Pandemic Influenza Readiness Report on Laboratory and Epidemiology Capacity

Abstract

Laboratory and epidemiologic data are vital to identify a novel influenza A virus and inform the public health response, whether it be to a localized outbreak or pandemic. The Centers for Disease Control and Prevention (CDC) developed the Pandemic Influenza Readiness Assessment (PIRA) to evaluate the state of the nation's preparedness for the next influenza pandemic. Representatives from all 62 Public Health Emergency Preparedness (PHEP) awardee jurisdictions were requested to complete the web-based questionnaire in July 2015. The PIRA consists of 7 modules covering key components of pandemic preparedness; this article summarizes results from the laboratory and epidemiology modules. Many of the jurisdictions reported they had the capacity to fulfill most of the laboratory and epidemiology tasks, including the ability to differentiate novel influenza A viruses from seasonal influenza viruses and electronically transfer laboratory, surveillance, and case investigation data. Pandemic preparedness includes transfer of electronic death records and conducting surveillance for influenza-associated mortality in adults. Although most jurisdictions self-reported that they had the epidemiologic and laboratory capabilities that were assessed, additional planning and technical assistance are needed to ensure all states and territories have and maintain all critical capacities. The results from this PIRA can inform how CDC and federal partners focus future training and outreach.

Laboratory and epidemiologic data are vital to identify a novel influenza A virus and inform the public health response, whether it be to a localized outbreak or pandemic. The CDC developed the Pandemic Influenza Readiness Assessment to evaluate preparedness for the next influenza pandemic. Although most jurisdictions self-reported that they had the epidemiologic and laboratory capabilities that were assessed, additional planning and technical assistance are needed to ensure all states and territories have and maintain critical capacities.

The 2009 H1N1 influenza pandemic and the identification and continued spread of human infections with avian influenza A (H7N9) in China since 2013 underscore the importance of influenza pandemic preparedness. During the fifth epidemic, from October 1, 2016, through September 30, 2017, the World Health Organization (WHO) reported 766 human infections with Asian H7N9 virus, making it the largest H7N9 epidemic to date.¹ This virus causes severe illness in people (reported case fatality ratio of 41%)² but is not efficiently transmitted from person to person. If the virus mutates to become more easily transmitted among people, it has the potential to cause severe disease around the world.

The Centers for Disease Control and Prevention (CDC), in partnership with state, local, and territorial health departments, advances public health emergency preparedness and operational readiness through the Public Health Emergency Preparedness (PHEP) program.³ In 2009, CDC provided supplemental funding to 62 PHEP awardees to improve response capacity for the H1N1 influenza pandemic. The PHEP-funded investments in pandemic influenza preparedness were critical in supporting collection and reporting of information that was used to characterize disease severity, spread, and at-risk populations.

In 2015 the Pandemic Influenza Readiness Assessment (PIRA) was administered to assess the current state of PHEP awardees' pandemic planning and vaccination delivery capacity. The PIRA was developed for this assessment by CDC's Division of State and Local Readiness (DSLR), Office of Public Health Preparedness and Response, in collaboration with other CDC divisions and programs, including the Influenza Coordination Unit, the Influenza Division, the Immunization Services Division, and the Division of Global Migration and Quarantine. The questionnaire is organized into 7 modules corresponding to priority pandemic planning areas. Each module describes an influenza scenario and assumptions that respondents are directed to consider when answering the assessment questions. This article addresses results from the epidemiology and laboratory modules.

Methods

There are 62 PHEP awardees, consisting of health departments in all 50 states, Washington, DC, 3 locally funded jurisdictions, and 8 territories or freely associated states. In July 2015, the 62 PHEP jurisdictions covering the entire population of the United States were invited to participate in completing the PIRA. The CDC sent PHEP directors an email that explained the purpose and intent of the assessment and requested names and contact information for individuals in their jurisdiction who were best suited to complete each PIRA module. The CDC invited the identified participants by email to complete the web-based questionnaire. Respondents were given 4 weeks to submit answers. Reminder emails were sent on days 7 and 14 to maximize response rates. Data were collected under OMB approval number 0920-0879. Because the precise population of awardees is known, all percentages are based on a complete denominator of 62. Population and jurisdictional information were collected from the 2010 US Census.

For each PIRA module, a scenario and assumptions were provided. The epidemiology and laboratory modules consisted of questions in the areas of willingness to follow CDC protocols for collecting and reporting data, investigating mortality, and laboratory capacity and epidemiologic capacity. A 5-point Likert scale was used to indicate the jurisdiction's level of capacity for each epidemiologic indicator, ranging from 1 indicating no capacity to 5 indicating full capacity; dichotomous questions were used. Data were analyzed using Excel.

Results

All 62 PHEP awardee jurisdictions submitted responses to the epidemiology and laboratory module of the PIRA. Of the 62 jurisdictions, 53 (85%) reported full capacity as of 2015 to collect detailed epidemiologic and clinical case information, such as onset date, symptoms, contacts, hospitalization or death, on a subset of initial cases identified during a large epidemic or pandemic. The 53 jurisdictions cover 88% of the US population. All jurisdictions reported they would follow at least some CDC protocols for electronically reporting laboratory, surveillance, and investigation data to CDC. Of the 57 jurisdictions that responded to a question about specifically using CDC protocols and questionnaires to collect detailed epidemiologic and clinical data at the onset of the pandemic, 56 (98%) said they would do so (Figure 1).

Figure 1.

Representation of the surveyed Public Health Emergency Preparedness (PHEP) awardees' (N = 62) willingness to follow CDC protocols of data collection and sharing for epidemiologic investigations pertaining to an influenza pandemic. (5 jurisdictions did not provide a response to the question about collecting detailed epidemiologic and clinical case information.)

Sixty (97%) jurisdictions covering 99.7% of the US population reported the ability to transport specimens to CDC on a regular basis during a pandemic, and 2 jurisdictions in the Pacific islands did not report on this capacity. Fifty-four (87%) jurisdictions reported the ability to test for and differentiate novel influenza A viruses (eg, A(H7), A(H5), A(H3)v) from seasonal influenza viruses. However, 7 (11%) jurisdictions reported an inability to perform this task, including 1 jurisdiction that also reported not having the capacity to transport specimens to CDC on a regular basis during a pandemic and another jurisdiction that reported being in the process of developing this capacity (Figure 2).

Figure 2.

Representation of the surveyed Public Health Emergency Preparedness (PHEP) laboratories' (N = 62) ability to differentiate between novel influenza A viruses versus seasonal influenza and capacity to transport samples to CDC

Fifty-one (82%) jurisdictions covering 81% of the US population reported full capacity for comprehensive contact tracing and epidemiologic investigations of initial confirmed cases of novel influenza. Fifty-two (84%) jurisdictions covering 75% of the US population reported full capacity to collect basic epidemiologic data, and 1 jurisdiction reported they had no capacity to perform this function. Fifty-three (85%) jurisdictions covering 88% of the US population reported high capacity to collect detailed epidemiologic and clinical case data on a subset of initial cases identified during a large epidemic or pandemic.

Four surveyed capacities addressed surveillance of influenza-related mortality. Sixty-one (98%) jurisdictions covering 99.9% of the population reported full capability to investigate influenza-related mortality in children, a nationally notifiable condition since 2004.⁴ Forty-three (69%) jurisdictions covering 57% of the population reported full capacity for conducting surveillance for influenza-related mortality in adults, and 49 (79%) jurisdictions covering 71% of the population reported full capacity for investigating a subset of influenza-associated deaths in adults. Only 37 (60%) jurisdictions covering 60% of the population reported full capacity to transfer electronic death records to CDC within 2 weeks of death, and 5 jurisdictions reported no capacity for this task.

Discussion

Reliable laboratory and epidemiologic data about cases across the spectrum of disease severity are needed to effectively identify and respond to novel influenza A virus outbreaks or an influenza pandemic. State and local jurisdictions have increased their capacity to collect and report these data since 2001.^4-8 These increases in capacity were made possible in part by the PHEP cooperative agreement, which has provided more than $11 billion to jurisdictions since 2002.³ In addition, seasonal influenza surveillance data collection and transfer systems, which will serve as the backbone for pandemic influenza surveillance, have advanced since 2001 in terms of geographic coverage, metrics monitored, and electronic transmission of data. Jurisdictions use these existing systems (eg, HL7 messaging of laboratory data through the Public Health Laboratory Interoperability Project and web-based reporting of novel influenza A virus infections on the Secure Access Management Services [SAMS] reporting application) to transmit seasonal influenza data to CDC year-round. With only minor changes, these systems would continue to be used during a pandemic.

Timely detection of a novel influenza A virus is imperative, regardless of whether the novel strain is the start of the next pandemic, as occurred with the 2009 H1N1 pandemic,⁹ or a more localized event such as variant influenza virus infections.^10,11 A total of 87% of jurisdictions reported the ability to differentiate and test between novel and seasonal influenza viruses, and 97% of jurisdictions reported the capacity to transport specimens to CDC. However, it is important that all state public health laboratories have these capabilities and that all local and territorial jurisdictions are able to coordinate with their regional or state public health partners to ensure these functions are carried out.

A delay in identifying or reporting laboratory results or epidemiologic data can have a significant impact on public health planning for and emergency management of these events. For the 1 jurisdiction that reported they will not follow CDC protocols and questionnaires, and the 5 that did not respond to the question about collecting and transmitting data at the outset of a pandemic, it is important to understand the reason for their reluctance to use these tools and determine if jurisdiction-specific protocols exist.

A high degree of preparedness exists for tasks related to contact tracing, collection of epidemiologic and clinical data, and investigating influenza-related deaths in children. However, influenza-related mortality surveillance in adults, investigation of a subset of these deaths, and reliable transfer of electronic death records pose a challenge for many jurisdictions. Maintaining critical systems and avenues of electronic data reporting, such as the Public Health Laboratory Interoperability Project (PHLIP),^12,13 along with the skills and abilities to properly ship samples to the CDC and other federal partners, is critical to the response and investigation.

While the PIRA provides valuable information to guide future technical assistance and research announcements related to pandemic preparedness, there are some limitations with these data. Most jurisdictions completing the PIRA were staff from state-level organizations; therefore, the results may not reflect local-level pandemic planning approaches and decisions. PHEP directors provided the names of individuals to complete the PIRA and instructions to have those individuals complete the survey, but it is possible that these individuals may not have had the most up-to-date information on each capacity. It is also possible the scenarios and assumptions provided to the respondents may not reflect the actual conditions and decisions during an influenza pandemic.

Despite these limitations, the PIRA informs planners at all levels of where there might be gaps in PHEP jurisdictions' capacities. Gaps identified included the ability to differentiate influenza strains and the ability to transport samples to CDC. These gaps can have a negative effect on the ability to respond effectively to the next influenza pandemic. It is important for the entire public health system to prepare for and be able to respond to an outbreak or pandemic, regardless of the severity, strain type, ages affected, and geographic origin. The ability for jurisdictions to respond during a pandemic must include capacity to identify and report novel influenza A virus infection and electronically transfer laboratory, surveillance, and case investigation data. Although the majority of jurisdictions self-reported a level of preparedness to perform these activities, it is clear that additional planning and technical assistance is needed to ensure all states and territories have this capacity. Future analysis of preparedness functions will include an assessment of whether jurisdictions with deficits had proportionately fewer resources or unique competing priorities that would explain the deficit and a more detailed assessment of their unmet needs in order to more strategically target future assistance.

Footnotes

Acknowledgments

The authors acknowledge Admiral Stephen Redd, MD, for his support of this project, and Sara Vagi, PhD, for initial analysis and Rachel Avchen, PhD, in the Applied Science and Evaluation Branch.

References

Kile

, Ren

, Liu

, et al. Update: increase in human infections with novel Asian lineage avian influenza A(H7N9) viruses during the fifth epidemic—China, October 1, 2016-August 7, 2017. MMWR Morb Mortal Wkly Rep, 2017; 66(35):928-932.

Xiang

, Li

, Ren

, et al. Assessing change in avian influenza A(H7N9) virus infections during the fourth epidemic—China, September 2015-August 2016. MMWR Morb Mortal Wkly Rep, 2016; 65(49):1390-1394.

US Centers for Disease Control and Prevention.. Public Health Emergency Preparedness (PHEP) Cooperative Agreement. CDC website. Updated June 15, 2018. https://www.cdc.gov/phpr/readiness/phep.htm. Accessed July 17, 2018.

US Centers for Disease Control and Prevention.. Influenza-associated pediatric mortality. CDC website. https://wwwn.cdc.gov/nndss/conditions/influenza-associated-pediatric-mortality/. Accessed July 17, 2018.

Polansky

, Outin-Blenman

, Moen

. Improved global capacity for influenza surveillance. Emerg Infect Dis, 2016; 22(6):993-1001.

World Health Organization.. Strengthening the WHO Global Influenza Surveillance Network (GISN). World Health Organization website. 2010. http://www.who.int/influenza/gisrs_laboratory/GISN_Meeting_Report_apr2011.pdf?ua=1. Accessed July 17, 2018.

World Health Organization.. FluNet. World Health Organization website. 2018. http://www.who.int/influenza/gisrs_laboratory/flunet/en. Accessed July 17, 2018.

Muir-Paulik

, Johnson

, Kennedy

, et al. Measuring laboratory-based influenza surveillance capacity: development of the ‘International Influenza Laboratory Capacity Review’ tool. Public Health, 2016; 130:72-77.

US Centers for Disease Control and Prevention. Update: novel influenza A (H1N1) virus infections—worldwide, May 6, 2009. MMWR Morb Mortal Wkly Rep, 2009; 58(17):453-458.

10.

US Centers for Disease Control and Prevention.. Variant influenza viruses in humans. CDC website. Updated July 5,. 2018. https://www.cdc.gov/flu/swineflu/variant-flu-in-humans.htm. Accessed July 17, 2018.

11.

World Health Organization.. Influenza virus infections in humans (February 2014). WHO website. www.who.int/influenza/human_animal_interface/virology_laboratories_and_vaccines/influenza_virus_infections_humans_feb14.pdf?ua=1. Accessed July 17, 2018.

12.

Association of Public Health Laboratories.. Electronic Laboratory Surveillance Messaging (ELSM). https://www.aphl.org/programs/informatics/Documents/INF_2013May15_ELSM-Overview.pdf. Accessed July 17, 2018.

13.

Lazo