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How CDC Uses Flu Forecasting

https://www.cdc.gov/flu/weekly/flusight/index.html?deliveryName=USCDC_7_3-DM14949

How CDC Forecasts Seasonal Influenza in the U.S.

The timing and severity of influenza in the United States can vary widely from season to season. Flu forecasting aims to predict the characteristics of influenza seasons before disease activity occurs and is captured by the U.S. influenza surveillance system. Since the 2013-2014 flu season, the Influenza Division at CDC has worked with CDC’s Epidemic Prediction Initiative and external researchers to improve the science and usability of flu forecasting, including the coordination of flu forecasting challenges. Recently, these challenges have been extended to the state level.

This page includes information on current and past influenza forecasting efforts, including working with external researchers and the flu season characteristics being forecasted.

Working with External Researches to Predict Flu in the U.S.

Every influenza season since 2013–2014, CDC’s Influenza Division has engaged with members of the scientific community on real-world influenza forecasting challenges known as FluSight. Originally, 11 teams participated, but interest in FluSight has grown in the six years since FluSight’s inception. We anticipate that more than 20 teams will participate during the 2019-2020 flu season.

Each challenge usually runs from late October through mid-May. Teams independently develop their forecasting approaches using a variety of methods and data sources, and teams submit forecasts to CDC on a weekly basis. At the conclusion of each challenge, CDC determines how accurate each team’s forecasts were by scoring forecasts against actual flu activity, announcing an overall winner.

FluSight brings together multiple forecasts and researchers, making real-time forecasts available in one central location and providing structured and standardized assessments of forecast accuracy. Recently, funding was awarded to Carnegie Mellon University and University at Massachusetts Amherst  to further improve the accuracy and communication of influenza forecasts at the national, regional, and state level.

What the Forecasts Aim to Predict

CDC and FluSight partners worked together to develop targets – or the outcome that a forecast is predicting (like season peak) – that would be meaningful to public health. Targets for the main FluSight Challenge at the national level are season onset, peak week, peak intensity, and short-term activity. These target definitions rely on the percent of visits to health-care providers that are for influenza-like illness from the CDC’s U.S. Outpatient ILI Surveillance Network (ILINet).

  • Season onset: The first week when ILINet is at or above baseline and remains there for at least two more weeks
  • Peak week: The week when ILINet is the highest for the whole season (it is possible to have more than one peak week in a given season if two weeks are “tied” for the highest value)
  • Peak intensity: The highest value that ILINet reaches during the season
  • Short-term ILI activity: The ILINet value one, two, three, and four weeks ahead of the date that they are available in FluView.

State-level forecasting efforts are recent, only having been available starting in the 2017-18 season. Some targets in these systems vary from the national-level.

Collaborating After Each Challenge to Understand Forecast Results and Prepare for Next Season

At the end of every forecasting season, CDC, FluSight partners, and stakeholders gather to review forecasting approaches, discuss the accuracy of forecasts from the past season, identity overall challenges and successes and plans for future seasons, such as the additions of new forecasting targets. These meetings improve the usefulness of forecasting by providing the opportunity for collaboration among forecasters and public health officials.

More Resources

Types of Influenza Viruses

CDC https://www.cdc.gov/flu/about/viruses/types.htm?deliveryName=USCDC_7_3-DM14949

illustration and cross section of flu virus

Human Seasonal Influenza Virus

figure 1 - phylogenetic tree , node common acestor, subclade, clade Figure 1 – This is a picture of a phylogenetic tree. In a phylogenetic tree, related viruses are grouped together on branches. Influenza viruses whose HA genes’ share the same genetic changes and who also share a common ancestor (node) are grouped into specific “clades” and “sub clades.” These clades and sub-clades are alternatively sometimes called “groups” and “sub-groups.”

 

understanding the naming of flu viruses virus type, place virus isolated, strain number, year isolated, virus subtype example a sydney o5 97 (h3n2)

Figure 3 – This image shows how influenza viruses are named. The name starts with the virus type, followed by the place the virus was isolated, followed by the virus strain number, the year isolated, and finally, the virus subtype.

 

There are four types of influenza viruses: A, B, C and D. Human influenza A and B viruses cause seasonal epidemics of disease (known as the flu season) almost every winter in the United States. Influenza A viruses are the only influenza viruses known to cause flu pandemics, i.e., global epidemics of flu disease. A pandemic can occur when a new and very different influenza A virus emerges that both infects people and has the ability to spread efficiently between people. Influenza type C infections generally cause mild illness and are not thought to cause human flu epidemics. Influenza D viruses primarily affect cattle and are not known to infect or cause illness in people.

Influenza A viruses are divided into subtypes based on two proteins on the surface of the virus: hemagglutinin (H) and neuraminidase (N). There are 18 different hemagglutinin subtypes and 11 different neuraminidase subtypes (H1 through H18 and N1 through N11, respectively). While there are potentially 198 different influenza A subtype combinations, only 131 subtypes have been detected in nature. Current subtypes of influenza A viruses that routinely circulate in people include: A(H1N1) and A(H3N2). Influenza A subtypes can be further broken down into different genetic “clades” and “sub-clades.” See the “Influenza Viruses” graphic below for a visual depiction of these classifications.

Clades and sub-clades can be alternatively called “groups” and “sub-groups,” respectively. An influenza clade or group is a further subdivision of influenza viruses (beyond subtypes or lineages) based on the similarity of their HA gene sequences. (See the Genome Sequencing and Genetic Characterization page for more information). Clades and subclades are shown on phylogenetic trees as groups of viruses that usually have similar genetic changes (i.e., nucleotide or amino acid changes) and have a single common ancestor represented as a node in the tree (see Figure 1). Dividing viruses into clades and subclades allows flu experts to track the proportion of viruses from different clades in circulation.

Note that clades and sub-clades that are genetically different from others are not necessarily antigenically different (i.e., viruses from a specific clade or sub-clade may not have changes that impact host immunity in comparison to other clades or sub-clades).

Currently circulating influenza A(H1N1) viruses are related to the pandemic 2009 H1N1 virus that emerged in the spring of 2009 and caused a flu pandemic (CDC 2009 H1N1 Flu website). This virus, scientifically called the “A(H1N1)pdm09 virus,” and more generally called “2009 H1N1,” has continued to circulate seasonally since then. These H1N1 viruses have undergone relatively small genetic changes and changes to their antigenic properties (i.e., the properties of the virus that affect immunity) over time.

Of all the influenza viruses that routinely circulate and cause illness in people, influenza A(H3N2) viruses tend to change more rapidly, both genetically and antigenically. Influenza A(H3N2) viruses have formed many separate, genetically different clades in recent years that continue to co-circulate.

Influenza B viruses are not divided into subtypes, but instead are further classified into two lineages: B/Yamagata and B/Victoria. Similar to influenza A viruses, influenza B viruses can then be further classified into specific clades and sub-clades. Influenza B viruses generally change more slowly in terms of their genetic and antigenic properties than influenza A viruses, especially influenza A(H3N2) viruses. Influenza surveillance data from recent years shows co-circulation of influenza B viruses from both lineages in the United States and around the world. However, the proportion of influenza B viruses from each lineage that circulate can vary by geographic location.

Naming Influenza Viruses

CDC follows an internationally accepted naming convention for influenza viruses. This convention was accepted by WHO in 1979 and published in February 1980 in the Bulletin of the World Health Organization, 58(4):585-591 (1980) (see A revision of the system of nomenclature for influenza viruses: a WHO Memorandum pdf icon[854 KB, 7 pages]external icon). The approach uses the following components:

  • The antigenic type (e.g., A, B, C, D)
  • The host of origin (e.g., swine, equine, chicken, etc.). For human-origin viruses, no host of origin designation is given. Note the following examples:
    • (Duck example): avian influenza A(H1N1), A/duck/Alberta/35/76
    • (Human example): seasonal influenza A(H3N2), A/Perth/16/2019
  • Geographical origin (e.g., Denver, Taiwan, etc.)
  • Strain number (e.g., 7, 15, etc.)
  • Year of collection (e.g., 57, 2009, etc.)
  • For influenza A viruses, the hemagglutinin and neuraminidase antigen description are provided in parentheses (e.g., influenza A(H1N1) virus, influenza A(H5N1) virus)
  • The 2009 pandemic virus was assigned a distinct name: A(H1N1)pdm09 to distinguish it from the seasonal influenza A(H1N1) viruses that circulated prior to the pandemic.
  • When humans are infected with influenza viruses that normally circulate in swine (pigs), these viruses are call variant viruses and are designated with a letter ‘v’ (e.g., an A(H3N2)v virus).

Influenza Vaccine Viruses

One influenza A(H1N1), one influenza A(H3N2), and one or two influenza B viruses (depending on the vaccine) are included in each season’s influenza vaccines. Getting a flu vaccine can protect against flu viruses that are like the viruses used to make vaccine. Information about this season’s vaccine can be found at Preventing Seasonal Flu with Vaccination. Seasonal flu vaccines do not protect against influenza C or D viruses. In addition, flu vaccines will NOT protect against infection and illness caused by other viruses that also can cause influenza-like symptoms. There are many other viruses besides influenza that can result in influenza-like illness (ILI) that spread during flu season.

 

 


Human H9N2 infections have been reported only in Hong Kong, China, Bangladesh, and Pakistan. Now it’s in India!

Potdar V, Hinge D, Satav A, Simões EF, Yadav PD, Chadha MS. Laboratory-confirmed avian influenza A(H9N2) virus infection, India, 2019. Emerg Infect Dis. 2019 Dec [date cited]. https://doi.org/10.3201/eid2512.190636

Abstract

“A 17-month-old boy in India with severe acute respiratory infection was laboratory confirmed to have avian influenza A(H9N2) virus infection. Complete genome analysis of the strain indicated a mixed lineage of G1 and H732. The strain also was found to be susceptible to adamantanes and neuraminidase inhibitors.”

Phylogenetic tree of hemagglutinin gene (A) and neuraminidase gene (B) gene of influenza virus A/India/TCM 2581/2019(H9N2) from India (black circle) and reference strains. The numbers above the branches are the bootstrap probabilities (%) for each branch, determined by using the MEGA 7.0 (https://megasoftware.net). Human cases from other countries are in bold. Scale bars indicate substitutions per site.

The case:  “……The child, a resident of Melghat, had fever, cough, breathlessness, and difficulty feeding for 2 days since illness onset on January 31, 2019. His high intermittent grade fever had no diurnal variation and no association with rash or mucocutaneous lesions. Examination revealed a conscious, restless child with a respiratory rate of 48 breaths/min and lower chest wall in-drawing with intermittent absence of breathing for >20 seconds. He was fully immunized for his age, with bacillus Calmette–Guérin, diphtheria, hepatitis B, poliovirus, and measles vaccines. Both length and weight for age were less than −3 SD. History of travel with his parents to a local religious gathering 1 week before symptom onset was elicited. The father had similar symptoms on return from the gathering but could not undergo serologic testing because of his migrant work. No history of poultry exposure was elicited. The child received an antibacterial drug and antipyretics and recovered uneventfully.….”


President Donald J. Trump Is Working to Modernize and Improve Influenza Vaccines

White House

MODERNIZING INFLUENZA VACCINES: President Donald J. Trump is safeguarding public health by helping ensure Americans have access to effective influenza vaccines. 

 

  • Today, President Trump signed an executive order to modernize influenza vaccines and help protect more Americans through vaccination.
  • At President Trump’s direction, the Administration will work to promote new technologies to improve vaccine manufacturing and effectiveness.
    • This will reduce reliance on more time-consuming, egg-based vaccine production.
    • Improving the speed of production will enable experts to better match vaccines to actively circulating viruses, an important piece of making the vaccines more effective.
    • The Administration will advance the development of new, more effective vaccines.
  • The Trump Administration will also work to increase Americans’ access to vaccines by reducing barriers to seasonal flu vaccine services.
  • To help put these objectives into action, President Trump is establishing a task force to identify policy priorities and monitor progress.

PROTECTING LIVES THROUGH PREVENTION: Influenza vaccines are vitally important to disease prevention, yet current production methods need to be improved.

  • Influenza vaccines are the best way to save lives, reduce the illness severity, and prevent influenza infections in the first place.
    • During the 2017–2018 flu season, influenza vaccinations prevented up to 7.1 million illnesses, 3.7 million medical visits, and 109,000 hospitalizations.
    • A Centers for Disease Control and Prevention study found that vaccines prevented more than 40,000 flu-associated deaths over a nine-year period.
  • It is especially important to be able to rapidly produce well-matched influenza vaccines using scalable technologies in the event of a future influenza pandemic.
  • Despite their important role in safeguarding the health of the American people, influenza vaccines are currently produced using more time-consuming, egg-based technology.
    • More rapid non-egg-based production methods would give experts more time to select the most relevant strains.

PROMOTING PUBLIC HEALTH: Improving the influenza vaccine is part of President Trump’s longstanding effort to combat public health threats and promote quality care for all Americans.

  • President Trump has released a National Biodefense Strategy and a Global Health Security Strategy to help combat biological threats and pandemics.
  • President Trump has made it a priority to increase the quality and accessibility of care for American patients.
    • This year, the President launched a kidney health initiative to help prevent kidney failure, improve treatment options, and expand access to life-saving transplants.
    • The Trump Administration is working to encourage new, innovative approaches to treating childhood cancer.
    • President Trump launched an initiative to end the HIV/AIDS epidemic in America over the next decade.
    • The Administration is supporting research on new treatments for opioid addiction.

Rubbing hands with ethanol-based sanitizers may not be effective hand hygiene after all.

ASM

“……the researchers from the Kyoto Profectural University of Medicine found that ethanol-based disinfectants, or hand sanitizers, would have be in contact for at least 4 minutes with the influenza A virus before killing it, a much longer duration than typical use. After 2 minutes of use, the virus was still active...….”

Ryohei Hirose, Takaaki Nakaya, Yuji Naito, Tomo Daidoji, Risa Bandou, Ken Inoue, Osamu Dohi, Naohisa Yoshida, Hideyuki Konishi, Yoshito Itoh
“…….If there is insufficient time before treating the next patient (i.e., if the infectious mucus is not completely dry), medical staff should be aware that effectiveness of AHR (rubbing) is reduced. Since AHW is effective against both dry and nondry infectious mucus, AHW (washing) should be adopted to compensate for these weaknesses of AHR…….”

Baloxavir showed broad-spectrum in vitro replication inhibition of 4 types of influenza viruses

Mishin VP, Patel MC, Chesnokov A, De La Cruz J, Nguyen HT, Lollis L, et al. Susceptibility of influenza A, B, C, and D viruses to baloxavir. Emerg Infect Dis. 2019 Oct [date cited]. https://doi.org/10.3201/eid2510.190607

“…….Baloxavir displayed broad antiviral activity against diverse influenza viruses, including all 4 types and animal-origin influenza A viruses with pandemic potential. Our findings suggest that baloxavir might offer the first therapeutic option against influenza C virus infections. Further studies are needed to provide comprehensive assessment of baloxavir susceptibility by using a large panel of representative influenza C viruses. Ongoing monitoring of baloxavir susceptibility of emerging avian and swine influenza A viruses with pandemic potential is needed to inform clinical management and public health preparedness efforts...…”


2018-2019 Influenza Season Week 20 ending May 18, 2019: Influenza activity remained low in United States and was similar to last week.

CDC

national levels of ILI and ARI

INFLUENZA Virus Isolated

Click on image to launch interactive tool

 


2018-2019 Influenza Season Week 19 ending May 11, 2019: Influenza activity continues to decrease in the United States.

CDC

national levels of ILI and ARI

INFLUENZA Virus Isolated

Click on image to launch interactive tool

 


CDC: 2018-2019 U.S. Flu Season: Preliminary Burden Estimates

37.2 million – 42.7 million
flu illnesses

person coughing icon
17.2 million – 20 million
flu medical visits

524,000 – 637,000
flu hospitalizations

36,100 – 59,600
flu deaths


2018-2019 Influenza Season Week 17 ending April 27, 2019

national levels of ILI and ARI

INFLUENZA Virus Isolated

Click on image to launch interactive tool


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