our publications
recent publications
The CLIMADE consortium brings together partners from across the globe that have long-term experience working with climate amplified epidemics and pathogen genomics. Partners include public health agencies, academic organizations, and industry. Here, we highlight some of our recent publications on pathogens that are amplified by climate.
Identification and genomic characterisation of known and novel highly divergent sapoviruses in frugivorous and insectivorous bats in Nigeria
Collaborators: Uwem E. George, Lander De Coninck, Oluwadamilola A. George, Taiye Adeyanju, Arthur Oragwa, Joshua Kamani, Joseph Igbokwe, Andrew Adamu,…
Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria
Collaborators: Bernard Anyebe Onoja, Judith Uche Oguzie, Uwem Etop George, Kaego Emmanuel Asoh, Philip Ajayi, Toluwanimi Faithful Omofaye, Imafidon Oluwatoyin…
Lassa virus in novel hosts: insights into the epidemiology of lassa virus infections in southern Nigeria
Collaborators: Anise Nkenjop Happi, Olusola Akinola Ogunsanya, Akeemat Opeyemi Ayinla, Ayotunde Elijah Sijuwola, Femi Mudasiru Saibu, Kazeem Akano, Cecilia Nwofoke,…
Nationwide surveillance identifies yellow fever and chikungunya viruses transmitted by various species ofAedesmosquitoes in Nigeria
Collaborators: Udoka C. Nwangwu, Judith U. Oguzie, William E. Nwachukwu, Cosmas O. Onwude, Festus A. Dogunro, Mawlouth Diallo, Chukwuebuka K.…
Genomics reveals zoonotic and sustained human mpox spread in West Africa
Collaborators: Edyth Parker, Ifeanyi F. Omah, Delia Doreen Djuicy, Andrew Magee, Christopher H. Tomkins-Tinch, James Richard Otieno, Patrick Varilly, Akeemat…
Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa
Collaborators: Delia Doreen Djuicy, Ifeanyi F. Omah, Edyth Parker, Christopher H Tomkins-Tinch, James Richard Otieno, Moïse Henri Moumbeket Yifomnjou, Loique…
Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas
Collaborators: Jenicca Poongavanan, Marcel Dunaiski, Graeme Dor, Moritz U.G. Kraemer, Marta Giovanetti, Ahyoung Lim, Oliver J. Brady, Bernardo Gutierrez, Jean…
Disaggregation Regression and Multi-Model Evaluation for Predicting Dengue Risk in Africa
Collaborators: Jenicca Poongavanan, Tim C.D. Lucas, Gaspary Mwanyika, Moritz U.G. Kraemer, José Lourenço, Marcel Dunaiski, Tulio de Oliveira, Houriiyah Tegally…
Infectious diseases in a warming world: A call for action
Collaborators: Monika Moir, Cheryl Baxter, Houriiyah Tegally, Tulio de Oliveira Summary: Abstract not available Publication Date: 2025-03-07Journal: South African Journal…
Craft: A Machine Learning Approach to Dengue Subtyping
Collaborators: Daniel J. van Zyl, Marcel Dunaiski, Houriiyah Tegally, Cheryl Baxter, Tulio de Oliveira, Joicymara S. Xavier Summary: AbstractMotivationThe dengue…
Building Pathogen Genomic Sequencing Capacity in Africa: Centre for Epidemic Response and Innovation Fellowship
Collaborators: Eric Agboli, Molalegne Bitew, Christian N. Malaka, Tiangay M. P. S. Kallon, Alhaji M. S. Jalloh, Baron Yankonde, Doreen…
A decade of dengue disease burden in Africa (2013–2023): a systematic review
Collaborators: Gaspary O. Mwanyika, Monika Moir, Abdualmoniem O. Musa, Jenicca Poongavanan, Graeme Dor, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira,…
Establishing a dengue genomic monitoring in Cuba: uncovering virus dynamics to enhance local response
Collaborators: Melissa Pérez, Mayling Álvarez, Lissette Perez, Ana Julia Benitez, Silvia Serrano, Talita Emile Ribeiro Adelino, Vagner Fonseca, Sonia Resik,…
GRAPEVNE - Graphical Analytical Pipeline Development Environment for Infectious Diseases
Collaborators: John-Stuart Brittain, Joseph Tsui, Rhys Inward, Bernardo Gutierrez, Gaspary Mwanyika, Houriiyah Tegally, Tuyen Huynh, George Githinji, Sofonias Kifle Tessema,…
Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review
Collaborators: Monika Moir, Nikita Sitharam, Laura Marije Hofstra, Graeme Dor, Gaspary Mwanyika, Yajna Ramphal, Martina L Reichmuth, James Emmanuel San,…
Travel-associated international spread of Oropouche virus beyond the Amazon
Collaborators: Felipe Campos de Melo Iani, Felicidade Mota Pereira, Elaine Cristina de Oliveira, Janete Taynã Nascimento Rodrigues, Mariza Hoffmann Machado,…
Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023
Collaborators: Lucious Chabuka, Wonderful T. Choga, Carla N. Mavian, Monika Moir, Christian Morgenstern, Houriiyah Tegaly, Abhinav Sharma, Eduan Wilkinson, Yeshnee…
Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023
Collaborators: Adugna Abera, Houriiyah Tegally, Geremew Tasew, Eduan Wilkinson, Abraham Ali, Feyisa Regasa, Molalegne Bitew, Mahlet Belachew, Lucious Chabuka, Gaspary…
Artificial intelligence for modelling infectious disease epidemics
Collaborators: Moritz U. G. Kraemer, Joseph L.-H. Tsui, Serina Y. Chang, Spyros Lytras, Mark P. Khurana, Samantha Vanderslott, Sumali Bajaj,…
Dengue virus importation risks in Africa: a modelling study
Collaborators: Jenicca Poongavanan, José Lourenço, Joseph L-H Tsui, Vittoria Colizza, Yajna Ramphal, Cheryl Baxter, Moritz U G Kraemer, Marcel Dunaiski,…
Rapid Spatial Expansion Beyond the Amazon Basin: Oropouche Virus joins other main arboviruses in epidemic activity across the Americas
Collaborators: Felipe Campos de Melo Iani, Felicidade Mota Pereira, Elaine Cristina de Oliveira, Janete Taynã Nascimento Rodrigues, Mariza Hoffmann Machado,…
Impacts of climate change-related human migration on infectious diseases
Collaborators: Joseph L.-H. Tsui, Rosario Evans Pena, Monika Moir, Rhys P. D. Inward, Eduan Wilkinson, James Emmanuel San, Jenicca Poongavanan,…
Understanding the Transmission Dynamics of the Chikungunya Virus in Africa
Collaborators: Yajna Ramphal, Houriiyah Tegally, James Emmanuel San, Martina Larissa Reichmuth, Marije Hofstra, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira,…
Disentangling seasonal introduction and establishment risk of dengue in Africa
Collaborators: Jenicca Poongavanan, José Lourenço, Joseph L.-H. Tsui, Vittoria Colizza, Yajna Ramphal, Cheryl Baxter, Moritz U.G. Kraemer, Marcel Dunaiski, Tulio…
A new lineage nomenclature to aid genomic surveillance of dengue virus
Collaborators: Verity Hill, Sara Cleemput, Vagner Fonseca, Houriiyah Tegally, Anderson F. Brito, Robert Gifford, Vi Thuy Tran, Duong Thi Hue…
An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal
Collaborators: Abdou Padane, Houriiyah Tegally, Yajna Ramphal, Ndiaye Seyni, Mariéma Sarr, Mame Matar Diop, Cyrille Kouligueul Diedhiou, Aminata Mboup, Ndèye…
Genomic characterization of Dengue virus circulation in Ethiopia
Collaborators: Adugna Abera, Houriiyah Tegally, Geremew Tasew, Eduan Wilkinson, Abraham Ali, Feyisa Regasa, Molalegne Bitew, Lucious Chabuka, Gaspary Mwanyika, Derek…
Aedes albopictus arrives in Lisbon: an emerging public health threat
Collaborators: Teresa Nazareth, Gonçalo Seixas, José Lourenço, Paulo J. G. Bettencourt Summary: The recent identification in Lisbon, Portugal, of the…
Monitoring Monkeypox: Safeguarding Global Health through Rapid Response and Global Surveillance
Collaborators: Marta Giovanetti, Eleonora Cella, Sonia Moretti, Fabio Scarpa, Alessandra Ciccozzi, Svetoslav Nanev Slavov, Francesca Benedetti, Davide Zella, Giancarlo Ceccarelli,…
Chikungunya vaccine: Is it time for it?
Collaborators: Francesco Branda, Fabio Scarpa, Chiara Romano, Alessandra Ciccozzi, Antonello Maruotti, Marta Giovanetti, Massimo Ciccozzi Summary: The Chikungunya virus (CHIKV),…
Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay
Collaborators: Cynthia Vazquez, Vagner Fonseca, Andrea Gomez de la Fuente, Sandra Gonzalez, Fatima Fleitas, Mauricio Lima, Natália R. Guimarães, Felipe…
Genomics-based timely detection of Dengue Virus type I genotypes I and V in Uruguay
Collaborators: Noelia Morel, Marta Giovanetti, Vagner Fonseca, Analía Burgueño, Mauricio Lima, Emerson Castro, Natália R. Guimarães, Felipe C. M. Iani,…
A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species
Collaborators: Joilson Xavier, Vagner Fonseca, Talita Adelino, Felipe C. M. Iani, Glauco C. Pereira, Myrian M. Duarte, Mauricio Lima, Emerson…
North-south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic
Collaborators: Isaac Miguel, Edwin P. Feliz, Robinson Agramonte, Pedro V. Martinez, Carlos Vergara, Yvonne Imbert, Lucia De la Cruz, Nurys…
Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023
Collaborators: Analía Burgueño, Marta Giovanetti, Vagner Fonseca, Noelia Morel, Mauricio Lima, Emerson Castro, Natália R. Guimarães, Felipe C. M. Iani,…
Mpox: An Overview of Pathogenesis, Diagnosis, and Public Health Implications
Collaborators: Francesco Branda, Chiara Romano, Massimo Ciccozzi, Marta Giovanetti, Fabio Scarpa, Alessandra Ciccozzi, Antonello Maruotti Summary: Mpox, caused by viruses…
Global Measles Surveillance: Trends, Challenges, and Implications for Public Health Interventions
Collaborators: Francesco Branda, Marta Giovanetti, Chiara Romano, Domenico Benvenuto, Alessandra Ciccozzi, Daria Sanna, Massimo Ciccozzi, Fabio Scarpa Summary: Measles, a…
Exploring the Chikungunya virus landscape in a dengue-endemic Brazilian area
Collaborators: Debora Glenda Lima de La Roque, Elaine Vieira Santos, Lucca Rocha Policastro, Péricles Natan Mendes da Costa, Mariane Evaristo,…
A new lineage nomenclature to aid genomic surveillance of dengue virus
Collaborators: Verity Hill, Sara Cleemput, Vagner Fonseca, Houriiyah Tegally, Anderson F. Brito, Robert Gifford, Vi Thuy Tran, Duong Thi Hue…
Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil
Collaborators: Felipe Campos de Melo Iani, Gabriel Montenegro de Campos, Talita Emile Ribeiro Adelino, Anielly Sarana da Silva, Simone Kashima,…
Tracing the evolution of the chikungunya virus in Argentina, 2016-2023: independent introductions and prominence of Latin American lineages
Collaborators: Cintia Fabbri, Marta Giovanetti, Victoria Luppo, Vagner Fonseca, Jorge Garcia, Cintia Barulli, Mariel Feroci, Sofia Perrone, Doraldina Casoni, Sergio…
Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread
Collaborators: Gabriel Schuab, Stephane Tosta, Keldenn Moreno, Vagner Fonseca, Luciane Amorim Santos, Svetoslav Nanev Slavov, Simone Kashima, Massimo Ciccozzi, José…
The historical ecological background of West Nile virus in Portugal indicates One Health opportunities
Collaborators: Martim A. Geraldes, Mónica V. Cunha, Carlos Godinho, Ricardo F. de Lima, Marta Giovanetti, José Lourenço Summary: West Nile…
Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report
Collaborators: Talita Adelino, Maurício Lima, Natália R. Guimarães, Joilson Xavier, Vagner Fonseca, Luiz Marcelo R. Tomé, Maira Alves Pereira, Vanessa…
Dengue Fever Surveillance in Mato Grosso do Sul: insights from genomic analysis and implications for Public Health Strategies
Collaborators: Larissa Domingues Castilho de Arruda, Marta Giovanetti, Vagner Fonseca, Marina Castilhos Souza Umaki Zardin, Gislene Garcia de Castro Lichs,…
Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023
Authors: Analía Burgueño, Marta Giovanetti, Vagner Fonseca, Noelia Morel, Mauricio Lima, Emerson Castro, Natália R. Guimarães, Felipe C. M. Iani, Victoria Bormida, Maria Noel Cortinas, Viviana Ramas, Leticia Coppola, Ana I. Bento, Leticia Franco, Jairo Mendez Rico, José Lourenço, Luiz Carlos Junior Alcantara, Hector Chiparelli. Journal: medRxiv, doi: https://doi.org/10.1101/2023.08.17.23294156 Abstract: Uruguay experienced its first Chikungunya virus…
Will climate change amplify epidemics and give rise to pandemics? Science Expert Voices
Authors: de Oliveira T, Tegally H.Journal: Science,381,6660, DOI: 10.1126/science.adk4500: (2023) Abstract While the world recovers from the COVID-19 pandemic, another crisis continues to…
Genomic epidemiology of the cholera outbreak in Malawi 2022-2023
Title: Genomic epidemiology of the cholera outbreak in Malawi 2022-2023Authors: Chabuka L, Choga WT, Mavian CN, Moir M, Tegally H, Wilkinson E, Naidoo Y, Inward R, Morgenstern…
Rapid epidemic expansion of Chikungunya virus-ECSA lineage in Paraguay
Journal: medRxiv, doi:10.1101/2023.04.16.23288635. .Authors: Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C,…
Genomic epidemiology sheds light on the recent spatio-temporal dynamics of Yellow Fever virus and the spatial corridor that fueled its ongoing emergence in southern Brazil
Journal: medRxiv,2023.01.13.23284525v1: (2023) Authors: Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi A, Tscha M, Soares G, Dorl G, Marques…
Infectious diseases science in Africa takes a leading place in the world
The Lancet, 2022. Authors: de Oliveira T. Journal: The Lancet,https://doi.org/10.1016/S0140-6736(22)00977-1I: (2022) Abstract During the COVID-19 pandemic, the lives of many loved ones…
A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil.
Microbiol Spectr., 2022. Authors: Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva…
West Nile Virus in Brazil
Authors: Costa WE, Giovanetti M, Silva Catenacci L, Fonseca V, Aburjaile FF, Chalhoub FLL, Xavier J, Campos de Melo Iani F, da…
Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses
Front. Public Health, 2021. Authors: Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, Adelino TER, Tosta S,…
Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay
Emerg Infect Dis, 2021. Authors: Graf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez…
Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil
Infect Genet Evol, 2021. Authors: Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF,…
Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes
Viruses, 2021. Authors: Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandao AP, Venancio da…
Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil
IJID, 2021. Authors: Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T,…
Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.
Pathogens, 2020. Authors: Fabri AA, Rodrigues CDS, Santos CC, Chalhoub FLL, Sampaio AS, Faria NRC, Torres MC, Fonseca V, Brasil P, Calvet…
Fatal outcome of chikungunya virus infection in Brazil
Clinical Infectious Diseases, 2020. Authors: Lima STS, Souza WM, Cavalcante JW, Candido DS, Fumagalli MJ, Carrera JP, Mello LMS, Araújo…
Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil
PLoS Negl Trop Dis, 2020. Authors: Goes de Jesus J, Gräf T, Giovanetti M, Mares-Guia MA, Xavier J, Lima Maia M, Fonseca…
A genomics network established to respond rapidly to public health threats in South Africa
Lancet Microbe, 2020. Authors: Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser…
Exposure to waste sites and their impact on health: a panel and geospatial analysis of nationally representative data from South Africa, 2008-2015
Lancet Planetary Health, 2020. Authors: Tomita A, Cuadros DF, Burns JK, Tanser F, Slotow R.Journal: Lancet Planetary Health,4: e223-34: (2020)…
Spatial clustering of food insecurity and its association with depression: a geospatial analysis of nationally representative South African data, 2008-2015
Scientific Reports, 2020. Authors: Tomita A, Cuadros DF, Mabhaudhi T, Sartorius B, Ncama BP, Dangour AD, Tanser F, Modi AT, Slotow…
Impact of community piped water coverage on re-infection with urogenital schistosomiasis in rural South Africa
Elife, 2020. Authors: Mogeni P, Vandormael A, Cuadros D, Appleton C, Tanser F.Journal: Elife,9. pii: e54012. doi: 10.7554/eLife.54012: (2020) Abstract Previously, we…
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region
Cell Reports, 2020. Authors: Giovanetti M, Faria NR, Lourenco J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour…
Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases.
Emerg Microbes Infect., 2020. Authors: Pereira Gusmão Maia Z, Mota Pereira F, do Carmo Said RF, Fonseca V, Gräf T, de…
Yellow fever virus re-emergence and spread in Southeast Brazil, 2016-2019
Journal of Virology, 2019. Authors: Giovanetti M, Lima de Mendonça MC, Fonseca V, Mares-Guia MA, Fabri A, Xavier J, Goes de Jesus J,…
Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas
PLoS Negl Trop Dis, 2021 Authors: de Oliveira EC, Fonseca V, Xavier J, Adelino T, Morales Claro I, Fabri A, Macario EM, Viniski…
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
Nature Communications, 2021 Authors: Adelino TAR, Giovanetti M, Fonseca V, Xavier J, de Abreu AS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da…
Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era
Epidemiology of Vector-Borne, 2019. Authors: Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M.Journal: Current Topics in the…
Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus.
Nature Microbiology, 2019. Authors: Kraemer MUG, Reiner RC Jr, Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson…
Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil
PLoS One, 2019 Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de…
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes
PLoS Negl Trop Dis, 2019. Authors: Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti…
Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018
Emerg Infect Dis., 2019 Authors: Hill SC, Neto de Vasconcelos J, Granja BG, Theze J, Jandondo D, Neto Z, Mirandela M,…
Genomic and epidemiological monitoring of yellow fever virus transmission potential
Science, 2018. Authors: Faria NR, Kraemer MUG, S C Hill, J Goes de Jesus, R S Aguiar, F C M…
Green environment and incident depression in South Africa: a geospatial analysis and mental health implications in a resource-limited setting
Lancet Planetary Health, 2017. Authors: Tomita A, Vandormael AM, Cuadros D, Di Minin E, Heikinheimo V, Tanser F, Slotow R, Burns…
Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study.
Lancet Infectious Diseases, 2017 Authors: Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje…
Potential for Zika virus introduction and transmission in resource-limited countries in Africa and the Asia-Pacific region: a modelling study.
Lancet Infectious Diseases, 2016. Authors: Bogoch II, Brady OJ, Kraemer MUG, German M, Creatore MI, Brent S, Watts AG, Hay…