Alpha and Delta variant shedding profiles in oral swabs and air samples.

Syrian hamsters were inoculated with 103 TCID50 via the intranasal route with Alpha or Delta. A. Comparison of swab viral load and virus shedding into the air. Inferred profile of air shedding in PFU/h compared to sgRNA levels and infectious virus titers (TCID50/mL) in oropharyngeal swabs collected 1, 2, 3, 4, 5, and 7 DPI. Semitransparent lines are 100 random draws from the inferred posterior distribution of hamster within-host kinetics for each of the metrics. Joined points are individual measured timeseries for experimentally infected hamsters; each set of joined points is one individual. Measurements and inferences shown grouped by variant and animal sex. Measurement points are randomly jittered slightly along the x (time) axis to avoid overplotting. B. Viral sgRNA and infectious virus (PFU) recovered from cage air sample filters over a 24 h period starting at 0, 1, 2, 3, 4, and 5 DPI. Points are measured values, normalized by the number of hamsters in the cage (2 or 3) to give per-capita values. Downward-pointing arrows represent virus below the limit of detection (0 observed plaques or estimated copy number corresponding to Ct ≥ 40). Semitransparent lines are posterior predictions for the sample that would have been collected if sampling started at that timepoint; these reflect the inferred underlying concentrations of sgRNA and infectious virus in the cage air at each timepoint and are calculated from the inferred infection kinetics for each of the hamsters housed within the cage. 100 random posterior draws shown for each cage. Cages housed 2 or 3 hamsters; all hamsters within a cage were of the same sex and infected with the same variant. Column titles show cage number and variant, with number of and sex of individuals in parentheses. Dotted lines limit of detection. Grey = Alpha, teal = Delta, p-values are indicated where significant. Abbreviations: sg, subgenomic; TCID, Tissue Culture Infectious Dose; PFU, plaque forming unit; F, female; M, male; DPI, days post inoculation.

Lung function and breathing changes after SARS-CoV-2 infection with Alpha and Delta.

Syrian hamsters were inoculated with 103 TCID50 via the intranasal route with Alpha or Delta. A. Lung function was assessed on day −1, 0, 1, 2, 3, 4, and 5 by whole body plethysmography. Principal component analysis was used to investigate individual variance. Depicted are principal component (PC) 1 and 2 for each day, showing individual animals (colors refer to legend on right, sex-separated) and clusters (black ellipses). B. Individual loading plots for contributions of top 6 variables to PC1 and 2 at each day. C. Relevant subset of lung function parameters. Line graphs depicting median and 95% CI fold change values (left) and area under the curve (AUC, right), Kruskal-Wallis test, p-values indicated where significant. Grey = Alpha, teal = Delta, beige = anesthesia control, light = male, dark = female. Abbreviations: Expiratory time (Te), inspiratory time (Ti), percentage of breath occupied by the transition from inspiration to expiration (TB), end expiratory pause (EEP), breathing frequency (f), peak inspiratory flow (PIFb), peak expiratory flow (PEFb), tidal volume (TVb), minute volume (MVb), enhanced pause (Penh), male (M), female (F).

Aerodynamic particle analysis of SARS-CoV-2 infected hamsters.

A. Syrian hamsters were inoculated with 103 TCID50 via the intranasal route with Alpha or Delta. Aerodynamic diameter profile of exhaled particles was analyzed on day 0, 1, 3, and 5. Heatmap shows rounded median percent of total particles across groups, including the anesthesia control group (N = 10, comprising 5 males and 5 females). Colors refer to scale below. B. For each animal, line graphs of the percent of particles in the <0.53 and 1-10 µm diameter range by variant group and sex indicated by color. Multiple linear regression performed for each diameter range with group and sex as predictors, F-statistic (3,26) = 9.47 for <0.53 µm model and F-statistic (3,26) = 2.62 for 1-10 µm model, with Tukey multiple comparison adjustment for the three variant-group comparisons (95% family-wise confidence level). For <0.53 range, Male-Female (estimate = −1.7, standard error = 0.888, two-sided p = 0.0659); Alpha-Control (estimate = 2.41, standard error = 1.09, two-sided p = 0.0874), Delta-Control (estimate = 5.40, standard error = 1.09, two-sided p = 0.0001), Delta-Alpha (estimate = 2.99, standard error = 1.09, two-sided p = 0.0280). For 1-10 range, Male-Female (estimate = 2.19, standard error = 1.23, two-sided p = 0.0875); Alpha-Control (estimate = −0.633, standard error = 1.51, two-sided p = 0.9079), Delta-Control (estimate = −3.098, standard error = 1.51, two-sided p = 0.1197), Delta-Alpha (estimate = −2.465, standard error = 1.51, two-sided p = 0.2498). Grey = Alpha, teal = Delta, beige = anesthesia control, red = female, blue = male.

Airborne attack rate of Alpha and Delta SARS-CoV-2 variants.

Donor animals (N = 7) were inoculated with either the Alpha or Delta variant with 103 TCID50 via the intranasal route and paired together randomly (1:1 ratio) in 7 attack rate scenarios (A-G). To each pair of donors, one day after inoculation, 4-5 sentinels were exposed for a duration of 4 h (i.e., h 24-28 post inoculation) in an aerosol transmission set-up at 200 cm distance. A. Schematic figure of the transmission set-up. B. Day 1 sgRNA detected in oral swabs taken from each donor after exposure ended. Individuals are depicted. Wilcoxon test, N = 7. Grey = Alpha, teal = Delta inoculated donors. C. Respiratory shedding measured by viral load in oropharyngeal swabs; measured by sgRNA on day 2, 3, and 5 for each sentinel. Animals are grouped by scenario. Colors refer to legend below. 3.3 = limit of detection of RNA (<10 copies/rxn). D. Schematic representation of majority variant for each sentinel as assessed by percentage of Alpha and Delta detected in oropharyngeal swabs taken at day 2 and day 5 post exposure by deep sequencing. Grey = Alpha, teal = Delta, white = no transmission.

Airborne competitiveness of Alpha and Delta SARS-CoV-2 variants.

A. Schematic. Donor animals (N = 8) were inoculated with Alpha and Delta variant with 5 x 102 TCID50, respectively, via the intranasal route (1:1 ratio), and three groups of sentinels (Sentinels 1, 2, and 3) were exposed subsequently at a 16.5 cm distance. Animals were exposed at a 1:1 ratio; exposure occurred on day 1 (Donors ◊ Sentinels 1) and day 2 (Sentinels ◊ Sentinels). B. Respiratory shedding measured by viral load in oropharyngeal swabs; measured by gRNA, sgRNA, and infectious titers on days 2 and day 5 post exposure. Bar-chart depicting median, 96% CI and individuals, N = 8, ordinary two-way ANOVA followed by Šídák’s multiple comparisons test. C/D/E. Corresponding gRNA, sgRNA, and infectious virus in lungs and nasal turbinates sampled five days post exposure. Bar-chart depicting median, 96% CI and individuals, N = 8, ordinary two-way ANOVA, followed by Šídák’s multiple comparisons test. Dark orange = Donors, light orange = Sentinels 1, grey = Sentinels 2, dark grey = Sentinels 3, p-values indicated where significant. Dotted line = limit of detection. F. Percentage of Alpha and Delta detected in oropharyngeal swabs taken at days 2 and day 5 post exposure for each individual donor and sentinel, determined by deep sequencing. Pie-charts depict individual animals. Grey = Alpha, teal = Delta. G. Lung and nasal turbinate samples collected on day 5 post inoculation/exposure. H. Summary of data of variant composition, violin plots depicting median and quantiles for each chain link (left) and for each set of samples collected (right). Shading indicates majority of variant (grey = Alpha, teal = Delta). I. Correlation plot depicting spearman r for each chain link (right, day 2 swab) and for each set of samples collected across all animals (left). Colors refer to legend on right. Abbreviations: TCID, Tissue Culture Infectious Dose.