Research Goal

In Prodger lab, we focus on understanding the complex interactions between host tissues, the immune system, and microbial communities, with an emphasis on translational research in infectious diseases and mucosal immunology. We develop innovative systems to study how bacteria and viruses interact with epithelial and immune cells. This multidisciplinary approach bridges cell biology, immunology, and microbiome research, with the ultimate goal of improving prevention and treatment strategies for human health.

Our first research goal is to understand natural resistance/susceptibility to HIV-1. Penile anaerobic bacteria can increase HIV-1 risk, but the exact species and mechanisms underpinning this risk are unknown. Our group is working to illuminate these and to develop targeted antimicrobials to prevent HIV-1.
Our second goal is to understand the unique barriers to curing individuals living with HIV-1 in sub-Saharan Africa. HIV-1 remains incurable due to the stable integration of viral DNA into the host genome. We are working to characterize persistent HIV-1 infection in Uganda, and plan to test HIV-1 cure strategies as they become available.

News and more

Summer 2026

Africa Day Celebration, Western University, London, Ontario

Western University hosted a celebration of Africa Day on May 25, 2026.

PhD students, Martina Cathy Nakibuuka, Shirley Constable, and Sarah Gowanlock presented their recent research findings on HIV.

African day celebration 25MAY2026

Africa day prodger lab

6th Symposium of the Canadian Society for Virology, CSV2026

Guelph University

Nasal Commensal Bacteria Differentially Modulate Epithelial Cells

PhD student, Zeynep Güneş Tepe Demir, presents her recent research on Nasal Commensal Bacteria and their effects on respiratory viral infections in the in vitro 3D nasal model CSV2026 Gunes tepedemir

33rd International Dynamics & Evolution of Human Viruses Conference, University of British Columbia

PhD student, Martina Cathy Nakibuuka, presented her recent research findings on the latent HIV reservoir.

33rd International Dynamics & Evolution of Human Viruses conference

35^th Canadian Conference on HIV/AIDS Research (CAHR 2026)

HIV Persistence During ART: Lessons from Longitudinal Studies in Rakai, Uganda

Jessica Prodger

Source: https://www.youtube.com/watch?v=cCT1g505d8c

From billboards to the biology of HIV

PhD student Sarah Gowanlock is working to close gaps in HIV detection in Uganda, after modelling abroad helped shape her path

Sarah Billboard

Source: https://www.schulich.uwo.ca/about/news-events-community/news/2026/from-billboards-to-the-biology-of-hiv.html

Western University to Uganda: Summer Internship

MSc student Henryroger Ssemunywa is working on human tissues and bioengineering this summer.

Henry internship

Partners

Rakai Health Sciences Program (RHSP)

RHSP collaboration with Prodger lab

Uganda has about 1.4 million people living with HIV, and 37,000-53,000 new infections annually. Uganda pioneered Africa's national AIDS program in 1986—supported by pioneering work from the Rakai Health Sciences Program (RHSP), which established one of the world's first population-based HIV cohorts—dramatically reducing the rates from over 20% in the 1990s through behaviour change and antiretroviral therapy (ART) scale-up, including a 64% drop in AIDS deaths since 2010. In Prodger Lab, we collaborate with the RHSP, a key Uganda-based group advancing HIV research and services. We aim to contribute to an HIV cure by targeting the latent reservoir and the microbiome-immune interactions to develop novel prevention and treatment strategies.

RHSP website: https://www.rhsp.org/

Women's College Hospital (WCH)

Women’s College Hospital (WCH) in Toronto hosts Canada’s first publicly funded hospital-based Transition-Related Surgery (TRS) Program, launched in 2019 to provide essential gender-affirming surgeries. In Prodger Lab, we collaborates with WCH TRS on innovative research, such as characterizing neovaginal microbiomes post-vaginoplasty to improve outcomes for transfeminine individuals. Our goal is to advance reproductive health and gender-affirming care through microbiome-immune system insights. Check out our TransBiota Facebook page for more information about these studies!

WCH website: https://womenscollegehospitalfoundation.com/

TransBiota news: https://www.facebook.com/share/1BzAKAjpVh/?mibextid=wwXIfr

Featured publications

The adult nasal mucosa is defined by distinct immune profiles that modulate in-vitro SARS-CoV-2 infection

Authors: Sarah N Gowanlock, Victor HK Lam, Zeynep Güneş Tepe, Daniel E Park, Vera Tai, Juan E Salazar, Tony Pham, Yazan Khan, Sydney Nelson, Caitlin Horn, David Zuanazzi, Diana Yang, Lance B Price, Rupert Kaul, Leigh Sowerby, Ryan M Troyer, Cindy M Liu, Jessica L Prodger

Description: The nasal mucosa is the primary entry site for many respiratory viruses, and immune molecules present at the time of exposure may dictate if infection occurs. However, the baseline immune state in healthy adults – and how it influences susceptibility to viruses – remains poorly defined.

Anaerobe‐Driven Inflammation and Epithelial Barrier Disruption in Genital HIV Acquisition
Authors: Shirley Constable, Yasamin Minazadeh, Lane B Buchanan, Henryroger Ssemunywa, Ronald M Galiwango, Rupert Kaul, Jessica L Prodger

Description: Genital microbiome dysbiosis is an important risk factor for the sexual acquisition of human immunodeficiency virus (HIV) in both the male and female genital tracts. The vaginal, penile and urethral mucosae are distinct microenvironments with characteristic microbiome compositions. However, all three sites can be colonised by a group of strictly anaerobic bacteria that are strongly associated with mucosal inflammation and HIV risk. Our understanding of the relationship between genital anaerobes and HIV acquisition has largely focused on mucosal target cell density and activation. Yet, genital anaerobes disrupt epithelial barrier integrity, a crucial component of mucosal defence.

Pathological phimosis is associated with foreskin immune cell infiltration but not microbiota composition

Authors: Rachel Penney, Lane B Buchanan, Jorge Rojas-Vargas, Jeff Lin, Yazan Khan, Jacob Davidson, Claire A Wilson, Vera Tai, Thatiane A Russo, Thomas J Hope, Hannah Wilcox, Bern Monari, Jacques Ravel, Kait F Al, Sumit Dave, Peter Zhan Tao Wang, Jeremy P Burton, Jessica L Prodger

Description: The penile microbiota has been implicated in genital inflammation and increased risk of HIV, HPV, HSV-2, and female-partner bacterial vaginosis in adult males, yet its development during childhood and potential role in pediatric foreskin pathologies remain unknown. We characterized the coronal sulcus microbiota of 75 pediatric males (median age 8.5 years; 43% with pathological phimosis) before and after circumcision and compared these profiles to 56 uncircumcised adult men. Pediatric penile microbiota were highly diverse, dominated by strict and facultative anaerobes, and loosely structured compared to adults, who exhibited two distinct, ecologically organized communities. Circumcision markedly reduced anaerobic taxa and increased Corynebacterium and Staphylococcus. Pathological phimosis (the inability to retract the foreskin due to scarring) was associated with increased densities of CD3+ T cells …

The Nugent score is an inappropriate diagnostic tool for neovaginal bacteria in transfeminine people

Authors: Reeya Parmar, Bern Monari, Emery Potter, Jorge Rojas-Vargas, Hannah Wilcox, David Zuanazzi, Annabel Poon, Ainslie C Shouldice, Vonetta L Edwards, Yonah Krakowsky, Jacques Ravel, Jessica L Prodger

Description: Many transfeminine people (assigned male at birth with feminine gender identities) undergo vaginoplasty, a surgical procedure constructing a neovagina, typically using penile and scrotal tissue. In cisgender females, gynecological symptoms (pain, discharge, malodor) are often attributed to bacterial vaginosis, which can be diagnosed using Nugent scoring of gram-stained vaginal smears. The Nugent score assesses the abundance of large gram-positive rods versus small or curved gram-variable rods, traditionally for the detection of Lactobacillus, Gardnerella vaginalis, and Mobiluncus, respectively. Although unvalidated, this method is frequently applied to neovaginal samples to diagnose gynecological symptoms and dysbiosis. This study assessed the Nugent score’s utility for diagnosing neovaginal dysbiosis in transfeminine people.

Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

Authors: Ghazal Sadri, Steven T Nadakal, William Lauer, Justin Kos, Parmit K Singh, Erin Elliott, Catherine W Kaiser, Easton E Ford, Nadia Richardson, Kaitlyn M Shields, Elizabeth Hudson, Noemi L Linden, Ali Danesh, James Powell, Peter Warburton, Juan Soto, Matthew Emery, Gintaras Deikus, Guinevere Q Lee, Susanna L Lamers, Steven J Reynolds, Ronald Galiwango, Jessica L Prodger, Stephen Tomusange, Taddeo Kityamuweesi, Tina Han, R Brad Jones, Aaron AR Tobian, Alan N Engelman, Robert Sebra, Susan Morgello, Andrew D Redd, David Sachs, Eric Rouchka, Melissa L Smith

Description: Human Immunodeficiency Virus type 1 (HIV-1) is responsible for the global HIV/AIDS epidemic and the establishment of an integrated HIV-1 reservoir remains the primary obstacle to cure. Upon therapy interruption, reactivation of the persistent HIV-1 reservoir propagates viral rebound and mediates continued immunological decline. While furthering understanding of the HIV-1 reservoir is essential for HIV-1 cure, commonly used sequencing strategies are often limited by the reliance on short-read sequencing across separate assays to determine integration sites and proviral integrity – something that does not always adequately resolve complex human genomic repeats or low complexity regions. Simultaneous identification of proviral integration sites and proviral integrity at the single molecule level would enable HIV-1 reservoir characterization with minimal imputation or bioinformatic reconstruction. Here we present HIV Single Molecule Real Time Capture (HIV SMRTcap), a novel molecular and computational pipeline that directly and simultaneously identifies HIV-1 integration sites, defines proviral integrity, and characterizes clonal expansion of HIV-1 provirus-containing cells with single molecule resolution. In combination with long-read, single-molecule, real-time (SMRT) sequencing and custom analytic pipelines, HIV SMRTcap enables a highly comprehensive characterization of HIV-1 reservoirs. Moreover, we demonstrate here that HIV SMRTcap performs robustly across the major global subtypes (HIV-1 subtype A, B, C, D and A/D recombinant viruses), and can use both cell- and tissue-derived inputs, including samples from antiretroviral …

Estimating HIV-1 Viremic Time from Reservoir Sequence Diversity with Uncertainty Quantification

Authors: Edward N Kankaka, Stephen Tomusange, Taddeo Kityamuweesi, Gabriel Quiros, Nicholas DiRico, Adam A Capoferri, Owen Baker, Erin E Brown, Jernelle Miller, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Craig Martens, Thomas C Quinn, Eileen P Scully, Amjad Khan, Art FY Poon, Jessica L Prodger, Ronald M Galiwango, Steven J Reynolds, Andrew D Redd

Description: Accurate estimation of HIV viremic time is valuable for understanding reservoir dynamics, and informing cure trials. Traditional approaches rely on serological assays or CD4 counts, which can lack quantitative precision. Sequence-based estimates using diversity in pre-treatment plasma RNA address this limitation, but are increasingly limited in the era of immediate ART initiation. Source

Experiences and evidence of transfeminine people’s challenges with chronic, recurrent neovaginal malodor: a cross-sectional qualitative study

Authors: Ainslie C Shouldice, Reeya Parmar, Hannah Wilcox, Aleena Ghafoor, Jorge Rojas-Vargas, Emery Potter, Deborah Penava, Jacques Ravel, Jessica L Prodger

Description: Penile inversion vaginoplasty, which uses penile and scrotal skin to surgically create a neovagina, is a medically necessary gender-affirming surgery for some transfeminine individuals. Much like cisgender women, roughly a third of transfeminine individuals who have undergone vaginoplasty report having experienced bothersome neovaginal malodor in the past 30 days. However, sources of neovaginal malodor remain unclear. This study sought to collect data on odour quality and characterize the experiences of transfeminine individuals with neovaginal malodor. Source

The Futility of Nugent Scoring as a Diagnostic Tool for Neovaginal Bacterial Dysbiosis in Transfeminine People

Authors: Jessica Prodger, Reeya Parmar, Bern Monari, Emery Potter, Jorge Rojas-Vargas, Hannah Wilcox, David Zuanazzi, Annabel Poon, Ainslie Shouldice, Vonetta Edwards, Yonah Krakowsky, Jacques Ravel

Description: Transfeminine people were assigned male at birth and experience a female or feminine gender identity. Many elect to undergo vaginoplasty, a surgical procedure that constructs a neovagina, typically using penile and scrotal tissue. Like cisgender females, transfeminine people experience gynecological symptoms, including pain, discharge, and malodor. In cisgender females, clinicians attribute these symptoms to bacterial dysbiosis and can be diagnosed by Nugent scoring of gram-stained vaginal smears. The Nugent score assesses the abundance of large gram-positive rod vs. small or curved gram-variable rod morphotypes, traditionally for the detection of Lactobacillus spp., Gardnerella vaginalis , and Mobiluncus spp. (curved rod), respectively. Although unvalidated for neovaginal samples, this method is frequently applied to diagnose dysbiosis in transfeminine people with vaginoplasty.

Source

Survival and transmission fitness of SARS-CoV-2 over the time-of-flight in an aerosolization chamber

Authors: Yiying Zhang, Justin M Donovan, Dylan W Weninger, Victor Lam, Richard Gibson, Steven Renaud, Daniel Paquette, Alex Lescanec, Cody Hird, Christopher T DeGroot, Jessica L Prodger, Franco Berruti, Eric Savory, Eric J Arts

Description: The impact of various environmental factors on SARS-CoV-2 transmission remains debated, partly due to limited physical experiments with infectious virus that closely replicate real-world conditions. Using a novel, self-contained containment level 3 chamber, we aerosolized the virus in different environmental conditions then collected droplets on nasal tissue, cell lines, or different materials to measure the transmission of infectious SARS-CoV-2. We found that SARS-CoV-2 survival was much shorter than previously reported for the potential of fomite transmission. Temperature, relative humidity and the presence of incinerated tobacco, cannabis, or vape products had no discernible impact on SARS-CoV-2 transmission through aerosolized droplets, but affected the survival of VSV, a non-respiratory enveloped virus. When compared to USA-WA1/2020 and the Omicron variant, Delta SARS-CoV-2 had the greatest …

Source

Penile microbiomes have important implications for HIV susceptibility and broader reproductive health

Authors: Rameen Jamil, Jessica L Prodger, Ronald M Galiwango, Cindy M Liu, Aaron AR Tobian, Rupert Kaul

Description: HIV is a major public health issue, with almost 40 million people currently living with HIV and 1.3 million new infections reported in 2024 [1]. Sub-Saharan Africa (SSA) accounts for over 50% of global cases, despite the considerable success of prevention programmes in the region [1]. Pre-exposure prophylaxis (PrEP) with antiretroviral medications reduces the risk of sexual HIV acquisition by over 90%, but rollout in SSA has been slow due to barriers such as stigma, high cost, lack of health infrastructure and low individual awareness of risk [2]. In addition, political pressures mean that global treatment and prevention programs are currently under great threat. Human cohort studies and animal models have shown that genital inflammation is a key determinant of HIV susceptibility in both men and women [3]. Proinflammatory cytokines and chemokines recruit HIV-target cells to the mucosa, including activated CD4+ T … Source