David Simons

Zoonoses, Infectious Diseases and Antimicrobial Resistance

Welcome to my personal website!

I am an epidemiologist and infectious disease ecologist. Currently a Postdoctoral Scholar at Penn State University working on the SCAPES project in Nigeria, I am transitioning to an independent role as the incoming Birgitta Sintring Fellow at Uppsala University in Sweden.

My research programme investigates the ecological and anthropogenic drivers of zoonotic viral spillover. I have organised my work into research themes accessible by selecting the headings below or in the navigation bar. You can read more about my clinical background and academic journey in the About me section.

📢 Recent Highlights

Rodent-Borne Zoonoses

My primary research focuses on the complex ecology and epidemiology of viruses transmitted by rodents. This work combines field ecology, molecular diagnostics, and mathematical modelling to understand the mechanisms of viral spillover and inform public health interventions.

Lassa Fever

Lassa Fever is a zoonotic infectious disease, endemic across much of West Africa, caused by Mammarenavirus lassaense (LASV). It is classed as a Viral Haemorrhagic Fever - similar to Ebola Virus - there are no current effective treatments for individuals infected with this virus and no licensed vaccines. Human cases of disease are regularly reported from Nigeria, Sierra Leone, Liberia and Guinea. Sporadic cases are reported from other West African countries, including; Benin, Togo, Mali and Ghana. The annual incidence of disease is not known with an estimated 100-900,000 cases annually. Epidemiological studies funded by the Coalition for Epidemic Preparedness Innovations are ongoing (ENABLE 1.0, ENABLE 1.5), these will help local public health agencies understand the true scale of this disease.

The zoonotic hosts of LASV are rodent species, primarily Mastomys natalensis (the multimammate mouse). Although virus (6) or evidence of prior viral infection (16) has been detected in additional species across the endemic region. The multimammate mouse is found throughout sub-Saharan Africa although this pathogen is limited to the western extent of its range. The reasons behind this are not well understood and this raises concerns that the endemic range of this pathogen has the potential to expand across a greater region.

Comprehensive list of Mammarenavirus lassaense findings in hosts across West Africa.
Year Country Species Assay References
Mastomys
2014 Guinea Mastomys erythroleucus Serology Fichet-Calvet E, 2014
2018 Nigeria Mastomys erythroleucus PCR Olayemi, 2018
1974 Sierra Leone Mastomys natalensis Virus Culture Monath, 1974
1974 Sierra Leone Mastomys natalensis Culture Monath, 1974
1975 Nigeria Mastomys natalensis Culture Wulff, 1975
2008 Guinea Mastomys natalensis PCR Fichet-Calvet, 2008
2014 Guinea Mastomys natalensis Serology Fichet-Calvet E, 2014
1988 Senegal Mastomys spp. Serology Saluzzo, 1988
Mus
2018 Nigeria Mus baoulei Serology Olayemi, 2018
2019 Benin Mus baoulei PCR Anges Yadouleton, 2019
1975 Nigeria Mus minutoides Virus Culture Wulff, 1975
1975 Nigeria Mus minutoides Culture Wulff, 1975
2014 Guinea Mus minutoides Serology Fichet-Calvet E, 2014
1988 Senegal Mus musculus Serology Saluzzo, 1988
2011 CĂ´te d'Ivoire Mus setulosus Serology Coulibaly-N'Golo, 2011
Rattus
1975 Nigeria Rattus rattus Virus Culture Wulff, 1975
1975 Nigeria Rattus rattus Culture Wulff, 1975
2018 Nigeria Rattus rattus Serology Olayemi, 2018
Arvicanthis
1988 Senegal Arvicanthis niloticus Serology Saluzzo, 1988
Gerbilliscus
1988 Senegal Gerbilliscus kempii Serology Saluzzo, 1988
Crocidura
2011 CĂ´te d'Ivoire Crocidura spp. Serology Coulibaly-N'Golo, 2011
Lophuromys
2011 CĂ´te d'Ivoire Lophuromys sikapusi Serology Coulibaly-N'Golo, 2011
Lemniscomys
2014 Guinea Lemniscomys striatus Serology Fichet-Calvet E, 2014
Praomys
2014 Guinea Praomys daltoni Serology Fichet-Calvet E, 2014
2018 Nigeria Praomys misonnei Serology Olayemi, 2018
2014 Guinea Praomys rostratus Serology Fichet-Calvet E, 2014
Hylomyscus
2016 Nigeria Hylomyscus pamfi PCR Olayemi, 2016
2018 Nigeria Hylomyscus pamfi Serology Olayemi, 2018
Malacomys
2021 Sierra Leone Malacomys edwardsi Serology Bangura, 2021

My research focusses on the ecology of rodent species within the endemic region and whether a better understanding of host dynamics can help us to quantify the risk of pathogen spillover into human populations. Understanding dynamics of both the host and virus will hopefully enable more targeted public health responses within the communities that need them most.

A) Reported human cases of Lassa Fever from 2011-2023. The first grey section (2013-2016) represents the period of the Ebola epidemic in West Africa, the second grey section (2020-) corresponds to the ongoing COVID-19 pandemic, the orange section represents an incomplete year of reporting. Data current as of 2023-07-13. B) The predicted distribution of Mastomys natalensis overlain over known endemic countries.

Project ArHa: Arenaviruses and Hantaviruses

With Dr. Stephanie Seifert we are leading a project synthesising published sampling records of small-mammals for arenaviruses and hantaviruses. This work is being supported by the Fellows-in-Residence programme of the Verena consortium.

We recently released our first major preprint from this initiative: Viral reservoir status in small mammals emerges as a predictable life-history trait after correcting for surveillance bias. By harmonising over 590,000 surveillance records, we demonstrated that viral reservoir status is a predictable biological trait strongly associated with a “fast” pace of life and synanthropy, independent of historical sampling biases.

Further macroecological analyses and the public release of the full ArHa database are forthcoming.

Rodent Ecology

Underpinning much of my research is a fundamental interest in rodent ecology. Understanding the population dynamics, community structure, and behavioural ecology of host species is critical for predicting disease risk. This theme explores my work on host ecology independent of a specific pathogen system.

It also houses my upcoming independent research programme, launching at Uppsala University, which focuses on developing microbial sensors to investigate the indirect detection of contact networks among bank voles. By mapping these hidden networks, we aim to better understand the environmental transmission dynamics of rodent-borne viruses.

Strategy & Policy

This theme translates ecological research into high-level frameworks for disease control and policy recommendations. Recent highlights include outlining an integrated ‘One Health Trial Design’ framework to accelerate Lassa fever vaccines (published in Nature Medicine) and establishing a set of intrinsically safe design commitments for transmissible vaccines published in Science.

Open Science and Data Tools

I am a strong proponent of FAIR data principles and reproducibility in computational ecology. Rather than extracting data behind closed doors, I focus on building open-source infrastructure for the wider research community.

  • Data Standards: I recently co-authored a minimum data standard for wildlife disease research published in Scientific Data, aimed at harmonising global surveillance efforts. I am involved in review exploring the use of geographic Ecological Momentary Assessments in addictive substance research, you can read our pre-registration here.
  • Public Datasets: All my spatial ecology and trapping data are hosted on open platforms, including GBIF and the PHAROS database.
  • Codebases & Apps: I maintain the open-source R codebase and interactive Shiny web applications for Project ArHa, allowing researchers to easily query and visualise global arenavirus and hantavirus data. You can explore my reproducible analysis pipelines on my GitHub.

Other Major Disease Systems

mpox

mpox is an endemic zoonosis, caused by the mpox virus (MPXV). Despite the name, the primary zoonotic reservoir is unknown, although several species are suspected as caompetent reservoirs. The virus has been isolated from wild animals on two occasions, first from a Rope Squirrel (Funisciurus anerythrus) and second from a Sooty Mangeby (Cercocebus atys). Several other species, including shrews, rodents and pigs, have been identified to have antibodies against the virus suggesting prior infection.

Adapted from Haider et al. 2022
Common name Scientific name Country References
Virus Isolation
Rope squirrel Funisciurus anerythrus Democratic Republic of Congo (DRC) Khodakevich et al. 1986
Sooty mangabey Cercocebus atys Cote d'Ivoire Radonić et al. 2014
Antibody Detection
Rope squirrel Funisciurus anerythrus DRC, Ghana, Reynolds et al. 2010
Giant pouched rats Cricetomys emini Ghana, DRC Reynolds et al. 2010
Sun squirrels Heliociurus spp Ghana Reynolds et al. 2010
Elephant shrews Petrodromus tetradactylus DRC Hutin et al. 2001
Domestic pigs Sus scrofa DRC Hutin et al. 2001
African dormouse Graphiurus lorraineus DRC Doty et al. 2017
Rusty-nosed rat Oenomys hypoxanthus DRC Doty et al. 2017
Grivet Cercopithecus aethiops Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977
Mona monkey Cercopithecus mona Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977
Lesser spot-nosed monkey Cercopithecus petaurista Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977
Greater spot-nosed monkey Cercopithecus nictitans Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977
Western red colobus Colobus badius Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977
King colobus Colobus polykomos Cote d'Ivoire, Liberia, Ghana, Mali Breman et al. 1977

Human infections are reported from several Central and West African nations, including the Democratic Republic of Congo, Nigeria and Cameroon. Reported cases have been increasing since the elimination of Smallpox and the end of routine vaccination against this virus. The Smallpox vaccine was found to provide some protection against Monkeypox disease and waning immunity in the region is suspected to be driving increasing human cases. Monkeypox transmission rarely occur outside of the endemic region, suggesting limited human-to-human transmission outside of endemic regions. In early 2022, a globally distributed outbreak was identified, predominantly in populations of gay or bisexual and other men who have sex with men.

My work with monkeypox has primarily been in my role as an epidemiologist with the UK Health Security Agency maintaining a linelist of cases and their contacts. With PANDORA-ID-NET we looked at what factors may be driving the recent outbreak.

COVID-19

COVID-19 is a disease caused by infection with the SARS-Coronavirus-2 virus. This novel coronavirus was identified from a cluster of clinically diagnosed viral pneumonia cases in Wuhan, China in late 2019. This viral epidemic was declared a pandemic in early 2020 following global transmission and rapidly rising confirmed cases. The pandemic has highlighted the interconnectedness of current society and the vulnerability to diseases of pandemic potential. Public health responses have included travel bans, quarantine of confirmed and suspected contacts and national or regional lockdowns. The WHO records over 600 million cases of this disease and in excess of 6.5 million deaths on their WHO Coronavirus Dashboard.

Vaccines were rapidly developed against this disease, although their reduced efficacy against more recently emerged viral variants has potentially reduced the protection that was expected from population level immunity. Effective treatments against this disease have been identified through global clinical trials, exemplified by the RECOVERY trial which provided evidence for the effectiveness of steroids, antivirals and antibody therapy.

My work with this disease includes some early modelling work on the potential international spread of the recently identified virus, involvement in the London School of Hygiene and Tropical Medicine’s Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, performing regular updates to a living review on the association of smoking and SARS-CoV-2 infection, working as an epidemiologist with the UKHSA on the emerging Omicron variant and clinical work as a member of the Infectious Diseases team at University College London Hospital.

Investigating the time to detection of different COVID-19 variants in the UK

Antimicrobial Resistance

Antimicrobial resistance is increasingly recognised as a threat to human health as effectiveness of treatment and prevention falls. My work in this theme relates to epidemiological monitoring of resistance patterns in food production in Malaysia and involvement in antimicrobial stewardship in clinical practice.

Other work

I have collected other projects I have worked on in this section.

African Swine Fever

African Swine Fever (ASF) is a highly contagious viral disease of domestic and wild pigs. Mortality is very high (up to 100%) and transmission is difficult to control. The virus can be transmitted through contact with environmental sources, fomites and infected meat products.

The virus forms a complex dynamic system including domesticated and farmed suids and wild boar, with the primary route of transmission through contaminated carcasses, meat products and fluids from infected swine alongside contaminated fomites. The presence of a wild reservoir population during the ongoing epidemic introduces challenges to the control of viral spread, particularly as this is occurring on a background of increasing wild board population densities particularly in Europe.

This project began as a summer internship with EcoHealth Alliance looking at whether reporting of cases from the World Animal Health Infromation System, maintained by the World Organisation for Animal Health could help us to quantify the risk of cases being detected in regions not previously reporting cases.

A conceptual model of ASF transmission in both sylvatic and agricultural settings.

Digital Health

I collaborate with Olga Perski, typically providing some data-science support to her interests of smoking cessation through digital health interventions.

Peste des Petits Ruminants

Peste des petits ruminants is caused by a morbilivirus which affects goats, sheep and other small ruminants. It has been targeted for global eradication by 2030. I assist with current work designed to assess the sensitivity and specificity of current assays against this virus to support elimination campaigns.

Consultancy

In addition to my academic research, I provide independent expert consultancy services in quantitative epidemiology and disease modelling for international health organisations and the biotechnology industry. Detailed information on services and contact details can be found on the Consultancy page.