As of February 2022, mRNA-based vaccine Comirnaty, developed by Pfizer/Biontech, was the leading COVID-19 vaccine by efficacy rate, showing around 95 percent of efficacy against COVID-19. This statistic illustrates the comparison of select COVID-19 vaccines worldwide, by efficacy.

This publication corresponds to the Common Data Model (CDM) specification of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection.” Research Question: “How effective have the SARS-CoV-2 vaccination programmes been in preventing SARS-CoV-2 infections?” Intervention (exposure): COVID-19 vaccine(s) Outcome: SARS-CoV-2 infection Subgroup analysis: Vaccination schedule (type of vaccine) Study Design: An observational retrospective longitudinal study to assess the effectiveness of the SARS-CoV-2 vaccine in preventing SARS-CoV-2 infections using routinely collected social, health and care data from several countries. A causal model was established using Directed Acyclic Graphs (DAGs) to map domain knowledge, theories and assumptions about the causal relationship between exposure and outcome. The DAG developed for the research question of interest is shown below. Cohort definition: All people eligible to be vaccinated (from 5 to 115 years old, included) or with, at least, one dose of a SARS-CoV-2 vaccine (any of the available brands) having or not a previous SARS-CoV-2 infection. Inclusion criteria: All people vaccinated with at least one dose of the COVID-19 vaccine (any available brands) in an area of residence. Any person eligible to be vaccinated (from 5 to 115 years old, included) with a positive diagnosis (irrespective of the type of test) for SARS-CoV-2 infection (COVID-19) during the period of study. Exclusion criteria: People not eligible for the vaccine (from 0 to 4 years old, included) Study period: From the date of the first documented SARS-CoV-2 infection in each country to the most recent date in which data is available at the time of analysis. Roughly from 01-03-2020 to 30-06-2022, depending on the country. Files included in this publication: Causal model (responding to the research question) SARS-CoV-2 vaccine effectiveness causal model v.1.0.0 (HTML) - Interactive report showcasing the structural causal model (DAG) to answer the research question SARS-CoV-2 vaccine effectiveness causal model v.1.0.0 (QMD) - Quarto RMarkdown script to produce the structural causal model Common data model specification (following the causal model) SARS-CoV-2 vaccine effectiveness data model specification (XLXS) - Human-readable version (Excel) SARS-CoV-2 vaccine effectiveness data model specification dataspice (HTML) - Human-readable version (interactive report) SARS-CoV-2 vaccine effectiveness data model specification dataspice (JSON) - Machine-readable version Synthetic dataset (complying with the common data model specifications) SARS-CoV-2 vaccine effectiveness synthetic dataset (CSV) [UTF-8, pipe | separated, N~650,000 registries] SARS-CoV-2 vaccine effectiveness synthetic dataset EDA (HTML) - Interactive report of the exploratory data analysis (EDA) of the synthetic dataset SARS-CoV-2 vaccine effectiveness synthetic dataset EDA (JSON) - Machine-readable version of the exploratory data analysis (EDA) of the synthetic dataset SARS-CoV-2 vaccine effectiveness synthetic dataset generation script (IPYNB) - Jupyter notebook with Python scripting and commenting to generate the synthetic dataset #### Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Common Data Model Specification v.1.1.0 change log #### Updated Causal model to eliminate the consideration of 'vaccination_schedule_cd' as a mediator Adjusted the study period to be consistent with the Study Protocol Updated 'sex_cd' as a required variable Added 'chronic_liver_disease_bl' as a comorbidity at the individual level Updated 'socecon_lvl_cd' at the area level as a recommended variable Added crosswalks for the definition of 'chronic_liver_disease_bl' in a separate sheet Updated the 'vaccination_schedule_cd' reference to the 'Vaccine' node in the updated DAG Updated the description of the 'confirmed_case_dt' and 'previous_infection_dt' variables to clarify the definition and the need for a single registry per person The scripts (software) accompanying the data model specification are offered "as-is" without warranty and disclaiming liability for damages resulting from using it. The software is released under the CC-BY-4.0 licence, which permits you to use the content for almost any purpose (but does not grant you any trademark permissions), so long as you note the license and give credit.

Protection provided by seasonal influenza vaccination (SIV) may be measured against numerous outcomes, and their heterogeneity may hamper decision-making. The aim of this study was to explore outcomes used for estimation of SIV efficacy/effectiveness (VE) and obtain expert consensus on their importance. An umbrella review was first conducted to collect and map outcomes considered in systematic reviews of SIV VE. A Delphi study was then performed to reach expert convergence on the importance of single outcomes, measured on a 9-point Likert scale, in principal target groups, namely children, working-age adults, older adults, subjects with co-morbidities and pregnant women. The literature review identified 489 outcomes. Following data reduction, 20 outcomes were selected for the Delphi process. After two Delphi rounds and a final consensus meeting, convergence was reached. All 20 outcomes were judged to be important or critically important. More severe outcomes, such as influenza-related hospital encounters and mortality with or without laboratory confirmation, were generally top-ranked across all target groups (median scores ≥8 out of 9). Rather than focusing on laboratory-confirmed infection per se, experimental and observational VE studies should include more severe influenza-related outcomes because they are expected to exercise a greater impact on decision-making.

Supplementary Table 2: The frequencies per 100 amino acids for all viral proteins, for all frequently mutated amino acid substitutions, calculated individually for each country. The frequencies for the two groups (labelled ‘Before May’ and ‘After May’) are provided in separate sheets.

Tabulated individual data points for data reported in the associated publication: Spackman E, Suarez DL, Lee CW, Pantin-Jackwood MJ, Lee SA, Youk S, Ibrahim S. Efficacy of inactivated and RNA particle vaccines against a North American Clade 2.3.4.4b H5 highly pathogenic avian influenza virus in chickens. Vaccine. 2023 Nov 30;41(49):7369-7376. doi: 10.1016/j.vaccine.2023.10.070. Epub 2023 Nov 4. PMID: 37932132.Description of methodsVirusesThe highly pathogenic avian influenza virus (HPAIV) isolate A/turkey/Indiana/22-003707-003/2022 H5N1 (TK/IN/22) and A/Gyrfalcon/Washington/41088/2014 H5N8 (GF/WA/14) isolate were each propagated and titrated in embryonating specific pathogen free (SPF) chicken eggs using standard procedures and titers were determined using the Reed-Muench method.VaccinesAn in-house vaccine was produced by de novo synthesizing the HA gene of TK/IN/22 that was modified to be low pathogenic (LP) and placing it in a PR8 backbone using rg methods as described . The vaccine (SEP-22-N9) contained 6 genes from PR8 and a de novo synthesized N9 NA from A/blue winged teal/Wyoming/AH0099021/2016 (H7N9). The rg virus was inactivated by treatment with 0.1% beta-propiolactone. Vaccines were produced with Montanide ISA 71 VG (Seppic Inc., Fairfield, NJ) adjuvant at ambient temperature in a L5M-A high shear mixer (Silverson Machines, Inc., East Longmeadow, MA) for 30sec at 1,000rpm, then for 3min at 4,000rpm using an emulsifying screen in accordance with the adjuvant manufacturer’s instructions.Sham vaccine was prepared in-house using sterile phosphate buffered saline as described above.Commercial vaccines were supplied by the manufacturers. The commercial inactivated vaccine (1057.R1 serial 590088) (rgH5N1) (Zoetis Inc., Parsippany, NJ) was produced with the GF/WA/14 (clade 2.3.4.4c HA gene) and the remaining 7 gene segments including the NA from PR8 (1). The Sequivity vaccine (serial V040122NCF) (RP) (Merck and Co. Inc., Rahway, NJ) is an updated version of their replication restricted alphavirus vector vaccine that expresses the TK/IN/22 H5 HA (modified to be low pathogenic LP).Challenge study designThree-week-old, mixed sex, SPF white leghorn chickens (Gallus gallus domesticus) were obtained from in-house flocks and were randomly assigned to vaccine groups.All vaccines were administered by the subcutaneous route at the nape of the neck. Commercial vaccines were given at the volumes instructed by the manufacturer (0.5ml each). In-house vaccine was given at a dose of 512 hemagglutination units per bird in 0.5ml. Three weeks post vaccination chickens were challenged with 6.7 log10 50% egg infectious doses (EID50) of TK/IN/22 in 0.1ml by the intrachoanal route.Oropharyngeal (OP) and cloacal (CL) swabs were collected from all birds at 2-, 4-, and 7-days post challenge (DPC). Swabs were also collected from dead and euthanized sham vaccinates at 1DPC.To evaluate antibody-based DIVA-VI tests, blood for serum was collected from the RP and SEP-22-N9 vaccinated groups at 7, 10 and 14DPC because the SEP-22-N9 vaccine does not elicit antibodies to N1 and the RP vaccine does not elicit antibodies to the N1 or NP proteins.Mortality and morbidity were recorded for 14DPC after which time the remaining birds were euthanized. If birds were severely lethargic or had neurological signs they were euthanized and were counted as mortality at the next observation time for mean death time calculations.Evaluation of antibody titers based on prime-boost order with the RP and inactivated vaccinesTo determine if there was a difference in antibody levels based on the order of vaccination with the RP vaccine and an inactivated vaccine, groups of 20 chickens (hatch-mates of the chickens in the challenge study) were given one dose of each vaccine three weeks apart (Supplementary Table 1). The first dose was administered at three weeks of age using the RP or SEP-22-N9 vaccine as described above. Then a second dose of either the same vaccine or the other vaccine was administered three weeks later (six weeks of age). All birds were bled for serum three weeks after the second vaccination (nine weeks of age). Antibody was quantified by hemagglutination inhibition (HI) assay as described below using the homologous antigen (TK/IN/22).Quantitative rRT-PCR (qRRT-PCR)RNA was extracted from OP and CL swabs using the MagMax (Thermo Fisher Scientific, Waltham, MA) magnetic bead extraction kit with the modifications described by Das et al., (2). Quantitative real-time RT-PCR was conducted as described previously (3) on a QuantStudio 5 (Thermo Fisher Scientific). A standard curve was generated from a titrated stock of TK/IN/22 and was used to calculate titer equivalents using the real time PCR instrument’s software.Hemagglutination inhibition assayHemagglutination inhibition assays were run in accordance with standard procedures. All pre-challenge sera were tested against the challenge virus. Sera from birds vaccinated with the rgH5N1 vaccine were also tested against the vaccine antigen, GF/WA/14. Titers of 8 or below were considered non-specific binding, therefore negative.Commercial ELISAPre-vaccination sera from 30 chickens were tested to confirm the absence of antibodies to AIV with a commercial AIV antibody ELISA (IDEXX laboratories, Westbrook, ME) in accordance with the manufacturer’s instructions. Pre- and post-challenge sera from the RP vaccine group (the only vaccine utilized here that does not induce antibodies to the NP) were also tested with this ELISA to characterize the detection of anti-NP antibodies post-challenge.Enzyme-linked lectin assay (ELLA) and neuraminidase inhibition (NI) to detect N1 antibody in serum from challenged chickensThe ELLA assay was performed in accordance with a previously published protocol with minor modifications (4). Absorbance data were fit to a non-linear regression curve with Prism 9.5 (GraphPad Software LLC, Boston, MA) to determine the effective concentration, and the 98% effective concentration (EC98) of the N1 source virus was subsequently used for NI assays.To detect N1 antibody with the optimized N1 NA concentrations, serum samples from the sham, SEP-22-N9, and RP vaccinated groups collected pre-challenge, 7, 10 and 14DPC, were heat inactivated at 56°C for one hour and diluted 1:20 and 1:40 using sample dilution buffer. Equal volumes of the N1 NA source virus at a concentration of 2X EC98 was added to each of the diluted serum samples. Then 100µl of the serum-virus mixture was added to the fetuin coated plates after the fetuin plates were washed as described above for the NA assay. Fetuin plates with the serum-virus mixture were then incubated overnight (approximately 17-19hr) at 37°C. The NA assay protocol described above was followed for the remaining NI assay steps.The percent NI activity of individual serum samples was determined by subtracting percent NA activity from 100. To calculate the percent NA activity, the average background absorbance value was subtracted from the sample absorbance value. The result was then divided by the average value of the NA source virus only (no serum) wells then multiplying by 100. A cut-off value for NI activity for positive detection of N1 antibody from chickens post-challenge was calculated by adding three standard deviations to the mean value obtained from pre-challenge sera of corresponding vaccine group for each dilution tested (1:20 and 1:40).References1. Kapczynski DR, Sylte MJ, Killian ML, Torchetti MK, Chrzastek K, Suarez DL. Protection of commercial turkeys following inactivated or recombinant H5 vaccine application against the 2015U.S. H5N2 clade 2.3.4.4 highly pathogenic avian influenza virus. Vet Immunol Immunopathol. 2017;191:74-9. Epub 2017/09/13. doi: 10.1016/j.vetimm.2017.08.001.2. Das A, Spackman E, Pantin-Jackwood MJ, Suarez DL. Removal of real-time reverse transcription polymerase chain reaction (RT-PCR) inhibitors associated with cloacal swab samples and tissues for improved diagnosis of Avian influenza virus by RT-PCR. Journal of Veterinary Diagnostic Investigation. 2009;21(6):771-8.3. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, et al. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. Journal of Clinical Microbiology. 2002;40(9):3256-60.4. Bernard MC, Waldock J, Commandeur S, Strauss L, Trombetta CM, Marchi S, et al. Validation of a Harmonized Enzyme-Linked-Lectin-Assay (ELLA-NI) Based Neuraminidase Inhibition Assay Standard Operating Procedure (SOP) for Quantification of N1 Influenza Antibodies and the Use of a Calibrator to Improve the Reproducibility of the ELLA-NI With Reverse Genetics Viral and Recombinant Neuraminidase Antigens: A FLUCOP Collaborative Study. Front Immunol. 2022;13:909297. Epub 2022/07/06.

Supplementary Table 1b: All frequently mutated amino acid residues that have encountered substitutions in 2% or more of all SARS-CoV-2 isolates, in at least one country, after May (Group A). The frequencies above 2% have been highlighted in ‘red’

Two commercially available vaccines based on the recombinant herpes virus of turkeys (rHVT) vector were tested against a recent North American clade 2.3.4.4b HPAI virus isolate: A/turkey/Indiana/22-003707-003/2022 H5N1 in specific pathogen free white leghorn (WL) chickens and commercial broiler chickens. One rHVT-H5 vaccine encodes a hemagglutinin (HA) gene designed by the computationally optimized broadly reactive antigen method (COBRA-HVT vaccine). The other encodes an HA gene of a clade 2.2 virus (2.2-HVT vaccine). There was 100% survival of both breeds in the COBRA-HVT vaccinated groups and in the 2.2-HVT vaccinated groups there was 94.8% and 90% survival of the WL and broilers respectively. Compared to the 2.2-HVT vaccinated groups, WL in the COBRA-HVT vaccinated group shed significantly lower mean viral titers by the cloacal route and broilers shed significantly lower titers by the oropharyngeal route than broilers. Virus titers detected in oral and cloacal swabs were otherwise similar among both vaccine groups and chicken breeds. To assess antibody-based tests to identify birds that have been infected after vaccination (DIVA-VI), sera collected after the challenge were tested with enzyme-linked lectin assay-neuraminidase inhibition (ELLA-NI) for N1 neuraminidase antibody detection and by commercial ELISA for detection of antibodies to the NP protein. As early as 7 days post challenge (DPC) 100% of the chickens were positive by ELLA-NI. ELISA was less sensitive with a maximum of 75% positive at 10DPC in broilers vaccinated with 2.2-HVT. Both vaccines provided protection from challenge to both breeds of chickens and ELLA-NI was sensitive at identifying antibodies to the challenge virus therefore should be evaluated further for DIVA-VI.MethodsViruses. All procedures using infectious material were reviewed and approved by the Institutional Biosafety Committee of US National Poultry Research Center (USNPRC), US Department of Agriculture-Agricultural Research Service, Athens, GA. The HPAI virus isolate A/turkey/Indiana/22-003707-003/2022 H5N1 (TK/IN/22) was provided by Dr. Mia Torchetti, National Veterinary Services Laboratories, US Department of Agriculture-Animal and Plant Health Inspection Service, Ames, IA. The A/Vietnam/1203/2004 H5N1 HPAI virus (Viet/04), A/Whooper Swan/Mongolia/244/2005 H5N1 (WS/Mongolia/05) HPAI virus, and A/Flycatcher/CA/14875-1/1994 H7N1 low pathogenic avian influenza virus isolates were provided by the repository at the USNPRC. Virus isolates were propagated and titrated in SPF embryonating chicken eggs using standard procedures [1]. Titers were determined using the Reed-Muench method [2].Vaccines. Two commercial rHVT-H5 vaccines were selected because they are licensed in the US (and may be licensed elsewhere) and were supplied by the manufacturers: 2.2-HVT (Vectormune HVT AIV, Ceva Animal Health LLC, Lenexa, KS) (serial 395-134); and COBRA-HVT (Vaxxitek HVT+IBD+H5, Boehringer-Ingelheim Animal Health USA, Ridgefield, CT) (serial EW003). The amino acid similarity between the vaccine antigens and the challenge virus HA1 was 91.7% (COBRA-HVT) and 91.2% (2.2-HVT).Challenge study design. All animal work was reviewed and approved by the USNPRC Institutional Animal Care and Use Committee. Mixed sex, SPF WL chickens (Gallus gallus domesticus) were obtained at hatch from in-house flocks. Broiler chicken eggs were obtained from a commercial hatchery at 18 days of incubation prior to administration of any in ovo vaccines and were hatched on-site. All birds were randomly assigned to vaccine groups based on breed. Vaccine groups are shown in Table 1. All vaccines were prepared and administered on the day of hatch by the subcutaneous route at the nape of the neck in accordance with the manufacturer’s instructions (0.2ml per chicken). Serum was collected from all chickens 25 days post vaccination to evaluate the antibody response to the vaccines.Four weeks post vaccination (four weeks of age) chickens were challenged with a target dose 6.0log10 50% egg infectious doses (EID50) per bird of TK/IN/22 in 0.1ml by the intrachoanal route (titration of the challenge virus after dilution confirmed the challenge dose to be 6.7log10 EID50 per bird). Oropharyngeal and CL swabs were collected from all birds at 2-, 4-, and 7-days post challenge (DPC). Swabs were also collected from dead and euthanized birds.To evaluate antibody-based DIVA-VI tests, serum was collected at 7-, 10- and 14DPC. Mortality and morbidity were recorded for 14DPC. Surviving birds were euthanized at 14DPC. If birds were severely lethargic or presented with neurological signs, they were euthanized and were counted as mortality at the next observation time for mean death time calculations. Euthanasia was performed by cervical dislocation in accordance with American Veterinary Medical Association guidelines.Quantitative rRT-PCR (qRRT-PCR). RNA was extracted from OP and CL swabs using the MagMax magnetic bead extraction kit (Thermo Fisher Scientific, Waltham, MA) with the wash modifications as described by Das et al., [3]. Quantitative real-time RT-PCR was conducted as described previously [4] on a QuantStudio 5 (Thermo Fisher Scientific) instrument. A standard curve was generated from a titrated stock of TK/IN/22 and was used to calculate titer equivalents using the real time PCR instrument’s software.Hemagglutination inhibition assay. Hemagglutination inhibition (HI) assays were run in accordance with standard procedures [5]. All pre-challenge sera collected at 25 days post vaccination were tested against the challenge virus and the closest isolates available to the vaccine antigens. The serum from the 2.2-HVT group was tested against WS/Mongolia/05 (99.3% similarity) and the serum from the COBRA-HVT group was tested against Viet/04 (98.2% similarity). Titers of eight or below were considered negative.Commercial ELISA. A commercial AIV antibody ELISA (AI Ab Test, IDEXX laboratories, Westbrook, ME) was used in accordance with the manufacturer’s instructions. Sera were tested to detect anti-NP antibodies pre-challenge (25days pos-vaccination) and at 7-, 10- and 14DPC.Enzyme-linked lectin assay (ELLA) for detection of neuraminidase inhibition (NI) antibody. The ELLA was performed as previously described with minor modifications [6, 7]. Briefly, the NA activity of a beta-propiolactone inactivated H7N1 virus (A/Flycatcher/CA/14875-1/1994) was quantified to determine the effective concentration (EC) of antigen. The 98% EC (EC98) of antigen was subsequently used for the ELLA-NI assays. For ELLA-NI assay, the antigen and serum mixture was incubated overnight (approximately18hr) at 37°C and the NA activity was determined following the procedure as described in Spackman et al. [7]. The average background absorbance value was subtracted from the sample absorbance value then that value was divided by the average values of wells with only NA antigen. This value was multiplied by a factor of 100 to calculate the percent NA activity. The percent NI activity of individual serum samples was determined by subtracting the percent NA activity from 100%. A cut-off value for positive NI activity was determined by adding three standard deviations to the mean NI activity of pre-challenge sera (i.e., NA antibody negative sera) of each corresponding group of chickens at 7-, 10- and 14DPC. Each serum was tested at dilutions of 1:20 and 1:40.References.1. Spackman E, Killian ML. Avian Influenza Virus Isolation, Propagation, and Titration in Embryonated Chicken Eggs. Methods Mol Biol. 2020;2123:149-64. Epub 2020/03/15.2. Reed LJ, Muench H. A simple method for estimating fifty percent endpoints. American Journal of Hygiene. 1938;27:493-7.3. Das A, Spackman E, Pantin-Jackwood MJ, Suarez DL. Removal of real-time reverse transcription polymerase chain reaction (RT-PCR) inhibitors associated with cloacal swab samples and tissues for improved diagnosis of Avian influenza virus by RT-PCR. Journal of Veterinary Diagnostic Investigation. 2009;21(6):771-8.4. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, et al. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. Journal of Clinical Microbiology. 2002;40(9):3256-60.5. Spackman E, Sitaras I. Hemagglutination Inhibition Assay. Methods Mol Biol. 2020;2123:11-28. Epub 2020/03/15.6. Bernard MC, Waldock J, Commandeur S, Strauss L, Trombetta CM, Marchi S, et al. Validation of a Harmonized Enzyme-Linked-Lectin-Assay (ELLA-NI) Based Neuraminidase Inhibition Assay Standard Operating Procedure (SOP) for Quantification of N1 Influenza Antibodies and the Use of a Calibrator to Improve the Reproducibility of the ELLA-NI With Reverse Genetics Viral and Recombinant Neuraminidase Antigens: A FLUCOP Collaborative Study. Front Immunol. 2022;13:909297. Epub 20220617.7. Spackman E, Suarez DL, Lee CW, Pantin-Jackwood MJ, Lee SA, Youk S, Ibrahim S. Efficacy of inactivated and RNA particle vaccines against a North American Clade 2.3.4.4b H5 highly pathogenic avian influenza virus in chickens. Vaccine. 2023. Epub 20231104.

Viruses. All procedures using infectious material were reviewed and approved by the Institutional Biosafety Committee of US National Poultry Research Center (USNPRC), US Department of Agriculture-Agricultural Research Service, Athens, GA. The HPAI virus isolate A/turkey/Indiana/22-003707-003/2022 H5N1 (TK/IN/22) was provided by Dr. Mia Torchetti, National Veterinary Services Laboratories, US Department of Agriculture-Animal and Plant Health Inspection Service, Ames, IA. The A/Vietnam/1203/2004 H5N1 HPAI virus (Viet/04), A/Whooper Swan/Mongolia/244/2005 H5N1 (WS/Mongolia/05) HPAI virus, and A/Flycatcher/CA/14875-1/1994 H7N1 low pathogenic avian influenza virus isolates were provided by the repository at the USNPRC. Virus isolates were propagated and titrated in SPF embryonating chicken eggs using standard procedures [1]. Titers were determined using the Reed-Muench method [2].Vaccines. Two commercial rHVT-H5 vaccines were selected because they are licensed in the US (and may be licensed elsewhere) and were supplied by the manufacturers: 2.2-HVT (Vectormune HVT AIV, Ceva Animal Health LLC, Lenexa, KS) (serial 395-134); and COBRA-HVT (Vaxxitek HVT+IBD+H5, Boehringer-Ingelheim Animal Health USA, Ridgefield, CT) (serial EW003). The amino acid similarity between the vaccine antigens and the challenge virus HA1 was 91.7% (COBRA-HVT) and 91.2% (2.2-HVT).Challenge study design. All animal work was reviewed and approved by the USNPRC Institutional Animal Care and Use Committee. Mixed sex, SPF WL chickens (Gallus gallus domesticus) were obtained at hatch from in-house flocks. Broiler chicken eggs were obtained from a commercial hatchery at 18 days of incubation prior to administration of any in ovo vaccines and were hatched on-site. All birds were randomly assigned to vaccine groups based on breed. Vaccine groups are shown in Table 1. All vaccines were prepared and administered on the day of hatch by the subcutaneous route at the nape of the neck in accordance with the manufacturer’s instructions (0.2ml per chicken). Serum was collected from all chickens 25 days post vaccination to evaluate the antibody response to the vaccines.Four weeks post vaccination (four weeks of age) chickens were challenged with a target dose 6.0log10 50% egg infectious doses (EID50) per bird of TK/IN/22 in 0.1ml by the intrachoanal route (titration of the challenge virus after dilution confirmed the challenge dose to be 6.7log10 EID50 per bird). Oropharyngeal and CL swabs were collected from all birds at 2-, 4-, and 7-days post challenge (DPC). Swabs were also collected from dead and euthanized birds.To evaluate antibody-based DIVA-VI tests, serum was collected at 7-, 10- and 14DPC. Mortality and morbidity were recorded for 14DPC. Surviving birds were euthanized at 14DPC. If birds were severely lethargic or presented with neurological signs, they were euthanized and were counted as mortality at the next observation time for mean death time calculations. Euthanasia was performed by cervical dislocation in accordance with American Veterinary Medical Association guidelines.Quantitative rRT-PCR (qRRT-PCR). RNA was extracted from OP and CL swabs using the MagMax magnetic bead extraction kit (Thermo Fisher Scientific, Waltham, MA) with the wash modifications as described by Das et al., [3]. Quantitative real-time RT-PCR was conducted as described previously [4] on a QuantStudio 5 (Thermo Fisher Scientific) instrument. A standard curve was generated from a titrated stock of TK/IN/22 and was used to calculate titer equivalents using the real time PCR instrument’s software.Hemagglutination inhibition assay. Hemagglutination inhibition (HI) assays were run in accordance with standard procedures [5]. All pre-challenge sera collected at 25 days post vaccination were tested against the challenge virus and the closest isolates available to the vaccine antigens. The serum from the 2.2-HVT group was tested against WS/Mongolia/05 (99.3% similarity) and the serum from the COBRA-HVT group was tested against Viet/04 (98.2% similarity). Titers of eight or below were considered negative.Commercial ELISA. A commercial AIV antibody ELISA (AI Ab Test, IDEXX laboratories, Westbrook, ME) was used in accordance with the manufacturer’s instructions. Sera were tested to detect anti-NP antibodies pre-challenge (25days pos-vaccination) and at 7-, 10- and 14DPC.Enzyme-linked lectin assay (ELLA) for detection of neuraminidase inhibition (NI) antibody. The ELLA was performed as previously described with minor modifications [6, 7]. Briefly, the NA activity of a beta-propiolactone inactivated H7N1 virus (A/Flycatcher/CA/14875-1/1994) was quantified to determine the effective concentration (EC) of antigen. The 98% EC (EC98) of antigen was subsequently used for the ELLA-NI assays. For ELLA-NI assay, the antigen and serum mixture was incubated overnight (approximately18hr) at 37°C and the NA activity was determined following the procedure as described in Spackman et al. [7]. The average background absorbance value was subtracted from the sample absorbance value then that value was divided by the average values of wells with only NA antigen. This value was multiplied by a factor of 100 to calculate the percent NA activity. The percent NI activity of individual serum samples was determined by subtracting the percent NA activity from 100%. A cut-off value for positive NI activity was determined by adding three standard deviations to the mean NI activity of pre-challenge sera (i.e., NA antibody negative sera) of each corresponding group of chickens at 7-, 10- and 14DPC. Each serum was tested at dilutions of 1:20 and 1:40.

In the United States, influenza vaccination rates differ greatly by age. For example, during the 2022-2023 flu season, around ** percent of those aged 65 years and older received an influenza vaccination, compared to just ** percent of those aged 18 to 49 years. The CDC recommends that everyone six months and older in the United States should get vaccinated against influenza every year, with a few exceptions. Although influenza is mild for most people it can lead to hospitalization and even death, especially among the young, the old, and those with certain preexisting conditions. The impact of flu vaccinations Flu vaccinations are safe and effective, preventing thousands of illnesses, medical visits, and deaths every year. However, the effectiveness of flu vaccines varies each year depending on what flu viruses are circulating that season and the age and health status of the person receiving the vaccination. During the 2022-2023 flu season it was estimated that influenza vaccination prevented almost *********** hospitalizations among those aged 65 years and older. In addition, flu vaccinations prevented ***** deaths among those aged 65 years and older as well as ** deaths among children six months to four years. The burden of influenza The impact of influenza is different from season to season. However, during the 2022-2023 flu season there were around ** million cases of influenza in the United States. Furthermore, there were around ****** deaths due to influenza, an increase from the previous year but significantly fewer than in ********* when influenza contributed to ****** deaths. Most of these deaths are among the elderly. In ********* the death rate due to influenza among those aged 65 years and older was around **** per 100,000 population. In comparison, those aged 18 to 49 years had an influenza death rate of just ** per 100,000 population.

As of July 13, 2022, approximately 53.7 million people in the United Kingdom had received the first dose of the COVID-19 vaccination. The UK was the first country in the world to approve the use of the Pfizer/BioNTech vaccine, and began inoculations on December 8, 2020. Nearly all the vaccines currently being used in the UK require two doses for full efficacy to occur, and according to the latest data around 50.3 million people had received their second dose of the immunization. Furthermore, 40.1 million booster vaccinations had been administered.

The total number of cases in the UK can be found here. For further information about the coronavirus (COVID-19) pandemic, please visit our dedicated Facts and Figures page.

This table illustrates the effectiveness of vaccination by comparing the number of cases of six vaccine-preventable diseases in Canada before and after the introduction of each vaccine.

Vaccinations Solutions for Pets Market Outlook

The global market size for vaccination solutions for pets was projected to be approximately USD 5.5 billion in 2023 and is forecasted to reach USD 9.8 billion by 2032, growing at a compound annual growth rate (CAGR) of 6.5% during the forecast period. The growth of this market can be attributed to increasing pet ownership, heightened awareness about pet health, and advances in veterinary medicine.

One of the primary growth factors driving the vaccination solutions for pets market is the increasing pet humanization trend. As pets are increasingly being considered as family members, owners are more willing to invest in their health and well-being. This shift in perception has led to a higher expenditure on pet healthcare services, including vaccinations. Furthermore, the rising incidences of zoonotic diseases have emphasized the importance of regular vaccinations, thereby driving market growth.

Another significant factor contributing to market expansion is the advancements in veterinary medicine and biotechnology. Innovations such as DNA vaccines and recombinant vaccines are proving to be more effective and safer, leading to higher adoption rates. These advancements not only enhance the efficacy of vaccines but also reduce the potential side effects, making them more acceptable to pet owners and veterinarians alike.

There is also a growing awareness about preventive healthcare among pet owners, influenced by various veterinary campaigns and government initiatives. Many countries have implemented mandatory vaccination programs for pets to curb the spread of infectious diseases. Additionally, the rise of social media and online platforms has made information about pet health more accessible, encouraging pet owners to adhere to vaccination schedules. These factors collectively are propelling the market forward.

Geographically, North America and Europe currently dominate the market due to the high pet ownership rates, well-established veterinary infrastructure, and significant investments in pet healthcare. However, the Asia Pacific region is expected to witness the highest growth rate, driven by increasing disposable incomes, urbanization, and a burgeoning middle class that is more inclined towards pet adoption and healthcare. The growing availability of veterinary services and products in emerging economies further supports this regional growth trend.

Product Type Analysis

The market for vaccination solutions for pets can be segmented into core vaccines and non-core vaccines. Core vaccines are those that are universally recommended for all pets, regardless of their geographical location or lifestyle. These include vaccines for rabies, distemper, parvovirus, and adenovirus. The demand for core vaccines remains consistently high due to their critical role in preventing life-threatening diseases. These vaccines are often mandated by law, further ensuring their widespread adoption.

Non-core vaccines, on the other hand, are administered based on the pet's risk of exposure to certain diseases. These include vaccines for Lyme disease, Bordetella, and feline leukemia virus (FeLV). The market for non-core vaccines is also growing, driven by the increasing awareness among pet owners about the specific health risks their pets may face. Veterinarians play a crucial role in guiding pet owners about the necessity of these vaccines based on the pet’s lifestyle and environment.

Advancements in vaccine technology are significantly impacting both core and non-core vaccine markets. The development of combination vaccines, which protect against multiple diseases in a single shot, is gaining popularity. These combination vaccines offer the dual benefits of reducing the number of injections a pet needs and ensuring comprehensive protection, thus increasing compliance with vaccination schedules.

The growing trend of personalized pet healthcare is also influencing the product type segment. Veterinarians are increasingly adopting tailored vaccination plans that take into account the individual pet’s health status, age, and lifestyle. This personalized approach is particularly relevant for non-core vaccines and is expected to drive market growth in this segment.

Report Scope

File includes Tables S1-S4. Table S1. General information of the five provinces/municipalities. This table provides general information, including areas, overall population, GDP per capita and population aged 6 months to 14 years, of the five provinces (the four studied province Shandong, Henan, Hunan, Sichuan and the compared municipality Beijing). Table S2. Epidemiologic inputs by province, season, and age group. This table showed the epidemiologic inputs that were used to calculate case numbers by province, season and age group from season 05/06 to 10/11, excluding 09/10 the pandemic season. Table S3. Current situation: influenza vaccination coverage rates among target populations by province, season and age group, influenza vaccine effectiveness by season for all ages. This table used data of vaccination coverage rate and effectiveness of influenza vaccine by province from season 05/06 to 11/12, excluding 09/10 the pandemic season. Table S4. Number of influenza cases and cases averted by vaccination program. It showed the calculation results of number of cases and cases averted by the vaccination program, comparing with no vaccination, from season 05/06 to 10/11, excluding 09/10 the pandemic season. Table S5. Current situation: Cost effectiveness of influenza vaccination program in season 05/06-10/11, 09/10 not included; by province, season and age group. Demonstration of results on cost- effectiveness of comparing the current pay-out-of-pocket policy with no vaccination. Table S6. A: cost-effectiveness of OPTION 1-reminder, by province and age group. Demonstration of results on cost-effectiveness of comparing the current situation with two OPTIONS: OPTION 1 reminder and OPTION 2- sending free influenza vaccination voucher and expanding vaccination sites. (DOCX)

Tuberculosis (TB) remains one of the deadliest infectious diseases worldwide, causing over a million deaths annually. The only licensed TB vaccine for human use, Bacille Calmette-Guérin (BCG), a mycobacteria-based live-attenuated vaccine, confers immunity to children but fails to efficiently protect adults from pulmonary TB. Several TB vaccine candidates have been developed over the last two decades, but some have failed to provide substantially better protection than BCG in clinical trials. Most of these vaccine candidates were initially evaluated for their protective capacity in mouse models of TB. With the availability of several mouse strains, vaccination routes and Mycobacterium tuberculosis (Mtb) challenge strains, to-date there is no consensus in the field about the predictive value of different murine models of TB, and it remains a matter of debate whether host genetics or vaccine-driven parameters primarily determine vaccine efficacy. Here we reviewed the performance of all TB vaccine candidates that have entered clinical trials over the last 25 years. We extracted protective efficacy data from all published studies that utilized mouse models to assess vaccination efficacy. The efficacy of each vaccine candidate to reduce lung bacterial burden depending on the mouse genotype, the vaccine administration route, and the Mtb challenge strain at different time-points was evaluated. Our data reveals insights into the effect of experimental parameters on vaccine performance and emphasizes the potential benefits of standardizing TB mouse models across vaccination-challenge studies to identify pre-clinical vaccine candidates with the highest potential to succeed.

Additional file 2: Table S2. Vaccine efficacy and effectiveness in children and adolescents

In line with encountering the world with the emergence of vaccine-resistance variants of SARS-CoV-2, 15,669,529 samples that received COVID-19 vaccines until April 2023 were investigated as two doses in the first phase and booster vaccinations in the second phase. The analysis shows that D614G and P681 mutations occurred in both phases. The E484 and Y655 mutations significantly emerged during the second phase. The 762-889 and 254-381 regions are revealed as conserved parts and could be considered in vaccine design. The Kruskal–Wallis test revealed a significant reduction in single mutations between populations with 20%–50% and those with 70%–100% vaccination coverage (p=0.017). The Mann–Whitney U test proposes a link between vaccination and suppression of viral mutation rates. Dynamic modeling suggests that key mutations have facilitated the virus’ evolution and immune escape. The study’s findings are crucial for understanding virus genome mutations, especially E614 and P681 in Delta and E484 and H655 in Omicron. This highlights the need to adjust strategies and strengthen global efforts in combating the pandemic.

Cats (Felis domesticus) are rich source of airborne allergens that prevailed in the environment and sensitized a number of people to allergy. In this study, a mouse model of allergic rhinitis caused by the cat allergens was developed for the first time and the model was used for testing therapeutic efficacy of a novel intranasal liposome-entrapped vaccines made of native Fel d 1 (major cat allergen) in comparison with the vaccine made of crude cat hair extract (cCE). BALB/c mice were sensitized with cCE mixed with alum intraperitoneally and intranasally. The allergic mice were treated with eight doses of either liposome (L)-entrapped native Fel d 1 (L-nFD1), L-cCE), or placebo on every alternate day. Vaccine efficacy evaluation was performed one day after provoking the treated mice with aerosolic cCE. All allergenized mice developed histological features of allergic rhinitis with rises of serum specific-IgE and Th2 cytokine gene expression. Serum IgE and intranasal mucus production of allergic mice reduced significantly after vaccination in comparison with the placebo mice. The vaccines also caused a shift of the Th2 response (reduction of Th2 cytokine expressions) towards the non-pathogenic responses: Th1 (down-regulation of the Th1 suppressive cytokine gene, IL-35) and Treg (up-regulation of IL-10 and TGF-β). In conclusions, a mouse model of allergic rhinitis to cat allergens was successfully developed. The intranasal, liposome-adjuvanted vaccines, especially the refined single allergen formulation, assuaged the allergic manifestations in the modeled mice. The prototype vaccine is worthwhile testing further for clinical use in the pet allergic patients.

Supplementary Table 9: The additional Spike protein mutations which had frequencies ≥ 2% as observed in the period of September-October. The mutations previously dealt with in the earlier sections have not been listed here.

A table of all potential covariates that were investigated with a brief definition. (XLSX)

Supporting figures and tables. Figure S1. Week 30 paired ELISpot responses to Gag in the assay comparison study (Panel A & B) and week 8 ELISpot responses to Gag in the Main study before and after calibration (Panel C & D). Panels A & B show the distribution of Gag responses based on the paired samples. One outlier of Gag response was removed before the calibration. Panel C shows the distribution of the 27 bonus samples before and after calibration. Panel D shows the distribution of the Week 8 samples before and after calibration. Figure S2: Distribution of ICS Reponses in Infected (Inf.) and Uninfected (Uninf.) Vaccine and Placebo Recipients. Panel A includes the mock ICS responses. Panel B includes the ICS responses against CMV stimulation. Panel C includes the ICS responses against HIV-1 antigens. Panel D includes the ICS responses against Ad5 antigens. Box plots show the 25th percentile (lower edge of the box), 50th percentile (horizontal line in the box), and 75th percentile (upper edge of the box) for the immune responses, with participants stratified according to HIV-1 infection status and treatment assignment. The tip of the vertical bars indicate the most extreme data points, which are no more than 1.5 times the interquartile range from the box. Figure S3: Correlations between Mock ELISpot Responses and Ad5-specific or CMV-specific ICS Responses among Vaccine Recipients. A fitted simple linear regression line is added with values in the upper corner indicating the Spearman's correlations coefficients (ρ) and p-values (p) from the exact test of ρ being zero. Figure S4: Correlations between the Number of IFN-γ-secreting Cells Measured by Mock ELISpot and the Proportions of IFN-γ-secreting Cells in Different Cell Subsets Measured by Mock ICS among Vaccine Recipients. A fitted simple linear regression line is added with values in the upper corner indicating the Spearman's correlations coefficients (ρ) and p-values (p) from the exact test of ρ being zero. Figure S5: Estimated instantaneous hazard ratios over time per 1-loge increase of immune responses from each baseline-covariate-adjusted model of a single immune variable as presented in Table 1. Figure S6: Distribution of Week 8 mock ELISpot responses by HLA class I categories among vaccine recipients. Red dots indicate infected cases and blue dots indicate uninfected non-cases. Mock responses do not seem to differ among different HLA class I categories. As shown in Table S3 in Information S1, HLA class I category was not a significant independent predictor of mock responses, in addition to Race and Ad5 seropositivity which were found to be associated with mock response. Table S1: Estimates of immune correlate hazard ratios (HR) for HIV-1 infection in vaccine recipients from multivariate Cox regression models of background-unadjusted HIV-specific immune responses. In addition to the ELISpot response variables, all models adjusted for baseline covariates as specified in the Methods section including circumcision status, Ad5 seropositivity, region, race, age, HSV-2 serostatus, recreational drug usage, unprotected receptive anal sex with HIV+ male partner, unprotected insertive anal sex with HIV+ male partner, and number of male partners. Due to missing data in other covariates, 82 (instead of 86) infections were included in these models. Model Foreground indicates antigen-stimulated immune responses without background adjustment. Adjusted indicates antigen-stimulated immune responses subtracted by mock responses. Table S2: Estimates of the effect of ELISpot Mock responses and HLA class I types on risk of HIV-1 infection among vaccine recipients. Table S3: Estimates based on a multivariate linear regression model of the effect of baseline covariates and HLA class I types on week 8 ELISpot mock responses among vaccine recipients. HLA class I type was assessed as an additional independent predictor in the best fitting model that includes race and Ad5 serostatus as presented in Table 3. (PDF)