In vitro and animal work had been performed beneath applicable biosafety situations in a BSL-3 facility on the Institut für Virologie, Freie Universität Berlin, Germany. All animal experiments had been carried out in compliance with related institutional, nationwide and worldwide pointers for the care and humane use of animals and accredited by the competent state authority, Landesamt für Gesundheit und Soziales, Berlin, Germany (allow quantity 0086/20).
Vero E6 (obtained from ATCC, CRL-1586), Vero E6-TMPRSS2 (obtained from the Nationwide Institute for Organic Requirements and Management (NIBSC), 100978) and Calu-3 (obtained from ATCC, HTB-55) cells had been cultured in minimal important medium (MEM) containing 10% fetal bovine serum, 100 IU ml−1 penicillin G and 100 µg ml−1 streptomycin at 37 °C and 5% CO2. As well as, the cell tradition medium for Vero E6-TMPRSS2 cells contained 1,000 µg ml−1 geneticin (G418) to make sure choice for cells expressing the genes for neomycin resistance and TMPRSS2.
The modified live-attenuated SARS-CoV-2 mutant sCPD9 and SARS-CoV-2 variants B.1 (BetaCoV/Munich/ChVir984/2020; B.1, EPI_ISL_406862), Beta (B.1.351; hCoV-19/Netherlands/NoordHolland_20159/2021) and Delta (B.1.617.2; SARS-CoV-2, Human, 2021, Germany ex India, 20A/452R (B.1.617)) had been propagated on Vero E6-TMPRSS2 cells. Omicron BA.1 (B.1.1.529.1; hCoV-19/Germany/BE-ChVir26335/2021, EPI_ISL_7019047) was propagated on CaLu-3 cells. All virus shares had been entire genome sequenced earlier than an infection experiments to substantiate genetic integrity within the majority of the inhabitants, particularly on the furin cleavage web site. Earlier than experimental an infection, virus shares had been saved at −80 °C.
9- to 11-week-old Syrian hamsters (Mesocricetus auratus; breed RjHan:AURA) had been bought from Janvier Labs and had been housed in teams of two to three animals in individually ventilated cages. The hamsters had free entry to meals and water. They had been allowed to get used to the housing situations for 7 d earlier than vaccination. For each experiments, the cage temperatures had been maintained at a relentless vary of twenty-two to 24 °C with a relative humidity between 40 and 55%.
Vaccination and an infection experiments
For an infection experiments, Syrian hamsters had been randomly assigned to teams, with 50–60% of the animals in every group being feminine. Within the first experiment, 15 hamsters had been mock-vaccinated or vaccinated with live-attenuated sCPD9 virus, Ad2-spike or mRNA. Vaccination with sCPD9 was utilized by intranasal instillation beneath anaesthesia (1 × 105 focus-forming models (f.f.u.), 60 µl)53. Ad2-spike (5 × 108 infectious models, 200 μl) and mRNA vaccine (5 μg mRNA, 100 μl) had been utilized intramuscularly. Mock-vaccinated hamsters had been vaccinated by intranasal instillation with sterile cell tradition supernatant obtained from uninfected Vero E6-TMPRSS2 cells. At 21 d after vaccination, hamsters had been challenge-infected with SARS-CoV-2 Delta variant (1 × 105 plaque-forming models (p.f.u.), 60 µl) by intranasal instillation beneath anaesthesia. Within the second experiment, 10 hamsters had been both mock-vaccinated or vaccinated with one of many three vaccines (see above) adopted by a booster vaccination 21 d later. At 14 d after booster vaccination, the hamsters had been challenged as described above.
To find out onward transmission of problem virus in vaccinated people, we vaccinated 3 animals per group in a prime-boost routine. To this finish, hamsters obtained both 1 × 104 f.f.u. sCPD9delFCS in 60 µl MEM intranasally, 5 μg BNT162b2 mRNA in 100 μl regular saline (0.9% NaCl in sterile water) intramuscularly or 60 µl plain MEM intranasally (mock). Vaccination was boosted utilizing the identical vaccines for every respective group 21 d after preliminary vaccination.
Vaccinated hamsters had been challenge-infected with 1 × 105 p.f.u. SARS-CoV-2 variant B.1 as described above. At 24 h after an infection, contaminated vaccinated hamsters had been introduced into contact with naïve animals and co-habitated to observe transmission for six consecutive days. Every day oral swabs had been obtained from every animal to observe virus shedding and transmission.
sCPD9 was grown on Vero E6-TMRSS2 cells and titrated on Vero E6 cells as described beforehand; last titres had been adjusted to 2 × 106 f.f.u. ml−1 in MEM. Recombinant Ad2-spike was generated, produced on 293T cells and purified as beforehand described23. BNT162b2 was obtained as a industrial product (Comirnaty) and dealt with precisely as advisable by the producer, besides that the ultimate focus of mRNA was adjusted to 50 µg ml−1 (100 µg ml−1 is the advisable focus to be used in people) by including injection-grade saline (0.9% NaCl in sterile water) instantly earlier than use.
To extend genetic stability of the sCPD9 assemble, the furin cleavage web site (FCS) of the spike protein was deleted to create sCPD9delFCS. This FCS-deleted vaccine virus was solely used for the transmission examine of this paper (Prolonged Information Fig. 5). Importantly, all vaccines used on this examine comprise the identical SARS-CoV-2 spike antigen derived from the ancestral B.1 (Wuhan) sequence.
sCPD9 was administered intranasally beneath basic anaesthesia (0.15 mg kg−1 medetomidine, 2.0 mg kg−1 midazolam and a couple of.5 mg kg−1 butorphanol) at a dose of 1 × 105 f.f.u. per animal in a complete quantity of 60 µl MEM. For transmission experiments (Prolonged Information Fig. 5), 1 × 104 f.f.u. sCPD9delFCS was utilized in the identical approach. Ad2-spike was injected intramuscularly at 5 × 108 infectious models in 200 µl injection buffer (3 mM KCl, 1 mM MgCl2, 10% glycerol in PBS). BNT162b2 was injected intramuscularly at a dose of 5 µg mRNA per animal in 100 µl physiological saline (0.9% NaCl in sterile water).
Nasal washes had been obtained from every hamster on this examine. To this finish, the cranium of every animal was cut up barely paramedian, such that the nasal septum remained intact on one aspect of the nostril. Subsequently, a 200 µl pipette tip was fastidiously slid beneath the nasal septum and 150 µl wash fluid (PBS with 30 µg ml−1 ofloxacin and 10 µg ml−1 voriconazole) was utilized. The wash was collected by the nostril and the washing process was repeated twice; roughly 100 µl of pattern was recovered after the third wash.
Nasal washes obtained from the prime-only vaccination trial had been subjected to enzyme-linked immunosorbent assay (ELISA) evaluation of SARS-CoV-2 spike-specific IgA antibodies. Nasal washes obtained from the prime-boost vaccination trial had been used for microneutralization assay to evaluate their capability to neutralize the SARS-CoV-2 ancestral variant B1.
For quantification of replication-competent virus, 50 mg of lung tissue had been used. Serial 10-fold dilutions had been ready after homogenizing the organ samples in a bead mill (Analytic Jena). The dilutions had been plated on Vero E6 cells grown in 24-well plates and incubated for two.5 h at 37 °C. Subsequently, cells had been overlaid with MEM containing 1.5% carboxymethylcellulose sodium (Sigma Aldrich) and glued with 4% formaldehyde resolution 72 h after an infection. To rely the plaque-forming models, plates had been stained with 0.75% methylene blue.
Histopathology, immunohistochemistry and in situ hybridization
Lungs had been processed as beforehand described53. After cautious elimination of the left lung lobe, tissue was fastened in PBS-buffered 4% formaldehyde resolution (pH 7.0) for 48 h. For conchae preparation, elements of the left cranium half had been fastened accordingly. Afterwards, lungs or conchae had been gently faraway from the nasal cavity and embedded in paraffin, minimize at 2 µm thickness and stained with hematoxylin and eosin (H&E). In situ hybridization on lungs was carried out as beforehand described54 utilizing the ViewRNA ISH Tissue Assay equipment (Invitrogen by Thermo Fisher) based on the producer’s directions, with minor changes. For SARS-CoV-2 RNA localization, probes detecting N gene sequences (NCBI database NC_045512.2, nucleotides 28,274–29,533, assay ID: VPNKRHM) had been used. Sequence-specific binding was managed through the use of a probe for detection of pneumolysin. Immunohistochemistry on conchae was carried out as described earlier55 (particulars in Supplementary Strategies).
Blinded microscopic evaluation was carried out by a board-certified veterinary pathologist (J.B.).
SARS-specific Ig measurement by ELISA from serum and nasal washes
An in-house ELISA was carried out to analyze SARS-specific IgG ranges in serum and SARS-specific IgA ranges in nasal washes after vaccination (particulars in Supplementary Strategies).
Neutralization assays from nasal washes
To evaluate the capability of nasal washes obtained from the prime-boost vaccination trial to neutralize genuine SARS-CoV-2 (B.1), nasal washes had been diluted 1:1 in 2× MEM containing 50 µg ml−1 enrofloxacin and 10 µg ml−1 voriconazole. Subsequent serial dilutions had been carried out in MEM containing 25 mg ml−1 enrofloxacin, 5 µg ml−1 voriconazole and 1% FBS. SARS-CoV-2 (50 p.f.u.) had been added to the nasal wash dilutions and dilutions from 1:2 to 1:256 had been plated on near-confluent Vero E6 cells seeded in 96-well cell tradition plates. At 3 d after inoculation, cells had been fastened and stained with methylene blue. To determine virus-neutralizing dilutions, the integrity of the cell monolayer was assessed by comparability with management wells that contained both no nasal wash or no virus. The final dilution with no proof of virus-induced cytopathic impact was thought-about the neutralizing titre for the respective pattern.
Serum neutralization assay
Serum samples had been examined for his or her means to neutralize totally different SARS-CoV-2 variants. Day 0 samples of the prime-boost trial couldn’t be examined for neutralizing antibodies in opposition to B.1.351 (Beta) on account of lack of fabric. Sera had been inactivated at 56 °C for 30 min. Twofold serial dilutions (1:8 to 1:1,024) had been plated on 96-well plates and 200 p.f.u. SARS-CoV-2 had been pipetted into every nicely. After an incubation time of 1 h at 37 °C, the dilutions had been transferred to 96-well plates containing sub-confluent Vero E6 cells and incubated for 72 h at 37 °C (B.1, Beta, Delta) or for 96 h at 37 °C (Omicron). The plates had been fastened with 4% formaldehyde resolution and stained with 0.75% methylene blue. Wells that confirmed no cytopathic impact had been thought-about neutralized.
IFN-γ ELISpot evaluation
Hamster IFN-γ ELISpot evaluation was carried out as described beforehand56. Briefly, the hamster IFN-γ ELISpotBASIC equipment (MABTECH) was used to detect IFN-γ secretion by 5 × 105 remoted splenocytes, every in co-culture with totally different stimuli. Medium-treated splenocytes served as unfavorable management and recombinant ovalbumin (10 mg ml−1) was used as unfavorable protein management stimulus. Normal stimulation of T cells was achieved utilizing 5 μg ml−1 concanavalin A (ConA, Sigma Aldrich). Recombinant SARS-CoV-2 (2019-nCoV) spike protein (S1 + S2 ECD, His tag; 10 mg ml−1; Sino Organic Europe) or 10 mg ml−1 recombinant SARS-CoV-2 (2019-nCoV) nucleocapsid protein (N) (Sino Organic Europe) had been used to re-stimulate SARS-CoV-2-specific T cells. Spots had been counted utilizing an Eli.Scan ELISpot scanner (AE.L.VIS) and the evaluation software program ELI.Analyse v5.0 (AE.L.VIS).
RNA extraction and qPCR
To quantify genomic copies in oropharyngeal swabs and 25 mg homogenized lung tissue, RNA was extracted utilizing innuPREP Virus DNA/RNA equipment (Analytic Jena) based on the producer’s directions. qPCR was carried out utilizing the NEB Luna Common Probe One-Step RT–qPCR equipment (New England Biolabs) with biking situations of 10 min at 55 °C for reverse transcription, 3 min at 94 °C for activation of the enzyme, and 40 cycles of 15 s at 94 °C and 30 s at 58 °C on a qTower G3 cycler (Analytic Jena) in sealed qPCR 96-well plates. Primers and probes had been used as beforehand reported57. Oligonucleotides (Sequence (5’-3’)): E_Sarbeco_F: ACAGGTACGTTAATAGTTAATAGCGT;
Mesocricetus auratus genome annotation
For quantification of gene expression, we used the MesAur 2.0 genome meeting and annotation obtainable by way of the NCBI genome database (https://www.ncbi.nlm.nih.gov/genome/11998?genome_assembly_id=1585474). The GFF file was transformed to GTF utilizing gffread 0.12.758. The place no overlaps had been produced, 3’-UTRs within the annotation had been prolonged by 1,000 bp as described beforehand59. Additional sharpening steps for the GTF file are described on the GitHub web page accompanying this paper (https://github.com/Berlin-Hamster-Single-Cell-Consortium/Dwell-attenuated-vaccine-strategy-confers-superior-mucosal-and-systemic-immunity-to-SARS-CoV-2). The ultimate gtf file used for the evaluation is on the market by GEO (https://www.ncbi.nlm.nih.gov/geo/question/acc.cgi?acc=GSE200596).
Bulk RNA extraction
To carry out RNA bulk sequencing, RNA was remoted from lung tissue utilizing Trizol reagent based on the producer’s directions (Ambion, Life Applied sciences). Briefly, 1 ml Trizol was added to the homogenized organ pattern and vortexed completely. After an incubation time of 20 min, 200 µl of chloroform had been added. The samples had been vortexed once more and incubated for 10 min at room temperature. Subsequently, tubes had been centrifuged at 12,000 × g for 15 min at 4 °C and 500 µl of the aqueous part had been transferred into a brand new tube containing 10 µg GlycoBlue. Isopropanol (500 µl) was added, adopted by vortexing, incubating and centrifuging the samples as described above. Thereafter, isopropanol was eliminated and 1 ml of ethanol (75%) was utilized. The tubes had been inverted shortly and centrifuged at 8,000 × g for 10 min. After releasing the pellet from ethanol, RNA was resuspended in 30 µl of RNase-free water and saved at −80 °C.
Cell isolation from blood and lungs
White blood cells had been remoted from EDTA-blood as beforehand described; steps included pink blood cell lysis and cell filtration earlier than counting. Lung cells (caudal lobe) had been remoted as beforehand described26,60; steps included enzymatic digestion, mechanical dissociation and filtration earlier than counting in trypan blue. Buffers contained 2 µg ml−1 actinomycin D to forestall de novo transcription throughout the procedures.
Cell isolation from nasal cavities
To acquire single-cell suspensions from the nasal mucosa of SARS-CoV-2-challenged hamsters, the cranium of every animal was cut up barely paramedian in order that the nasal septum remained intact on the left aspect of the nostril. The appropriate aspect of the nostril was fastidiously faraway from the skull and saved in ice-cold 1× PBS with 1% BSA and a couple of µg ml−1 actinomycin D till additional use. Nostril elements had been transferred into 5 ml Corning Dispase resolution supplemented with 750 U ml−1 Collagenase CLS II and 1 mg ml−1 DNase, and incubated at 37 °C for 15 min. For preparation of cells from the nasal mucosa, the conchae had been fastidiously faraway from the nasal cavity and re-incubated in digestion medium for 20 min at 37 °C. Conchae tissue was dissociated by pipetting and urgent by a 70 µm filter with a plunger. Ice-cold PBS with 1% BSA and a couple of µg ml−1 actinomycin D was added to cease the enzymatic digestion. The cell suspension was centrifuged at 400 × g at 4 °C for 15 min and the supernatant discarded. The pelleted nasal cells had been resuspended in 5 ml pink blood cell lysis buffer and incubated at room temperature for two min. Lysis response was stopped with 1× PBS with 0.04% BSA and cells centrifuged at 400 × g at 4 °C for 10 min. Pelleted cells had been resuspended in 1× PBS with 0.04% BSA and 40 µm-filtered. Dwell cells had been counted in trypan blue and viability charges decided utilizing a counting chamber. Cell focus for scRNA-seq was adjusted by dilution.
Single-cell RNA sequencing
Remoted cells from blood, lungs and nasal cavities of Syrian hamsters had been subjected to scRNA-seq utilizing the ten× Genomics Chromium Single Cell 3’ Gene Expression system with characteristic barcoding know-how for cell multiplexing (particulars in Supplementary Strategies).
Evaluation of single-cell RNA sequencing knowledge
Sequencing reads had been initially processed utilizing bcl2fastq 2.20.0 and the multi command of the Cell Ranger 6.0.2 software program. For the cellplex demultiplexing, the task thresholds had been partially adjusted (for particulars, see the GitHub web page at https://github.com/Berlin-Hamster-Single-Cell-Consortium/Dwell-attenuated-vaccine-strategy-confers-superior-mucosal-and-systemic-immunity-to-SARS-CoV-2). Additional processing was accomplished in R 4.0.4 Seurat R 4.0.6 bundle61, in addition to R packages ggplot2 3.3.5, dplyr 1.0.7, DESeq2 1.30.1, lme4 1.1–27.1 and dependencies, and in Python 3.9.13 in addition to Python packages scanpy 1.9.1, scvelo 0.2.4 and dependencies. Within the subsequent step, cells had been filtered by a unfastened high quality threshold (minimal of 250 detected genes per cell) and clustered. Cell sorts had been then annotated per cluster and filtered utilizing cell type-specific thresholds (cells beneath the median or within the lowest quartile inside a cell sort had been eliminated). The remaining cells had been processed utilizing the SCT/combine workflow62 and cell sorts once more annotated on the ensuing Seurat object. All code for downstream evaluation is on the market on GitHub at https://github.com/Berlin-Hamster-Single-Cell-Consortium/Dwell-attenuated-vaccine-strategy-confers-superior-mucosal-and-systemic-immunity-to-SARS-CoV-2.
Statistics and reproducibility
Particulars on statistical evaluation of sequencing knowledge together with pre-processing steps are described within the particular person Strategies part. Analyses of virological, histopathological, ELISA, cell frequencies and cell quantity statistics had been carried out with GraphPad Prism 9. Statistical particulars are offered in respective determine legends. No statistical technique was used to predetermine pattern dimension. Information distribution was assumed to be regular however this was not formally examined. No knowledge had been excluded from the analyses. All experiments involving reside animals had been randomized, different experiments weren’t randomized. The investigators had been blinded to allocation of hamsters throughout animal experiments and first consequence evaluation (scientific improvement, virus titrations, qPCR, ELISpot, serology and histopathology). Investigators weren’t blinded to allocation in different experiments and analyses.
Additional info on analysis design is on the market within the Nature Portfolio Reporting Abstract linked to this text.