Temitope O. C. Faleye, Ph.D. Turning genomic insight into public health action.
Seeing What Surveillance Misses
Dr. Temitope O. C. Faleye
About

Meet Dr. Temitope O. C. Faleye

Virologist · Public Health Scientist · Author

Viruses constantly evolve, spread, and sometimes remain hidden within the environments we share.

My work explores those hidden pathways by combining genomics, surveillance in humans, animals, and wastewater with computational biology to improve outbreak preparedness and strengthen global health security.

Through studies spanning Africa and North America, I have sought to understand not only what surveillance systems reveal, but also what they may miss.

These experiences inspired the book The Blind Spot and the Genome-to-Action initiative, which aims to translate scientific discovery into practical public health action.

The goal is to make the invisible visible before outbreaks become crises.

At a Glance
80+Peer-reviewed publications
15+Years of experience
2Continents of research experience
GlobalPublic health focus
Research Profiles
Featured Book

How the search for polio changed what we could see.

The Blind Spot is the story of how the global effort to eradicate polio—one of the most ambitious public health campaigns in history—revealed a deeper truth: the ways we search for viruses shape what we find, and what we miss.

Grounded in science and real-world experience, this book invites readers to rethink surveillance not simply as a technical process, but as a lens that influences our understanding of infectious diseases and our ability to prepare for future threats.

Glossary & Additional Reading Watch Chapter 4 ↗
Explore the glossary, additional reading, and illustrated audiobook chapters accompanying The Blind Spot.
The Blind Spot book cover
The Blind Spot — Reference Material

Glossary & Additional Reading

Reference material accompanying The Blind Spot: How the Search for Polio Changed What We Could See.

Glossary

Plain-language definitions of the scientific and public-health terms used throughout The Blind Spot.

A
Acute Flaccid Paralysis (AFP)
A sudden loss of muscle strength or movement, usually affecting the arms or legs. Because poliovirus can cause AFP, every case is investigated to determine whether polio is responsible.
Alternative Cell Lines
Different laboratory-grown cells used to cultivate viruses. Some viruses grow better in certain cell types than others, so changing the cell line can reveal viruses that would otherwise remain hidden.
Attenuation
The process of weakening a virus so that it can stimulate immunity without causing disease. The oral polio vaccine uses attenuated viruses.
B
Bacteriophages (Phages)
Viruses that infect bacteria instead of humans, animals, or plants.
Bias
A systematic tendency for a method or process to favor one outcome over another. Scientific bias often reflects the strengths and limitations of the tools being used rather than intentional error.
Biodiversity
The variety of living organisms within an environment. Viral biodiversity refers to the wide range of viruses present in nature.
Bioinformatics
The use of computers and specialized software to analyze biological data, especially genome sequences.
Blind Spot
An important part of reality that remains hidden because of the way observations are made. The central theme of this book is that surveillance methods can create blind spots.
C
Capsid
The protective protein shell surrounding a virus's genetic material.
Capsid Protein
A protein that forms the virus's outer shell and helps protect its genome.
CD155 (Poliovirus Receptor)
A protein found on the surface of certain human cells that serves as the receptor for poliovirus.
Cell Culture
A laboratory technique in which living cells are grown under controlled conditions outside the body. Circulating Vaccine-Derived Poliovirus (cVDPV) A weakened vaccine virus that has circulated long enough in under-immunized populations to regain the ability to spread and occasionally cause paralysis.
Clinical Surveillance
Monitoring disease by examining patients who become ill.
Coding-Complete Genome
A viral genome sequence that contains the complete protein-coding region but may be missing some or all of the non-coding sequences at one or both ends of the genome.
Community Transmission
The spread of infection within a population without a clearly identifiable source.
Culture-Independent Detection
Methods that detect viruses directly from clinical or environmental samples without first growing them in cells.
Cytopathic Effect (CPE)
Visible changes that occur in cells after they become infected by a virus.
D
Diagnostic Test
A laboratory method used to determine whether a particular pathogen is present.
Disease Surveillance
The continuous monitoring of diseases to guide public health decisions.
Diversity
The variety of different viruses circulating within a population.
DNA Virus
A virus whose genetic material is DNA.
E
Ecological Intelligence
An approach to surveillance that studies pathogens within the wider biological communities in which they exist.
Ecology
The study of interactions among organisms and their environments.
Ecosystem
A community of interacting organisms. In this book, viral ecosystems are central to understanding pathogen evolution.
Elimination
Reducing disease transmission to zero within a defined geographic area while continued surveillance remains necessary.
Endemic
A disease that persists at a relatively stable level within a population.
Environmental Surveillance
The systematic testing of environmental samples, such as wastewater, river water, or sewage, for evidence of pathogens circulating in communities.
Epidemic
A sudden increase in disease cases above the expected level.
Eradication
The permanent worldwide elimination of a disease so that no further interventions are needed. Smallpox has been eradicated; polio is approaching eradication.
Evolution
Gradual genetic change over time through mutation, recombination, and natural selection.
Enterovirus
A large group of RNA viruses that includes polioviruses and many other human pathogens.
Enterovirus C (EV-C)
The enterovirus species that includes the three polioviruses and numerous non-polio relatives.
F
Field of View
The portion of reality that a scientific method can reveal.
Fitness
The ability of a virus to survive, reproduce, and spread successfully.
G
Genome
The complete genetic material of an organism or virus.
Genome Sequencing
Determining the complete order of genetic material within a virus.
Genomic Epidemiology
The study of disease spread using genome sequences.
Genomic Surveillance
Monitoring pathogens through genome sequencing.
Genomics
The study of complete genomes.
Genotype
A classification based on genetic sequence.
Global Polio Eradication Initiative (GPEI)
The international campaign to eliminate poliovirus.
Global Polio Laboratory Network (GPLN)
The worldwide network of laboratories supporting global polio surveillance.
H
Hidden Diversity
Viruses that exist but remain undetected because current surveillance methods do not reveal them.
Host
The organism infected by a virus.
Host Range
The collection of organisms or cell types that a virus can infect.
I
Immunity
Protection against infection provided by the immune system.
Incidence
The number of new cases of a disease occurring over a given period.
Infectious Disease
A disease caused by bacteria, viruses, fungi, parasites, or other pathogens.
Inactivated Polio Vaccine (IPV)
A vaccine made from killed poliovirus that protects against paralysis.
L
L20B Cell Line
A laboratory-grown mouse cell line genetically engineered to produce the human poliovirus receptor (CD155).
Laboratory Bias
A tendency for laboratory methods to detect some viruses more readily than others.
Lineage
A genetically related group of viruses sharing a recent ancestor.
Long-Range RT-PCR
A molecular technique that first converts viral RNA into complementary DNA (cDNA) and then amplifies long stretches of the viral genome in a single reaction
Long-Read Sequencing
A sequencing technology capable of reading very long stretches of DNA or RNA in a single pass.
M
Metagenomics
Sequencing all genetic material within a sample.
Metaviromics
The study of all viruses present within a sample using genomic methods.
Molecular Clock
The accumulation of mutations over time that allows scientists to estimate evolutionary history.
Molecular Epidemiology
The study of disease spread using molecular and genetic information.
Mutation
A change in a virus's genetic sequence.
N
Natural Selection
The process by which genetic changes that improve survival become more common over time.
Next-Generation Sequencing (NGS)
A group of technologies that can rapidly determine the nucleotide sequence of millions of DNA or RNA molecules simultaneously.
Non-Polio Enterovirus (NPEV)
Any enterovirus other than poliovirus.
O
Observation Bias
A misleading picture created because some things are easier to detect than others.
One Health
An approach recognizing that human, animal, and environmental health are interconnected.
Oral Polio Vaccine (OPV)
A vaccine containing weakened live polioviruses that generates strong intestinal immunity.
Outbreak
A localized increase in disease cases.
P
Pandemic
An epidemic that spreads across multiple countries or continents.
Pathogen
An organism capable of causing disease.
Pathogen Discovery
The identification of previously unknown disease-causing organisms.
Phage Therapy
The use of bacteriophages (viruses that infect bacteria) to treat bacterial infections.
Phylogenetic Tree
A branching diagram illustrating evolutionary relationships.
Poliomyelitis (Polio)
A disease caused by poliovirus that can lead to paralysis.
Poliovirus
One of three closely related viruses belonging to Enterovirus C.
Population Immunity
The level of immunity within a community that limits disease spread.
R
RD Cell Line
A laboratory-grown human cell line originally established from a rhabdomyosarcoma (skeletal muscle tumor).
Recombination
A process in which two related viruses infect the same cell and exchange portions of their genomes, producing a new virus that contains genetic material from both parents.
Reassortment
The exchange of entire genome segments between viruses with segmented genomes such as influenza.
Reservoir
A population, species, or environment in which a pathogen naturally persists.
RNA Virus
A virus whose genetic material is RNA.
S
Sample
Material collected for laboratory testing.
Scientific Lens
A way of observing the natural world.
Selection Pressure
Any environmental factor that influences which viral variants survive.
Sequencing
Determining the order of genetic building blocks within DNA or RNA.
Serotype
A classification based on immune recognition.
Spillover
The transmission of a pathogen from one species to another.
Strain
A particular genetic variant within a virus type.
Surveillance
The systematic collection and analysis of disease information.
Surveillance Bias
A systematic tendency for a surveillance method to detect some pathogens more readily than others.
Surveillance Intensity
The amount of effort devoted to searching for pathogens.
Surveillance Visibility
The degree to which a pathogen can be detected.
Surveillance Visibility Problem
The central concept explored in this book: some viruses appear rare simply because they are difficult to detect using existing surveillance methods.
T
Taxonomy
The scientific classification of organisms according to their evolutionary relationships.
Therapeutic Virus
A virus deliberately used to treat disease, such as viruses designed to kill cancer cells or deliver beneficial genes.
Transmission
The spread of a pathogen from one host to another.
U
Under-Immunized Population
A community where vaccination coverage is too low to prevent sustained virus transmission.
V
Vaccine-Derived Poliovirus
A poliovirus descended from the weakened virus used in OPV after prolonged circulation.
Variant
A virus differing genetically from another member of the same type.
Viral Ecology
The study of how viruses interact with one another, their hosts, and their environments.
Viral Evolution
The process by which viruses change genetically over time.
Viral Genome
The complete genetic blueprint of a virus.
Viral Shedding
The release of viruses from an infected individual into the environment.
Virome
The complete collection of viruses present within a host or environment.
Virology
The scientific study of viruses.
Virus Isolation
The process of recovering a live virus from a clinical or environmental sample by growing it in susceptible cells under laboratory conditions.
W
Wastewater Epidemiology
The use of wastewater to monitor the health of entire populations.
Wastewater Surveillance
The analysis of sewage or wastewater to monitor pathogens circulating within a community.
Window of Observation
A metaphor used throughout this book describing the fact that every scientific method reveals some aspects of nature while leaving others outside its frame.
Z
Zoonosis
An infectious disease that can spread between animals and humans.
Zoonotic Spillover
The event in which a pathogen crosses from an animal host into humans.
100 Days Mission
An international initiative aiming to develop diagnostics, treatments, and vaccines within 100 days of recognizing a new pandemic threat.
Additional Reading

The chapter-by-chapter literature that supports and extends the ideas developed in the book.

Chapter 1: The Contradiction

  1. Fernandez-Garcia MD, Kebe O, Fall AD, Ndiaye K. Identification and molecular characterization of non- polio enteroviruses from children with acute flaccid paralysis in West Africa, 2013-2014. Sci Rep. 2017 Jun 19;7(1):3808. doi: 10.1038/s41598-017-03835-1.
  2. Faleye TOC, Adewumi MO, Japhet MO, David OM, Oluyege AO, Adeniji JA, Famurewa O. Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria. Virol J. 2017 Sep 12;14(1):175. doi: 10.1186/s12985-017-0846-x.
  3. Wollants E, Beller L, Beuselinck K, Bloemen M, Lagrou K, Reynders M, Van Ranst M. A decade of enterovirus genetic diversity in Belgium. J Clin Virol. 2019 Dec;121:104205. doi: 10.1016/j.jcv.2019.104205.
  4. de Schrijver S, Vanhulle E, Ingenbleek A, Alexakis L, Johannesen CK, Broberg EK, Harvala H, Fischer TK, Benschop KSM; ENPEN Study Collaborators. Epidemiological and Clinical Insights into Enterovirus Circulation in Europe, 2018-2023: A Multicenter Retrospective Surveillance Study. J Infect Dis. 2025 Jul 30;232(1):e104-e115. doi: 10.1093/infdis/jiaf179.
  5. Adil MN, Abbas MA, Alam MM, Rana MS, Salman M, Umair M, Khurshid A, Mahmood N, Arshad Y, Ahmed M, Mirza HA, Mujtaba G, Ali MQ, Anwar MM, Anas M. Molecular Detection of Non-Polio Enteroviruses and Emergence of Novel Enterovirus D111 in Stool Samples From Children Reported With Acute Flaccid Paralysis Symptoms During 2021 in Pakistan. J Med Virol. 2025 Sep;97(9):e70566. doi: 10.1002/jmv.70566.
  6. Abedi GR, Watson JT, Pham H, Nix WA, Oberste MS, Gerber SI. Enterovirus and Human Parechovirus Surveillance - United States, 2009-2013. MMWR Morb Mortal Wkly Rep. 2015 Sep 4;64(34):940-3. doi: 10.15585/mmwr.mm6434a3. PMID: 26334674.
  7. Brouwer L, Moreni G, Wolthers KC, Pajkrt D. World-Wide Prevalence and Genotype Distribution of Enteroviruses. Viruses. 2021 Mar 8;13(3):434. doi: 10.3390/v13030434.
  8. Burns CC, Shaw J, Jorba J, Bukbuk D, Adu F, Gumede N, Pate MA, Abanida EA, Gasasira A, Iber J, Chen Q, Vincent A, Chenoweth P, Henderson E, Wannemuehler K, Naeem A, Umami RN, Nishimura Y, Shimizu H, Baba M, Adeniji A, Williams AJ, Kilpatrick DR, Oberste MS, Wassilak SG, Tomori O, Pallansch MA, Kew O. Multiple independent emergences of type 2 vaccine-derived polioviruses during a large outbreak in northern Nigeria. J Virol. 2013 May;87(9):4907-22. doi: 10.1128/JVI.02954- Epub 2013 Feb 13.
  9. Combelas N, Holmblat B, Joffret ML, Colbère-Garapin F, Delpeyroux F. Recombination between poliovirus and coxsackie A viruses of species C: a model of viral genetic plasticity and emergence. Viruses. 2011 Aug;3(8):1460-84. doi: 10.3390/v3081460. Epub 2011 Aug 17.
  10. Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses. 2019 Sep 14;11(9):859. doi: 10.3390/v11090859.
  11. Adeniji JA, Faleye TO. Enterovirus C strains circulating in Nigeria and their contribution to the emergence of recombinant circulating vaccine-derived polioviruses. Arch Virol. 2015 Mar;160(3):675-83. doi: 10.1007/s00705-014-2322-x. Epub 2015 Jan 7.
  12. Bessaud M, Joffret ML, Blondel B, Delpeyroux F. Exchanges of genomic domains between poliovirus and other cocirculating species C enteroviruses reveal a high degree of plasticity. Sci Rep. 2016 Dec 13;6:38831. doi: 10.1038/srep38831.

Chapter 2: Meet the Enteroviruses

  1. Tapparel C, Siegrist F, Petty TJ, Kaiser L. Picornavirus and enterovirus diversity with associated human diseases. Infect Genet Evol. 2013 Mar;14:282-93. doi: 10.1016/j.meegid.2012.10.016. Epub 2012 Nov 29.
  2. The Pirbright Institute. Enterovirus [Internet]. Woking (UK): Picornaviridae Study Group; [cited 2026 Aug 6]. Available from: https://www.picornaviridae.com/ensavirinae/enteroviru s/enterovirus.htm
  3. International Committee on Taxonomy of Viruses (ICTV). Genus: Enterovirus [Internet]. In: ICTV Report. London: ICTV; [cited 2026 Aug 6]. Available from: https://ictv.global/report/chapter/picornaviridae/picorn aviridae/enterovirus

Chapter 3: The Rise of Modern Poliovirus Surveillance

  1. World Health Organization. Polio laboratory manual [Internet]. 4th ed. Geneva: World Health Organization; 2004 [cited 2026 Aug 6]. Available from: https://polioeradication.org/wp- content/uploads/2024/05/Polio_Lab_Manual04.pdf
  2. World Health Organization Regional Office for Europe. Enterovirus surveillance guidelines: guidelines for enterovirus surveillance in support of the Polio Eradication Initiative [Internet]. Copenhagen (Denmark): World Health Organization Regional Office for Europe; 2015 [cited 2026 Aug 6]. Available from: https://iris.who.int/handle/10665/344375
  3. Wood DJ, Hull B. L20B cells simplify culture of polioviruses from clinical samples. J Med Virol. 1999 Jun;58(2):188-92.
  4. Oberste MS, Maher K, Kilpatrick DR, Pallansch MA. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J Virol. 1999 Mar;73(3):1941-8. doi: 10.1128/JVI.73.3.1941- 1948.1999.
  5. Harvala H, Broberg E, Benschop K, Berginc N, Ladhani S, Susi P, Christiansen C, McKenna J, Allen D, Makiello P, McAllister G, Carmen M, Zakikhany K, Dyrdak R, Nielsen X, Madsen T, Paul J, Moore C, von Eije K, Piralla A, Carlier M, Vanoverschelde L, Poelman R, Anton A, López- Labrador FX, Pellegrinelli L, Keeren K, Maier M, Cassidy H, Derdas S, Savolainen-Kopra C, Diedrich S, Nordbø S, Buesa J, Bailly JL, Baldanti F, MacAdam A, Mirand A, Dudman S, Schuffenecker I, Kadambari S, Neyts J, Griffiths MJ, Richter J, Margaretto C, Govind S, Morley U, Adams O, Krokstad S, Dean J, Pons-Salort M, Prochazka B, Cabrerizo M, Majumdar M, Nebbia G, Wiewel M, Cottrell S, Coyle P, Martin J, Moore C, Midgley S, Horby P, Wolthers K, Simmonds P, Niesters H, Fischer TK. Recommendations for enterovirus diagnostics and characterisation within and beyond Europe. J Clin Virol. 2018 Apr;101:11-17. doi: 10.1016/j.jcv.2018.01.008. Epub 2018 Feb 6.
  6. Faleye TO, Adewumi MO, Adeniji JA. Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? Viruses. 2016 Jan 12;8(1):18. doi: 10.3390/v8010018.
  7. Lulla V, Dinan AM, Hosmillo M, Chaudhry Y, Sherry L, Irigoyen N, Nayak KM, Stonehouse NJ, Zilbauer M, Goodfellow I, Firth AE. An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells. Nat Microbiol. 2019 Feb;4(2):280-292. doi: 10.1038/s41564-018-0297-1. Epub 2018 Nov 26.

Chapter 4: The Bias Nobody Meant to Create

  1. Faleye TO, Adeniji JA. Enterovirus Species B Bias of RD Cell Line and Its Influence on Enterovirus Diversity Landscape. Food Environ Virol. 2015 Dec;7(4):390-402. doi: 10.1007/s12560-015-9215-3. Epub 2015 Sep 24.
  2. Majumdar M, Martin J. Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland. Front Microbiol. 2018 Aug 21;9:1956. doi: 10.3389/fmicb.2018.01956.
  3. Adewumi OM, Faleye TOC, Ope-Ewe OO, et al.; Non- polio enterovirus species C infection in AFP cases and its implication for the emergence of recombinant circulating vaccine-derived polioviruses. Hosts and Viruses 2020;7(1):1-6. doi: 10.17582/journal.hv/2020/7.1.1.6

Chapter 5: Finding the Missing EV-Cs

  1. Adeniji JA, Faleye TO. Impact of cell lines included in enterovirus isolation protocol on perception of nonpolio enterovirus species C diversity. J Virol Methods. 2014 Oct;207:238-47. doi: 10.1016/j.jviromet.2014.07.016. Epub 2014 Jul 24.
  2. Adewumi OM, Faleye TOC, Ope-Ewe OO, et al.; Non- polio enterovirus species C infection in AFP cases and its implication for the emergence of recombinant circulating vaccine-derived polioviruses. Hosts and Viruses 2020;7(1):1-6. doi: 10.17582/journal.hv/2020/7.1.1.6
  3. Adeniji JA, Oragwa AO, George UE, Ibok UI, Faleye TOC, Adewumi MO. Preponderance of enterovirus C in RD- L20B-cell-culture-negative stool samples from children diagnosed with acute flaccid paralysis in Nigeria. Arch Virol. 2017 Oct;162(10):3089-3101. doi: 10.1007/s00705-017-3466-2. Epub 2017 Jul 10.
  4. Donbraye E, Olasunkanmi OI, Opabode BA, Ishola TR, Faleye TOC, Adewumi OM, Adeniji JA. Abundance of enterovirus C in RD-L20B cell culture-negative stool samples from acute flaccid paralysis cases in Nigeria is geographically defined. J Med Microbiol. 2018 Jun;67(6):854-865. doi: 10.1099/jmm.0.000737. Epub 2018 Apr 30.
  5. Sadeuh-Mba SA, Bessaud M, Massenet D, Joffret ML, Endegue MC, Njouom R, Reynes JM, Rousset D, Delpeyroux F. High frequency and diversity of species C enteroviruses in Cameroon and neighboring countries. J Clin Microbiol. 2013 Mar;51(3):759-70. doi: 10.1128/JCM.02119-12. Epub 2012 Dec 19.
  6. Razafindratsimandresy R, Joffret ML, Andriamandimby SF, Andriamamonjy S, Rabemanantsoa S, Richard V, Delpeyroux F, Heraud JM, Bessaud M. Enterovirus detection in different regions of Madagascar reveals a higher abundance of enteroviruses of species C in areas where several outbreaks of vaccine-derived polioviruses occurred. BMC Infect Dis. 2022 Nov 8;22(1):821. doi: 10.1186/s12879-022-07826-0.S
  7. Faleye TOC, Driver EM, Bowes DA, Holm RH, Talley D, Yeager R, Bhatnagar A, Smith T, Varsani A, Halden RU, Scotch M. Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan- enterovirus amplicon-based long-read Illumina sequencing. Emerg Microbes Infect. 2022 Dec;11(1):1339-1342. doi: 10.1080/22221751.2022.2071173.
  8. Faleye TOC, Bowes DA, Driver EM, Adhikari S, Adams D, Varsani A, Halden RU, Scotch M. Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020. Viruses. 2021 Sep 10;13(9):1803. doi: 10.3390/v13091803.

Chapter 6: Engineering a Better Virus

  1. Yeh MT, Bujaki E, Dolan PT, Smith M, Wahid R, Konz J, Weiner AJ, Bandyopadhyay AS, Van Damme P, De Coster I, Revets H, Macadam A, Andino R. Engineering the Live- Attenuated Polio Vaccine to Prevent Reversion to Virulence. Cell Host Microbe. 2020 May 13;27(5):736- 751.e8. doi: 10.1016/j.chom.2020.04.003. Epub 2020 Apr 23.
  2. Martin J, Burns CC, Jorba J, Shulman LM, Macadam A, Klapsa D, Majumdar M, Bullows J, Frolov A, Mate R, Bujaki E, Castro CJ, Bullard K, Konz J, Hawes K, Gauld J, Blake IM, Mercer LD, Kurji F, Voorman A, Diop OM, Oberste MS, Modlin J, Macklin G, Eisenhawer M, Bandyopadhyay AS, Zipursky S. Genetic Characterization of Novel Oral Polio Vaccine Type 2 Viruses During Initial Use Phase Under Emergency Use Listing - Worldwide, March-October 2021. MMWR Morb Mortal Wkly Rep. 2022 Jun 17;71(24):786-790. doi: 10.15585/mmwr.mm7124a2.
  3. Burns CC, Diop OM, Sutter RW, Kew OM. Vaccine- derived polioviruses. J Infect Dis. 2014 Nov 1;210 Suppl 1:S283-93. doi: 10.1093/infdis/jiu295.
  4. Davlantes E, Jorba J, Henderson E, Bullard K, Deka MA, Kfutwah A, Martin J, Bessaud M, Shulman LM, Hawes K, Diop OM, Bandyopadhyay AS, Zipursky S, Burns CC. Notes from the Field: Circulating Vaccine-Derived Poliovirus Type 2 Emergences Linked to Novel Oral Poliovirus Vaccine Type 2 Use - Six African Countries, 2021-2023. MMWR Morb Mortal Wkly Rep. 2023 Sep 22;72(38):1041-1042. doi: 10.15585/mmwr.mm7238a4.
  5. Tushabe P, Majumdar M, Carlyle S, Shulman L, Ssekagiri A, Joffret ML, Klapsa D, Cremer J, Arowolo KO, Bujaki E, Bukenya H; EPI Laboratory team; Nanteza MB, Turyahabwe I, Namuwulya P, Birungi M, Eliku JP, Aine F, Tibanagwa M, Nakabazzi L, Gaizi J, Ssebuuma AM, Dhatemwa R, Okia C, Nyachwo M, Nanteza MB, Turyahabwe I, Namuwulya P, Birungi M, Eliku JP, Aine F, Tibanagwa M, Nakabazzi L, Gaizi J, Ssebuuma AM, Dhatemwa R, Okia C, Nyachwo M, Hawes KM, Bakamutumaho B, Duizer E, Bessaud M, Bandyopadhyay AS, Macadam A, Byabamazima CR, Martin J, Bwogi J. Higher stability of novel live-attenuated oral poliovirus type 2 (nOPV2) despite the emergence of a neurovirulent double recombinant strain in Uganda. Nat Microbiol. 2026 Feb;11(2):406-414. doi: 10.1038/s41564-025-02219-w. Epub 2026 Jan 19.
  6. Doté JW, Joffret M-L, Mazitchi A, Klapsa D, Kouatcho G, Kalthan E, Jouvenet N, Martin J, Gouandjika-Vasilache I, Bessaud M. Emergence of vaccine-derived poliovirus strains from the novel oral polio vaccine in the Central African Republic. mBio. 2026 May 13;17(5):e0066926. doi: 10.1128/mbio.00669-26. Epub 2026 Apr 23. PMID: 42023833;
  7. Castro CJ, Oderinde BS, Poston KD, Mawashi KY, Bullard K, Akinola M, Meade C, Liu H, Hu F, Bullows JE, Gonzalez Z, Pang H, Sarris S, Agha C, Dybdahl-Sissoko N, Perry DB, McDuffie L, Henderson E, Burns CC, Jorba J, Baba M. Complete genome sequences of nine double recombinant vaccine-derived novel oral poliovirus type 2 genomes from Nigeria 2023-2024. Microbiol Resour Announc. 2024 Dec 12;13(12):e0088124. doi: 10.1128/mra.00881-24. Epub 2024 Oct 29.

Chapter 7: Silent Circulation in the IPV Era

  1. Ryerson AB, Lang D, Alazawi MA, Neyra M, Hill DT, St George K, Fuschino M, Lutterloh E, Backenson B, Rulli S, Ruppert PS, Lawler J, McGraw N, Knecht A, Gelman I, Zucker JR, Omoregie E, Kidd S, Sugerman DE, Jorba J, Gerloff N, Ng TFF, Lopez A, Masters NB, Leung J, Burns CC, Routh J, Bialek SR, Oberste MS, Rosenberg ES; 2022 U.S. Poliovirus Response Team. Wastewater Testing and Detection of Poliovirus Type 2 Genetically Linked to Virus Isolated from a Paralytic Polio Case - New York, March 9-October 11, 2022. MMWR Morb Mortal Wkly Rep. 2022 Nov 4;71(44):1418-1424. doi: 10.15585/mmwr.mm7144e2.
  2. Manor Y, Handsher R, Halmut T, Neuman M, Bobrov A, Rudich H, Vonsover A, Shulman L, Kew O, Mendelson E. Detection of poliovirus circulation by environmental surveillance in the absence of clinical cases in Israel and the Palestinian authority. J Clin Microbiol. 1999 Jun;37(6):1670-5. doi: 10.1128/JCM.37.6.1670- 1675.1999.
  3. Manor Y, Shulman LM, Kaliner E, Hindiyeh M, Ram D, Sofer D, Moran-Gilad J, Lev B, Grotto I, Gamzu R, Mendelson E. Intensified environmental surveillance supporting the response to wild poliovirus type 1 silent circulation in Israel, 2013. Euro Surveill. 2014 Feb 20;19(7):20708. doi: 10.2807/1560- 7917.es2014.19.7.20708.
  4. Hird TR, Grassly NC. Systematic review of mucosal immunity induced by oral and inactivated poliovirus vaccines against virus shedding following oral poliovirus challenge. PLoS Pathog. 2012;8(4):e1002599. doi: 10.1371/journal.ppat.1002599. Epub 2012 Apr 19.
  5. Zuckerman NS, Bucris E, Morad-Eliyahu H, Weiss L, Vasserman R, Fratty IS, Aguvaev I, Cohen-Said Z, Matar R, Erster O, Shulman LM, Yishai R, Hecht-Sagie L, Alroy- Preis S, Mendelson E, Lustig Y, Sofer D, Bar-Or I, Weil M. Environmental surveillance of a circulating vaccine- derived poliovirus type 2 outbreak in Israel between 2022 and 2023: a genomic epidemiology study. Lancet Microbe. 2024 Oct;5(10):100893. doi: 10.1016/S2666- 5247(24)00116-2. Epub 2024 Sep 13.
  6. Seo GE, Mandes R, Wright ND, Hawkins JP, Landgraff A, Lidder R, Mohammed U, Mangat CS, Michel AS, Fafard J, Hole D, Tyler AD, Vlok M, Grudeski E, Booth TF, Majer A. Sporadic detection of vaccine-derived poliovirus type 2 using next-generation sequencing in Canadian wastewater in August of 2022. Sci Rep. 2025 Apr 15;15(1):12913. doi: 10.1038/s41598-025-92912-x.
  7. John TJ, Dharmapalan D. Lessons from Vaccine-Related Poliovirus in Israel, UK and USA. Vaccines (Basel). 2022 Nov 20;10(11):1969. doi: 10.3390/vaccines10111969.

Chapter 8: Seeing the Invisible

  1. Bellekom B, Troman C, Fitz S, Akello JO, Grassly NC, Shaw AG. Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater. Sci Total Environ. 2026 Jan 20;1013:181333. doi: 10.1016/j.scitotenv.2025.181333. Epub 2026 Jan 6.
  2. Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio. 2023 Dec 19;14(6):e0146823. doi: 10.1128/mbio.01468-23.
  3. Shaw AG, Mampuela TK, Lofiko EL, Pratt C, Troman C, Bujaki E, O'Toole Á, Akello JO, Aziza AA, Lusamaki EK, Makangara JC, Akonga M, Lay Y, Nsunda B, White B, Jorgensen D, Pukuta E, Riziki Y, Rankin KE, Rambaut A, Ahuka-Mundeke S, Muyembe JJ, Martin J, Grassly NC, Mbala-Kingebeni P. Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study. Nat Microbiol. 2023 Sep;8(9):1634- doi: 10.1038/s41564-023-01453-4. Epub 2023 Aug 17.
  4. Chien Y-S, Chen F-J, Wu H-C, Lin C-H, Chang W-C, Perera D, Yang J-Y, Lee M-S, Liao Y-C. Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses. Microbiol Spectr. 2023 Dec 12;11(6):e0250723. doi: 10.1128/spectrum.02507-23. Epub 2023 Oct 13.
  5. Isaacs SR, Kim KW, Cheng JX, Bull RA, Stelzer-Braid S, Luciani F, Rawlinson WD, Craig ME. Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples. Sci Rep. 2018 Aug 8;8(1):11889. doi: 10.1038/s41598-018-30322-y.
  6. Arita M, Kilpatrick DR, Nakamura T, Burns CC, Bukbuk D, Oderinde SB, Oberste MS, Kew OM, Pallansch MA, Shimizu H. Development of an efficient entire-capsid- coding-region amplification method for direct detection of poliovirus from stool extracts. J Clin Microbiol. 2015 Jan;53(1):73-8. doi: 10.1128/JCM.02384-14. Epub 2014 Oct 22.
  7. Nix WA, Oberste MS, Pallansch MA. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol. 2006 Aug;44(8):2698-704. doi: 10.1128/JCM.00542-06.
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Chapter 9: Beyond Polio: From Pandemic Preparedness to Therapeutic Viruses...

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  3. Shaw AG, Cooper LV, Gumede N, Bandyopadhyay AS, Grassly NC, Blake IM. Time Taken to Detect and Respond to Polio Outbreaks in Africa and the Potential Impact of Direct Molecular Detection and Nanopore Sequencing. J Infect Dis. 2022 Aug 26;226(3):453-462. doi: 10.1093/infdis/jiab518.
  4. Skurnik M, Alkalay-Oren S, Boon M, Clokie M, Sicheritz- Pontén T, Dąbrowska K, et al. Phage therapy. Nat Rev Methods Primers. 2025; 5:9. doi:10.1038/s43586-024- 00377-5.
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  6. Salmond GPC, Fineran PC. A century of the phage: past, present and future. Nat Rev Microbiol. 2015;13(12):777- doi: 10.1038/nrmicro3564.
  7. Ireland T. The good virus: the untold story of phages: the most abundant life forms on Earth and what they can do for us. London: Hodder & Stoughton; 2023
  8. Strathdee S, Patterson T, Barker T. The perfect predator: a scientist's race to save her husband from a deadly superbug: a memoir. New York: Hachette Books; 2019.
  9. Chen C, Cillis J, Deshpande S, Park AK, Valencia H, Kim SI, et al. Oncolytic virotherapy in solid tumors: a current review. BioDrugs. 2025;39:857-876. doi:10.1007/s40259-025-00743-z.
  10. Xiao D, Zhang H, Liu Y, Li Y, Li G, Ning Y, et al. Oncolytic viruses: advanced strategies in cancer therapy. Signal Transduct Target Ther. 2026;11:45. doi:10.1038/s41392- 025-02343-3
  11. Mukherjee S. The emperor of all maladies: a biography of cancer. New York: Scribner; 2010.
  12. Arney K. Rebel cell: cancer, evolution and the science of life. London: Weidenfeld & Nicolson; 2020.
Research

Seeing Beyond What Current Surveillance Reveals

My research explores how viruses evolve, circulate, and remain hidden—and how genomics, surveillance, and computational approaches can help us detect emerging threats earlier.

Wastewater surveillance and pathogen discovery

01 — Surveillance & Pathogen Discovery

Developing and applying approaches to detect viruses in humans, animals, and wastewater—including those that conventional surveillance systems may overlook.

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Viral genomics and evolution

02 — Viral Genomics & Evolution

Understanding how viruses evolve, diversify, recombine, and move through populations using genomic and computational approaches.

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Outbreak preparedness and global health

03 — Outbreak Preparedness & Global Health

Translating genomic and surveillance insights into earlier warning, stronger preparedness, and practical public health action.

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