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Kanki Lab

Our research works toward improving our understanding of the pathobiology of important viral diseases in Africa and training students and research scientists. We collaborate with African scientists to address research questions that can translate to evidence-based real-world solutions, improved health outcomes, and sustained policy change.   

Location

Harvard T. H. Chan School of Public Health 
   
651 Huntington Avenue  
FXB Building, Room 405B
Boston, Massachusetts 02115 
 

Prof. Phyllis Kanki in her office at Harvard T. H. Chan School of Public Health

About the Kanki Lab

Phyllis Kanki’s research is focused on the virology, pathogenesis, and molecular epidemiology of HIV and other viral infections in Africa. In the mid-1980s, as a doctoral student with Max Essex at SPH, she was part of the team to discover the Simian Immunodeficiency Virus (SIV) in captive immunodeficient macaque monkeys and characterize its relationship to HIV. Her further research described African Cercopithecine primates as the natural host of SIV, leading to the first evidence of an SIV-related virus in humans in Senegal, West Africa. HIV-2 is the closest human immunodeficiency virus related to HIV-1 and based on long-term research collaborations with Professor Souleymane Mboup at Université Cheikh Anta Diop in Senegal, her work provided the initial characterization of this newly described zoonotic virus.

Research Associate Charlotte Change working in the Kanki Lab
Research Associate Charlotte Change working in the Kanki Lab

AIDS Prevention Initiative in Nigeria (APIN)

APIN: Collaborating to deliver HIV-1 care and treatment, and to build local capacity 

In 2000, Phyllis Kanki created and directed the AIDS Prevention Initiative in Nigeria (APIN), with a $25 million grant from the Bill & Melinda Gates Foundation. She led the Harvard President’s Emergency Plan for AIDS Relief (PEPFAR) program from 2004-2013, providing prevention, care, and HIV antiretroviral therapy in Nigeria, Botswana, and Tanzania. Harvard PEPFAR is one of the largest grants ever awarded to Harvard. The program engaged in capacity building for clinical, laboratory, and research capabilities and supported treatment for over 300,000 AIDS patients. Phyllis Kanki is currently collaborating with Nigerian scientists on implementation science work to optimize HIV outcomes.

EBOV and ZIKV

Response to Ebola and Zika Epidemics

Following previous epidemics of Ebola (EBOV) and Zika (ZIKV) virus, Phyllis Kanki’s research has documented the presence of ZIKV infection in Senegalese and Nigerian fever patients over ~25 years, demonstrating the endemicity of this unique arbovirus in the region. Research studies have described the longevity, specificity, and cross-reactivity of T cell responses to ZIKV and dengue (DENV) and characterized the T cell responses in survivors and exposed healthcare workers from the 2015 Nigeria EBOV outbreak. A recent prospective study of pregnant women in Jos, Nigeria has characterized acute ZIKV, DENV, and Chikungunya virus infections with an association to abnormal birth outcomes.

COVID-19 Research

SARS-CoV-2 in Nigeria

In response to the SARS-CoV-2 pandemic, Phyllis Kanki collaborated with BIDMC investigators to study the relationship of SARS-CoV-2 genetic variation, antigenemia, and viral infectivity. In studies with Dr Jin-Ah Park, she looked at SARS-CoV-2 infection in human respiratory epithelial cells to better understand cellular responses associated with risk factors for COVID disease. She also engaged in studies of SARS CoV-2 infection in Nigerian healthcare workers which answered important questions on the immunopathogenesis of SARS CoV-2 infection and induction of vaccine immunity in this high-risk population. 

Kanki Lab members wearing lab personal protective equipment
Kanki Lab members wearing lab personal protective equipment

Our Research

SARS-CoV-2 in Nigerian Health Care Workers

In early 2021, we surveyed healthcare workers at Lagos State University Teaching Hospital, and SARS-CoV-2 vaccine recipients, by Western blot serology and by measuring T-cell responses. One surprising finding was evidence of pre-existing immunity to SARS-CoV-2 in as much as 15% of the general population, suggesting that prior infection by other coronaviruses could provide cellular immunity to SARS-CoV-2.  

Chikungunya virus (CHKV) and abnormal infant outcomes 

In a cohort study of 1006 pregnant women, tested in Nigerian clinics from 2019 through 2022, women were screened for Zika, Dengue, or CHKV. 119 tested positive for CHKV, and 36 were subjected to detailed laboratory tests. Abnormalities in infants, including stillbirth, cleft lip, microcephaly, preterm delivery, polydactyly with sepsis, and jaundice, were found to be associated with CHKV.  

Point-of-Care Viral Load Monitoring in Patients with HIV-1 in Nigeria 

HIV-1 viral load is an essential tool in monitoring viral suppression in 696 people living with HIV. Traditional testing is performed at central laboratories and can result in long turnaround times. A study from 2018-2019 in two clinics in Nigeria compared an alternative method, the Cepheid GeneXpert system, which can deliver results in 2-3 hours, with standard testing, in a randomized, controlled trial. We found that this point-of-care test delivered rapid results to patients failing their treatment and enabled them to switch more quickly to more effective treatment regimens, and improved documentation and patient retention.  

Phyllis Kanki at BPH retreat
Prof. Kanki talking with students at the BPH retreat

Publications Highights