This folder is used to store additional data relevant to the RSV modeling efforts. It contains multiple folders:
- one for vaccine coverage
- one for RSV data from different CDC sources, including the python code to extract and update the data.
- one for location and population data
- one for birth rate data
- one archive for past version and past round associated files
The folder vaccine_coverage/ provides weekly state-specific cumulative coverage for specific rounds.
For round 2, the file vaccine_coverage/RSV_round2_vax_coverage_seniors_2024_25.csv provides weekly vaccine coverage (cumulative percentage, cumulative no of doses, size of eligible population) for seniors from summer 2024 to the end of the projection period for RSVnet states. Separate values are provided for seniors 60-74 high risk and 75+.
Coverage should be considered additive to that of last season. The same coverage values apply to all intervention scenarios (A-D), while the counterfactual (F) assumes no coverage.
- RSV_RD2_maternal_vaccine_2024_25.csv
has weekly state-specific coverage for maternal vaccine. The weekdate is the
Saturday at the end of each week. This date represents the date when the mother
was vaccinated, so that the vaccine effect on the infant would start on average
one month later after the baby is born. Columns are provided for total state pop
size (
Total_pop), annual number of births (Births_per_year), Scenarios ("A"through"D"), No of weekly vaccine doses administered (Maternal_vaccine_weekly_doses), No of eligible mothers throughout the season (Eligible_mothers_entire_season, calculated as the no of moms who are eligible for vaccination at any time point of the campaign), weekly incident coverage (Weekly_incident_cov, calculated as weekly doses divided by the number of eligible mothers), and cumulative coverage (calculated as the cumulative sum of weekly incidence coverage) - RSV_RD2_nirsevimab_aggregated_2024_25.csv
has a similar structure as the maternal vaccine file for nirsevimab.
Note that the column
Dose_Typeindicates whether a baby is vaccinated at birth (at a constant rate throughout the season; New Born) or during the catch-up campaign (accelerated immunization in the first month of the season; Catch Up).Eligible_babies_entire_seasonreflects the number of babies in each category (catchup/newborn) who are eligible for nirsevimab at any time point during the campaign. Weekly incident and cumulative coverages are estimated based on this eligible population - RSV_RD2_nirsevimab_byweekofage_2024_25.csv is a version of the above file where the catch-up babies have been disaggregated by single week of age. This is the age at receipt of nirsevimab. Eligible babies counts the number of babies would are of that age in any given week of the season, which represents one week of babies.
In all files, the first and last weeks of the campaign have lower vaccination rates than other weeks to account for the fact that the campaign starts and ends at precise dates which do not exactly match with the start of a week (eg Aug 15, Sep 1... etc).
For teams that require US-level vaccine coverage, we advise to either do a weighted mean of the state coverage proportions, where the weights are the state population sizes. Or you can also sum all the state-level no of doses and state-level populations
The folder location_census/ contains two files:
- location_census/locations.csv containing the state and national full name, 2 letter abbreviation and fips code as used in the hub. The file also contains the population size
- location_census/state_pop_data
contains the population size per year, state (and national level), age from
2010 to 2022 (included). The data are coming from the US Census Bureau:
- Annual Estimates of the Civilian Population by Single Year of Age and Sex for the United States and States: April 1, 2010 to July 1, 2020: available here
- Annual Estimates of the Civilian Population by Single Year of Age and Sex for the United States and States: April 1, 2020 to July 1, 2022: available here
The folder birth_rate/ contains multiple files:
- natality_ files containing total number of births per state and per year from the Centers for Disease Control and Prevention, National Center for Health Statistics. National Vital Statistics System, Natality on CDC WONDER Online Database
- birth_rate_2016_2022.txt containing the birth rate per state and year from the Centers for Disease Control and Prevention, National Center for Health Statistics. National Vital Statistics System, Natality on CDC WONDER Online Database
- birth_rate_1995_2022.txt containing the calculated birth rate and standardized birth rate from the "natality_" and other "birth_rate" files from 1995 to 2022 per year and per state.
The folder rsv/ contains the RSV data divided in three sub-folders: one per each CDC source and the python code to extract and update the data.
The data is updated weekly by the update-rsv-data GitHub Action, which runs weekly on Friday morning, 9:00 am UTC.
The Weekly Rates of Laboratory-Confirmed RSV Hospitalizations from the RSV-NET Surveillance System is also downloaded weekly and output in a PARQUET file with the download date added in the name of the file: rsv/rsv-net/DATE_weekly_rates_lab_confirmed_rsv_hosp.parquet.
The Respiratory Syncytial Virus Hospitalization Surveillance Network (RSV-NET) is a network that conducts active, population-based surveillance for laboratory-confirmed RSV-associated hospitalizations in children younger than 18 years of age and adults. The network currently includes 58 counties in 12 states, and data are collected and reported during the October 1-April 30 season each year. In some years, additional months of data are collected.
The output file contains the rate and cumulative rate of RSV hospitalization at national level and for 12 states by season, by week and by age category, sex, race.
For more information about RSV-NET, please consult the CDC RSV-NET Overview and Methods webpage.
The Weekly Respiratory Virus Vaccination Data, Children 6 Months-17 Years and Adults 18 Years and Older, National Immunization Survey is also downloaded weekly and output in a PARQUET file: rsv/rsv-vax/weekly_respiratory_virus_vaccination_data.parquet.
The weekly respiratory virus vaccination data come from the National Immunization Survey-Adult COVID Module (NIS-ACM), National Immunization Survey-Child COVID Module (NIS-CCM), and the National Immunization Survey-Flu (NIS-Flu). The NIS-ACM provides data on Influenza (flu), COVID-19, and RSV vaccination for adults aged ≥18 years in the United States.
The output file contains vaccination survey data on Influenza, COVID-19, and RSV vaccination for adults aged ≥18 years in the United States and Children 6 Months-17 Years for a specific subset.
For more information, please consult the homepage of the data and the surveys method webpage information
Other links of interest:
- Weekly Respiratory Syncytial Virus (RSV) Vaccination Coverage among Pregnant or Recently Pregnant Persons 18-49 Years, by Race and Ethnicity
- Monthly Nirsevimab Receipt and Intent Reported by Females Aged 18-49 Years Who Have a Baby <8 Months During the RSV Season, United States
- Weekly Cumulative RSV Vaccination Coverage and Intent, Overall, by Selected Demographics and Jurisdiction, Among Adults 75 and Older and 60-74 Years with High-Risk Conditions Ever Vaccinated, United States
- Weekly Differences in Cumulative Respiratory Syncytial Virus (RSV) Vaccination Coverage and Comparison, Overall, by Jurisdiction, Among Adults 75 Years and Older and Adults 60─74 Years with High-Risk Conditions
The repository also contains 3 CSV files about 2023-2024 Weekly RSV vaccination data.
- 2023_24_observed_coverage_60plus_NIS.csv
- 2023_2024_observed_coverage_maternal_vaccine_nirsevimab_NIS.csv contains the monthly estimates of receipt for nirsevimab reported by adult females aged 18–49 years with infants under the age of 8 months. Data is from the National Immunization Survey-Adult COVID Module (NIS-ACM). Also contains maternal vaccine coverage estimates for pregnant persons 18-49 years old based on EHR data from the Vaccine Safety Datalink, obtained from National Center for Immunization and Respiratory Diseases (NCIRD)
- 2023_24_nirsevimab_coverage.csv from Monthly Cumulative Number and Percent of Children <20 Months Who Received Nirsevimab by Age Group and Jurisdiction assessed through the Immunization Information System (IIS) obtained from National Center for Immunization and Respiratory Diseases (NCIRD). Note that the IIS underestimates the true coverage. The file also contains monthly national estimates of eceipt for nirsevimab reported by adult females ged 18–49 years with infants under the age of 8 months obtained from the National Immunization Survey-Adult COVID Module (NIS-ACM).
The NIS and IIS estimates are based on different groups of children recommended to receive nirsevimab. The IIS estimates include only "catch-up: babies" ie excludes babies who would become eligible on or after October 1, 2023 (i.e., babies born October 2023 - March 2024 are excluded). Further, IIS is based on an administrative database which may miss a fraction of immunizations.
The Percent Positivity of Respiratory Syncytial Virus Nucleic Acid Amplification Tests by HHS Region, National Respiratory and Enteric Virus Surveillance System is also downloaded weekly and output in a PARQUET file: rsv/nrevss/weekly_positivity.parquet.
More than 450 public health, clinical, and commercial laboratories located throughout the United States voluntarily participate in surveillance for respiratory syncytial virus (RSV) through CDC's National Respiratory and Enteric Virus Surveillance System (NREVSS). The data contain weekly, aggregate counts of RSV tests performed and RSV detections as reported to NREVSS since April 11, 2020.
For more information, please consult the homepage of the data and the NREVSS webpage information
Both the 2023 Respiratory Virus Response - NSSP Emergency Department Visit Trajectories by State and Sub State Regions- COVID-19, Flu, RSV, Combined, 2023 Respiratory Virus Response - NSSP Emergency Department Visits - COVID-19, Flu, RSV, Combined – by Demographic Category are downloaded weekly and output in PARQUET files:
2023 Respiratory Virus Response - NSSP Emergency Department (ED) Visit Trajectories by State and Sub-State Regions- COVID-19, Flu, RSV, Combined. This dataset provides the percentage of emergency department patient visits for the specified pathogen of all ED patient visits for the specified geography each part of the country that were observed for the given week from data submitted to the National Syndromic Surveillance Program (NSSP).
For more information, please consult the NSSP homepage
For round 1, the file
vaccine_coverage/RSV_round1_Coverage_2023_2024.csv
provides vaccine coverage (percentage) from summer 2023 to the end of the
projection period to apply to infants 0-6 months (rsv_cov_infants_pes and
resv_cov_infants_opt) and seniors over 60 years (rsv_cover_over_60_pes and
rsv_cov_over60_opt). Values represent the optimistic and pessimistic
assumptions prescribed in RSV round 1
The rsv_n_dose_infants_opt is the cumulative weekly number of monoclonal
doses administered to infants 0-6 months during October through March in the
optimistic scenario. This includes birth doses and catch up doses.
rsv_n_dose_infants_pes is the same for the pessimistic scenario.
The R code to generate the rsv_n_dose_infants_ is also available in the
vaccine_coverage/ folder in an
add_doses.R file.
For the NREVSS and NSSP data, for each CSV file, an as_of column has been added
containing the date the data point has been last downloaded, see table 1 for example.
Table 1: File downloaded on 2023-10-06 and stored in the repository on 2023-10-06
| ... | report_date | as_of |
|---|---|---|
| 2021-10-02 | 2023-10-06 | |
| 2021-10-09 | 2023-10-06 | |
The source data are expressed using a rolling time period, meaning each week the data contains only the last one or two years of data. For example table 2, starts a week after table 1 and will contain an additional most recent week of data.
Table2: File downloaded on 2023-10-13
| ... | report_date | as_of |
|---|---|---|
| 2021-10-09 | 2023-10-13 | |
| 2021-10-13 | 2023-10-13 | |
To preserve all the data in the repository, the rolling time series is updated weekly and the "historical" data are kept in the CSV file. For example, table 3 contains the "historical" data from table 1 and the last updated version of the time series from table 2.
Table3: Stored file containing all the information on 2023-10-13
| ... | report_date | as_of |
|---|---|---|
| 2021-10-02 | 2023-10-06 | |
| 2021-10-09 | 2023-10-13 | |
| 2021-10-13 | 2023-10-13 | |
The National Respiratory and Enteric Virus Surveillance System (NREVSS) provides data at national and state level.
Participating laboratories report weekly to CDC the total number of RSV tests performed that week, and the number of those tests that were positive. Because reporting delays may be expected for some laboratories, data shown for the most recent weeks, in particular the most recent two weeks, may be less complete than others.
As of May 10, 2024, the data previously included on the page was moved to the a new NREVSS Interactive Dashboard. We last downloaded the data on May 10, 2024 and will not be updated.
The National RSV Trends were extracted from the NREVSS-RSV National Trends webpage.
Two tables are extracted:
- Percent positive respiratory syncytial virus tests in the United States, by week (rsv/nrevss/rsv_data_us.csv)
- RSV detections in the United States, by week (rsv/nrevss/rsv_numerator_data_us.csv)
The National RSV Trends were extracted from the NREVSS-RSV State Trends webpage.
State-level trends are only displayed when two or more labs report RSV testing data for at least 36 of the prior 52 weeks presented by diagnostic method.
For each state, three tables are extracted:
- Percent positive antigen detection RSV tests, by 3-week moving average (rsv/nrevss/rsv_antigen_3_week_average.csv)
- Percent positive RSV PCR tests, by 3-week moving average (rsv/nrevss/rsv_pcr_3_week_average.csv)
- RSV detections, by 5-week average (rsv/nrevss/rsv_numerator_data_5_week_average.csv)
All the states data are compiled together into one file.
National Emergency Department Visits for COVID-19, Influenza, and Respiratory Syncytial Virus (NSSP) [Archived]
The national and state level data are extracted from the National Emergency Department Visits webpage.
[...] emergency department visit data for multiple respiratory conditions as tracked by the National Syndromic Surveillance Program (NSSP). NSSP is a collaboration among CDC, federal partners, state and local health departments, and academic and private sector partners to collect, analyze, and share electronic data received from multiple health care settings. Data are monitored for a subset of emergency departments across the United States.
As Oct 2, 2024, the data extraction was stopped, last downloaded the data on Oct 2, 2024 and will not be updated.
Three tables are extracted from this page:
- Weekly Emergency Department Visits by Age Group (rsv/nssp/resp_ed_count_weekly_national.csv)
- Weekly Emergency Department Visits by Age Group and Respiratory Illness, as a Percent of All Emergency Department Visits (rsv/nssp/resp_ed_percent_weekly_national.csv)
- Weekly Emergency Department Visits by Viral Respiratory Illness Type and State, as a Percent of All Emergency Department Visits (rsv/nssp/resp_ed_percent_weekly_state.csv)