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.
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…
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic
Genes, 2020. Authors: Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy…
New Genomes from The Congo Basin Expand History of CRF01_AE Origin and Dissemination
AIDS Res Hum Retroviruses, 2020. Authors: Junqueira DM, Wilkinson E, Vallari AS, Deng XD, Achari A, Yu G, McArthur C, Kaptué L,…
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…
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Bioinformatics, 2020. Authors: Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T.Journal: Bioinformatics,btaa145, https://doi.org/10.1093/bioinformatics/btaa145: (2020). Abstract…
Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls
Front. Microbiol., 2020. Authors: San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T. Journal: Front. Microbiol.,…
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,…
Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.
Bioinformatics, 2019 Authors: Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme…
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…
Impact of point-of-care Xpert MTB/RIF on tuberculosis treatment initiation: a cluster randomised trial
Am J Respir Crit Care Med, 2017. Authors: Lessells RJ, Cooke GS, McGrath N, Nicol MP, Newell ML, Godfrey-Faussett P.Journal: Am J…
High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients
Clinical Infectious Diseases, 2017. Authors: Hofstra LM, Rivas ES, Nijhuis M, Bank LEA, Wilkinson E, Kelly K, Mudrikova T, Schuurman R, de Oliveira…
Sensitive next generation sequencing method reveals deep genetic diversity of HIV-1 in the Democratic Republic of the Congo
Journal of Virology, 2017. Authors: Rodgers MA, Wilkerson E, Vallari A, McArthur C, Sthreshley L, Brennan CA, Cloherty G, de Oliveira T.Journal: Journal…
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…
Microbial genome-wide association studies: lessons from human GWAS.
Nature Reviews Genetics, 2017 Authors: Power RA, Parkhill J, de Oliveira T.Journal: Nature Reviews Genetics,nrg.2016.132:doi:10.1038/nrg.2016.132 (2017) Abstract The reduced costs of sequencing…
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…