Journal: Cell

Article Title: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

doi: 10.1016/j.cell.2021.12.027

Figure Lengend Snippet: Epidemiology of the COVID-19 Provincetown outbreak and overview of the dataset (A) SARS-CoV-2 genomes in this dataset by collection date. (B) Distribution of all cases in Barnstable County (gray bars) and estimate of reproductive number ( R t ) (red line) over the course of the outbreak. (C) Flow diagram of sample sets presented here. Gray shading indicates sample sets reported and analyzed in this study. (D) Cycle threshold (Ct) value of the N1 gene for the 313 individuals known to be fully vaccinated by BNT162b2, mRNA-1273, or AD26.CoV2.S; includes linear regression with 95% confidence interval. All Ct values were collected using the same platform and assay. See also Figure S1 .

Article Snippet: Illumina sequencing libraries were prepared using the NEBNext ARTIC v3 SARS-CoV-2 FS Library Prep Kit.

Techniques:

Journal: Cell

Article Title: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

doi: 10.1016/j.cell.2021.12.027

Figure Lengend Snippet: Genomic epidemiology and limited onward impact of the Provincetown outbreak (A) Time tree of SARS-CoV-2 outbreak-associated genomes (blue dots) in the global context. Inset, frequencies of Pango lineages among outbreak-associated genomes. An interactive version of this tree is available at: https://auspice.broadinstitute.org/sars-cov-2/ma-delta/20211005/cluster-unique-usher . (B) Percentage of all Delta-lineage genomes from MA detected by baseline genomic surveillance with the mutational signature of the dominant outbreak cluster (red line). Percentages are calculated and shown per day based on sample collection date. Dashed line: cumulative new cases in MA over the same period (available at: https://www.mass.gov/info-details/covid-19-response-reporting ). (C) Numbers of genomes (left) and percentage of Delta-lineage genomes (right) per state that are estimated to descend from the largest cluster in the Provincetown outbreak. Barplots show lower-bound (solid) and upper-bound (faded) estimates, calculated as described in STAR Methods. Note that the scale of the x axis in the plot on the right is in percentages, with a maximum of 1%. See also and ; .

Article Snippet: Illumina sequencing libraries were prepared using the NEBNext ARTIC v3 SARS-CoV-2 FS Library Prep Kit.

Techniques:

Journal: Cell

Article Title: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

doi: 10.1016/j.cell.2021.12.027

Figure Lengend Snippet: Outbreak introductions and onward spread, related to (A) Left: time tree of outbreak-associated SARS-CoV-2 genomes in a global context colored by association with the Provincetown outbreak (as in A). Right: each introduction into Provincetown as inferred from the phylogenetic tree based on a change in ancestral inference of a branch to “outbreak-associated.” Gray dots represent the most recent common ancestor of the clade that was inferred to be from outside of Provincetown. All outbreak-associated samples downstream of each node are shown in the full phylogenetic tree. (B) The percentage of all Delta-lineage baseline surveillance genomes from MA with the mutational signature of the five Delta-lineage clusters among outbreak-associated cases. Three mutations (C8752T, C20451T, and A26759G) are shared by the majority of all outbreak-associated genomes, referred to as the dominant cluster. The remaining four clusters were defined by their characteristic mutations, with cluster 2 defined by G4124A and A5608G; cluster 3 by T7858C and A29257C; cluster 4 by T23131C; and cluster 5 by A26759G, C20451T, C7600T, and T27940C. Percentages per day based on sample collection date and new cumulative cases in MA were plotted over time from July 3rd to August 31st, 2021.

Article Snippet: Illumina sequencing libraries were prepared using the NEBNext ARTIC v3 SARS-CoV-2 FS Library Prep Kit.

Techniques:

Journal: Cell

Article Title: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

doi: 10.1016/j.cell.2021.12.027

Figure Lengend Snippet: Genomic support for transmission links and transmission predictions by vaccination status and symptoms, related to Figure 3 (A) Maximum-likelihood phylogenetic tree of the only high-confidence transmission pair from contact tracing without strong statistical support in outbreaker2 transmission reconstruction. This pair was in a cluster of six identical consensus genomes with very similar collection dates. No symptom onset date was known for either of the individuals in the pair. Even when incorporating contact tracing information into the model, another sample was predicted as almost equally likely to have been the ancestor of this case. (B) Maximum-likelihood phylogeny of the large cluster of cases associated with a single index case in a close-contact setting. Cases from this epidemiological cluster are colored in dark red. (A) and (B) are part of a larger phylogenetic tree available at https://auspice.broadinstitute.org/sars-cov-2/ma-delta/20211005/cluster-unique-usher . (C) Gray bars, fractions, and 90% confidence intervals indicate the proportion of individuals that were the origin of at least one transmission event predicted by outbreaker2 with a probability of >70%. Individuals are separated by vaccination status (left), days from final vaccination date to collection date (middle), or presence or absence of symptoms in vaccinated individuals (right). 90% binomial confidence intervals were calculated using the exact method through the binom package in R. Using simulations incorporating outbreaker2’s confidence in putative transmission links, we calculate that an infected unvaccinated individual was 0.18–2.11 times as likely to transmit as an infected vaccinated individual. Among fully vaccinated individuals, an infected asymptomatic individual was 0–0.99 times as likely to transmit as an infected symptomatic individual. Our estimates of relative risk are predicated on outbreaker2 correctly estimating the probability that it has chosen the correct index case of each putative transmission.

Article Snippet: Illumina sequencing libraries were prepared using the NEBNext ARTIC v3 SARS-CoV-2 FS Library Prep Kit.

Techniques: Transmission Assay, Infection

Journal: Cell

Article Title: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

doi: 10.1016/j.cell.2021.12.027

Figure Lengend Snippet:

Article Snippet: Illumina sequencing libraries were prepared using the NEBNext ARTIC v3 SARS-CoV-2 FS Library Prep Kit.

Techniques: Isolation, Quantitative RT-PCR, Diagnostic Assay, RNA Sequencing Assay, Software

Journal: Frontiers in Immunology

Article Title: Heterologous booster with a novel formulation containing glycosylated trimeric S protein is effective against Omicron

doi: 10.3389/fimmu.2023.1271209

Figure Lengend Snippet: Specific ancestral Spike (SW) IgG and IgG isotypes levels induced by homologous and heterologous vaccination schedule. (A) K18-hACE2 mice (n =7/group) were immunized on Days 0 and 14 with commercial vaccines mRNA1273 or AZD1222 plus a booster with formulations containing purified spike protein from ancestral (SW) or Delta (SD) SARS-CoV-2 variant on Day 60 delivered intramuscularly. (B) SW specific IgG levels induced by 2 dose primary series. Serum collected on Days 14 and 45 after the second dose was analyzed by ELISA. (C) SW specific IgG, (D) IgG1 and (E) IgG2c levels induced by 3-dose homologous and heterologous schemes. Sera from immunized and non-immunized were collected 14 Days after the 3 rd dose and analyzed by ELISA. Serum antibody levels are expressed as EC50 ± SD for each group. For statistical analysis, antibody levels were analyzed by a one-way ANOVA with Bonferroni’s multiple comparisons test. The * symbol indicate significant differences among immunized: ****p<0.0001, *** p<0.001, *p<0.05. The # symbol indicate significant differences between non-immunized and immunized animals: #### p <0,0001.

Article Snippet: RT-qPCR detection of SARS-CoV-2 was performed using kit LightMix® Modular SARS-CoV-2 (COVID19) E-gene, LightMix® Modular SARS-CoV (COVID19) RdRp (TIB MOLBIOL), and RNAsa P following the protocol developed by Dr. Corman et al. from the Institute of Virology, Charité, Berlin, Germany, by the World Health Organization ( https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf ) on a real time thermal cycler CFX96 (Biorad).

Techniques: Vaccines, Purification, Variant Assay, Enzyme-linked Immunosorbent Assay

Journal: Frontiers in Immunology

Article Title: Heterologous booster with a novel formulation containing glycosylated trimeric S protein is effective against Omicron

doi: 10.3389/fimmu.2023.1271209

Figure Lengend Snippet: Homologus and heterologous immunization induces Ag-specific Th1 (IFN-γ)/Th17 (IL-17)/Th2 (IL-5). (A) K18-hACE2 mice (n =7/group) were immunized on Days 0 and 14 with commercial vaccines mRNA1273 or AZD1222 plus a booster with formulations containing purified spike protein from ancestral (SW) or Delta (SD) SARS-CoV-2 variant on Day 60 delivered intramuscularly. Mice were challenged 14 days after the 3 rd dose with SARS-CoV-2 Omicron BA.1 variant, 5 days after challenge mice were sacrificed and spleens were harvested. Levels of secreted IFN-γ (B) , IL-17 (C) and IL-5 (D) following splenocytes stimulation with medium or recombinant spike protein from W o D variants were determined by ELISA. Bars are means ± SEM of pg/ml. The * symbol indicate significant differences among immunized: ***p<0.001, **p<0.01, *p<0.05. The # symbol indicate significant differences between non-immunized and immunized animals: ####p<0.0001, ###p<0.001, ##p<0.01, #p<0.05.

Article Snippet: RT-qPCR detection of SARS-CoV-2 was performed using kit LightMix® Modular SARS-CoV-2 (COVID19) E-gene, LightMix® Modular SARS-CoV (COVID19) RdRp (TIB MOLBIOL), and RNAsa P following the protocol developed by Dr. Corman et al. from the Institute of Virology, Charité, Berlin, Germany, by the World Health Organization ( https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf ) on a real time thermal cycler CFX96 (Biorad).

Techniques: Vaccines, Purification, Variant Assay, Recombinant, Enzyme-linked Immunosorbent Assay

Journal: Frontiers in Immunology

Article Title: Heterologous booster with a novel formulation containing glycosylated trimeric S protein is effective against Omicron

doi: 10.3389/fimmu.2023.1271209

Figure Lengend Snippet: Protection assay against Omicron BA.1 SARS-CoV-2 infection in the intranasal challenge mouse model. (A) K18-hACE2 mice (n =7/group) were immunized on Days 0 and 14 with commercial vaccines mRNA1273 or AZD1222 plus a booster with formulations containing purified spike protein from ancestral (SW) or Delta (SD) SARS-CoV-2 variant on Day 60 delivered intramuscularly. Mice were challenged 14 days after the 3 rd dose with SARS-CoV-2 Omicron BA.1 variant, 5 days after challenge mice were sacrificed and nasal washes and lungs were collected. (B, E) Changes in body weight were expressed as the percentage of body weight in comparison to day 0 (mean ± SEM.). Post-challenge weights were zoomed in for each treatment in the right part of the graph. (C, F) nasal and (D, G) lungs SARS-CoV-2 viral load after Omicron BA.1 challenge in animals vaccinated with schedules that contain mRNA-1273 (C, D) or AZD1222 (F, G) . Results are expressed as Log number Rdrp copies/ml nasal wash or as Log number Rdrp copies/mg lungs. One-way or Two-way ANOVA followed by Bonferroni post-test, were used for statistical analysis. ****p < 0.0001, ***p<0.001, **p < 0.01, *p<0.05.

Article Snippet: RT-qPCR detection of SARS-CoV-2 was performed using kit LightMix® Modular SARS-CoV-2 (COVID19) E-gene, LightMix® Modular SARS-CoV (COVID19) RdRp (TIB MOLBIOL), and RNAsa P following the protocol developed by Dr. Corman et al. from the Institute of Virology, Charité, Berlin, Germany, by the World Health Organization ( https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf ) on a real time thermal cycler CFX96 (Biorad).

Techniques: Infection, Vaccines, Purification, Variant Assay, Comparison

Journal: Frontiers in Immunology

Article Title: Heterologous booster with a novel formulation containing glycosylated trimeric S protein is effective against Omicron

doi: 10.3389/fimmu.2023.1271209

Figure Lengend Snippet: Pathology score in lungs and brains for non-immunized and immunized animals. K18-hACE2 mice (n = 7/group) were immunized on Days 0 and 14 with commercial vaccines mRNA1273 or AZD1222, along with a booster containing purified spike protein from ancestral (SW) or Delta (SD) variants of SARS-CoV-2 on Day 60, administered intramuscularly. Fourteen days after the third dose, mice were challenged with the Omicron BA.1 variant of SARS-CoV-2. Five days after the challenge, mice were euthanized, and their lungs and brains were collected. An experienced pathologist performed blinded assessments of the lesions detected in the lungs (A) and brains (B) using a scale ranging from 0 to 3 (where 0 indicates no lesion, 1 mild, 2 moderate, and 3 severe). The data obtained are expressed as the percentage of animals that exhibited each degree of lesion.

Article Snippet: RT-qPCR detection of SARS-CoV-2 was performed using kit LightMix® Modular SARS-CoV-2 (COVID19) E-gene, LightMix® Modular SARS-CoV (COVID19) RdRp (TIB MOLBIOL), and RNAsa P following the protocol developed by Dr. Corman et al. from the Institute of Virology, Charité, Berlin, Germany, by the World Health Organization ( https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf ) on a real time thermal cycler CFX96 (Biorad).

Techniques: Vaccines, Purification, Variant Assay