snippet: Human coronavirus strain 229E (HCoV-229E) from ATCC ((#VR-740, Lot #70053995) was used for in-house virus batch propagation.

Techniques: Infection, Control, Marker

Journal: iScience

Article Title: Broad-spectrum antiviral activity of antisense oligonucleotides targeting GBF1 against SARS-CoV-2 and influenza viruses

doi: 10.1016/j.isci.2026.114851

Figure Lengend Snippet: Identification of host factors involved in SARS-CoV-2 and HCoV-229E replication (A) Schematic overview of the siRNA screening. HEK293 A/T cells were seeded in 24-well plates and transfected twice with siRNAs targeting 91 host genes previously identified as being involved in influenza virus replication. Cells were then infected with SARS-CoV-2 (100 plaque-forming unit [PFU]/100 μL) one day after the second transfection. Supernatants were collected at 2 days post-infection (dpi) and titrated by plaque assay. (B) Results of the SARS-CoV-2 siRNA screen. The 91 host factors were divided into four batches, each including a non-targeting siRNA as a negative control (N) and siRNA targeting SARS-CoV-2 nsp12 as a positive control (P). Viral titers were calculated based on the difference between each siRNA and its corresponding negative control. Each dot represents the mean of duplicate wells from a single independent experiment. Data are presented as the mean ± standard deviation (SD) of at least three independent experiments. (C) The seven host factors identified in the SARS-CoV-2 siRNA screen were further examined in HCoV-229E, along with the negative control siRNA (N) and positive control siRNA (P) targeting the HCoV-229E N gene. Following the same method described in (A), MRC-5 cells were infected with HCoV-229E (50 tissue culture infectious dose (TCID 50 )/100 μL). Supernatants were collected at 3 dpi and titrated by TCID 50 assay. Viral titers were calculated based on the difference between each siRNA and the negative control. Each dot represents the mean of duplicate wells from a single independent experiment. Data are presented as the mean ± SD of three independent experiments. (D) Cell viability was measured in duplicate wells across two independent experiments using CellTiter-Glo following siRNA transfection. See also and .

Article Snippet: HCoV-229E , ATCC , VR-740.

Techniques: Transfection, Virus, Infection, Plaque Assay, Negative Control, Positive Control, Standard Deviation

Journal: bioRxiv

Article Title: On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

doi: 10.64898/2026.01.02.697259

Figure Lengend Snippet: a , Titers of HCoV-229E virions propagated in Huh-7 cells at 33℃ or 37℃. Virus stocks derived from equal volumes of cell culture supernatants were serially diluted and used to infect Huh-7 cells. Statistical significance was determined by Pair t test (** indicates P value < 0.01). b , Schematic overview of sample preparation conditions used to examine temperature- and receptor-dependent conformational dynamics of S on HCoV-229E virions. Virions were subjected to defined temperature treatments (33lJ or 4lJ), fixation protocols, and incubation with or without soluble hAPN. Samples were categorized as apo or hAPN-incubated and as live or fixed, as indicated. The abundances of RBD-closed (light gray), RBD-up (gray), S2-compact (cyan), S2-loose (orange), hAPN-unbound (light steel blue), and hAPN-bound (steel blue) conformations in the viral sample treated with host temperature and receptor (HCoV-229E live -hAPN-33lJ_8h) are depicted in a donut chart. Similar analysis for apo viral samples incubated at different temperatures (4lJ and 33lJ) are also shown. The relative maps and their proportions are annotated.

Article Snippet: The laboratory strain HCoV-229E (ATCC VR740) was obtained from the China Center for Type Culture Collection (CCTCC) and stored at −80 until further use.

Techniques: Virus, Derivative Assay, Cell Culture, Sample Prep, Incubation

Journal: bioRxiv

Article Title: On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

doi: 10.64898/2026.01.02.697259

Figure Lengend Snippet: a , An exemplary tomogram slice (14 Å thickness) shows HCoV-229E live -hAPN33lJ_8h virions in vitreous ice. Scale bar: 100 nm. b , An exemplary virion (boxed in a ) was reconstructed by projecting the RBD-closed, S2-compact S (cyan), the RBD-closed, S2-loose S (orange), and the lipid envelope (gray) onto their refined coordinates. c , STA map and atomic model (cyan) of the RBD-closed, S2-compact S reconstructed from hAPN-unbound S in the HCoV-229E live -hAPN-33lJ_8h dataset. The map is shown in side and bottom views. The model dimensions (length excluding stalk, residues 17-1033; width at S2 subunit base, between residues 1024) are shown. d , STA map of the RBD-closed, S2-loose S from the same dataset, shown in equivalent orientations and rigidly fitted with the recombinant 2P S model (orange, PDB: 6U7H). The same model dimensions as c are shown. e , STA map of the one-RBD-up, S2-compact S reconstructed from apo virions (HCoV-229E live -4lJ_8h). The map is shown in side and top views. This map was rigidly fitted with the composite model built by superimposing the up-RBD component of recombinant S2-loose S-hAPN model (PDB: 8WDE) onto on-virion RBD-closed, S2-compact model with some modifications. f , Left: proportion of RBD-up S among different S2 conformations in the HCoV-229E live -hAPN-33lJ_8h sample. States are classified as RBD-closed state (white), RBD-up states (black). Right: STA maps of hAPN-unbound S exhibiting one-RBD-up state in either the S2-compact or S2-loose conformation from HCoV-229E live -hAPN-33lJ_8h virions. The S2-compact map (one-RBD-up, hAPN unbound) was rigidly fitted with the composite model built by superimposing the up-RBD component of recombinant S2-loose S-hAPN model (PDB: 8WDE) onto on-virion RBD-closed, S2-compact model with some modifications, while the S2-loose map was rigidly fitted with the S component of recombinant S2-loose S-hAPN model (PDB: 8WDE). The HCoV-229E S-trimer is depicted with its three protomers colored cyan, green, and orange (RBD-up).

Article Snippet: The laboratory strain HCoV-229E (ATCC VR740) was obtained from the China Center for Type Culture Collection (CCTCC) and stored at −80 until further use.

Techniques: Recombinant

Journal: bioRxiv

Article Title: On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

doi: 10.64898/2026.01.02.697259

Figure Lengend Snippet: a , Distribution of prefusion S in the S2-compact and S2-loose conformations across HCoV-229E samples subjected to different temperature treatments and fixation protocols, as indicated. Proportion: S2-compact (cyan); S2-loose (yellow). b , Chronological alignment of S2 conformational states across sequential temperature treatments. Four samples collected at different time points in a are indicated by dashed line on the horizontal axis of the broken line graph. The proportions of S adopting the S2-compact (cyan) and S2-loose (orange) conformations are labeled. c , Titers of HCoV-229E virions following temperature treatment. Virions in the left box (HCoV-229E live -33lJ) were amplified and maintained at 33lJ, while virions in the right box (HCoV-229E live -4lJ_12h) were amplified at 33lJ and then cooled at 4lJ for 12 h until the infection experiment. Statistical significance was determined by paired t test (** indicates P value < 0.01).

Article Snippet: The laboratory strain HCoV-229E (ATCC VR740) was obtained from the China Center for Type Culture Collection (CCTCC) and stored at −80 until further use.

Techniques: Labeling, Amplification, Infection

Journal: bioRxiv

Article Title: On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

doi: 10.64898/2026.01.02.697259

Figure Lengend Snippet: a , Quantification of S-hAPN complex formation under different incubation conditions. Pie charts illustrate their proportion of hAPN-unbound/bound states. Proportion: hAPN-unbound (light steel blue) and hAPN-bound (steel blue). b , The atomic structure of soluble hAPN ectodomain dimers. The relative map was determined to 3.75 Å resolution by single-particle analysis. The two protomers are colored pink and blue, respectively. The distance between the N-terminal amino acids of each protomer is indicated by a red dashed line. c , Left: proportion of hAPN-bound S across two S2-conformations in the HCoV-229E live -hAPN-33lJ_8h sample. States are classified as hAPN-unbound state (white) and hAPN-bound state (dark gray). Right: STA maps of hAPN-bound S exhibiting one-RBD-state in either the S2-compact or S2-loose conformation from HCoV-229E live -hAPN-33lJ_8h virions. The S2-compact map (one-RBD-up, hAPN bound) was rigidly fitted with the composite model built by superimposing the up-RBD component of recombinant S2-loose S-hAPN model (PDB: 8WDE) onto the on-virion model with some modifications, while the S2-loose map (one-RBD-up, hAPN bound) was rigidly fitted with recombinant S2-loose S-hAPN model (PDB: 8WDE). The HCoV-229E S-trimer models are depicted with its three protomers colored cyan, green, and orange (RBD-up). The hAPN monomers are colored magenta (bound to S) and white (unbound). d , Left: an exemplary tomogram slice (14 Å thickness) of the 24 h incubated HCoV-229E live -hAPN-33lJ_24h shows Gemini S-hAPN (red circle), where two S are bridged by an hAPN dimer (light blue). Scale bar: 100 nm. Right: STA map of Gemini S-hAPN complex resolved from HCoV-229E live -hAPN-33lJ_24h virions. The map was rigidly fitted with the composite model built by superimposing the recombinant apo hAPN ectodomain model and the up-RBD of recombinant S2-loose S-hAPN model (PDB: 8WDE) onto on-virion RBD-closed, S2-compact model with some modifications. This model is colored as in c . e , Quantification of prefusion and postfusion S on apo and hAPN-incubated HCoV-229E virions under different temperature conditions. Boxplots display the 5% outliers, minimums, first quartiles, medians, third quartiles, and maximums of the data. The average proportions for each condition are annotated.

Article Snippet: The laboratory strain HCoV-229E (ATCC VR740) was obtained from the China Center for Type Culture Collection (CCTCC) and stored at −80 until further use.

Techniques: Incubation, Single Particle, Recombinant

Journal: bioRxiv

Article Title: On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

doi: 10.64898/2026.01.02.697259

Figure Lengend Snippet: S. Proposed model illustrating the coordinated roles of temperature and receptor engagement in regulating conformational transitions of the HCoV-229E S on-virions. At low temperature (4lJ), prefusion S trimers predominantly adopt an RBD-closed, S2-compact conformation. Exposure to physiological temperature (33lJ) gradually shifts the equilibrium toward the S2-loose conformation. In both S2 conformations, S can sample RBD-up states, enabling engagement with hAPN and formation of Solo or Gemini S-hAPN complexes. Receptor binding promotes S1 dissociation and S2 rearrangements, driving membrane fusion and conversion to the postfusion state. This model highlights the synergistic effects of temperature, receptor interaction, and incubation time in governing alphacoronavirus spike activation and viral entry. The RBD-closed, S2-compact model was determined from the on-virion prefusion S of HCoV-229E live -hAPN-33lJ_8h, while the RBD-closed, S2-loose model was from recombinant 2P S model (PDB: 6U7H) and the two S2-loose, one-RBD-up models (hAPN-unbound or hAPN-bound) were from recombinant S2-loose, S-hAPN model (PDB: 8WDE). The two S2-compact, one-RBD-up models (hAPN-unbound or hAPN-bound) were built by superimposing the recombinant apo hAPN ectodomain model and the up-RBD component of recombinant S2-loose, S-hAPN model (PDB: 8WDE) onto on-virion RBD-closed, S2-compact model with some modifications. The postfusion S model was from the homologous SARS-CoV-2 structure (PDB: 8FDW). The HCoV-229E S-trimer models are depicted with three protomers colored cyan, green, and orange. The hAPN monomers are colored magenta when bound to S, and white when unbound.

Article Snippet: The laboratory strain HCoV-229E (ATCC VR740) was obtained from the China Center for Type Culture Collection (CCTCC) and stored at −80 until further use.

Techniques: Binding Assay, Membrane, Incubation, Activation Assay, Recombinant