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Draft:CADDE Project

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Brazil–UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) is a bilateral research network established in 2019 to integrate genomic surveillance with epidemiology for rapid detection and control of emerging and re-emerging viral diseases in Brazil and internationally.[1] CADDE was funded by the UK Medical Research Council (MRC) and the São Paulo Research Foundation (FAPESP), bringing together public health laboratories (e.g., Instituto Adolfo Lutz), universities (e.g., University of São Paulo, University of Campinas, Federal University of Minas Gerais, Imperial College London, University of Oxford, University of Birmingham, London School of Hygiene and Tropical Medicine) and international collaborators.

CADDE is noted for its contributions to COVID-19 research and response in Brazil, in particular the detection of Latin America's first COVID-19 cases in <48 hours on 28 February 2020 via rapid nanopore sequencing and open data sharing[2][3], the observation that high proportion of Manaus had been exposed to SARS-CoV-2 during its deadly first epidemic wave in 2020[4], and the early detection and genomic characterisation of the P.1/Gamma lineage of concern first detected in Manaus in January 2020[5][6]. In 2020, CADDE also discovered the first cases of the SARS-CoV-2 Alpha variant in Brazil[7]. In 2022, CADDE detected and sequenced the first monkeypox virus (MPXV) genomes in Brazil during the Clade IIb/sh2017 multicountry outbreak.[8]

History and mission

[edit]

The CADDE programme (April 2019 to March 2023) was a UK–Brazil programme that developed scalable “real-time” genomics capacity embedded within Brazil’s public health system.

CADDE was jointly led by Professor Ester Sabino (University of São Paulo) and Professor Nuno R. Faria (Imperial College London) and jointly funded by the São Paulo Research Foundation (FAPESP) alongside UKRI/MRC.[9]

With an original focus on arboviruses such as dengue, Zika, chikungunya, yellow fever and Oropouche[1][3], CADDE was able to pivot portable sequencing, open analytical pipelines, and epidemiological modelling to support risk assessment and incident response during the COVID-19 pandemic, particularly during the first epidemic waves.

CADDE's mission was to leapfrog legacy techniques and work towards a system of arbovirus research and surveillance fit for the 21st century, one based around genome sequencing and big data epidemiology.

COVID-19 response

[edit]

In February 2020, CADDE teams sequenced genomes from the first confirmed COVID-19 cases detected in Brazil, posting analyses publicly within 48 hours of sampling and confirmation.[2][3] Before sustained transmission in Brazil, CADDE and collaborators anticipated likely importation routes using air travel and incidence data.[10] In mid-2020 CADDE contributed to a nationwide genomic and mobility analysis clarifying the multiple introductions and early spread of SARS-CoV-2 across Brazil,[11] and to comprehensive studies of epidemiology and clinical characteristics of early SARS-CoV-2 cases Brazil.[12]

In late 2020–early 2021, CADDE co-led the first description of the P.1 (Gamma) lineage in Manaus and its associated resurgence despite high prior seroprevalence,[6][13] alongside a large serological analysis estimating a ~76% attack rate in Manaus by October 2020.[14] CADDE researchers also contributed to international genomic epidemiology studies in the UK and USA,[15][16] and to analyses of human mobility and control measures in China.[17]

Arbovirus research

[edit]

CADDE's work on dengue virus has spanned field investigations,[18][19] lineage nomenclature,[20] transmission modelling to inform forecasting and control strategies,[21] and clinical interactions.[22] Work on yellow fever has combined risk mapping, vector surveillance and enzootic transmission studies. For example, high-resolution maps of environmental suitability for the sylvatic vectors Haemagogus and Sabethes delineated areas at risk of transmission and spillover in Brazil.[23] The team detected yellow fever virus in Aedes scapularis in north-western São Paulo state, raising considerations about potential bridge or urban vector roles.[24] During the 2016–2018 resurgence, the team contributed to characterise the transmission of yellow fever virus in non-human primates in Bahia state, clarifying enzootic dynamics.[25]

More recent studies include a report on the 2024–2025 resurgence in São Paulo state and a large study on climatic drivers of sylvatic yellow fever spread during the large 2016–2018 epidemic in Brazil.[26][27] At global levels, CADDE contributed to updated, high-resolution maps of overlapping environmental suitability for dengue, chikungunya, Zika and yellow fever.[28]

Mpox (monkeypox)

[edit]

In June 2022 CADDE collaborators generated and shared the first mpox virus genome from Brazil, supporting early situational awareness during the multicountry outbreak.[8] Media coverage also highlighted accelerated sequencing workflows enabled by the network.[29]

International collaborations

[edit]

CADDE’s approach and personnel supported or collaborated with programmes beyond Brazil, including:

  • Panama: genomic epidemiology of early SARS-CoV-2 introductions and transmission.[30]
  • Caribbean: implementation of regional genomic surveillance led by UWI Trinidad & Tobago, with CADDE contributors.[31]
  • Angola: detection of local transmission of dengue virus serotype 2, with CADDE contributors.[19]
  • WHO and global policy: contributions to implementation guidance on SARS-CoV-2 sequencing and assessments of global surveillance disparities.[32][33]
  • United Kingdom: phylodynamic reconstruction and mobility-informed analyses of the UK epidemic with COG-UK partners.[34][35][36]
  • United States: early genomic epidemiology of introductions in California and co-development of open qPCR assays for rapid VOC discrimination.[37][38]
  • South Africa: collaborations on tracking the emergence and global dispersal of variants, including Omicron, with KRISP and regional partners.[39][40]

Recognition

[edit]

CADDE’s COVID-19 work was profiled by Imperial College London and the University of Oxford.[41][42] Science highlighted CADDE findings via article pages and editor summaries (e.g., “Spread of SARS-CoV-2 in Brazil” (2020) and “Unmitigated spread in Brazil” (2021)).[11][14] Independent rankings listed the Manaus P.1 study among the most influential Science papers of 2021.[43] A Newton Fund impact film documented CADDE’s real-time outbreak response in Brazil.[44] UKRI also featured CADDE in international case studies.[45][46] In July 2020, the UK Ambassador to Brazil publicly highlighted the CADDE-led study as an example of international collaboration and a science-led response.[47][48]

The State of São Paulo’s Secretariat of Economic Development and ACIESP created the Ester Sabino Prize for Women Scientists (2021), honouring the leadership of CADDE co-founder Ester C. Sabino.[49] CADDE-associated scientist Jaqueline Góes de Jesus has received multiple public recognitions, including the Forbes Brasil “20 Mulheres de Sucesso 2022”,[50], the Barbie Role Model honour by Mattel,[51] and Science Ambassador (MCTI) and Team Halo (UN Verified) science-communication roles.[52] Both Ester and Jaqueline were recognised in the famous cartoon Turma da Mônica in tribute on the International Day of Women and Girls in Science (2020).[53] CADDE research contributions have received recognition in the Smithsonian’s “Vaccines & Us” initiative and the "Luminaries” initiative linked to the G7 Global Vaccine Confidence Campaign.[54]

Selected media

[edit]

Over 5,000 news articles reported on the CADDE programme's study findings. Some of the selected media include:

  • The Guardian — “Brazil variant evaded up to 61% of immunity in previous Covid cases, study finds.” (2 March 2021)[55]
  • BBC News — “Covid Brazil variant 'may spread more easily'.”[56]
  • The New York Times — Coverage of the Brazil (Gamma/P.1) variant and reinfection.[57]
  • Folha de S.Paulo — “Novo método pode ajudar a prever casos de variantes da Covid-19.” (in Portuguese)[58]
  • Folha de S.Paulo — “Nova onda de Covid-19 em Manaus reacende debate sobre imunidade de rebanho.” (in Portuguese)[59]

Selected publications

[edit]
  • Candido DS et al. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science.[11]
  • Faria NR et al. (2021). Genomics and epidemiology of the P.1 lineage in Manaus, Brazil. Science.[6]
  • Sabino EC et al. (2021). Resurgence of COVID-19 in Manaus despite high seroprevalence. The Lancet.[13]
  • Buss LF et al. (2021). Three-quarters attack rate in the Brazilian Amazon. Science.[14]
  • du Plessis L et al. (2021). Lineage dynamics of the COVID-19 epidemic in the UK. Science.[15]
  • de Souza WM et al. (2020). Epidemiological and clinical characteristics in Brazil. Nat Human Behav.[12]

See also

[edit]

Category:Medical research institutes in Brazil Category:Medical research institutes in the United Kingdom Category:Genomics Category:SARS-CoV-2 Category:Public health in Brazil

  1. ^ a b "UK–Brazil Joint Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)". UKRI Gateway to Research. UK Research and Innovation. Retrieved 28 October 2025.
  2. ^ a b Faria, Nuno R. (28 February 2020). "First cases of coronavirus disease (COVID-19) in Brazil, South America (2 genomes, 3rd March 2020)". Virological.org. Retrieved 28 October 2025.
  3. ^ a b c "Results and impact (MR/S019510/1)". UKRI Gateway to Research. UKRI. Retrieved 28 October 2025. "With CADDE, it took us 2 days to get from sample to sequence…"
  4. ^ Buss, Lewis (2020). "Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic". Science. 371 (6526): 288–292. Bibcode:2021Sci...371..288B. doi:10.1126/science.abe9728. PMC 7857406. PMID 33293339.
  5. ^ "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological.org. January 2021. Retrieved 28 October 2025.
  6. ^ a b c Faria, Nuno R. (2021). "Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil". Science. 372 (6544): 815–821. Bibcode:2021Sci...372..815F. doi:10.1126/science.abh2644. PMC 8139423. PMID 33853970.
  7. ^ Claro, ingra (2021). "Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020". Emerg Infect Dis. 3 (27): 970–972. doi:10.3201/eid2703.210038. PMC 7920684. PMID 33496249.
  8. ^ a b "First monkeypox virus genome sequence from Brazil". Virological.org. June 2022. Retrieved 28 October 2025.
  9. ^ "Brazil–UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)". FAPESP. 2019. Retrieved 28 October 2025.
  10. ^ Candido, Darlan S. (2020). "Routes for COVID-19 importation in Brazil". Journal of Travel Medicine. 27 (3) taaa042. doi:10.1093/jtm/taaa042. PMC 7184379. PMID 32211799.
  11. ^ a b c Candido, Darlan S. (2020). "Evolution and epidemic spread of SARS-CoV-2 in Brazil". Science. 369 (6508): 1255–1260. Bibcode:2020Sci...369.1255C. doi:10.1126/science.abd2161. PMC 7402630. PMID 32703910.
  12. ^ a b de Souza, W. M. (2020). "Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil". Nature Human Behaviour. 4 (8): 856–865. doi:10.1038/s41562-020-0928-4. PMID 32737472.
  13. ^ a b Sabino, E. C. (2021). "Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence". The Lancet. 397 (10273): 452–455. doi:10.1016/S0140-6736(21)00183-5. PMC 7906746. PMID 33515491.
  14. ^ a b c Buss, L. F. (2021). "Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic". Science. 371 (6526): 288–292. Bibcode:2021Sci...371..288B. doi:10.1126/science.abe9728. PMC 7857406. PMID 33293339.
  15. ^ a b du Plessis, L. (2021). "Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK". Science. 371 (6530): 708–712. Bibcode:2021Sci...371..708D. doi:10.1126/science.abf2946. PMC 7877493. PMID 33419936.
  16. ^ Deng, X. (2020). "Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California". Science. 369 (6503): 582–587. Bibcode:2020Sci...369..582D. doi:10.1126/science.abb9263. PMC 7286545. PMID 32513865.
  17. ^ Kraemer, M. U. G. (2020). "The effect of human mobility and control measures on the COVID-19 epidemic in China". Science. 368 (6490): 493–497. Bibcode:2020Sci...368..493K. doi:10.1126/science.abb4218. PMC 7239080. PMID 32213647.
  18. ^ Rezende, Helder Ricas (2020). "First report of Aedes albopictus infected by Dengue and Zika virus in a rural outbreak in Brazil". PLOS ONE. 15 (3): e0229847. Bibcode:2020PLoSO..1529847R. doi:10.1371/journal.pone.0229847. PMC 7067471. PMID 32163449.{{cite journal}}: CS1 maint: article number as page number (link)
  19. ^ a b Neto, Zoraima; Martinez, Pedro A.; Hill, Sarah C.; Jandondo, Domingos; Thézé, Julien (18 May 2022). "Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019". PLOS Neglected Tropical Diseases. 16 (5): e0010255. doi:10.1371/journal.pntd.0010255. PMC 9166355. PMID 35584153.{{cite journal}}: CS1 maint: article number as page number (link)
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  21. ^ Harish, Vinyas; Colón-González, Felipe J.; Moreira, Filipe R. R.; Gibb, Rory; Kraemer, Moritz U. G. (28 May 2024). "Human movement and environmental barriers shape the emergence of dengue". Nature Communications. 15 (1) 4205. Bibcode:2024NatCo..15.4205H. doi:10.1038/s41467-024-48465-0. PMC 11133396. PMID 38806460.
  22. ^ Nicolete, Vanessa C.; Rodrigues, Priscila T.; Johansen, Igor C.; Corder, Rodrigo M.; Tonini, Juliana (6 December 2021). "Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated With Increased COVID-19 Risk in a Population-Based Cohort Study". Clinical Infectious Diseases. 73 (11): 2045–2054. doi:10.1093/cid/ciab410. PMC 8135953. PMID 33956939.
  23. ^ Li, Sabrina L.; Acosta, André L.; Hill, Sarah C.; Brady, Oliver J.; de Almeida, Marco A. B. (7 January 2022). "Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil". PLOS Neglected Tropical Diseases. 16 (1): e0010019. doi:10.1371/journal.pntd.0010019. PMID 35020416.{{cite journal}}: CS1 maint: article number as page number (link)
  24. ^ Cunha, Marcelo S. (2020). "Genomic evidence of yellow fever virus in Aedes scapularis (Diptera: Culicidae)". Acta Tropica. 205: 105413. doi:10.1016/j.actatropica.2020.105413. ISSN 0001-706X. PMID 32088278.{{cite journal}}: CS1 maint: article number as page number (link)
  25. ^ Goes de Jesus, Jaqueline; Gräf, Tiago; Giovanetti, Marta; Mares-Guia, Maria A.; Xavier, Janderson (11 August 2020). "Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil". PLOS Neglected Tropical Diseases. 14 (8): e0008405. doi:10.1371/journal.pntd.0008405. PMC 7418952. PMID 32780745.{{cite journal}}: CS1 maint: article number as page number (link)
  26. ^ Cunha, Mariana Sequetin; Guerra, Juliana Mariotti; Lima Siconelli, Márcio Junio; Da Fonseca, Benedito Antonio Lopes; De Almeida Dias, Jessica Caroline; De Freitas, Gisele Dias; Sabino, Ester; Manulli, Erika R.; Pereira, Geovana M.; Valença, Ian N.; Silvestre Matsumoto, Patrícia Sayuri; Faria, Nuno R.; De Azevedo Fernandes, Natália Coelho Couto (17 March 2025). "Yellow fever virus resurgence in São Paulo State, Brazil, 2024–2025". medRxiv. doi:10.1101/2025.03.14.25323956.
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  28. ^ Lim, Ahyoung; Shearer, Freya M.; Sewalk, Kara; Pigott, David M.; Clarke, Joseph (10 April 2025). "The overlapping global distribution of dengue, chikungunya, Zika and yellow fever". Nature Communications. 16 (1): 3418. Bibcode:2025NatCo..16.3418L. doi:10.1038/s41467-025-58609-5. PMC 11986131. PMID 40210848.
  29. ^ "Novel technique permits sequencing of monkeypox virus in only 18 hours". Agência FAPESP. 22 June 2022. Retrieved 28 October 2025.
  30. ^ Franco, D.; Gonzalez, C.; Abrego, L. E.; Carrera, J. P.; Diaz, Y.; Caicedo, Y.; Moreno, A.; Chavarria, O.; Gondola, J.; Castillo, M.; Valdespino, E.; Gaitán, M.; Martínez-Mandiche, J.; Hayer, L.; Gonzalez, P.; Lange, C.; Molto, Y.; Mojica, D.; Ramos, R.; Mastelari, M.; Cerezo, L.; Moreno, L.; Donnelly, C. A.; Pascale, J. M.; Faria, N. R.; Lopez-Verges, S.; Martinez, A. A.; Gorgas COVID19 team and Panama COVID19 Laboratory Network (2021). "Genomic epidemiology of early introductions of SARS-CoV-2 into Panama". Emerging Infectious Diseases. 27 (7): 1931–1941. doi:10.3201/eid2702.203767. PMC 7853578. PMID 33496228.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  31. ^ Sahadeo, N. S. D. (2023). "Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings". PLOS Global Public Health. 3 (2): e0001455. doi:10.1371/journal.pgph.0001455. PMC 10022082. PMID 36963002.{{cite journal}}: CS1 maint: article number as page number (link)
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  34. ^ du Plessis, L. (2021). "Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK". Science. 371 (6530): 708–712. Bibcode:2021Sci...371..708D. doi:10.1126/science.abf2946. PMC 7877493. PMID 33419936.
  35. ^ Kraemer, M. U. G. (2021). "Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7". Science. 373 (6557): 889–895. doi:10.1126/science.abj0113. PMC 9269003. PMID 34301854.
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  37. ^ Deng, X. (2020). "Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California". Science. 369 (6503): 582–587. Bibcode:2020Sci...369..582D. doi:10.1126/science.abb9263. PMC 7286545. PMID 32513865.
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  43. ^ "Most Influential Science Papers of 2021". PaperDigest. 2022. Retrieved 28 October 2025.
  44. ^ Real-time response to disease outbreaks in Brazil (CADDE). Newton Fund. 2023. Retrieved 28 October 2025.
  45. ^ UKRI International Strategic Framework (PDF) (Report). UK Research and Innovation. September 2022. p. 16. Retrieved 28 October 2025.
  46. ^ Annual Report and Accounts 2021–22 (PDF) (Report). UK Research and Innovation. January 2023. p. 19. Retrieved 28 October 2025.
  47. ^ "UK–Brazil CADDE project (MR/S019510/1) — Engagement and policy influence". UKRI Gateway to Research. UK Research and Innovation. Retrieved 28 October 2025. Tweet from the UK Ambassador on our work highlighting our study as an example of "international collaboration and focus in science…"
  48. ^ @VijayR_HMG (24 July 2020). "Tweet highlighting CADDE study" (Tweet). Retrieved 28 October 2025 – via Twitter.
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