Scenario B

Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, Baltyre. Residents are outraged and worried. There have already been 20 deaths.

The cause of the outbreak appears to be Influenza A virus. (Please refer to the WHO Influenza Fact Sheet for more information about the pathogen.)

False-coloured transmission electron microscopy (TEM) image of an influenza virus particle. Image credit: [CDC](https://phil.cdc.gov/Details.aspx?pid=10073)

Figure 1: False-coloured transmission electron microscopy (TEM) image of an influenza virus particle. Image credit: CDC

Each member of your group will play one of the following roles as you attempt to tackle the disease outbreak and save your city:

  1. Provost (head of the city council)
  2. Representative from a national public health org. (Public Health Scotland)
  3. Epidemiologist (on secondment from Public Health Scotland)
  4. Director of the city’s main hospital (Queen’s College)
  5. City planner/civil servant
  6. Microbiologist (working in one of the NHS Scotland clinical labs)
  7. Public communications expert (past and current sci comm campaigns)
  8. Doctor at a major surgery in Baltyre
  9. Epidemiologist from the local university, an expert on influenza virus A transmission

You must work together, using the information that has been provided for you in the attached information packets, and decide what action(s) should be taken to control the outbreak currently plaguing your city, Baltyre. Your actions should be evidence-based – use the peer-reviewed literature to decide on measures that will stop the pandemic in your scenario.

Your action points may include directives to gather more information (e.g., contact tracing of current cases, microbiological testing of food/water, etc.), or specific directives (e.g. public health measures, non-pharmaceutical interventions, etc.). Use the data/expertise of all group members. Be clear, concise, and specific.

You may choose to include mathematical modeling as part of your decision making (for example, using an epidemic calculator or other models); if you do so, you should provide details of your modelling and predictions when you submit your group’s pro forma.

You should submit 3-5 specific actions to control the pandemic, using the workshop 3 pro forma (also available on MyPlace). Submit this by noon, Friday March 1st, via the submission link on MyPlace.

Information Packet B1

You are the provost of Baltyre, elected in 2016.

Photograph of Baltyre city centre. Image credit: DALL-E

Figure 2: Photograph of Baltyre city centre. Image credit: DALL-E

The current population of Baltyre (as of December 2022) is 167519. The demographic data for the city is shown below.

Baltyre demographics (Source: Office for National Statistics)Baltyre demographics (Source: Office for National Statistics)

Figure 3: Baltyre demographics (Source: Office for National Statistics)

You were elected as a member of the popular “New Progress” party and made a number of election promises regarding a “Green New Deal” for Baltyre.

Voting intention by Baltyre residents (Source: YouGov polling)

Figure 4: Voting intention by Baltyre residents (Source: YouGov polling)

There are currently 43 elected councillors, representing the 5 main political parties in Baltyre as follows:

Political Party Number of Seats
Gold 3
Vocal Action 14
New Progress 19
Truth to Power 6
Social Redistribution 1



The overall budget (expenditures) for the 2022-2023 financial year was £494891220. A summary of expeditures by category for this financial year is shown below.

Public expenditures by category for the 2022-2023 financial year (Source: Baltyre City Council)

Figure 5: Public expenditures by category for the 2022-2023 financial year (Source: Baltyre City Council)

Your office has recently received a great deal of correspondence regarding the pandemic in Baltyre. A representative sample of these e-mails is shown below.

From:
To:
Cc: Subject: This Horrible Pandemic

Dear Provost,

I am outraged to hear about this new pandemic in Baltyre. There seems to be no end to the suffering that pandemics inflict on our city in these days.

I wish that your office is going to do something about all of the poor people dying at once.

Yours sincerely,
Su

From:
To:
Cc:
Subject: Pandemic Disaster for Businesses

Dear Provost,

This new pandemic in Baltyre has the potential to ruin our businesses. I run a records shop on the high street and almost literally went bankrupt due to COVID.

I hope you realise that you need to put businesses first now - we were unfairly forced to bear the costs of the last pandemic.

I hope very much that your office is going to do something about all of the poor people dying very soon, keeping in mind the economic interests of businesses in our city and the fact that we cannot afford restrictions that cripple our businesses.

Respectfully,
Graham (Jewels, proprietor)

From:
To:
Cc:
Subject: Stop This Madness

Dear Provost,

I dread that you and your office are going to use this new pandemic as yet another excuse for government overreach into citizens’ lives. The mental health consequences of the last pandemic were underappreciated, but very real - people suffered due to the lockdowns and children’s development was affected by the wearing of face masks and the closing of schools.

You must not allow the city to suffer through another round of lockdowns, face-masks, and other punitive restrictions that destroy people’s lives.

Respectfully,
Eleanor (a concerned voter)

From:
To:
Cc:
Subject:

Dear Provost,

I have just learned that my my gran has passed away due to the new pandemic in Baltyre. You cannot begin to imagine the grief that we are feeling.

You cannot begin to imagine the grief that we are feeling.

I don’t understand why we haven’t learned how to deal with pandemics better, after all our experiences with COVID-19, I don’t understand how this could have happened.

Kind regards,
Graham

As Provost of Baltyre, you are of course familiar with the work of the Standing Committee on Pandemic Preparedness. You are also familiar with:

Information Packet B2

You are a representative from Public Health Scotland, sent to Baltyre to help with the influenza outbreak.

Your briefing packet includes the following documents:

  • Public Health Scotland Influenza A-Z

  • Uyeki, Timothy M et al. “Influenza.” Lancet (London, England) vol. 400,10353 (2022): 693-706.

  • Tyrrell CS, Allen JLY, Gkrania-Klotsas E. Influenza: epidemiology and hospital management. Medicine (Abingdon). 2021 Dec;49(12):797-804. doi: 10.1016/j.mpmed.2021.09.015.

  • Kassianos, George et al. “Implementation of the United Kingdom’s childhood influenza national vaccination programme: A review of clinical impact and lessons learned over six influenza seasons.” Vaccine vol. 38,36 (2020): 5747-5758. doi:10.1016/j.vaccine.2020.06.065

Information Packet B3

You are an epidemiologist working for Public Health Scotland, sent to Baltyre to help with the influenza outbreak.

A team of scientists working together have in a PHS lab have isolated and cultured influenza virus (using a standard tissue culture model) from a number of patient samples taken during this outbreak; isolated influenza RNA from these cultures; reverse-transcribed this to DNA, and sequenced this DNA using an Illumina MiSeq platform; assembled the short paired-end reads; and compared these assemblies to the extant influenza sequences available in the NCBI databases. The results of these experiments are summarised in the table below.

Patient NCBI accession of closest database match to the NA genome segment
1 KU171017.1
2 KU171017.1
3 UZY70773.1
4 KU171017.1
5 KU171017.1
6 UZY70773.1
7 KU171017.1
8 KU171017.1
9 KU171017.1
10 UUB84697.1



Your briefing packet also includes the following documents:

  • Lean, Fabian Z X et al. “Gross pathology of high pathogenicity avian influenza virus H5N1 2021-2022 epizootic in naturally infected birds in the United Kingdom.” One health (Amsterdam, Netherlands) vol. 14 100392. 27 Apr. 2022, doi:10.1016/j.onehlt.2022.100392

  • Wolken, Madeline et al. “Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections.” Water research vol. 231 (2023): 119648. doi:10.1016/j.watres.2023.119648

  • Chen, Kuang-Yu et al. “High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing.” Proceedings of the National Academy of Sciences of the United States of America vol. 120,6 (2023): e2211098120. doi:10.1073/pnas.2211098120

  • Smyk, Julia M et al. “Evolution of Influenza Viruses-Drug Resistance, Treatment Options, and Prospects.” International journal of molecular sciences vol. 23,20 12244. 13 Oct. 2022, doi:10.3390/ijms232012244

  • Weekly National Flu Reports (UKHSA)

Information Packet B4

You are the director of Baltyre’s main hospital, the Queen’s College, which has 550 beds across 9 different wards and 10 operating theatres.

The Queen's College hospital in Baltyre. Image credit: [DALL-E

Figure 6: The Queen’s College hospital in Baltyre. Image credit: [DALL-E

The annual operating budget for financial year 2022-2023 was £1.5 million, and average expenditures are shown by category in the figure below.

Hospital expenditures by category for financial year 2022-2023 (Source: NHS Scotland)

Figure 7: Hospital expenditures by category for financial year 2022-2023 (Source: NHS Scotland)

The Queen’s College has units specialising in coronary care; maternity care; dermatology; gastroenterology; an ear, nose, and throat clinic; an eye clinic; and an orthopedic unit.

There are currently 25 ICU beds (with ventilators) available, an increase from the 14 ICU beds in the Queen’s College in November 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in the figure below.

ICU bed occupancy for the Baltyre Queen's College hospital (Source: NHS Scotland)

Figure 8: ICU bed occupancy for the Baltyre Queen’s College hospital (Source: NHS Scotland)

There are approximately 1.3m admissions to the Queen’s College hospital annually, the majority of these being to the emergency (A&E) department.

Admissions to the Baltyre Queen's College hospital by category (Source: NHS Scotland)

Figure 9: Admissions to the Baltyre Queen’s College hospital by category (Source: NHS Scotland)

A&E waiting times have been called “disastrously high” in recent months, both by the press and by tthe hospital ombudsman.

ICU waiting times for the Baltyre Queen's College hospital (Source: NHS Scotland)

Figure 10: ICU waiting times for the Baltyre Queen’s College hospital (Source: NHS Scotland)

The Queen’s College has been set a goal of 25% reduction in sepsis mortality (compared to past years)and 50% reduction in the nosocomial transmission of superbugs such as methicillin-resistant Staphylococcus aureus (MRSA), Clostridiodes difficile (C. diff), and Candida auris (C. auris).

Key Performance Indicators (KPIs) related to infectious diseases for the Baltyre Queen's College hospital (Source: NHS Scotland)

Figure 11: Key Performance Indicators (KPIs) related to infectious diseases for the Baltyre Queen’s College hospital (Source: NHS Scotland)

There are currently 170 patients in the Queen’s College with confirmed or suspected influenza, with 15 of these patients currently in the ICU.

The hospital follows the guidelines set out in the National Infection Prevention and Control Manual.

As a hospital director, you are familiar with the literature surrounding hospital pandemic preparedness, and regularly read papers such as:

  • Mer, Mervyn et al. “Critical Care Pandemic Preparation: Considerations and Lessons Learned from COVID-19.” Critical care clinics vol. 38,4 (2022): 761-774.

  • Tacconelli, Evelina et al. “Challenges of data sharing in European Covid-19 projects: A learning opportunity for advancing pandemic preparedness and response.” The Lancet regional health. Europe vol. 21 (2022): 100467.

  • Adelaja, I., Sayma, M., Walton, H., McLachlan, G., de Boisanger, J., Bartlett-Pestell, S., Roche, E., Gandhi, V., Wilson, G. J., Brookes, Z., Yeen Fung, C., Macfarlane, H., Navaratnam, A., James, C., Scolding, P., & Sara, H. (2020). A comprehensive hospital agile preparedness (CHAPs) tool for pandemic preparedness, based on the COVID-19 experience. Future healthcare journal, 7(2), 165–168.

Information Packet B5

You are a civil servant working in Baltyre, working closely with the provost, city council and various agencies including the NHS, the UK Health Security Agency (UKHSA), and the Scottish Environment Protection Agency (SEPA).

Some of the key Baltyre facts and figures at a glance are summarized in the table below.

Community Amenities Details
Schools 7 primary schools, 5 secondary schools, 1 college
Care Homes 3, each with ~40 bed capacity
Restaurants and Cafes 86
Parks and Playgrounds 7
Economic Indicators Details
GDP/capita £45453
Unemployment Rate 8%
Traffic and Transport Details
Traffic fatalities (average/month) 5



Your briefing packet on influenza includes the following information.

Information Packet B6

You are a microbiologist working in the virology department at the Greater Baltyre Clinical Laboratory. Your laboratory is equipped to handle a range of culture samples (including anaerobic and microaerobic bacteria, as well as viruses), and you routinely process 1754 samples monthly.

You are familiar with the culture requirements for growth of influenza viruses in tissue culture, and the range of influenza virus testing methods.

A plaque assay for influenza virus. Image credit: [CDC](https://phil.cdc.gov/Details.aspx?pid=23215)

Figure 12: A plaque assay for influenza virus. Image credit: CDC

You are also familiar with the literature surrounding influenza virus identification, and often read papers such as:

  • Morehouse, Zachary P et al. “A narrative review of nine commercial point of care influenza tests: an overview of methods, benefits, and drawbacks to rapid influenza diagnostic testing.” Journal of osteopathic medicine vol. 123,1 39-47. 19 Aug. 2022.

  • Ison MG, Hayden FG, Hay AJ, Gubareva LV, Govorkova EA, Takashita E, McKimm-Breschkin JL. Influenza polymerase inhibitor resistance: Assessment of the current state of the art - A report of the isirv Antiviral group. Antiviral Res. 2021 Oct;194:105158.

  • Van Poelvoorde, Laura A E et al. “Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza.” Trends in biotechnology vol. 38,4 (2020): 360-367.

Information Packet B7

You are a public communications expert, often employed by the Baltyre city council to manage the PR response to different initiatives or crises.

As a public communications expert, you are familiar with the literature surrounding science communication in a pandemic, including papers such as:

  • Matta, G. Science communication as a preventative tool in the COVID19 pandemic. Humanit Soc Sci Commun 7, 159 (2020).

  • Abdool Karim, Salim S. “Public understanding of science: Communicating in the midst of a pandemic.” Public understanding of science (Bristol, England) vol. 31,3 (2022): 282-287.

  • Royan, Regina et al. “Use of Twitter Amplifiers by Medical Professionals to Combat Misinformation During the COVID-19 Pandemic.” Journal of medical Internet research vol. 24,7 e38324. 22 Jul. 2022, doi:10.2196/38324

  • Tait, Margaret E et al. “Serving the public? A content analysis of COVID-19 public service announcements airing from March - December of 2020 in the U.S.” Preventive medicine reports vol. 29 (2022): 101971.

You have assembled the following information/resources for this meeting:

  • Influenza Pandemic Communication and Public Outreach (CDC)

  • Lawes-Wickwar, Sadie et al. “A Rapid Systematic Review of Public Responses to Health Messages Encouraging Vaccination against Infectious Diseases in a Pandemic or Epidemic.” Vaccines vol. 9,2 72. 20 Jan. 2021, doi:10.3390/vaccines9020072

  • Bielecki, K et al. “Impact of an influenza information pamphlet on vaccination uptake among Polish pupils in Edinburgh, Scotland and the role of social media in parental decision making.” BMC public health vol. 20,1 1381. 10 Sep. 2020, doi:10.1186/s12889-020-09481-z

Information Packet B8

You are one of the doctors at the largest surgery in Baltyre. In the past fortnight, 60 of your patients have recently presented to the surgery with symptoms consistent with influenza. You have therefore recently been familiarising yourself with the relevant literature:

Information Packet B9

You are an epidemiologist working at the University of Baltyre, and have been studying influenza A transmission dynamics for the past 9 years. As such, you are very familiar with the relevant literature, including papers such as:

  • Castro-Sanguinetti GR, González-Veliz R, Callupe-Leyva A, et al. Highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b from Peru forms a monophyletic group with Chilean isolates in South America. Sci Rep. 2024;14(1):3635. Published 2024 Feb 13. doi:10.1038/s41598-024-54072-2

  • Yang Q, Wang B, Lemey P, et al. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun. 2024;15(1):1126. Published 2024 Feb 6. doi:10.1038/s41467-024-45462-1

  • Seo YR, Cho AY, Si YJ, et al. Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea, 2022-2023. Emerg Infect Dis. 2024;30(2):299-309. doi:10.3201/eid3002.231274

  • Croville G, Walch M, Sécula A, et al. An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022. Front Cell Infect Microbiol. 2024;14:1257586. Published 2024 Jan 22. doi:10.3389/fcimb.2024.1257586

  • Wang X, Kim KW, Walker G, Stelzer-Braid S, Scotch M, Rawlinson WD. Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing. Influenza Other Respir Viruses. 2024;18(1):e13252. doi:10.1111/irv.13252

  • Szablewski CM, McBride DS, Trock SC, et al. Evolution of influenza A viruses in exhibition swine and transmission to humans, 2013-2015. Zoonoses Public Health. Published online December 18, 2023. doi:10.1111/zph.13104

  • Perofsky AC, Huddleston J, Hansen C, et al. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. Preprint. medRxiv. 2023;2023.10.02.23296453. Published 2023 Oct 3. doi:10.1101/2023.10.02.23296453