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.

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.

NO LONGER UPDATED.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.

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

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

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.

The demographic characteristics, clinical features, course, and outcomes of severe H1N1 influenza infection requiring intensive care have not been defined rigorously and systematically. While the majority of patients in early reports of critically ill novel influenza A (H1N1) have respiratory involvement, up to 10-20% may present with non-respiratory organ failures, such as shock, seizures, or acute renal failure. The burden of disease and resource utilization of these patients remains largely unknown. The purpose of this surveillance registry is to characterize the demographics, clinical features, outcomes, and resource utilization of patients with H1N1 influenza infection who require intensive care.

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.

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

Studies of pathogen transmission typically overlook that wildlife hosts can include both migrant and resident populations when attempting to model circulation. Through the application of stable isotopes in flight feathers, we estimated the migration strategy of mallards (Anas platyrhynchos) - resident, intermediate-distance migrant or long-distance migrant, occurring on California wintering grounds. Our study demonstrates that mallards, a principal host of avian influenza virus (AIV) in nature, contribute differently to virus gene flow depending on migration strategy. No difference in AIV prevalence was detected between resident (9.6%), intermediate-distance (9.6%) and long-distance migrants (7.4%). Viral diversity among the three groups was also comparable, possibly owing to viral pool mixing when birds converge at wetlands during winter. These findings challenge the view that migratory animals are exposed to a higher number and diversity of pathogens. However, migrants and residents contributed differently to the virus gene pool at wintering wetlands. Migrants introduced virus from northern breeding grounds (Alaska and the NW Pacific Rim) into the wintering population, facilitating gene flow at continental scales, but circulation of imported virus appeared to be limited. In contrast, resident mallards acted as AIV reservoirs facilitating year-round circulation of limited subtypes (i.e. H5N2) at lower latitudes. This study supports a model of virus exchange in temperate regions driven by the convergence of wild birds with separate geographic origins and exposure histories.

Here, we present a systematic and quantitative test of the hypothesis that the composition and activities of the endoplasmic reticulum (ER) proteostasis network impact mutational tolerance of secretory pathway client proteins. We focus on influenza hemagluttinin (HA), a viral coat protein that folds in the host’s ER via a complex but well-characterized pathway. By integrating chemical methods to modulate the unfolded protein response with deep mutational scanning to assess mutational tolerance, we discover that upregulation of ER chaperones broadly enhances HA mutational tolerance across numerous sites and secondary/tertiary structure elements, including sites targeted by host antibodies. Remarkably, this host chaperone-enhanced mutational tolerance is observed at the same HA sites where mutational tolerance is most reduced by propagation at a fever-like temperature. Thus, host ER proteostasis mechanisms and temperature modulate HA mutational tolerance in opposite directions. This finding has important implications for influenza evolution, because influenza immune escape is contingent on HA possessing sufficient mutational tolerance to acquire antibody resistance while still maintaining the capacity to fold and function. More broadly, this work provides the first experimental evidence that the composition and activities of the ER proteostasis network critically define the mutational tolerance and, therefore, the evolution of secretory pathway client proteins. RNA-seq characterizing a clonal HEK293T-Rex cell line, expressing DHFR ATF6f, Tet XBP1s, and the tetracycline repressor. These cell lines were treated with small molecules for 24 hours (in triplicate) to modulate the proteostasis environment in a stress-independent manner, at either 37C or 39C. XBP1s was activated by treatment with 0.1 ug/mL Doxycycline; ATF6f/XBP1s were activated by treatment with 0.1 ug/mL Doxycycline and 1 uM TMP; basal cells were vehicle-treated (0.01% DMSO). These cells were previously characterized in Shoulders et al. Cell Reports, 2013.

Antigenic relationships between B/Yamagata isolates and B/Wisconsin/01/2010, B/Massachusetts/02/2012 and B/Phuket/3073/2013 and amino acid substitutions on HA1 gene, refer to B/Wisconsin/01/2010 strain.

H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterize ecological and environmental predictors of virus spread between geographic regions through constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). Findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the US, H5Nx viruses spread at a greater rate between US-based regions and no evidence demonstrated spread back to any European region. We establish that geographic proximity is a predictor of virus spread between regions, which implies that inter-continental transport across the Atlantic Ocean is relatively rare. Increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and North America during an actively evolving inter-continental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses. Methods Publicly available H5Nx sequence data and phylogenetic analysis All publicly available avian-derived (domestic and wild) H5Nx HA segment sequences from Europe and North America between 2016 and 2022 were downloaded from the Influenza Research Database (IRD) on May 12, 2022 (n=321). We added 170 publicly available H5Nx HA sequences from 2021–2022 downloaded from GISAID on May 15, 2022, as these were unavailable on IRD at the time of sequence acquisition, and 15 unpublished H5N1 HA sequences from avian surveillance in Massachusetts, USA by our research group in 2022 (described elsewhere), totaling 546 HA sequences. Metadata for each sequence was collected, including sampling date, season, host species, and geographic sampling location. Only IAV sequences from wild avian species or environmental matrices were included. Duplicate sequences, sequences with less than 75% unambiguous bases, all vaccine derivative and recombinant sequences, and sequences with unavailable isolation date, location, or host species were excluded, resulting in 506 sequences. Downsampling was performed to ensure relative evenness of geographic state groupings while preserving genetic diversity of the dataset, using geographic state and year for random stratification. To root and historically time-calibrate the tree, H5 subtype HA avian sequences from IRD were downloaded for the period 1979–2015 from Europe and North America and randomly downsampled by year, resulting in 33 historic sequences. These sequences were ‘masked’ to ensure their contribution to the tree structure but not to quantification of diffusion rates or the GLM. The total downsampled dataset, including the outgroup (GISAID sequences from North America (n=170), unpublished Massachusetts sequences acquired by our group (n=15), publicly available H5Nx sequences from Europe 2016-2022 (n=162)), and historic sequences (n=33) resulted in a total of 380 sequences (Supplementary table 1). Multiple sequence alignments were performed using MUSCLE in Geneious Prime 2022.05.14 (https://www.geneious.com) and trimmed to the open reading frame.