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
The folder vaccine_coverage/ provides weekly state-specific cumulative coverage for specific rounds.
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_indants_ is also available in the
vaccine_coverage/ folder in an
add_doses.R file.
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.
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 are 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 are 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)
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.
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)
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