The following dashboards provide data on contagious respiratory viruses, including acute respiratory diseases, COVID-19, influenza (flu), and respiratory syncytial virus (RSV) in Massachusetts. The data presented here can help track trends in respiratory disease and vaccination activity across Massachusetts.

Access available resources below such as data reports, and Public Health Council presentations.

NO LONGER UPDATED. See the State Respiratory Illness Reporting site (https://www.mass.gov/info-details/respiratory-illness-reporting) for more recent information.

This is a dataset for the City of Somerville Infectious Illness Dashboard. This dataset combines multiple public data sources concerning COVID and flu in Massachusetts and, where possible, in the Somerville area specifically. Data sources include the Center for Disease Control, the Massachusetts Department of Public Health, and the Massachusetts Water Resources Authority.

The main entity of this document is a taxonomy with accession number 1865945

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.

Note: After November 1, 2024, this dataset will no longer be updated due to a transition in NHSN Hospital Respiratory Data reporting that occurred on Friday, November 1, 2024. For more information on NHSN Hospital Respiratory Data reporting, please visit https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html.

Due to a recent update in voluntary NHSN Hospital Respiratory Data reporting that occurred on Wednesday, October 9, 2024, reporting levels and other data displayed on this page may fluctuate week-over-week beginning Friday, October 18, 2024. For more information on NHSN Hospital Respiratory Data reporting, please visit https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html. Find more information about the updated CMS requirements: https://www.federalregister.gov/documents/2024/08/28/2024-17021/medicare-and-medicaid-programs-and-the-childrens-health-insurance-program-hospital-inpatient. 
. This dataset represents weekly respiratory virus-related hospitalization data and metrics aggregated to national and state/territory levels reported during two periods: 1) data for collection dates from August 1, 2020 to April 30, 2024, represent data reported by hospitals during a mandated reporting period as specified by the HHS Secretary; and 2) data for collection dates beginning May 1, 2024, represent data reported voluntarily by hospitals to CDC’s National Healthcare Safety Network (NHSN). NHSN monitors national and local trends in healthcare system stress and capacity for up to approximately 6,000 hospitals in the United States. Data reported represent aggregated counts and include metrics capturing information specific to COVID-19- and influenza-related hospitalizations, hospital occupancy, and hospital capacity. Find more information about reporting to NHSN at: https://www.cdc.gov/nhsn/covid19/hospital-reporting.html

Source: COVID-19 hospitalization data reported to CDC’s National Healthcare Safety Network (NHSN).

• Data source description(updated October 18, 2024): As of October 9, 2024, Hospital Respiratory Data (HRD; formerly Respiratory Pathogen, Hospital Capacity, and Supply data or ‘COVID-19 hospital data’) are reported to HHS through CDC’s National Healthcare Safety Network based on updated requirements from the Centers for Medicare and Medicaid Services (CMS). These data are voluntarily reported to NHSN as of May 1, 2024 until November 1, 2024, at which time CMS will require acute care and critical access hospitals to electronically report information via NHSN about COVID-19, Influenza, and RSV, hospital bed census and capacity, and limited patient demographic information, including age. Data for collection dates prior to May 1, 2024, represent data reported during a previously mandated reporting period as specified by the HHS Secretary. Data for collection dates May 1, 2024, and onwards represent data reported voluntarily to NHSN; as such, data included represents reporting hospitals only for a given week and might not be complete or representative of all hospitals. NHSN monitors national and local trends in healthcare system stress and capacity for approximately 6,000 hospitals in the United States. Data reported by hospitals to NHSN represent aggregated counts and include metrics capturing information specific to hospital capacity, occupancy, hospitalizations, and admissions. Find more information about reporting to NHSN: https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html. Find more information about the updated CMS requirements: https://www.federalregister.gov/documents/2024/08/28/2024-17021/medicare-and-medicaid-programs-and-the-childrens-health-insurance-program-hospital-inpatient.
• Data quality: While CDC reviews reported data for completeness and errors and corrects those found, some reporting errors might still exist within the data. CDC and partners work with reporters to correct these errors and update the data in subsequent weeks. Data since December 1, 2020, have had error correction methodology applied; data prior to this date may have anomalies that are not yet resolved. Data prior to August 1, 2020, are unavailable.
• Metrics and inclusion criteria: Many hospital subtypes, including acute care and critical access hospitals, are included in the metric calculations included in this dataset. Psychiatric, rehabilitation, and religious non-medical hospital types, as well as Veterans Administration, Defense Health Agency, and Indian Health Service hospitals, are excluded from calculations. For a given metric calculation, hospitals that reported those data at least one day during a given week are included.
• Find full details on NHSN hospital data reporting guidance at https://www.hhs.gov/sites/default/files/covid-19-faqs-hospitals-hospital-laboratory-acute-care-facility-data-reporting.pdf

Notes: May 10, 2024: Due to missing hospital data for the April 28, 2024 through May 4, 2024 reporting period, data for Commonwealth of the Northern Mariana Islands (CNMI) are not available for this period in the Weekly NHSN Hospitalization Metrics report released on May 10, 2024.

May 17, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), Minnesota (MN), and Guam (GU) for the May 5,2024 through May 11, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 1, 2024.

May 24, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), and Minnesota (MN) for the May 12, 2024 through May 18, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 24, 2024.

May 31, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Virgin Islands (VI), Massachusetts (MA), and Minnesota (MN) for the May 19, 2024 through May 25, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 31, 2024.

June 7, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Virgin Islands (VI), Massachusetts (MA), Guam (GU), and Minnesota (MN) for the May 26, 2024 through June 1, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 7, 2024.

June 14, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), and Minnesota (MN) for the June 2, 2024 through June 8, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 14, 2024.

June 21, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Guam (GU), Virgin Islands (VI), and Minnesota (MN) for the June 9, 2024 through June 15, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 21, 2024.

June 28, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 16, 2024 through June 22, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 28, 2024.

July 5, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 23, 2024 through June 29, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 5, 2024.

July 12, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 30, 2024 through July 6 , 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 12, 2024.

July 19, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 7, 2024 through July 13, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 19, 2024.

July 26, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 13, 2024 through July 20, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 26, 2024.

August 2, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), West Virginia (WV), and Minnesota (MN) for the July 21, 2024 through July 27, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 2, 2024.

August 9, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), Guam (GU), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 28, 2024 through August 3, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 9, 2024.

August 16, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the August 4, 2024 through August 10, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 16, 2024.

August 23, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the August 11, 2024 through August 17, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics

This is a dataset for the City of Somerville Infectious Illness Dashboard. This dataset combines multiple public data sources concerning COVID and flu in Massachusetts and, where possible, in the Somerville area specifically. Data sources include the Center for Disease Control, the Massachusetts Department of Public Health, and the Massachusetts Water Resources Authority.

Influenza A virus (IAV) is known to circulate among human and animal reservoirs, yet there are few studies that address the potential for urban rodents to carry and shed IAV. Rodents are often used as influenza models in the lab, but the few field studies that have looked for evidence of IAV in rodents have done so primarily in rural areas following outbreaks of IAV in poultry. This study sought to assess the prevalence of IAV recovered from wild Norway rats in a dense urban location (Boston). To do this, we sampled the oronasal cavity, paws, and lungs of Norway rats trapped by the City of Boston's Inspectional Services from December 2016 to September 2018. All samples were screened by real-time, reverse transcriptase PCR targeting the conserved IAV matrix segment. A total of 163 rats were trapped, 18 of which (11.04%) were RT-PCR positive for IAV in either oronasal swabs (9), paw swabs (9), both (2), or lung homogenates (2). A generalized linear model indicated that month and geographic location were correlated with IAV-positive PCR status of rats. A seasonal trend in IAV-PCR status was observed with the highest prevalence occurring in the winter months (December–January) followed by a decline over the course of the year, reaching its lowest prevalence in September. Sex and weight of rats were not significantly associated with IAV-PCR status, suggesting that rodent demography is not a primary driver of infection. This pilot study provides evidence of the need to further investigate the role that wild rats may play as reservoirs or mechanical vectors for IAV circulation in urban environments across seasons.

Note: After November 1, 2024, this dataset will no longer be updated due to a transition in NHSN Hospital Respiratory Data reporting that occurred on Friday, November 1, 2024. For more information on NHSN Hospital Respiratory Data reporting, please visit https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html.

Due to a recent update in voluntary NHSN Hospital Respiratory Data reporting that occurred on Wednesday, October 9, 2024, reporting levels and other data displayed on this page may fluctuate week-over-week beginning Friday, October 18, 2024. For more information on NHSN Hospital Respiratory Data reporting, please visit https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html. Find more information about the updated CMS requirements: https://www.federalregister.gov/documents/2024/08/28/2024-17021/medicare-and-medicaid-programs-and-the-childrens-health-insurance-program-hospital-inpatient. 

This dataset represents weekly respiratory virus-related hospitalization data and metrics aggregated to national and state/territory levels reported during two periods: 1) data for collection dates from August 1, 2020 to April 30, 2024, represent data reported by hospitals during a mandated reporting period as specified by the HHS Secretary; and 2) data for collection dates beginning May 1, 2024, represent data reported voluntarily by hospitals to CDC’s National Healthcare Safety Network (NHSN). NHSN monitors national and local trends in healthcare system stress and capacity for up to approximately 6,000 hospitals in the United States. Data reported represent aggregated counts and include metrics capturing information specific to COVID-19- and influenza-related hospitalizations, hospital occupancy, and hospital capacity. Find more information about reporting to NHSN at: https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html.

Source: COVID-19 hospitalization data reported to CDC’s National Healthcare Safety Network (NHSN).

• Data source description (updated October 18, 2024): As of October 9, 2024, Hospital Respiratory Data (HRD; formerly Respiratory Pathogen, Hospital Capacity, and Supply data or ‘COVID-19 hospital data’) are reported to HHS through CDC’s National Healthcare Safety Network based on updated requirements from the Centers for Medicare and Medicaid Services (CMS). These data are voluntarily reported to NHSN as of May 1, 2024 until November 1, 2024, at which time CMS will require acute care and critical access hospitals to electronically report information via NHSN about COVID-19, Influenza, and RSV, hospital bed census and capacity, and limited patient demographic information, including age. Data for collection dates prior to May 1, 2024, represent data reported during a previously mandated reporting period as specified by the HHS Secretary. Data for collection dates May 1, 2024, and onwards represent data reported voluntarily to NHSN; as such, data included represents reporting hospitals only for a given week and might not be complete or representative of all hospitals. NHSN monitors national and local trends in healthcare system stress and capacity for approximately 6,000 hospitals in the United States. Data reported by hospitals to NHSN represent aggregated counts and include metrics capturing information specific to hospital capacity, occupancy, hospitalizations, and admissions. Find more information about reporting to NHSN: https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html. Find more information about the updated CMS requirements: https://www.federalregister.gov/documents/2024/08/28/2024-17021/medicare-and-medicaid-programs-and-the-childrens-health-insurance-program-hospital-inpatient. 
• Data quality: While CDC reviews reported data for completeness and errors and corrects those found, some reporting errors might still exist within the data. CDC and partners work with reporters to correct these errors and update the data in subsequent weeks. Data since December 1, 2020, have had error correction methodology applied; data prior to this date may have anomalies that are not yet resolved. Data prior to August 1, 2020, are unavailable.
• Metrics and inclusion criteria: Many hospital subtypes, including acute care and critical access hospitals, are included in the metric calculations included in this dataset. Psychiatric, rehabilitation, and religious non-medical hospital types, as well as Veterans Administration, Defense Health Agency, and Indian Health Service hospitals, are excluded from calculations. For a given metric calculation, hospitals that reported those data at least one day during a given week are included.
• Find full details on NHSN Hospital Respiratory Data (HRD) reporting guidance, including additional information on bed type definitions at https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html.

Notes: May 10, 2024: Due to missing hospital data for the April 28, 2024 through May 4, 2024 reporting period, data for Commonwealth of the Northern Mariana Islands (CNMI) are not available for this period in the Weekly NHSN Hospitalization Metrics report released on May 10, 2024.

May 17, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), Minnesota (MN), and Guam (GU) for the May 5,2024 through May 11, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 1, 2024.

May 24, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), and Minnesota (MN) for the May 12, 2024 through May 18, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 24, 2024.

May 31, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Virgin Islands (VI), Massachusetts (MA), and Minnesota (MN) for the May 19, 2024 through May 25, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on May 31, 2024.

June 7, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Virgin Islands (VI), Massachusetts (MA), Guam (GU), and Minnesota (MN) for the May 26, 2024 through June 1, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 7, 2024.

June 14, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), and Minnesota (MN) for the June 2, 2024 through June 8, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 14, 2024.

June 21, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Guam (GU), Virgin Islands (VI), and Minnesota (MN) for the June 9, 2024 through June 15, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 21, 2024.

June 28, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 16, 2024 through June 22, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on June 28, 2024.

July 5, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 23, 2024 through June 29, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 5, 2024.

July 12, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), West Virginia (WV), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the June 30, 2024 through July 6, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 12, 2024.

July 19, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 7, 2024 through July 13, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 19, 2024.

July 26, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 13, 2024 through July 20, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on July 26, 2024.

August 2, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), West Virginia (WV), and Minnesota (MN) for the July 21, 2024 through July 27, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 2, 2024.

August 9, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), Guam (GU), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the July 28, 2024 through August 3, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 9, 2024.

August 16, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the August 4, 2024 through August 10, 2024 reporting period are not available for the Weekly NHSN Hospitalization Metrics report released on August 16, 2024.

August 23, 2024: Data for Commonwealth of the Northern Mariana Islands (CNMI), Massachusetts (MA), American Samoa (AS), Virgin Islands (VI), and Minnesota (MN) for the August 11, 2024 through August 17, 2024 reporting period are not available for the Weekly

This dataset represents preliminary estimates of cumulative U.S. COVID-19 disease burden for the 2024-2025 period, including illnesses, outpatient visits, hospitalizations, and deaths. The weekly COVID-19-associated burden estimates are preliminary and based on continuously collected surveillance data from patients hospitalized with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. The data come from the Coronavirus Disease 2019 (COVID-19)-Associated Hospitalization Surveillance Network (COVID-NET), a surveillance platform that captures data from hospitals that serve about 10% of the U.S. population. Each week CDC estimates a range (i.e., lower estimate and an upper estimate) of COVID-19 -associated burden that have occurred since October 1, 2024.

Note: Data are preliminary and subject to change as more data become available. Rates for recent COVID-19-associated hospital admissions are subject to reporting delays; as new data are received each week, previous rates are updated accordingly.

References

1. Reed C, Chaves SS, Daily Kirley P, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369. https://doi.org/10.1371/journal.pone.0118369 
2. Rolfes, MA, Foppa, IM, Garg, S, et al. Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness. Influenza Other Respi Viruses. 2018; 12: 132– 137. https://doi.org/10.1111/irv.12486
3. Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331-7337. doi:10.1016/j.vaccine.2018.10.026 
4. Collier SA, Deng L, Adam EA, Benedict KM, Beshearse EM, Blackstock AJ, Bruce BB, Derado G, Edens C, Fullerton KE, Gargano JW, Geissler AL, Hall AJ, Havelaar AH, Hill VR, Hoekstra RM, Reddy SC, Scallan E, Stokes EK, Yoder JS, Beach MJ. Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States. Emerg Infect Dis. 2021 Jan;27(1):140-149. doi: 10.3201/eid2701.190676. PMID: 33350905; PMCID: PMC7774540.
5. Reed C, Kim IK, Singleton JA,  et al. Estimated influenza illnesses and hospitalizations averted by vaccination–United States, 2013-14 influenza season. MMWR Morb Mortal Wkly Rep. 2014 Dec 12;63(49):1151-4. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm 
6. Reed C, Angulo FJ, Swerdlow DL, et al. Estimates of the Prevalence of Pandemic (H1N1) 2009, United States, April–July 2009. Emerg Infect Dis. 2009;15(12):2004-2007. https://dx.doi.org/10.3201/eid1512.091413  
7. Devine O, Pham H, Gunnels B, et al. Extrapolating Sentinel Surveillance Information to Estimate National COVID-19 Hospital Admission Rates: A Bayesian Modeling Approach. Influenza and Other Respiratory Viruses. https://onlinelibrary.wiley.com/doi/10.1111/irv.70026. Volume18, Issue10. October 2024.
8. https://www.cdc.gov/covid/php/covid-net/index.html">COVID-NET | COVID-19 | CDC 
9. https://www.cdc.gov/covid/hcp/clinical-care/systematic-review-process.html 
10. https://academic.oup.com/pnasnexus/article/1/3/pgac079/6604394?login=false">Excess natural-cause deaths in California by cause and setting: March 2020 through February 2021 | PNAS Nexus | Oxford Academic (oup.com)
11. Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial with R and BUGS. Elsevier, Amsterdam, Section 3.3.5.

We performed single-cell RNA sequencing (scRNA-Seq) on nasal wash cells freshly collected from adults with COVID-19, influenza A, or no disease (healthy). Major cell types and subtypes were defined using cluster analysis and classic transcriptional markers. Seq-Well single-cell RNA-Seq analysis of cells taken from nasal wash samples from healthy donors and patients diagnosed with either COVID-19 or influenza A

BackgroundInfluenza virus is one of the most common pathogens that cause viral pneumonia. During pneumonia, host immune inflammation regulation involves microbiota in the intestine and glycolysis in the lung tissues. In the clinical guidelines for pneumonia treatment in China, Ma Xing Shi Gan Decoction (MXSG) is a commonly prescribed traditional Chinese medicine formulation with significant efficacy, however, it remains unclear whether its specific mechanism of action is related to the regulation of intestinal microbiota structure and lung tissue glycolysis.ObjectiveThis study aimed to investigate the mechanism of action of MXSG in an animal model of influenza virus-induced pneumonia. Specifically, we aimed to elucidate how MXSG modulates intestinal microbiota structure and lung tissue glycolysis to exert its therapeutic effects on pneumonia.MethodsWe established a mouse model of influenza virus-induced pneumoni, and treated with MXSG. We observed changes in inflammatory cytokine levels and conducted 16S rRNA gene sequencing to assess the intestinal microbiota structure and function. Additionally, targeted metabolomics was performed to analyze lung tissue glycolytic metabolites, and Western blot and enzyme-linked immunosorbent assays were performed to assess glycolysis-related enzymes, lipopolysaccharides (LPSs), HIF-1a, and macrophage surface markers. Correlation analysis was conducted between the LPS and omics results to elucidate the relationship between intestinal microbiota and lung tissue glycolysis in pneumonia animals under the intervention of Ma Xing Shi Gan Decoction.ResultsMXSG reduced the abundance of Gram-negative bacteria in the intestines, such as Proteobacteria and Helicobacter, leading to reduced LPS content in the serum and lungs. This intervention also suppressed HIF-1a activity and lung tissue glycolysis metabolism, decreased the number of M1-type macrophages, and increased the number of M2-type macrophages, effectively alleviating lung damage caused by influenza virus-induced pneumonia.ConclusionMXSG can alleviate glycolysis in lung tissue, suppress M1-type macrophage activation, promote M2-type macrophage activation, and mitigate inflammation in lung tissue. This therapeutic effect appears to be mediated by modulating gut microbiota and reducing endogenous LPS production in the intestines. This study demonstrates the therapeutic effects of MXSG on pneumonia and explores its potential mechanism, thus providing data support for the use of traditional Chinese medicine in the treatment of respiratory infectious diseases.

This dataset represents preliminary estimates of cumulative U.S. RSV –associated disease burden estimates for the 2024-2025 season, including outpatient visits, hospitalizations, and deaths. Real-time estimates are preliminary and based on continuously collected surveillance data from patients hospitalized with laboratory-confirmed respiratory syncytial virus (RSV) infections. The data come from the Respiratory Syncytial Virus Hospitalization Surveillance Network (RSV-NET), a surveillance platform that captures data from hospitals that serve about 8% of the U.S. population. Each week CDC estimates a range (i.e., lower estimate and an upper estimate) of RSV-associated disease burden estimates that have occurred since October 1, 2024.

Note: Data are preliminary and subject to change as more data become available. Rates for recent RSV-associated hospital admissions are subject to reporting delays; as new data are received each week, previous rates are updated accordingly.

Note: Preliminary burden estimates are not inclusive of data from all RSV-NET sites. Due to model limitations, sites with small sample sizes can impact estimates in unpredictable ways and are excluded for the benefit of model stability. CDC is working to address model limitations and include data from all sites in final burden estimates.

References

1. Reed C, Chaves SS, Daily Kirley P, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369. https://doi.org/10.1371/journal.pone.0118369 
2. Rolfes, MA, Foppa, IM, Garg, S, et al. Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness. Influenza Other Respi Viruses. 2018; 12: 132– 137. https://doi.org/10.1111/irv.12486
3. Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331-7337. doi:10.1016/j.vaccine.2018.10.026 
4. Collier SA, Deng L, Adam EA, Benedict KM, Beshearse EM, Blackstock AJ, Bruce BB, Derado G, Edens C, Fullerton KE, Gargano JW, Geissler AL, Hall AJ, Havelaar AH, Hill VR, Hoekstra RM, Reddy SC, Scallan E, Stokes EK, Yoder JS, Beach MJ. Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States. Emerg Infect Dis. 2021 Jan;27(1):140-149. doi: 10.3201/eid2701.190676. PMID: 33350905; PMCID: PMC7774540.
5. Reed C, Kim IK, Singleton JA,  et al. Estimated influenza illnesses and hospitalizations averted by vaccination–United States, 2013-14 influenza season. MMWR Morb Mortal Wkly Rep. 2014 Dec 12;63(49):1151-4. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm 
6. Reed C, Angulo FJ, Swerdlow DL, et al. Estimates of the Prevalence of Pandemic (H1N1) 2009, United States, April–July 2009. Emerg Infect Dis. 2009;15(12):2004-2007. https://dx.doi.org/10.3201/eid1512.091413  
7. Devine O, Pham H, Gunnels B, et al. Extrapolating Sentinel Surveillance Information to Estimate National COVID-19 Hospital Admission Rates: A Bayesian Modeling Approach. Influenza and Other Respiratory Viruses. https://onlinelibrary.wiley.com/doi/10.1111/irv.70026. Volume18, Issue10. October 2024.
8. https://www.cdc.gov/covid/php/covid-net/index.html">COVID-NET | COVID-19 | CDC 
9. https://www.cdc.gov/covid/hcp/clinical-care/systematic-review-process.html 
10. https://academic.oup.com/pnasnexus/article/1/3/pgac079/6604394?login=false">Excess natural-cause deaths in California by cause and setting: March 2020 through February 2021 | PNAS Nexus | Oxford Academic (oup.com)
11. Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial with R and BUGS. Elsevier, Amsterdam, Section 3.3.5.

WHISPers stands for Wildlife Health Information Sharing Partnership - event reporting system. It is a web-based repository for sharing basic information about historic and ongoing wildlife mortality (death) and morbidity (illness) events. The system possesses a searchable archive of wildlife mortality and morbidity event data that is available to the public. The information is opportunistically collected and does not reflect all the mortality events that occur in North America. WHISPers is driven by a subset of data housed in NWHC’s ‘Epizoo’ database (http://data.usgs.gov/datacatalog/#q=EPIZOO).

Parental perceptions and knowledge toward influenza and IV.

Factors associated with IV (ever received) of the index child (among all participants).

Differences in clearance of lung viral particles in vaccinated mice 4 days post-challenge with live ma-pH1N1.

Human primary macrophages were infected with influenza A virus (H3N2/Udorn strain, HA 256) for 6 hrs or left untreated. Cells were collected and lysed with HEPES lysis buffer (50 mM HEPES, 150 mM NaCl, 1 mM EDTA, 1 % NP-40, pH 7.4) including protease and phosphatase inhibitor cocktails. The cell lysates were centrifuged and the supernatant was collected and the protein content was measured with Bio-Rad DC™ protein assay (Bio-Rad). The proteins were reduced, alkylated, and enzymatically digested in-solution with trypsin. The digestion was stopped by adding FA (final c = 1 %). The samples were centrifuged 9168 x g for 10 min and desalted with Sep-Pak Vac RP C18 cartridges (Waters, MA, USA), following fractionation by strong cation exchange chromatography (SCX). The peptides were separated on a 200 x 4.6 mm, 5 μm, 200 Å PolySULFOETHYL A™ column (PolyLC, USA). The fractions were vacuum centrifuged and desalted as before, following phosphopeptide-enrichment with PHOS-Select™ Iron Affinity Gel (Sigma Aldrich, MO, USA). LC-MS/MS was performed with a Q Exactive hybrid quadrupole-orbitrap tandem mass spectrometer coupled to an EASY-nLC 1000 nanoflow liquid chromatograph (Thermo Fisher Scientific). A 100 μm x 3 cm trap column and a 75 μm x 15 cm analytical column were in-house packed with Magic C18AQ resin (200 Å, 5 μm; Michrom Bioresources). The mobile phases were 2% acetonitrile, 0.2% formic acid (A) and 95% acetonitrile, 0.2% formic acid (B). LC gradient elution condition was 2% B (0 min), 20% B (70 min), 40% B (100 min), and then 100% B (105-110 min), with a flow rate of 300 nl/min. Data dependent acquisition was performed in positive ion mode. MS spectra were acquired from m/z 300 to m/z 2000 at a resolution of 70,000 at m/z 200 with a target value of 1,000,000 and maximum injection time of 120 ms. The 10 most abundant precursor ions of which charge states were 2+ or higher were selected for higher energy collisional dissociation (HCD) with an isolation window of 2 and normalized collision energy of 30. MS/MS spectra were acquired at a resolution of 17,500 at m/z 200 with a target value of 50,000, maximum injection time of 250 ms, and the lowest mass fixed at m/z 100. Dynamic exclusion duration was 30 s.

Influenza epidemics represent a significant threat to global public health, primarily caused by the influenza viruses A and B. Although antiviral drugs targeting the influenza virus, such as zanamivir and oseltamivir, are clinically available, the emergence of virus evolution and drug resistance necessitates the development of host-directed therapies. Protein kinases are essential components of host signaling pathways, including the orchestration of virus–host interactions. By screening a library of kinase inhibitors, we identified that OTS167, a pharmacological inhibitor of maternal embryonic leucine zipper kinase (MELK), strongly inhibits the infections caused by multiple influenza virus subtypes in cell culture. This antiviral activity was further confirmed by treatment with another MELK pharmacological inhibitor, MELK-8a, and siRNA-mediated MELK gene silencing. In mice challenged with the influenza A virus, treatment with OTS167 inhibited both viral replication and lung inflammation. Mechanistically, inhibition of MELK by OTS167 downregulates the downstream effector CDK1, thereby inhibiting influenza virus M1 mRNA splicing to reduce viral replication and virus particle assembly. Finally, we demonstrated that combining OTS167 with zanamivir or oseltamivir resulted in additive antiviral activity. In conclusion, we identified MELK as a crucial host kinase that supports the influenza virus infection. OTS167, a pharmacological inhibitor of MELK currently undergoing phase II clinical trials for treating cancer, potently inhibits influenza virus infections in vitro and in mice, representing a promising lead for developing novel influenza antivirals.

Estimated number of medically-attended (MA) influenza cases averted by vaccination, 2005/06–2010/11 influenza seasons (95% confidence interval in parentheses).