Influenza, also called the flu, is one of the most infectious diseases worldwide. Its symptoms range from mild to severe, and include sore throat, cough, runny nose, fever, headache, and muscle pain, but can also cause severe illness and death among high-risk populations such as the elderly and children. During the 2023-2024 flu season, there were 40 million cases of influenza in the United States. Influenza deaths Although influenza does not require medical attention for most people, it can be deadly, and causes thousands of deaths every year. The impact of influenza varies from year to year. The number of influenza deaths during the 2023-2024 flu season was 27,965. The vast majority of deaths attributed to influenza during the 2023-2024 flu season occurred among those aged 65 years and older. Vaccination An annual influenza vaccination remains the most effective way of preventing influenza. During the 2022-2023 flu season, influenza vaccinations prevented an estimated 2,479 deaths among U.S. adults aged 65 years and older. Although, flu vaccinations are accessible and cheap, a large share of the United States population still fails to get vaccinated every year. In 2022-2023, only 35 percent of those aged 18 to 49 years received a flu vaccination, much lower compared to children and the elderly.

The burden of influenza in the United States can vary from year to year depending on which viruses are circulating, how many people receive an influenza vaccination, and how effective the vaccination is in that particular year. During the 2023-2024 flu season, around 28,000 people lost their lives to the disease. Although most people recover from influenza without needing medical care, the disease can be deadly among young children, the elderly, and those with weakened immune systems or chronic illnesses. Deaths due to influenza Even though most people recover from influenza without medical care, influenza and pneumonia can be deadly, especially for older people and those with certain preexisting conditions. Influenza is a common cause of pneumonia and although most cases of influenza do not develop into pneumonia, those that do are often more severe and more deadly. Deaths due to influenza are most common among the elderly, with a mortality rate of around 32 per 100,000 population during the 2023-2024 flu season. In comparison, the mortality rate for those aged 50 to 64 years was 9.1 per 100,000 population. Flu vaccinations The most effective way to prevent influenza is to receive an annual influenza vaccination. These vaccines have proven to be safe and are usually cheap and easily accessible. Nevertheless, every year a large share of the population in the United States still fails to get vaccinated against influenza. For example, in the 2022-2023 flu season, only 35 percent of those aged 18 to 49 years received a flu vaccination. Unsurprisingly, children and the elderly are the most likely to get vaccinated. It is estimated that during the 2022-2023 flu season, vaccinations prevented over 929 thousand influenza cases among children aged 6 months to 4 years.

The graph illustrates the number of flu-related deaths in the United States for each flu season from 2010-2011 to 2023-2024*. The x-axis represents the flu seasons, labeled from '10-11 to '23*-24*, while the y-axis shows the annual number of flu deaths. Throughout this period, flu deaths vary significantly, ranging from a low of 4,900 in the 2021-2022* season to a high of 51,000 in both the 2014-2015 and 2017-2018 seasons. Other notable figures include 36,000 deaths in 2010-2011, 42,000 in 2012-2013, and a recent increase to 28,000 in the 2023*-2024* season. The data exhibits considerable fluctuations with no consistent upward or downward trend, highlighting the variability in flu mortality rates over the years. This information is presented in a line graph format, effectively showcasing the yearly changes and peaks in flu-related deaths across the United States.

*Data for the 2021-2022 and 2022-2023 seasons are estimated.

During the 2023-2024 flu season in the United States, an estimated 27,965 people died from influenza. The vast majority of deaths due to influenza occur among the elderly, with those aged 65 years and older accounting for 19,038 deaths during the 2023-2024 flu season. During this time, the mortality rate from influenza among those aged 65 years and older was around 32 per 100,000 population, compared to a mortality rate of two per 100,000 population among those aged 18 to 49 years. Influenza deaths Although most people recover from influenza without the need of medical care, influenza and pneumonia are still major causes of death in the United States. Influenza is a common cause of pneumonia and cases in which influenza develops into pneumonia tend to be more severe and more deadly. However, the impact of influenza varies from year to year depending on which viruses are circulating. For example, during the 2017-2018 flu season around 52,000 people died due to influenza, whereas in 2023-2024 total deaths amounted to 28,000. Preventing death The most effective way to prevent influenza is to receive an annual influenza vaccination. These vaccines have proven to be safe and are usually cheap and easily accessible. Each year, flu vaccinations prevent thousands of influenza cases, hospitalizations and deaths. It was estimated that during the 2022-2023 flu season, vaccinations prevented the deaths of around 2,479 people aged 65 years and older.

The seasonal influenza (flu) vaccine is designed to protect against those influenza viruses predicted to circulate during the upcoming flu season, but identifying which viruses are likely to circulate is challenging. We use features from phylogenetic trees reconstructed from hemagglutinin (HA) and neuraminidase (NA) sequences, together with a support vector machine, to predict future circulation. We obtain accuracies of 0.75–0.89 (Area under the curve AUC 0.83–0.91) over 2016–2020. We explore ways to select potential candidates for a seasonal vaccine and find that the machine learning model has a moderate ability to select strains that are close to future populations. However, consensus sequences among the most recent three years also do well at this task. We identify similar candidate strains to those proposed by the World Health Organization, suggesting that this approach can help inform vaccine strain selection., This repository contains the code, data and materials developed for 'Phylogenetic identification of influenza virus candidates for seasonal vaccines'. We downloaded all hemagglutinin (HA) and neuraminidase (NA) human H3N2 sequences collected from 1980 to February 2020 from the Global Initiative on Sharing Avian Influenza Data (GISAID). Accession numbers and references to the GISAID submitting laboratories for the sequences used in this study are included in this repository. As per GISAID access terms, the sequences used in this study are not reproduced here but may be downloaded from the GISAID server.This repository contains all code to compute the features, train and test the machine learning models, predict the next year's flu vaccine candidates, and generate the plots for the paper. Derived data e.g. all the influenza trees for the experiments in years 2016 to 2020 are included. , All data files are in CSV format. All code was written in R (open-source), and influenza trees are included in RDATA files to be read into R. Accession numbers and references to the GISAID submitting laboratories for the sequences used in this study are included in a zip folder. To recreate the analysis in full, these accession numbers may be used to download the influenza sequences directly from GISAID. , # Phylogenetic identification of influenza virus candidates for seasonal vaccines - supporting data and code

This repository contains the code, data and materials developed for 'Phylogenetic identification of influenza virus candidates for seasonal vaccines'. The seasonal influenza (flu) vaccine is designed to protect against those influenza viruses predicted to circulate during the upcoming flu season, but identifying which viruses are likely to circulate is challenging. We use features from phylogenetic trees reconstructed from hemagglutinin (HA) and neuraminidase (NA) sequences, together with a support vector machine, to predict future circulation. We obtain accuracies of 0.75-0.89 (Area under the curve AUC 0.83-0.91) over 2016-2020. We explore ways to select potential candidates for a seasonal vaccine and find that the machine learning model has a moderate ability to select strains that are close to future populations. However, consensus sequences among the most recent three y...

Over 12 million people in the United States died from all causes between the beginning of January 2020 and August 21, 2023. Over 1.1 million of those deaths were with confirmed or presumed COVID-19.

Vaccine rollout in the United States Finding a safe and effective COVID-19 vaccine was an urgent health priority since the very start of the pandemic. In the United States, the first two vaccines were authorized and recommended for use in December 2020. One has been developed by Massachusetts-based biotech company Moderna, and the number of Moderna COVID-19 vaccines administered in the U.S. was over 250 million. Moderna has also said that its vaccine is effective against the coronavirus variants first identified in the UK and South Africa.

India reported over 2,752 cases of swine flu, also known as influenza A (H1N1) between in 2020, with 44 deaths. The country saw an outbreak of this disease in 2015, recording over 42 thousand cases and 2,990 deaths.

The influenza A (H1N1) strain of virus was first recognized in 1919 but was declared as a global pandemic by the World Health Organization in 2009, lasting until August 2010 across the world.

Chicago residents who are up to date with influenza vaccines by ZIP Code, based on the reported home address and age group of the person vaccinated, as provided by the medical provider in the Illinois Comprehensive Automated Immunization Registry Exchange (I-CARE). “Up to date” refers to individuals aged 6 months and older who have received 1+ doses of influenza vaccine during the current season, defined as the beginning of July (MMWR week 27) through the end of the following June (MMWR week 26). Data Notes: Weekly cumulative totals of people up to date are shown for each combination ZIP Code and age group. Note there are rows where age group is "All ages" so care should be taken when summing rows. Weeks begin on a Sunday and end on a Saturday. Coverage percentages are calculated based on the cumulative number of people in each ZIP Code and age group who are considered up to date as of the week ending date divided by the estimated number of people in that subgroup. Population counts are obtained from the 2020 U.S. Decennial Census. For ZIP Codes mostly outside Chicago, coverage percentages are not calculated because reliable Chicago-only population counts are not available. Actual counts may exceed population estimates and lead to coverage estimates that are greater than 100%, especially in smaller ZIP Codes with smaller populations. Additionally, the medical provider may report a work address or incorrect home address for the person receiving the vaccination, which may lead to over- or underestimation of vaccination coverage by geography. All coverage percentages are capped at 99%. The Chicago Department of Public Health (CDPH) uses the most complete data available to estimate influenza vaccination coverage among Chicagoans, but there are several limitations that impact our estimates. Influenza vaccine administration is not required to be reported in Illinois, except for publicly funded vaccine (e.g., Vaccines for Children, Section 317). Individuals may receive vaccinations that are not recorded in I-CARE, such as those administered in another state, or those administered by a provider that does not submit data to I-CARE, causing underestimation of the number individuals who received an influenza vaccine for the current season. All data are provisional and subject to change. Information is updated as additional details are received and it is, in fact, very common for recent dates to be incomplete and to be updated as time goes on. At any given time, this dataset reflects data currently known to CDPH. Numbers in this dataset may differ from other public sources due to when data are reported and how City of Chicago boundaries are defined. For all datasets related to influenza, see https://data.cityofchicago.org/browse?limitTo=datasets&sortBy=alpha&tags=flu . Data Source: Illinois Comprehensive Automated Immunization Registry Exchange (I-CARE), U.S. Census Bureau 2020 Decennial Census

Monthly Cumulative Number and Percent of Persons Who Receive ≥1 Influenza Vaccination Doses and Comparison Between 2023-2024 and Two Previous Seasons, by Jurisdiction, United States

• Influenza vaccination coverage for children and adults is assessed through U.S. jurisdictions’ Immunization Information Systems (IIS) data, submitted from jurisdictions to CDC monthly in aggregate by age group. More information about the IIS can be found at https://www.cdc.gov/vaccines/programs/iis/about.html.

• Influenza vaccination coverage estimate numerators include the number of people receiving at least one dose of influenza vaccine in a given flu season, based on information that state, territorial, and local public health agencies report to CDC. Some jurisdictions’ data may include data submitted by tribes. Estimates include persons who are deceased but received a vaccination during the current season. People receiving doses are attributed to the jurisdiction in which the person resides unless noted otherwise. Quality and completeness of data may vary across jurisdictions. Influenza vaccination coverage denominators are obtained from 2020 U.S. Census Bureau population estimates.

• Monthly estimates shown are cumulative, reflecting all persons vaccinated from July through a given month of that flu season. Cumulative estimates include any historical data reported since the previous submission. National estimates are not presented since not all U.S. jurisdictions are currently reporting their IIS data to CDC. Jurisdictions reporting data to CDC include U.S. states, some localities, and territories.

• Because IIS data contain all vaccinations administered within a jurisdiction rather than a sample, standard errors were not calculated and statistical testing for differences in estimates across years were not performed.

• Laws and policies regarding the submission of vaccination data to an IIS vary by state, which may impact the completeness of vaccination coverage reflected for a jurisdiction. More information on laws and policies are found at https://www.cdc.gov/vaccines/programs/iis/policy-legislation.html.

• Coverage estimates based on IIS data are expected to differ from National Immunization Survey (NIS) estimates for children (https://www.cdc.gov/flu/fluvaxview/dashboard/vaccination-coverage-race.html)
and adults (https://www.cdc.gov/flu/fluvaxview/dashboard/vaccination-adult-coverage.html) because NIS estimates are based on a sample that may not be representative after survey weighting and vaccination status is determined by survey respondent rather than vaccine records or administrations, and quality and completeness of IIS data may vary across jurisdictions. In general, NIS estimates tend to overestimate coverage due to overreporting and IIS estimates may underestimate coverage due to incompleteness of data in certain jurisdictions.

Chicago residents who are up to date with influenza vaccines by Healthy Chicago Equity Zone (HCEZ), based on the reported address, race-ethnicity, and age group of the person vaccinated, as provided by the medical provider in the Illinois Comprehensive Automated Immunization Registry Exchange (I-CARE). Healthy Chicago Equity Zones is an initiative of the Chicago Department of Public Health to organize and support hyperlocal, community-led efforts that promote health and racial equity. Chicago is divided into six HCEZs. Combinations of Chicago’s 77 community areas make up each HCEZ, based on geography. For more information about HCEZs including which community areas are in each zone see: https://data.cityofchicago.org/Health-Human-Services/Healthy-Chicago-Equity-Zones/nk2j-663f “Up to date” refers to individuals aged 6 months and older who have received 1+ doses of influenza vaccine during the current season, defined as the beginning of July (MMWR week 27) through the end of the following June (MMWR week 26). Data notes: Weekly cumulative totals of people up to date are shown for each combination of race-ethnicity and age group within an HCEZ. Note that each HCEZ has a row where HCEZ is “Citywide” and each HCEZ has a row where age is "All" and race-ethnicity is “All Race/Ethnicity Groups” so care should be taken when summing rows. Weeks begin on a Sunday and end on a Saturday. Coverage percentages are calculated based on the cumulative number of people in each population subgroup (age group by race-ethnicity within an HCEZ) who are up to date, divided by the estimated number of people in that subgroup. Population counts are from the 2020 U.S. Decennial Census. Actual counts may exceed population estimates and lead to >100% coverage, especially in small race-ethnicity subgroups of each age group within an HCEZ. All coverage percentages are capped at 99%. Summing all race/ethnicity group populations to obtain citywide populations may provide a population count that differs slightly from the citywide population count listed in the dataset. Differences in these estimates are due to how community area populations are calculated. The Chicago Department of Public Health (CDPH) uses the most complete data available to estimate influenza vaccination coverage among Chicagoans, but there are several limitations that impact our estimates. Influenza vaccine administration is not required to be reported in Illinois, except for publicly funded vaccine (e.g., Vaccines for Children, Section 317). Individuals may receive vaccinations that are not recorded in I-CARE, such as those administered in another state, or those administered by a provider that does not submit data to I-CARE, causing underestimation of the number individuals who received an influenza vaccine for the current season. All data are provisional and subject to change. Information is updated as additional details are received and it is, in fact, very common for recent dates to be incomplete and to be updated as time goes on. At any given time, this dataset reflects data currently known to CDPH. Numbers in this dataset may differ from other public sources due to when data are reported and how City of Chicago boundaries are defined. For all datasets related to influenza, see https://data.cityofchicago.org/browse?limitTo=datasets&sortBy=alpha&tags=flu . Data Source: Illinois Comprehensive Automated Immunization Registry Exchange (I-CARE), U.S. Census Bureau 2020 Decennial Census

Between January and August 2020, there has been approximately 48.2 thousand deaths in England and Wales with COVID-19 as an underlying cause. As illustrated in the table, the number of deaths as a result of COVID-19 are much higher than from either pneumonia or influenza. There has been over three times the number of deaths from COVID-19 than pneumonia and influenza so far in 2020. The overall number of confirmed COVID-19 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 dataset includes aggregated weekly respiratory virus laboratory data that the Chicago Department of Public Health (CDPH) uses to monitor influenza, COVID-19, respiratory syncytial virus (RSV), and other respiratory virus activity in Chicago. The data represents respiratory viral PCR tests performed by several hospital laboratories in Chicago as well as two commercial laboratories serving Chicago facilities. Data are voluntarily reported on a weekly basis and do not contain patient demographic or geographic information. The data reported represent both Chicago and non-Chicago residents tested by the reporting facility. The respiratory viruses included are influenza, RSV, SARS-CoV-2, parainfluenza, rhinovirus/enterovirus, adenovirus, human metapneumovirus, and seasonal coronaviruses. Influenza laboratory data are available from 2010-2011 to present; for all other respiratory viruses data are available from 2019-2020 to present. All data are provisional and subject to change. Information is updated as additional details are received. At any given time, this dataset reflects data currently known to CDPH. Numbers in this dataset may differ from other public sources.

Influenza and pneumonia caused around 12.3 deaths in the U.S. per 100,000 population in 2019. Influenza and pneumonia are among the leading causes of death in the United States, accounting for around 1.6 percent of all deaths in 2020. Influenza, or the flu, is a viral infection that is highly contagious and especially common in the winter season. Influenza is a common cause of pneumonia, although most cases of the flu do not develop into pneumonia. Pneumonia is an infection or inflammation of the lungs and is particularly deadly among young children and the elderly.

Influenza cases

Influenza is very common in the United States, with an estimated 35 million cases reported in 2019-2020. Common symptoms of the flu include cough, fever, runny or stuffy nose, sore throat and headache. Symptoms can be mild but can also be severe enough to require medical attention. In 2019-2020, there were around 16 million influenza-related medical visits in the United States.

Prevention

To prevent contracting the flu people can take everyday precautions such as regularly washing their hands and avoiding those who are sick, but the best way to prevent the flu is by receiving the flu vaccination every year. Receiving a flu vaccination is especially important for young children and the elderly as they are most susceptible to flu complications and associated death. In 2021, around 75 percent of those aged 65 years and older received a flu vaccine, while only 38 percent of those aged 18 to 49 years had done so.

In the United States, the highest rate of hospitalizations due to influenza are among those aged 65 years and older. During the 2023-2024 flu season, the rate of hospitalizations due to influenza among this age group was about 401 per 100,000 population, compared to a rate of around 47 per 100,000 for those aged 5 to 17 years. Influenza is a common viral infection that usually does not require medical treatment. However, for the very young, the old, and those with certain pre-existing conditions, influenza can be serious and even deadly. The burden of influenza in the United States The impact of influenza in the United States varies from year to year depending on the strain that is most prevalent during that season and the immunity in the population. Preliminary estimates show that around 28,000 people died from influenza during the 2023-2024 flu season. However, during the 2017-2018 flu season, an estimated 52,000 people lost their lives to influenza. The importance of flu vaccines The best way to avoid catching the flu and to reduce the virus’s overall burden on society is by receiving an annual flu vaccination. The CDC currently recommends that everyone over 6 months of age should get a flu vaccination every year, preferably by the end of October. The flu vaccine is safe, efficient, and reduces the number of illnesses, hospitalizations, and deaths caused by the virus. For example, during the 2022-2023 flu season, it was estimated that vaccinations averted almost 65 thousand influenza-related hospitalizations. However, despite the proven benefits and wide availability of flu vaccinations, a large percentage of people in the United States fail to receive a vaccination every year. During the 2022-2023 flu season, only about 35 percent of those aged 18 to 49 years were vaccinated against influenza, compared to 70 percent of those aged 65 years and older.

The CHI, HIPC-I (Stanford and Yale), Emory, Yellow fever and SLE data sets used in the study. Unpack this file to your working directory and keep the directory structure. The R codes can be downloaded from github (https://github.com/kotliary/baseline) into the R directory.This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772If you use our data (including CITE-seq data) or code for your work please cite the following publication:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)AbstractResponses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.General contact: John Tsang (john.tsang@nih.gov)Questions about software/code: Yuri Kotliarov (yuri.kotliarov@nih.gov)

NNDSS - TABLE 1R. Hepatitis C, perinatal infection to Influenza-associated pediatric mortality - 2020. In this Table, provisional cases* of notifiable diseases are displayed for United States, U.S. territories, and Non-U.S. residents. Notice: Data from California published in week 29 for years 2019 and 2020 were incomplete when originally published on July 24, 2020. On August 4, 2020, incomplete case counts were replaced with a "U" indicating case counts are not available for specified time period. Note: This table contains provisional cases of national notifiable diseases from the National Notifiable Diseases Surveillance System (NNDSS). NNDSS data from the 50 states, New York City, the District of Columbia and the U.S. territories are collated and published weekly on the NNDSS Data and Statistics web page (https://wwwn.cdc.gov/nndss/data-and-statistics.html). Cases reported by state health departments to CDC for weekly publication are provisional because of the time needed to complete case follow-up. Therefore, numbers presented in later weeks may reflect changes made to these counts as additional information becomes available. The national surveillance case definitions used to define a case are available on the NNDSS web site at https://wwwn.cdc.gov/nndss/. Information about the weekly provisional data and guides to interpreting data are available at: https://wwwn.cdc.gov/nndss/infectious-tables.html. Footnotes: U: Unavailable — The reporting jurisdiction was unable to send the data to CDC or CDC was unable to process the data. -: No reported cases — The reporting jurisdiction did not submit any cases to CDC. N: Not reportable — The disease or condition was not reportable by law, statute, or regulation in the reporting jurisdiction. NN: Not nationally notifiable — This condition was not designated as being nationally notifiable. NP: Nationally notifiable but not published. NC: Not calculated — There is insufficient data available to support the calculation of this statistic. Cum: Cumulative year-to-date counts. Max: Maximum — Maximum case count during the previous 52 weeks. * Case counts for reporting years 2019 and 2020 are provisional and subject to change. Cases are assigned to the reporting jurisdiction submitting the case to NNDSS, if the case's country of usual residence is the U.S., a U.S. territory, unknown, or null (i.e. country not reported); otherwise, the case is assigned to the 'Non-U.S. Residents' category. Country of usual residence is currently not reported by all jurisdictions or for all conditions. For further information on interpretation of these data, see https://wwwn.cdc.gov/nndss/document/Users_guide_WONDER_tables_cleared_final.pdf. †Previous 52 week maximum and cumulative YTD are determined from periods of time when the condition was reportable in the jurisdiction (i.e., may be less than 52 weeks of data or incomplete YTD data). § Please refer to the CDC WONDER publication for weekly updates to the footnote for this condition.