Maciej F Boni

Associate Professor of Biology

Maciej F Boni

Research Summary

Human influenza epidemiology and evolution, evaluating population-level malaria treatment strategies with individual-based microsimulation models, phylogenetic analysis of avian influenza evolution in southern Vietnam, economic epidemiology of avian influenza, evaluating population-level efficacy of a potential dengue vaccine with mathematical models

Huck Affiliations

Links

Publication Tags

Epidemics Sars Virus Mutation Population Artemisinine Climate Cluster Analysis Norovirus Viruses Infections Pandemics Genes Antibodies Plasmodium Falciparum Genome Dengue Epidemiology Panama Incidence Parasites Gastroenteritis Vietnam Malaria Genetic Recombination Disease Outbreaks

Most Recent Papers

Mathematical epidemiology for a later age

Noah A. Rosenberg, Maciej F. Boni, 2022, Theoretical Population Biology on p. 81-83

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers, Christian L. Althaus, Ugochukwu J. Anyaneji, Phillip A. Bester, Maciej F. Boni, Mohammed Chand, Wonderful T. Choga, Rachel Colquhoun, Michaela Davids, Koen Deforche, Deelan Doolabh, Louis du Plessis, Susan Engelbrecht, Josie Everatt, Jennifer Giandhari, Marta Giovanetti, Diana Hardie, Verity Hill, Nei Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Charity Joseph, Rageema Joseph, Legodile Koopile, Sergei L. Kosakovsky Pond, Moritz U.G. Kraemer, Lesego Kuate-Lere, Oluwakemi Laguda-Akingba, Onalethatha Lesetedi-Mafoko, Richard J. Lessells, Shahin Lockman, Alexander G. Lucaci, Arisha Maharaj, Boitshoko Mahlangu, Tongai Maponga, Kamela Mahlakwane, Zinhle Makatini, Gert Marais, Dorcas Maruapula, Kereng Masupu, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Adriano Mendes, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele Mosepele, Gerald Motsatsi, Modisa S. Motswaledi, Thongbotho Mphoyakgosi, Nokukhanya Msomi, Peter N. Mwangi, Yeshnee Naidoo, Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San, Lesley Scott, Roger Shapiro, Lavanya Singh, Pamela Smith-Lawrence, Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila, Derek Tshiabuila, Joseph Tsui, Stephanie van Wyk, Steven Weaver, Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E. Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser, Florette Treurnicht, Marietje Venter, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira, 2022, Nature on p. 679-686

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.

D Martin, S Lytras, A Lucaci, W Maier, B Grüning, S Shank, S Weaver, O MacLean, R Orton, P Lemey, Maciej Boni, H Tegally, G Harkins, C Scheepers, J Bhiman, J Everatt, D Amoako, J San, J Giandhari, A Sigal, C Williamson, N Hsiao, A von Gottberg, A De Klerk, R Shafer, D Robertson, R Wilkinson, B Sewell, R Lessells, A Nekrutenko, A Greaney, T Starr, J Bloom, B Murrell, E Wilkinson, R Gupta, T de Oliveira, S Kosakovsky Pond, 2022, bioRxiv : the preprint server for biology

SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics

Nathan B. Wikle, Thu Nguyen-Anh Tran, Bethany Gentilesco, Scott M. Leighow, Emmy Albert, Emily R. Strong, Karel Brinda, Haider Inam, Fuhan Yang, Sajid Hossain, Philip Chan, William P. Hanage, Maria Messick, Justin R. Pritchard, Ephraim M. Hanks, Maciej F. Boni, 2022, Science advances

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, MacIej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei Yuan Hsiao, Anne Von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio De Oliveira, Sergei L.Kosakovsky Pond, 2022, Molecular Biology and Evolution

SARS-CoV-2 attack rate and population immunity in southern New England, March 2020 - May 2021.

T Tran, N Wikle, F Yang, H Inam, S Leighow, B Gentilesco, P Chan, E Albert, E Strong, J Pritchard, W Hanage, E Hanks, F Crawford, Maciej Boni, 2021, medRxiv : the preprint server for health sciences

Age-seroprevalence curves for the multi-strain structure of influenza A virus

Dao Nguyen Vinh, Nguyen Thi Duy Nhat, Erwin de Bruin, Nguyen Ha Thao Vy, Tran Thi Nhu Thao, Huynh Thi Phuong, Pham Hong Anh, Stacy Todd, Tran Minh Quan, Nguyen Thi Le Thanh, Nguyen Thi Nam Lien, Nguyen Thi Hong Ha, Tran Thi Kim Hong, Pham Quang Thai, Marc Choisy, Tran Dang Nguyen, Cameron P. Simmons, Guy E. Thwaites, Hannah E. Clapham, Nguyen Van Vinh Chau, Marion Koopmans, Maciej F. Boni, 2021, Nature Communications

Optimal SARS-CoV-2 vaccine allocation using real-time attack-rate estimates in Rhode Island and Massachusetts

Thu Nguyen Anh Tran, Nathan B. Wikle, Emmy Albert, Haider Inam, Emily Strong, Karel Brinda, Scott M. Leighow, Fuhan Yang, Sajid Hossain, Justin R. Pritchard, Philip Chan, William P. Hanage, Ephraim M. Hanks, Maciej F. Boni, 2021, BMC Medicine

SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics.

N Wikle, T Tran, B Gentilesco, S Leighow, J Albert, E Strong, K Břinda, H Inam, F Yang, S Hossain, P Chan, W Hanage, M Messick, J Pritchard, E Hanks, Maciej Boni, 2021, medRxiv : the preprint server for health sciences

Assessing the effect of climate variables on the incidence of dengue cases in the metropolitan region of panama city

Vicente Navarro Valencia, Yamilka Díaz, Juan Miguel Pascale, Maciej F. Boni, Javier E. Sanchez-Galan, 2021, International Journal of Environmental Research and Public Health

Most-Cited Papers

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson, 2020, Nature Microbiology on p. 1408-1417

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

Olivo Miotto, Jacob Almagro-Garcia, Magnus Manske, Bronwyn MacInnis, Susana Campino, Kirk A. Rockett, Chanaki Amaratunga, Pharath Lim, Seila Suon, Sokunthea Sreng, Jennifer M. Anderson, Socheat Duong, Chea Nguon, Char Meng Chuor, David Saunders, Youry Se, Chantap Lon, Mark M. Fukuda, Lucas Amenga-Etego, Abraham V.O. Hodgson, Victor Asoala, Mallika Imwong, Shannon Takala-Harrison, François Nosten, Xin Zhuan Su, Pascal Ringwald, Frédéric Ariey, Christiane Dolecek, Tran Tinh Hien, Maciej F. Boni, Cao Quang Thai, Alfred Amambua-Ngwa, David J. Conway, Abdoulaye A. Djimdé, Ogobara K. Doumbo, Issaka Zongo, Jean Bosco Ouedraogo, Daniel Alcock, Eleanor Drury, Sarah Auburn, Oliver Koch, Mandy Sanders, Christina Hubbart, Gareth Maslen, Valentin Ruano-Rubio, Dushyanth Jyothi, Alistair Miles, John O'Brien, Chris Gamble, Samuel O. Oyola, Julian C. Rayner, Chris I. Newbold, Matthew Berriman, Chris C.A. Spencer, Gilean McVean, Nicholas P. Day, Nicholas J. White, Delia Bethell, Arjen M. Dondorp, Christopher V. Plowe, Rick M. Fairhurst, Dominic P. Kwiatkowski, 2013, Nature Genetics on p. 648-655

Impact of human mobility on the emergence of dengue epidemics in Pakistan

Amy Wesolowski, Taimur Qureshi, Maciej F. Boni, Pål Roe Sundsøy, Michael A. Johansson, Syed Basit Rasheed, Kenth Engø-Monsen, Caroline O. Buckee, Burton H. Singer, 2015, Proceedings of the National Academy of Sciences of the United States of America on p. 11887-11892

Role for migratory wild birds in the global spread of avian influenza H5N8

Samantha J. Lycett, Rogier Bodewes, Anne Pohlmann, Jill Banks, Krisztián Bányai, Maciej F. Boni, Ruth Bouwstra, Andrew C. Breed, Ian H. Brown, Hualan Chen, Ádám Dán, Thomas J. DeLiberto, Nguyen Diep, Marius Gilbert, Sarah Hill, Hon S. Ip, Chang Wen Ke, Hiroshi Kida, Mary Lea Killian, Marion P. Koopmans, Jung Hoon Kwon, Dong Hun Lee, Youn Jeong Lee, Lu Lu, Isabella Monne, John Pasick, Oliver G. Pybus, Andrew Rambaut, Timothy P. Robinson, Yoshihiro Sakoda, Siamak Zohari, Chang Seon Song, David E. Swayne, Mia Kim Torchetti, Hsiang Jung Tsai, Ron A.M. Fouchier, Martin Beer, Mark Woolhouse, Thijs Kuiken, 2016, Science on p. 213-217

Recombination within the pandemic norovirus GII.4 lineage

John Sebastian Eden, Mark M. Tanaka, Maciej F. Boni, William D. Rawlinson, Peter A. White, 2013, Journal of Virology on p. 6270-6282

Genomic epidemiology of artemisinin resistant malaria

Roberto Amato, Olivo Miotto, Charles J. Woodrow, Jacob Almagro-Garcia, Ipsita Sinha, Susana Campino, Daniel Mead, Eleanor Drury, Mihir Kekre, Mandy Sanders, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Voahangy Andrianaranjaka, Tobias Apinjoh, Elizabeth Ashley, Sarah Auburn, Gordon A. Awandare, Vito Baraka, Alyssa Barry, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C. Bull, Kesinee Chotivanich, David J. Conway, Alister Craig, Nicholas P. Day, Abdoulaye Djimdé, Christiane Dolecek, Arjen M. Dondorp, Chris Drakeley, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Rick M. Fairhurst, Abul Faiz, Caterina I. Fanello, Tran Tinh Hien, Abraham Hodgson, Mallika Imwong, Deus Ishengoma, Pharath Lim, Chanthap Lon, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Pascal Michon, Victor Mobegi, 2016, eLife

Malaria eradication within a generation

Richard G.A. Feachem, Ingrid Chen, Omar Akbari, Amelia Bertozzi-Villa, Samir Bhatt, Fred Binka, Maciej F. Boni, Caroline Buckee, Joseph Dieleman, Arjen Dondorp, Alex Eapen, Neelam Sekhri Feachem, Scott Filler, Peter Gething, Roly Gosling, Annie Haakenstad, Kelly Harvard, Arian Hatefi, Dean Jamison, Kate E. Jones, Corine Karema, Richard Nchabi Kamwi, Altaf Lal, Erika Larson, Margaret Lees, Neil F. Lobo, Angela E. Micah, Bruno Moonen, Gretchen Newby, Xiao Ning, Muhammad Pate, Martha Quiñones, Michelle Roh, Ben Rolfe, Dennis Shanks, Balbir Singh, Kenneth Staley, James Tulloch, Jennifer Wegbreit, Hyun Ju Woo, Winnie Mpanju-Shumbusho, 2019, The Lancet on p. 1056-1112

Genomic analysis of local variation and recent evolution in Plasmodium vivax

Richard D. Pearson, Roberto Amato, Sarah Auburn, Olivo Miotto, Jacob Almagro-Garcia, Chanaki Amaratunga, Seila Suon, Sivanna Mao, Rintis Noviyanti, Hidayat Trimarsanto, Jutta Marfurt, Nicholas M. Anstey, Timothy William, MacIej F. Boni, Christiane Dolecek, Hien Tinh Tran, Nicholas J. White, Pascal Michon, Peter Siba, Livingstone Tavul, Gabrielle Harrison, Alyssa Barry, Ivo Mueller, Marcelo U. Ferreira, Nadira Karunaweera, Milijaona Randrianarivelojosia, Qi Gao, Christina Hubbart, Lee Hart, Ben Jeffery, Eleanor Drury, Daniel Mead, Mihir Kekre, Susana Campino, Magnus Manske, Victoria J. Cornelius, Bronwyn MacInnis, Kirk A. Rockett, Alistair Miles, Julian C. Rayner, Rick M. Fairhurst, Francois Nosten, Ric N. Price, Dominic P. Kwiatkowski, 2016, Nature Genetics on p. 959-964

In vivo susceptibility of plasmodium falciparum to artesunate in Binh Phuoc Province, Vietnam

Tran Tinh Hien, Nguyen Thanh Thuy-Nhien, Nguyen Hoan Phu, MacIej F. Boni, Ngo Viet Thanh, Nguyen Thuy Nha-Ca, Le Hong Thai, Cao Quang Thai, Pham Van Toi, Phung Duc Thuan, Le Thanh Long, Le Thanh Dong, Laura Merson, Christiane Dolecek, Kasia Stepniewska, Pascal Ringwald, Nicholas J. White, Jeremy Farrar, Marcel Wolbers, 2012, Malaria Journal

The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012

John Sebastian Eden, Joanne Hewitt, Kun Lee Lim, Maciej F. Boni, Juan Merif, Gail Greening, Rodney M. Ratcliff, Edward C. Holmes, Mark M. Tanaka, William D. Rawlinson, Peter A. White, 2014, Virology on p. 106-113

News Articles Featuring Maciej F Boni

Mysteries Linger About Covid’s Origins, W.H.O. Report Says

“The lack of political cooperation from China continues to stifle any meaningful progress,” one expert said. In its first report, a team of international scientists assembled by the World Health Organization to advise on the origins of the coronavirus said on Thursday that bats likely carried an ancestor of the coronavirus that may have then spilled over into a mammal sold at a wildlife market. But the team said that more Chinese data was needed to study how the virus spread to people, including the possibility that a lab leak played a role.

The real COVID surge is (much) bigger than it looks. But don't panic

Cases of COVID-19 are — yet again — on the rise. The U.S. is seeing an average of more than 100,000 reported new cases across the country every day. That's nearly double the rate a month ago and four times higher than this time last year.

Anthony Fauci said the pandemic was over in U.S., then backpedaled. What do experts say?

Epidemiologists in Philly and beyond cringed when Anthony Fauci said the U.S was “out of the pandemic phase.” But how will we know?

Omicron subvariant BA.2: Is COVID-19 surge in Europe coming to US?

In mid-January, when the omicron variant was driving the Philadelphia area’s latest wave of COVID-19, a boxy white device in Frederic Bushman’s lab already had detected a hint to the pandemic’s next chapter: The region’s first case of a subvariant of omicron, what would eventually be known as BA.2.

Is the latest COVID-19 surge in Europe coming to the U.S.?

We may not see a big wave, but "there's going to be a bump," says one expert.

How will we know the COVID pandemic is over? And how do we get there?

It’s been a long two years. Two years of stress. Two years of upending your daily routine, adopting a new one, and then upending the new one.

Omicron genetics and early transmission patterns are characterized in new study

The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-2 variants as a result of adaptive evolution, in which beneficial mutations are passed on to future generations through natural selection, rather than through recombination between previous variants, according to a large international team of researchers. The study, which published recently in Nature, is the first to describe the genomic profile of Omicron and explore the origins of the variant.

Omicron may be less severe in South Africa. That may not be the case for the U.S.

It's been about a month since scientists first detected the highly mutated coronavirus variant dubbed "omicron." Since then, scientists have come to learn that omicron spreads faster than the delta variant and is the quickest-spreading variant the world has yet faced. It also has a huge ability to bypass immune protection and cause breakthrough infections.

New technique better assesses exposure of a population to a virus

Accurately assessing the exposure of a population to a particular virus is difficult because the tools for doing so do not account for the fact that many viruses comprise multiple circulating strains, or the fact that people can be vaccinated or naturally immune, among other factors. Using influenza as a model, a team of researchers led by Penn State has developed a new technique that overcomes many of these roadblocks.

Plenty of Evidence for Recombination in SARS-CoV-2

Different variants of the virus behind the COVID-19 pandemic are swapping chunks of genetic material, but it’s not yet clear what implications that may have for public health.